CN117242085A

CN117242085A - Modified nucleosides

Info

Publication number: CN117242085A
Application number: CN202280025813.9A
Authority: CN
Inventors: 凯特·弗劳尔; 杰夫·卡特; 约翰·罗洛夫; 埃米·热利纳; 内博伊沙·亚尼奇
Original assignee: Private Placement Protein Body Operation Co ltd
Current assignee: Private Placement Protein Body Operation Co ltd
Priority date: 2021-04-13
Filing date: 2022-04-12
Publication date: 2023-12-15

Abstract

Compounds comprising a pyrimidine modified at the 5-position are provided. In addition, polynucleotides, such as aptamers, comprising at least one pyrimidine modified at the 5-position are provided. Methods of selecting and using such polynucleotides, such as aptamers, are also provided.

Description

Modified nucleosides

Cross-reference to related applications

The present application claims priority from U.S. provisional application Ser. No. 63/174,495 filed on day 13 of 4.2021 and U.S. provisional application Ser. No. 63/174,792 filed on day 14 of 4.2021, each of which is incorporated herein by reference in its entirety for any purpose.

Technical Field

The present disclosure relates generally to the field of oligonucleotides comprising modified nucleosides, such as aptamers capable of binding to target molecules. In some embodiments, the disclosure relates to oligonucleotides, such as aptamers, comprising one or more base-modified nucleosides, and methods of making and using such aptamers.

Background

Modified nucleosides have been used as therapeutic agents, diagnostic agents, and for incorporation into oligonucleotides to improve properties (e.g., stability) of the oligonucleotides.

SELEX (exponential enriched ligand system evolution) is a method of identifying oligonucleotides (called "aptamers") that selectively bind to target molecules. The SELEX process is described, for example, in U.S. patent No. 5,270,163. The SELEX method involves selecting and identifying oligonucleotides from a random mixture of oligonucleotides to achieve nearly any desired binding affinity and selectivity criteria. By incorporating specific types of modified nucleosides into the oligonucleotides identified in the SELEX process, the stability, net charge, hydrophilicity, or lipophilicity of the nuclease can be altered to provide differences in the three-dimensional structure and target binding capacity of the oligonucleotides.

There remains a need in the art for alternative modified nucleosides and modified nucleotides that can be incorporated into oligonucleotides, such as aptamers. The present disclosure is directed to meeting one or more of these needs or providing other benefits.

Disclosure of Invention

The foregoing and other objects, features and advantages of the invention will become more apparent from the following detailed description, which proceeds with reference to the accompanying drawings.

Certain non-limiting exemplary embodiments are as follows:

embodiment 1. A compound comprising a pyrimidine nucleoside modified at the 5-position, or a salt thereof, wherein the pyrimidine modified at the 5-position is substituted with a moiety comprising two phenyl groups covalently linked to each other through a first linker, and wherein the moiety is covalently linked to the 5-position of the pyrimidine through a second linker.

Embodiment 2. The compound of embodiment 1 wherein the first linker comprises at least one atom or bond selected from carbon and oxygen.

Embodiment 3. The compound of any one of embodiments 1-2, wherein the pyrimidine modified at the 5-position comprises a moiety at the 5-position selected from the group consisting of a phenylbenzyl moiety, a phenoxybenzyl moiety, and a diphenylmethyl moiety.

Embodiment 4. The compound of any of embodiments 1-3 wherein the second linker comprises a group selected from the group consisting of an amide linker, a carbonyl linker, a propynyl linker, an alkyne linker, an ester linker, a urea linker, a carbamate linker, a guanidine linker, an amidine linker, a sulfoxide linker, and a sulfone linker.

Embodiment 5. The compound of any one of embodiments 1-3, wherein the second linker comprises an amide linker.

Embodiment 6. The compound of embodiment 5 wherein the amide linker further comprises one or more carbon atoms or 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 carbon atoms.

Embodiment 7. The compound of any one of embodiments 1-6 comprising a uridine modified in the 5-position.

Embodiment 8. The compound of any one of embodiments 1-7, comprising a cytidine modified at the 5-position.

Embodiment 9 a compound comprising a structure of formula IA or formula IB:

or a salt of any of these,

wherein the method comprises the steps of

Each L is independently- (CH) ₂ ) _n -, wherein n is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10;

each R ₁ Independently selected from the group consisting of:

wherein is represents the R ₁ A point of attachment of a group to the L group;

each X is independently selected from the group consisting of: -H, -OH, -OMe, -O-allyl, -O-ethyl, -O-propyl, -OCH ₂ CH ₂ OCH ₃ -fluoro, -t-butyldimethylsilyloxy, -NH ₂ And-azido;

each R ₂ Is independently selected from the group consisting of-OH, -acetyl, -OBz, -OP (N (CH) ₂ CH ₃ ) ₂ )(OCH ₂ CH ₂ CN)、-OP(N(R _x ) ₂ )(OCH ₂ CH ₂ CN), wherein each R _x Independently is (C) _1-6 ) Alkyl, t-butyldimethylsilyloxy, -O-ss, -OR, -SR, -ZP (Z') (Z ") -O-R; wherein ss is a solid support, Z, Z' and Z "are each independently selected from O and S, and R is an adjacent nucleotide;

each R ₃ Independently selected from the group consisting of-OH, -O-trityl-O-4, 4' -dimethoxytrityl, -O-triphosphate, -OR, -SR, -NH ₂ -NHR and-Z-P (Z ') (Z ") O-R, wherein Z, Z' and Z" are each independently selected from O and S, and R is an adjacent nucleotide.

Embodiment 10. The compound of embodiment 9 wherein n is 1, 2, or 3.

Embodiment 11. The compound of any one of embodiments 9-10 wherein X is-H.

Embodiment 12. The compound of any one of embodiments 9-10, wherein X is-OMe.

Embodiment 13. The method of any one of embodiments 9-12A compound wherein each R ₁ Independently selected from the group consisting of

The compound of any one of embodiments 1-13, wherein the 5-position modified pyrimidine is selected from the group consisting of BPEdU, 2'-OMe-BPE-U, 2' -F-BPE-U, PBndU, 2'-OMe-PBn-U, 2' -F-PBn-U, POPdU, 2'-OMe-POP-U, 2' -F-POP-U, DPPdU, 2'-OMe-DPP-U, 2' -F-DPP-U, DBMdU, 2'-OMe-DBM-U, 2' -F-DBM-U, BHdU, 2'-OMe-BH-U, 2' -F-BH-U, BPEdC, 2'-OMe-BPE-C, 2' -F-BPE-C, PBndC, 2'-OMe-PBn-C, 2' -F-PBn-C, POPdC, 2'-OMe-POP-C, 2' -OMe-POP-C, DPPdC, 2'-OMe-DPP-C, 2' -F-DPP-C, DBMdC, 2 '-OMe-C, 2' -OMe-BH-C, 2 '-OMe-C, 2' -F-BH-C, and BH-C.

Embodiment 15 a compound comprising a structure of formula IIA or formula IIB:

or a salt of any of these,

wherein the method comprises the steps of

each R ₁ Independently selected from the group consisting of:

each X is independently selected from the group consisting of: -H, -OH, -OMe, -O-allyl, -O-ethyl, -O-propyl, -OCH ₂ CH ₂ OCH ₃ -fluoro, -t-butyldimethylsilyloxy, -NH ₂ And-azido.

Embodiment 16. The compound of embodiment 15 wherein n is 1, 2, or 3.

Embodiment 17 the compound of any one of embodiments 15-16, wherein X is-H.

Embodiment 18. The compound of any one of embodiments 15-16, wherein X is-OMe.

Embodiment 19 the compound of any one of embodiments 15-18 wherein each R ₁ Independently selected from the group consisting of

Embodiment 20 a compound comprising the structure:

or a salt of any of these;

wherein each X is independently selected from the group consisting of: -H, -OH, -O-methyl, -O-allyl, -O-ethyl, -O-propyl, -OCH ₂ CH ₂ OCH ₃ -fluoro, -t-butyldimethylsilyloxy, -NH ₂ And-azido.

Embodiment 21. The compound of embodiment 20 wherein X is-H.

Embodiment 22. The compound of embodiment 20 wherein X is-OMe.

Embodiment 23 an oligonucleotide comprising a compound of any of embodiments 1-14.

Embodiment 24. The oligonucleotide of embodiment 23 comprising RNA, DNA, or a combination thereof.

The oligonucleotide of any one of embodiments 23-24, which is 15 to 100, or 15 to 90, or 15 to 80, or 15 to 70, or 15 to 60, or 15 to 50, or 20 to 100, or 20 to 90, or 20 to 80, or 20 to 70, or 20 to 60, or 20 to 50, or 30 to 100, or 30 to 90, or 30 to 80, or 30 to 70, or 30 to 60, or 30 to 50, or 40 to 100, or 40 to 90, or 40 to 80, or 40 to 70, or 40 to 60, or 40 to 50 nucleotides in length.

Embodiment 26. The oligonucleotide of any one of embodiments 23-25, which is an aptamer that binds to a target.

Embodiment 27. An aptamer comprising a compound of any one of embodiments 1 to 14.

The aptamer of any one of embodiments 26-27, wherein the aptamer has a length of 15 to 100, or 15 to 90, or 15 to 80, or 15 to 70, or 15 to 60, or 15 to 50, or 20 to 100, or 20 to 90, or 20 to 80, or 20 to 70, or 20 to 60, or 20 to 50, or 30 to 100, or 30 to 90, or 30 to 80, or 30 to 70, or 30 to 60, or 30 to 50, or 40 to 100, or 40 to 90, or 40 to 80, or 40 to 70, or 40 to 60, or 40 to 50 nucleotides.

Embodiment 29 the aptamer of any one of embodiments 26-28, comprising a 5-position modified pyrimidine selected from the group consisting of: BPEdU, 2'-OMe-BPE-U, 2' -F-BPE-U, PBndU, 2'-OMe-PBn-U, 2' -F-PBn-U, POPdU, 2'-OMe-POP-U, 2' -F-POP-U, DPPdU, 2'-OMe-DPP-U, 2' -F-DPP-U, DBMdU, 2'-OMe-DBM-U, 2' -F-DBM-U, BHdU, 2'-OMe-BH-U, 2' -F-BH-U, BPEdC, 2'-OMe-BPE-C, 2' -F-BPE-C, PBndC, 2'-OMe-PBn-C, 2' -F-PBn-C, POPdC, 2'-OMe-POP-C, DPPdC, 2' -OMe-DPP-C, 2'-F-DPP-C, DBMdC, 2' -OMe-DBM-C, BHdC, 2'-OMe-BH-C and 2' -F-BH-C.

Embodiment 30 the aptamer of any one of embodiments 26-29, comprising at least one 5-position modified uridine selected from the group consisting of: BPEdU, 2'-OMe-BPE-U, 2' -F-BPE-U, PBndU, 2'-OMe-PBn-U, 2' -F-PBn-U, POPdU, 2'-OMe-POP-U, 2' -F-POP-U, DPPdU, 2'-OMe-DPP-U, 2' -F-DPP-U, DBMdU, 2'-OMe-DBM-U, 2' -F-DBM-U, BHdU, 2'-OMe-BH-U, 2' -F-BH-U, and at least one 5-position modified cytidine selected from the group consisting of: BPEdc, 2'-OMe-BPE-C, 2' -F-BPE-C, PBndC, 2'-OMe-PBn-C, 2' -F-PBn-C, POPdC, 2'-OMe-POP-C, 2' -F-POP-C, DPPdC, 2'-OMe-DPP-C, 2' -F-DPP-C, DBMdC, 2'-OMe-DBM-C, 2' -F-DBM-C, BHdC, 2'-OMe-BH-C and 2' -F-BH-C.

Embodiment 31. The aptamer of any one of embodiments 26-30, wherein the aptamer comprises a region of at least 10, at least 15, at least 20, at least 25, or at least 30 nucleotides in length, or 5 to 30, 10 to 30, 15 to 30, 5 to 20, or 10 to 20 nucleotides in length, at the 5 'end of the aptamer, wherein the region at the 5' end of the aptamer lacks a 5-position modified pyrimidine.

The aptamer of any one of embodiments 26-31, wherein the aptamer comprises a region of at least 10, at least 15, at least 20, at least 25, or at least 30 nucleotides in length, or 5 to 30, 10 to 30, 15 to 30, 5 to 20, or 10 to 20 nucleotides in length at the 3 'end of the aptamer, wherein the region at the 3' end of the aptamer lacks a 5-position modified pyrimidine.

Embodiment 33. An aptamer comprising at least one first 5-position modified pyrimidine and at least one second 5-position modified pyrimidine, wherein the first 5-position modified pyrimidine and the second 5-position modified pyrimidine are different 5-position modified pyrimidines, and wherein the at least one first 5-position modified pyrimidine is a compound according to any one of embodiments 1-14.

Embodiment 34. The aptamer of embodiment 33, wherein the at least one second 5-position modified pyrimidine is selected from the group consisting of one or more of the following: bndC, 2'-OMe-Bn-C, 2' -F-Bn-C, PEdC, 2'-OMe-PE-C, 2' -F-PE-C, PPdC, 2'-OMe-PP-C, 2' -F-PP-C, napdC, 2'-OMe-Nap-C, 2' -F-Nap-C, 2Napdc, 2'-OMe-2Nap-C, 2' -F-2Nap-C, NEdC, 2'-OMe-NE-C, 2' -F-NE-C, 2NEdC, 2'-OMe-2NE-C, 2' -F-2NE-C, tyrdC, 2'-OMe-Tyr-C, 2' -F-Tyr-C, bndU 2'-OMe-Bn-U, 2' -F-Bn-U, napdU, 2'-OMe-Nap-U, 2' -F-Nap-U, PEdU, 2'-OMe-PE-U, 2' -F-PE-U, ibdU, 2'-OMe-Ib-U, 2' -F-Ib-U, FBndU, 2'-OMe-FBn-U, 2' -F-FBn-U, 2NapdU, 2'-OMe-2Nap-U, 2' -F-2Nap-U, NEdU, 2'-OMe-NE-U, 2' -F-NE-U, MBndU, 2'-OMe-MBn-U, 2' -F-MBn-U, BFdU, 2'-OMe-BF-U, 2' -F-BF-U, BTdU, 2'-OMe-BT-U, 2' -F-BT-U, PPdU, 2'-OMe-PP-U, 2' -F-PP-U, MOEdU, 2'-OMe-MOE-U, 2' -F-MOE-U, tyrdU, 2'-OMe-Tyr-U, 2' -F-Tyr-U, trpdU, 2'-OMe-Trp-U, 2' -F-Trp-U, thrdU, 2'-OMe-Thr-U and 2' -F-Thr-U.

Embodiment 35 the aptamer of any one of embodiments 33-34, wherein the at least one second 5-position modified pyrimidine is selected from the group consisting of one or more of the following: napdc, 2'-OMe-Nap-C, 2' -F-Nap-C, 2Napdc, 2'-OMe-2Nap-C, 2' -F-2Nap-C, tyrdC, 2'-OMe-Tyr-C, 2' -F-Tyr-C, PPdC, 2'-OMe-PP-C, 2' -F-PP-C, napdU, 2'-OMe-Nap-U, 2' -F-Nap-U, PPdU, 2'-OMe-PP-U, 2' -F-PP-U, MOEdU, 2'-OMe-MOE-U, 2' -F-MOE-U, tyrdU, 2'-OMe-Tyr-U, 2' -F-Tyr-U, trpdU, 2'-OMe-Trp-U, 2' -F-Trp-U, thrdU, 2'-OMe-Thr-U and 2' -F-Thr-U.

Embodiment 36. The aptamer of any one of embodiments 26-35, wherein the aptamer has improved nuclease stability and/or a longer half-life in human serum and/or improved affinity and/or improved dissociation rate compared to an aptamer having the same length and comprising an unmodified pyrimidine in place of the nucleobase sequence of the 5-position modified pyrimidine.

Embodiment 37. A composition comprising the aptamer of any one of embodiments 26-36.

Embodiment 38. The composition of embodiment 37, wherein each aptamer comprises a random region.

Embodiment 39 the composition of embodiment 38, wherein the random region is 20 to 100, or 20 to 90, or 20 to 80, or 20 to 70, or 20 to 60, or 20 to 50, or 20 to 40, or 30 to 100, or 30 to 90, or 30 to 70, or 30 to 60, or 30 to 50, or 30 to 40 nucleotides in length.

Embodiment 40. A composition comprising an aptamer and a target, wherein the aptamer and the target are capable of forming a complex, and wherein the aptamer is the aptamer of any one of embodiments 26-35.

Embodiment 41 a composition comprising a first aptamer, a second aptamer, and a target, wherein the first aptamer, the second aptamer, and the target are capable of forming a trimeric complex; and wherein the first aptamer is an aptamer comprising a compound of any one of embodiments 1-14; and wherein the second aptamer comprises at least one second 5-position modified pyrimidine.

Embodiment 42. The composition of embodiment 41 wherein the target is selected from the group consisting of a protein, a peptide, a carbohydrate, a small molecule, a cell, and a tissue.

Embodiment 43 the composition of any one of embodiments 41-42, wherein the target is a target protein selected from the group consisting of IL-33, XIAP, K-Ras, and TNF-alpha.

Embodiment 44 a pharmaceutical composition comprising at least one aptamer of any one of embodiments 26-35 or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable carrier.

Embodiment 45 the pharmaceutical composition of embodiment 44 for use in the treatment or prevention of a disease or disorder mediated by a protein selected from the group consisting of IL-33, XIAP, K-Ras, and TNF-alpha.

Embodiment 46. A method of treating or preventing a disease or disorder in a subject comprising administering to a subject in need thereof the aptamer of any one of embodiments 26-35 or the pharmaceutical composition of any one of embodiments 44-45.

Embodiment 47. The method of embodiment 46, wherein the disease or disorder is mediated by a protein selected from the group consisting of IL-33, XIAP, K-Ras and TNF-alpha.

Embodiment 48. The method of any one of embodiments 46-47, wherein the disease or disorder is Traumatic Brain Injury (TBI) or rheumatoid arthritis.

Embodiment 49. A method comprising: (a) Contacting an aptamer capable of binding to a target molecule with a sample; (b) Incubating the aptamer with the sample to allow aptamer-target complex formation; (c) Enriching the aptamer-target complex in the sample; and (d) detecting the presence of the aptamer, the aptamer-target complex, or the target molecule, wherein detection of the aptamer, the aptamer-target complex, or the target molecule indicates the presence of the target molecule in the sample, and wherein no detection of the aptamer, the aptamer-target complex, or the target molecule indicates the absence of the target molecule in the sample; wherein the aptamer comprises a compound of any one of embodiments 1-14 or is an aptamer of any one of embodiments 26-35.

Embodiment 50. The method of embodiment 49, wherein the method comprises at least one additional step selected from the group consisting of: adding a competitor molecule to the sample; capturing the aptamer-target complex on a solid support; and adding a competitor molecule and diluting the sample; wherein the at least one additional step is performed after step (a) or step (b).

Embodiment 51. The method of embodiment 50 wherein the competitor molecule is selected from polyanionic competitors.

Embodiment 52. The method of embodiment 51, wherein the polyanionic competitor is selected from the group consisting of an oligonucleotide, a polydextrose, a DNA, a heparin, and a dNTP.

Embodiment 53. The method of embodiment 52, wherein the polyglucan is dextran sulfate; and the DNA is herring sperm DNA or salmon sperm DNA.

Embodiment 54 the method of any of embodiments 49-53 wherein the target molecule is selected from the group consisting of a protein, a peptide, a carbohydrate, a small molecule, a cell, and a tissue.

Embodiment 55 the method of any of embodiments 49-54, wherein the sample is selected from the group consisting of whole blood, leukocytes, peripheral blood mononuclear cells, plasma, serum, sputum, breath, urine, semen, saliva, meningeal fluid, amniotic fluid, glandular fluid, lymph, nipple aspirate, bronchial aspirate, synovial fluid, joint aspirate, cells, cell extracts, stool, tissue biopsies, and cerebral spinal fluid.

Embodiment 56. A method for detecting a target in a sample, comprising: (a) Contacting the sample with a first aptamer to form a mixture, wherein the first aptamer is capable of binding to the target to form a first complex; (b) Incubating the mixture under conditions allowing the first complex to form; (c) Contacting the mixture with a second aptamer, wherein the second aptamer is capable of binding to the first complex to form a second complex; (d) Incubating the mixture under conditions allowing the second complex to form; (e) Detecting the presence or absence of the first aptamer, the second aptamer, the target, the first complex, or the second complex in the mixture, wherein the presence of the first aptamer, the second aptamer, the target, the first complex, or the second complex is indicative of the presence of the target in the sample; wherein the first aptamer comprises a compound of any one of embodiments 1-14; and wherein the second aptamer comprises at least one second 5-position modified pyrimidine; wherein the first aptamer, the second aptamer, and the target are capable of forming a trimeric complex.

Embodiment 57 the method of embodiment 56 wherein the target molecule is selected from the group consisting of a protein, a peptide, a carbohydrate, a small molecule, a cell, and a tissue.

Embodiment 58 the method of any one of embodiments 56-57, wherein said first aptamer, said second aptamer, and said target are capable of forming a trimeric complex.

Embodiment 59. The method of any one of embodiments 56-58, wherein the second aptamer comprises at least one second 5-position modified pyrimidine selected from the group consisting of one or more of: bndC, 2'-OMe-Bn-C, PEdC, 2' -OMe-PE-C, PPdC, 2'-OMe-PP-C, napdC, 2' -OMe-Nap-C, 2Napdc, 2'-OMe-2Nap-C, NEdC, 2' -OMe-NE-C, 2NEdC, 2'-OMe-2NE-C, tyrdC, 2' -OMe-Tyr-C, bndU, 2'-OMe-Bn-U, napdU, 2' -OMe-Nap-U, PEdU, 2'-OMe-PE-U, ibdU, 2' -OMe-Ib-U, FBndU, 2'-OMe-FBn-U, 2NapdU, 2' -OMe-2Nap-U, NEdU, 2'-OMe-NE-U, MBndU, 2' -OMe-MBn-U, BFdU, 2'-OMe-BF-U, BTdU, 2' -OMe-BT-U, PPdU, 2'-OMe-PP-U, MOEdU, 2' -OMe-MOE-U, tyrdU, 2'-OMe-Ib-U, FBndU, 2' -OMe-FBn-U, 2 '-OMe-52, 2' -OMe-35 and Tre-4535.

Embodiment 60. The method of any one of embodiments 56-59, wherein the second aptamer comprises at least one second 5-position modified pyrimidine selected from the group consisting of one or more of the following: napdc, 2'-OMe-Nap-C, 2Napdc, 2' -OMe-2Nap-C, tyrdC, 2'-OMe-Tyr-C, PPdC, 2' -OMe-PP-C, napdU, 2'-OMe-Nap-U, PPdU, 2' -OMe-PP-U, MOEdU, 2'-OMe-MOE-U, tyrdU, 2' -OMe-Tyr-U, trpdU, 2'-OMe-Trp-U, thrdU and 2' -OMe-Thr-U.

Embodiment 61 a method for identifying one or more aptamers capable of binding to a target molecule, comprising: (a) Contacting a library of aptamers with the target molecule to form a mixture, and allowing formation of aptamer-target complexes, wherein the aptamer-target complexes are formed when the aptamers have affinity for the target molecule; (b) Separating the aptamer-target complex from the remainder of the mixture (or enriching the aptamer-target complex); (c) dissociating the aptamer-target complex; and (d) identifying the one or more aptamers capable of binding to the target molecule; wherein the aptamer library comprises a plurality of polynucleotides, and the aptamer library is the composition of any one of embodiments 37-43.

Embodiment 62. The method of embodiment 61, wherein each polynucleotide comprises an immobilization region at the 5' end of the polynucleotide.

Embodiment 63 the method of embodiment 62, wherein the length of the immobilization region at the 5' end of each polynucleotide is at least 10, at least 15, at least 20, at least 25, or at least 30 nucleotides, or 5 to 30, 10 to 30, 15 to 30, 5 to 20, or 10 to 20 nucleotides in length.

Embodiment 64 the method of any one of embodiments 61-63, wherein each polynucleotide comprises an immobilization region at the 3' end of the polynucleotide.

Embodiment 65 the method of embodiment 64, wherein the length of the immobilization region at the 3' end of the polynucleotide is at least 10, at least 15, at least 20, at least 25 or at least 30 nucleotides in length, or 5 to 30, 10 to 30, 15 to 30, 5 to 20 or 10 to 20 nucleotides in length.

Embodiment 66. The method of any one of embodiments 61-65, wherein each polynucleotide comprises a random region.

Embodiment 67. The method of embodiment 66, wherein the random region is 20 to 100, or 20 to 90, or 20 to 80, or 20 to 70, or 20 to 60, or 20 to 50, or 20 to 40, or 30 to 100, or 30 to 90, or 30 to 70, or 30 to 60, or 30 to 50, or 30 to 40 nucleotides in length.

Embodiment 68. The method of any one of embodiments 61-67, wherein each polynucleotide is 15 to 100, or 15 to 90, or 15 to 80, or 15 to 70, or 15 to 60, or 15 to 50, or 20 to 100, or 20 to 90, or 20 to 80, or 20 to 70, or 20 to 60, or 20 to 50, or 30 to 100, or 30 to 90, or 30 to 80, or 30 to 70, or 30 to 60, or 30 to 50, or 40 to 100, or 40 to 90, or 40 to 80, or 40 to 70, or 40 to 60, or 40 to 50 nucleotides in length.

Embodiment 69 the method of any one of embodiments 61-68, wherein each polynucleotide is an aptamer that binds to a target, and wherein the library comprises at least 1000 aptamers, wherein each aptamer comprises a different nucleotide sequence.

Embodiment 70 the method of any one of embodiments 61-69 wherein steps (a), (b) and/or (c) are repeated at least once, twice, three times, four times, five times, six times, seven times, eight times, nine times or ten times.

Embodiment 71 the method of any one of embodiments 61-70, wherein the one or more aptamers capable of binding to the target molecule are amplified.

Embodiment 72 the method of any one of embodiments 61-71, wherein the mixture comprises a polyanionic competitor molecule.

Embodiment 73. The method of embodiment 72, wherein the polyanionic competitor is selected from the group consisting of an oligonucleotide, a polyglucan, a DNA, a heparin, and a dNTP.

Embodiment 74 the method of embodiment 73 wherein the polyglucan is dextran sulfate; and the DNA is herring sperm DNA or salmon sperm DNA.

Embodiment 75. The method of any of embodiments 61-74 wherein the target molecule is selected from the group consisting of a protein, a peptide, a carbohydrate, a small molecule, a cell, and a tissue.

Embodiment 76 the compound of any one of embodiments 1-14, the aptamer of any one of embodiments 26-35, the composition of any one of embodiments 37-45, or the method of any one of embodiments 46-75, wherein the pyrimidine modified at the 5-position is capable of being incorporated by a polymerase.

Embodiment 77 a kit comprising a compound of any one of embodiments 1-14, a compound of any one of embodiments 15-22, an oligonucleotide of any one of embodiments 23-25, an aptamer of any one of embodiments 26-35, a composition of any one of embodiments 37-43, and optionally one or more of the following: (a) A pharmaceutically acceptable carrier, such as a solvent or solution; (b) Pharmaceutically acceptable excipients, such as stabilizers or buffers; (c) At least one container, vial or device for holding and/or mixing the kit components; and (d) a delivery device.

Embodiment 78 the kit of embodiment 77, optionally further comprising one or more of the following: (e) A labeling agent useful for detecting a target molecule bound to an aptamer; (f) a solid support, such as a microarray or bead; and (g) reagents related to the quantification of the polymerase chain reaction products, such as intercalating fluorescent dyes or fluorescent DNA probes.

Embodiment 79 a compound comprising a structure of formula III, formula IV, or formula V:

/>

or a salt of any of these, wherein:

each R ₁ Independently selected from:

wherein is represents the R ₁ A point of attachment of a group to the L group; and is also provided with

Each X is independently selected from the group consisting of-H, -OH, -OMe-O-allyl, -O-ethyl, -O-propyl, -OCH ₂ CH ₂ OCH ₃ -fluoro, -t-butyldimethylsilyloxy, -NH ₂ And-azido.

Embodiment 80 the compound of claim 79 wherein n is 1, 2, or 3.

Embodiment 81 the compound of any one of claims 79-80 wherein X is-H.

The compound of any one of claims 79 to 80, wherein X is-OMe.

Embodiment 83 the compound of any one of claims 79-82 wherein R ₁ Selected from the group consisting of

Drawings

FIGS. 1A-1I. Dose-dependent binding of round 7 enriched SELEX libraries to various protein targets. For each binding curve, the fraction of library-protein complexes was plotted as a function of protein concentration. Equilibrium binding constants (Kd values) were determined by fitting the data to a four parameter S-type dose response model. (A) Comparison of PP-dUTP-containing and DPP-dUTP-containing libraries for XIAP targets in round 7 enriched SELEX libraries. (B) Comparison of PP-dUTP-containing and PBn-dUTP-containing libraries for XIAP targets in round 7 enriched SELEX libraries. (C) Comparison of PP-dUTP-containing and DPP-dUTP-containing libraries for IL-33 targets in round 7 enriched SELEX libraries. (D) Comparison of PP-dUTP-containing and PBn-dUTP-containing libraries for IL-33 targets in round 7 enriched SELEX libraries. (E) Comparison of PP-dUTP-containing and POP-dUTP-containing libraries for K-Ras targets in round 7 enriched SELEX libraries. (F) Comparison of PP-dUTP-containing and DPP-dUTP-containing libraries for K-Ras targets in round 7 enriched SELEX libraries. (G) Comparison of PP-dUTP-containing and PBn-dUTP-containing libraries for K-Ras targets in round 7 enriched SELEX libraries. (H) Comparison of PP-dUTP-containing and BPE-dUTP-containing libraries for K-Ras targets in round 7 enriched SELEX libraries. (I) Comparison of PP-dUTP-containing and POP-dUTP-containing libraries for TNF- α targets in round 7 enriched SELEX libraries.

FIG. 2. Certain exemplary 5-position modified uridine and cytidine groups that can be incorporated into an aptamer.

FIG. 3 certain exemplary modifications that may be present at the 5-position of uridine. The chemical structure of the C-5 modification includes an exemplary amide linkage linking the modification to the 5-position of uridine. The 5-position moiety shown includes two phenyl groups covalently linked to each other. The 5-position moiety shown includes a phenylbenzyl moiety (e.g., BPE, PBnd, DBM), a 4-phenoxybenzyl moiety (e.g., POP), a diphenylpropyl moiety (e.g., DPP), a benzhydryl moiety (e.g., BH).

FIG. 4 some exemplary modifications that may exist at the 5-position of cytidine. The chemical structure of the C-5 modification includes an exemplary amide linkage linking the modification to the 5-position of the cytidine. The 5-position moiety shown includes two phenyl groups covalently linked to each other. The 5-position moiety shown includes a phenylbenzyl moiety (e.g., BPE, PBnd, DBM), a 4-phenoxybenzyl moiety (e.g., POP), a diphenylpropyl moiety (e.g., DPP), a benzhydryl moiety (e.g., BH).

FIG. 5 certain exemplary modifications that may be present at the 5-position of uridine. The chemical structure of the C-5 modification includes an exemplary amide linkage linking the modification to the 5-position of uridine. The 5-position moieties shown include benzyl moieties (e.g., bn, PE, and PP), naphthyl moieties (e.g., nap, 2Nap, NE), butyl moieties (e.g., iBu), fluorobenzyl moieties (e.g., FBn), tyrosyl moieties (e.g., tyr), 3, 4-methylenedioxybenzyl (e.g., MBn), morpholino moieties (e.g., MOE), benzofuranyl moieties (e.g., BF), indole moieties (e.g., trp), and hydroxypropyl moieties (e.g., thr).

FIG. 6 some exemplary modifications that may be present at the 5-position of cytidine. The chemical structure of the C-5 modification includes an exemplary amide linkage linking the modification to the 5-position of the cytidine. The 5-position moieties shown include benzyl moieties (e.g., bn, PE, and PP), naphthyl moieties (e.g., nap, 2Nap, NE, and 2 NE), and tyrosyl moieties (e.g., tyr).

FIGS. 7A-7F. Dose-dependent binding of round 8 (TNFa and sL-selectin) or round 6 (B7-H4) enriched SELEX libraries to various protein targets. For each binding curve, the fraction of library-protein complexes was plotted as a function of protein concentration. Equilibrium binding constants (Kd values) were determined by fitting the data to a four parameter S-type dose response model. (A) Comparison of Bn-dCTP, PP-dCTP and DPP-dCTP containing libraries for TNFα targets in the enriched SELEX library of round 8. (B) Comparison of Bn-dCTP, PP-dCTP and PBn-dCTP containing libraries for TNFα targets in the enriched SELEX library of round 8. (C) Comparison of Bn-dCTP, PP-dCTP and POP-dCTP containing libraries for tnfα targets in round 8 enriched SELEX libraries. (D) Comparison of Bn-dCTP and PBn-dCTP containing libraries for B7-H4 targets in round 8 enriched SELEX libraries. (E) Comparison of libraries containing PP-dCTP and PBn-dCTP for sL-selectin targets in the enriched SELEX library of round 8. (F) Comparison of PP-dCTP-containing and POP-dCTP-containing libraries for sL-selectin targets in the enriched SELEX library of round 8.

Detailed Description

Unless otherwise indicated, technical terms are used according to conventional usage. The definition of terms commonly used in molecular biology can be found in the following references: benjamin Lewis, genes V, published by Oxford University Press, 1994 (ISBN 0-19-854287-9); kendrew et al (editions), the Encyclopedia of Molecular Biology, published by Blackwell Science Ltd., 1994 (ISBN 0-632-02182-9); and Robert A. Meyers (editions), molecular Biology and Biotechnology: a Comprehensive Desk Reference, published by VCH Publishers, inc., 1995 (ISBN 1-56081-569-8).

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure belongs. The singular terms "a," "an," and "the" include plural referents unless the context clearly dictates otherwise. "comprising A or B" is meant to include A, or B, or A and B. It is also understood that all base sizes or amino acid sizes and all molecular weights or molecular mass values given for nucleic acids or polypeptides are approximations and are provided for the purpose of description.

Furthermore, ranges provided herein are to be understood as shorthand for all values that fall within the range. For example, a range of 1 to 50 is understood to include any number, combination of numbers, or subranges (and fractions thereof unless the context clearly indicates otherwise) from the group consisting of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50. Unless otherwise indicated, any concentration range, percentage range, ratio range, or integer range should be understood to include the value of any integer within the recited range, and to include fractions thereof (such as tenths and hundredths of integers) as appropriate. Furthermore, unless otherwise indicated, any numerical range recited herein in connection with any physical feature (such as a polymer subunit, size, or thickness) should be understood to include any integer within the range. As used herein, unless otherwise indicated, "about" or "consisting essentially of" means ± 20% of the specified range, value, or structure. As used herein, the terms "comprising" and "including" are open ended and are used synonymously.

Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present disclosure, suitable methods and materials are described below. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions of terms, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting.

As used herein, the term "nucleotide" refers to ribonucleotides or deoxyribonucleotides or modified forms thereof and analogs thereof. The substances included in the nucleotide include purines (e.g., adenine, hypoxanthine, guanine and derivatives and analogues thereof) and pyrimidines (e.g., cytosine, uracil, thymine and derivatives and analogues thereof). As used herein, unless explicitly indicated otherwise, the term "cytidine" generally refers to a ribonucleotide, deoxyribonucleotide, or modified ribonucleotide that comprises a cytosine base. The term "cytidine" includes 2' -modified cytidine, such as 2' -fluoro, 2' -methoxy, and the like. Similarly, unless explicitly indicated otherwise, the term "modified cytidine" or a particular modified cytidine also refers to a ribonucleotide, deoxyribonucleotide, or modified ribonucleotide (e.g., 2 '-fluoro, 2' -methoxy, etc.) that comprises a modified cytosine base. Unless specifically indicated otherwise, the term "uridine" generally refers to ribonucleotides, deoxyribonucleotides or modified ribonucleotides comprising a uracil base. The term "uridine" includes 2' -modified uridine such as 2' -fluoro, 2' -methoxy, etc. Similarly, unless explicitly indicated otherwise, the term "modified uridine" or a particular modified uridine also refers to ribonucleotides, deoxyribonucleotides or modified ribonucleotides (such as 2 '-fluoro, 2' -methoxy, etc.) comprising a modified uracil base.

As used herein, the term "5-position modified cytidine" or "C-5 modified cytidine" refers to a cytidine having a modification at the C-5 position of the cytidine, e.g., as shown in fig. 2 and 4. In some embodiments, the C5 modified cytidine (e.g., in its triphosphate form) can be incorporated into the oligonucleotide by a polymerase (e.g., KOD DNA polymerase). Non-limiting exemplary 5-position modified cytidine includes those shown in fig. 4. Non-limiting exemplary C-5 modified cytidine includes, but is not limited to, 5- [ N- (4-phenylbenzyl) carboxamide ] -2' -deoxycytidine (referred to as "PBndC" and shown in fig. 4, where x=h); 5- [ N- (4-phenylbenzyl) carboxamide ] -2 '-O-methylcytidine (referred to as "2' -OMe-PBn-C" and shown in fig. 4, wherein x=ome); 5- [ N- (4-phenylbenzyl) carboxamide ] -2 '-fluorocytidine (referred to as "2' -F-PBn-C" and shown in fig. 4, where x=f); 5- [ N- (4-phenoxybenzyl) carboxamide ] -2' -deoxycytidine (referred to as "POPdC" and shown in fig. 4, wherein x=h); 5- [ N- (4-phenoxybenzyl) carboxamide ] -2 '-O-methylcytidine (referred to as "2' -OMe-POP-C" and shown in fig. 4, wherein x=ome); 5- [ N- (4-phenoxybenzyl) carboxamide ] -2 '-fluorocytidine (referred to as "2' -F-POP-C" and shown in fig. 4, where x=f); 5- [ N- (3, 3-diphenylpropyl) carboxamide ] -2' -deoxycytidine (referred to as "DPPdC" and shown in fig. 4, where x=h); 5- [ N- (3, 3-diphenylpropyl) carboxamide ] -2 '-O-methylcytidine (referred to as "2' -OMe-DPP-C" and shown in fig. 4, wherein x=ome); 5- [ N- (3, 3-diphenylpropyl) carboxamide ] -2 '-fluorocytidine (referred to as "2' -F-DPP-C" and shown in fig. 4, wherein x=f); 5- { N- [ (1, 1 '-biphenyl) -4-yl) ethyl ] carboxamide } -2' -deoxycytidine (referred to as "BPEdC" and shown in fig. 4, wherein x=h); 5- { N- [ (1, 1' -biphenyl) -4-yl) ethyl ] carboxamide } -2' -O-methylcytidine (referred to as "2' -OMe-BPE-C" and shown in fig. 4, wherein x=ome); 5- { N- [ (1, 1' -biphenyl) -4-yl) ethyl ] carboxamide } -2' -fluorocytidine (referred to as "2' -F-BPE-C" and shown in fig. 4, wherein x=f); 5- [ N- (3-phenylbenzyl) carboxamide ] -2' -deoxycytidine (referred to as "DBMdC" and shown in fig. 4, wherein x=h); 5- [ N- (3-phenylbenzyl) carboxamide ] -2 '-O-methylcytidine (referred to as "2' -OMe-DBM-C" and shown in fig. 4, wherein x=ome); 5- [ N- (3-phenylbenzyl) carboxamide ] -2 '-fluorocytidine (referred to as "2' -F-DBM-C" and shown in fig. 4, wherein x=f); 5- [ N- (3, 3-diphenylmethyl) formamide ] -2' -deoxycytidine (referred to as "BHdC" and shown in fig. 4, where x=h); and 5- [ N- (3, 3-diphenylmethyl) formamide ] -2 '-O-methylcytidine (referred to as "2' -OMe-BH-C" and shown in fig. 4, wherein x=ome); and 5- [ N- (3, 3-diphenylmethyl) formamide ] -2 '-fluorocytidine (referred to as "2' -F-BH-C" and shown in fig. 4, where x=f). Non-limiting exemplary 5-position modified cytidine that can also be included include those shown in fig. 6. Non-limiting exemplary 5-position modified cytidine that can be further included include, but are not limited to, 5- (N-benzylformamide) -2' -deoxycytidine (referred to as "BndC"); 5- (N-benzylformamide) -2 '-O-methylcytidine (referred to as "2' -OMe-Bn-C"); 5- (N-benzyl formamide) -2 '-fluorocytidine (referred to as "2' -F-Bn-C"); 5- (N-2-phenethylformamide) -2' -deoxycytidine (referred to as "PEdC"); 5- (N-2-phenethylformamide) -2 '-O-methylcytidine (referred to as "2' -OMe-PE-C"); 5- (N-2-phenethylformamide) -2 '-fluorocytidine (referred to as "2' -F-PE-C"); 5- (N-3-phenylpropyl formamide) -2' -deoxycytidine (referred to as "PPdC"); 5- (N-3-phenylpropyl formamide) -2 '-O-methylcytidine (referred to as "2' -OMe-PP-C"); 5- (N-3-phenylpropyl formamide) -2 '-fluorocytidine (referred to as "2' -F-PP-C"); 5- (N-1-naphthylmethylformamide) -2' -deoxycytidine (referred to as "Napdc"); 5- (N-1-naphthylmethylformamide) -2 '-O-methylcytidine (referred to as "2' -OMe-Nap-C"); 5- (N-1-naphthylmethylformamide) -2 '-fluorocytidine (referred to as "2' -F-Nap-C"); 5- (N-2-naphthylmethylformamide) -2' -deoxycytidine (referred to as "2 Napdc"); 5- (N-2-naphthylmethylformamide) -2 '-O-methylcytidine (referred to as "2' -OMe-2 Nap-C"); 5- (N-2-naphthylmethylformamide) -2 '-fluorocytidine (referred to as "2' -F-2 Nap-C"); 5- (N-1-naphthyl-2-ethylformamide) -2' -deoxycytidine (referred to as "NEdC"); 5- (N-1-naphthyl-2-ethylformamide) -2 '-O-methylcytidine (referred to as "2' -OMe-NE-C"); 5- (N-1-naphthyl-2-ethylformamide) -2 '-fluorocytidine (referred to as "2' -F-NE-C"); 5- (N-2-naphthyl-2-ethylformamide) -2' -deoxycytidine (referred to as "2 NEdC"); 5- (N-2-naphthyl-2-ethylformamide) -2 '-O-methylcytidine (referred to as "2' -OMe-2 NE-C"); 5- (N-2-naphthyl-2-ethylformamide) -2 '-fluorocytidine (referred to as "2' -F-2 NE-C"); 5- (N-tyrosyl carboxamide) -2' -deoxycytidine (referred to as "TyrdC"); 5- (N-tyrosyl carboxamide) -2 '-O-methylcytidine (referred to as "2' -OMe-Tyr-C"); and 5- (N-tyrosyl carboxamide) -2 '-fluorocytidine (referred to as "2' -F-Tyr-C").

In some embodiments, the C5 modified cytidine (e.g., in its triphosphate form) can be incorporated into the oligonucleotide by a polymerase (e.g., KOD DNA polymerase).

The chemical modification of C-5 modified cytidine described herein can also be combined with 2' -position sugar modification (e.g., 2' -O-methyl or 2' -fluoro), modification at exocyclic amine, substitution of 4-thiouridine, and the like, alone or in any combination.

As used herein, the term "C-5 modified uridine" or "uridine modified at the 5-position" refers to a uridine having a modification at the C-5 position of uridine, for example, as shown in fig. 2 and 3. In some embodiments, the C5 modified uridine (e.g., in its triphosphate form) can be incorporated into an oligonucleotide by a polymerase (e.g., KOD DNA polymerase). Non-limiting exemplary 5-modified uridine include those shown in fig. 3. Non-limiting exemplary 5-modified uridine include, but are not limited to

5- [ N- (4-phenylbenzyl) carboxamide ] -2' -deoxyuridine (PBndU),

5- [ N- (4-phenylbenzyl) carboxamide ] -2 '-O-methyluridine (2' -OMe-PBn-U),

5- [ N- (4-phenylbenzyl) carboxamide ] -2 '-fluorouridine (2' -F-PBn-U),

5- [ N- (4-phenoxybenzyl) carboxamide ] -2' -deoxyuridine (POPdU),

5- [ N- (4-phenoxybenzyl) carboxamide ] -2 '-O-methyluridine (2' -OMe-POP-U),

5- [ N- (4-phenoxybenzyl) carboxamide ] -2 '-fluorouridine (2' -F-POP-U),

5- [ N- (3, 3-diphenylpropyl) formamide ] -2' -deoxyuridine (DPPdU),

5- [ N- (3, 3-diphenylpropyl) carboxamide ] -2 '-O-methyluridine (2' -OMe-DPP-U),

5- [ N- (3, 3-diphenylpropyl) carboxamide ] -2 '-fluorouridine (2' -F-DPP-U),

5- { N- [ (1, 1 '-biphenyl) -4-yl) ethyl ] carboxamide } -2' -deoxyuridine (BPEdU),

5- { N- [ (1, 1' -biphenyl) -4-yl) ethyl ] carboxamide } -2' -O-methyluridine (2 ' -OMe-BPE-U),

5- { N- [ (1, 1' -biphenyl) -4-yl) ethyl ] carboxamide } -2' -fluorouridine (2 ' -F-BPE-U),

5- [ N- (3-phenylbenzyl) carboxamide ] -2' -deoxyuridine (DBMdU),

5- [ N- (3-phenylbenzyl) carboxamide ] -2 '-O-methyluridine (2' -OMe-DBM-U),

5- [ N- (3-phenylbenzyl) carboxamide ] -2 '-fluorouridine (2' -F-DBM-U),

5- [ N- (3, 3-diphenylmethyl) formamide ] -2' -deoxyuridine (BHdU),

5- [ N- (3, 3-diphenylmethyl) formamide ] -2 '-O-methyluridine (2' -OMe-BH-U),

5- [ N- (3, 3-diphenylmethyl) carboxamide ] -2 '-fluorouridine (2' -F-BH-U).

Non-limiting exemplary 5-position modified uridine that may also be included include those shown in fig. 5.

Non-limiting exemplary 5-position modified uridine that may also be included include, but are not limited to, 5- (N-benzylformamide) -2' -deoxyuridine (BndU), 5- (N-benzylformamide) -2' -O-methyluridine (2 ' -OMe-Bn-U), 5- (N-benzylformamide) -2' -fluorouridine (2 ' -F-Bn-U), 5- (N-phenethylformamide) -2' -deoxyuridine (PEdU), 5- (N-phenethylformamide) -2' -O-methyluridine (2 ' -OMe-PE-U), 5- (N-phenethylformamide) -2' -fluorouridine (2 ' -F-PE-U), 5- (N-phenylthiomethylformamide) -2' -deoxyuridine (thdU), 5- (N-phenylthiomethylformamide) -2' -O-methyluridine (2 ' -OMe-Th-U), 5- (N-phenylthiomethylformamide) -2' -fluorouridine (2 ' -F-U), 5 ' -isobutylglycine (2 ' -d-U), 5- (N-isobutylcarboxamide) -2' -O-methyluridine (2 ' -OMe-iBu-U), 5- (N-isobutylcarboxamide) -2' -fluorouridine (2 ' -F-iBu-U), 5- (N-tyrosylmethylcarboxamide) -2' -deoxyuridine (TyrdU), 5- (N-tyrosylmethylcarboxamide) -2' -O-methyluridine (2 ' -OMe-Tyr-U), 5- (N-tyrosylmethylcarboxamide) -2' -fluorouridine (2 ' -F-Tyr-U), 5- (N-3, 4-methylenedioxybenzyl carboxamide) -2' -deoxyuridine (MBndU), 5- (N-3, 4-methylenedioxybenzyl carboxamide) -2' -O-methyluridine (2 ' -OMe-MBn-U), 5- (N-3, 4-methylenedioxybenzyl carboxamide) -2' -fluorouridine (2 ' -F-MBn-U), 5- (N-4-fluorobenzyl carboxamide) -2' -fluorouridine (2 ' -F-Tyr-U), 5- (N-3, 4-methylenedioxybenzyl carboxamide) -2' -deoxyuridine (MBndU), 5- (N-3, 4-methylenedioxybenzyl carboxamide) -2' -methyluridine (2 ' -MBndU), 5- (N-3, 4-methylenedioxybenzyl carboxamide) -2' -O-methyluridine (2 ' -OMe-MBn-U), 5- (N-4-fluorobenzyl formamide) -2' -fluorouridine (2 ' -F-FBn-U), 5- (N-3-phenylpropyl formamide) -2' -deoxyuridine (PPdU), 5- (N-3-phenylpropyl formamide) -2' -O-methyluridine (2 ' -OMe-PP-U), 5- (N-3-phenylpropyl formamide) -2' -fluorouridine (2 ' -F-PP-U), 5- (N-imidazolylethylformamide) -2' -deoxyuridine (ImdU), 5- (N-imidazolylethylformamide) -2' -O-methyluridine (2 ' -OMe-Im-U), 5- (N-imidazolylethylformamide) -2' -fluorouridine (2 ' -F-Im-U), 5- (N-tryptophanamide) -2' -deoxyuridine (TrpdU), 5- (N-tryptophanamide) -2' -O-methyluridine (2 ' -OMe-Trp-U), 5- (N-R-threo-carbamoyl) -2 '-deoxyuridine (ThrdU), 5- (N-R-threo-carbamoyl) -2' -O-methyluridine (2 '-OMe-Thr-U), - (N-R-threo-carbamoyl) -2' -fluorouridine (2 '-F-Thr-U), 5- (N- [1- (3-trimethylammonium) propyl ] carboxamide) -2' -deoxyuridine chloride, 5- (N- [1- (3-trimethylammonium) propyl ] carboxamide) -2 '-O-methyluridine chloride 5- (N- [1- (3-trimethylammonium) propyl ] carboxamide) -2' -fluorouridine chloride, 5- (N-naphthylmethylformamide) -2 '-deoxyuridine (NapdU), 5- (N-naphthylmethylformamide) -2' -O-methyluridine (2 '-OMe-Nap-U), 5- (N-naphthylmethylformamide) -2' -fluorouridine (2 '-F-Nap-U), 5- (N- [1- (2, 3-dihydroxypropyl) ] carboxamide) -2' -deoxyuridine), 5- (N- [1- (2, 3-dihydroxypropyl) ] carboxamide) -2 '-O-methyluridine, 5- (N- [1- (2, 3-dihydroxypropyl) ] carboxamide) -2' -fluorouridine, 5- (N-2-naphthylmethylformamide) -2 '-deoxyuridine (2 NapdU), 5- (N-2-naphthylmethylformamide) -2' -O-methyluridine (2 '-OMe-2 Nap-U), 5- (N-2-naphthylmethylformamide) -2' -fluorouridine (2 '-F-2 Nap-U), 5- (N-1-naphthylethylformamide) -2' -deoxyuridine (NEdU), 5- (N-1-naphthylethylformamide) -2 '-O-methyluridine (2' -OMe-NE-U), 5- (N-1-naphthylethylformamide) -2 '-fluorouridine (2' -F-NE-U), 5- (N-2-naphthylethylformamide) -2 '-deoxyuridine (2 NEdU), 5- (N-1-naphthylethylformamide) -2' -deoxyuridine (2 '-N-1-naphthylethylformamide) -2' -N-methyluridine (OMe-E-U), 5- (N-2-naphthylethylformamide) -2 '-fluorouridine (2' -F-2 NE-U), 5- (N-3-benzofuranylethylformamide) -2 '-deoxyuridine (BFdU), 5- (N-3-benzofuranylethylformamide) -2' -O-methyluridine (2 '-OMe-BF-U), 5- (N-3-benzofuranylethylformamide) -2' -fluorouridine (2 '-F-BF-U), 5- (N-3-benzothiylethylformamide) -2' -deoxyuridine (BTdU), 5- (N-3-benzothiophenylethylformamide) -2 '-O-methyluridine (2' -OMe-BT-U), 5- (N-3-benzothiophenylethylformamide) -2 '-fluorouridine (2' -F-BT-U).

As used herein, the terms "modification", "modified", "modification" and any variant thereof when used in reference to an oligonucleotide mean that at least one of the four constituent nucleotide bases (i.e., A, G, T/U and C) of the oligonucleotide is an analog or ester of a naturally occurring nucleotide. In some embodiments, the modified nucleotide confers nuclease resistance to the oligonucleotide. Additional modifications may include backbone modifications, methylation, unusual base pairing combinations, such as the isocytosine and isocarbadine, and the like. Modifications may also include 3 'and 5' modifications, such as capping. Other modifications may include substitution of one or more naturally occurring nucleotides with an analog; internucleotide modifications such as, for example, those with uncharged linkages (e.g., methyl phosphonates, phosphotriesters, phosphoamidates (phosphonates), carbamates (cabamates), etc.) and with charged linkages (e.g., phosphorothioates, phosphorodithioates, etc.), those with intercalators (e.g., acridine, psoralen, etc.), those containing chelators (e.g., metals, radiometals, boron, oxidized metals, etc.), those containing alkylating agents (akylators), and those with modified linkages (e.g., alpha anomeric nucleic acids, etc.). Furthermore, any hydroxyl groups normally present on the sugar of the nucleotide may be replaced by phosphonate groups, phosphate groups; protected by standard protecting groups; or activated to prepare additional linkages to additional nucleotides or to a solid support. The 5 'and 3' terminal OH groups may be phosphorylated or substituted with amines, organic capping moieties of about 1 to about 20 carbon atoms, polyethylene glycol (PEG) polymers in the range of about 10kDa to about 80kDa in some embodiments, PEG polymers in the range of about 20kDa to about 60kDa in some embodiments, or other hydrophilic or hydrophobic biological or synthetic polymers.

As used herein, "nucleic acid," "oligonucleotide," and "polynucleotide" are used interchangeably to refer to a polymer of nucleotides and include DNA, RNA, DNA/RNA hybrids and modifications of these types of nucleic acids, oligonucleotides, and polynucleotides, including the attachment of various entities or moieties to nucleotide units at any position. The terms "polynucleotide", "oligonucleotide" and "nucleic acid" include double-stranded or single-stranded molecules and triple-helical molecules. Nucleic acids, oligonucleotides and polynucleotides are terms that are broader than the term aptamer, and thus the terms nucleic acids, oligonucleotides and polynucleotides include polymers of nucleotides that are aptamers, but the terms nucleic acids, oligonucleotides and polynucleotides are not limited to aptamers.

The polynucleotides may also contain similar forms of ribose or deoxyribose commonly known in the art, including 2' -O-methyl-, 2' -O-allyl, 2' -O-ethyl, 2' -O-propyl, 2' -O-CH ₂ CH ₂ OCH ₃ 2 '-fluoro, 2' -NH ₂ Or 2' azido, carbocyclic sugar analogs, alpha anomeric sugars, epimeric sugars (e.g., arabinose, xylose or lyxose), pyranose, furanose, sedoheptulose, acyclic analogs, and abasic nucleoside analogs (e.g., methyl nucleosides). As described herein, one or more phosphodiester linkages may be replaced with a substituted linking group. These alternative linking groups include those wherein the phosphate is substituted with P (O) S ("thioester"), P (S) S ("dithioester"), (O) NR ^X ₂ ("amidates"), P (O) R ^X 、P(O)OR ^X ', CO or CH ₂ ("methylal") substitution embodiments, wherein each R ^X Or R is ^X ' is independently H, or a substituted or unsubstituted alkyl (C1-C20), aryl, alkenyl, cycloalkyl, cycloalkenyl, or aralkyl optionally containing an ether (-O-) linkage. Not all linkages in a polynucleotide need be identical. Substitution of similar forms of sugar, purine and pyrimidine may be advantageous in designing the final product, for example, alternative backbone structures such as polyamide backbones may also be advantageous in designing the final product.

Polynucleotides may also contain similar forms of carbocyclic sugar analogs, alpha-anomeric sugars, epimeric sugars (e.g., arabinose, xylose or lyxose), pyranose, furanose, sedoheptulose, acyclic analogs, and abasic nucleoside analogs (e.g., methyl nucleosides).

Modification of the nucleotide structure, if present, may be imparted either before or after assembly of the polymer. The sequence of nucleotides may be interrupted by non-nucleotide components. The polynucleotide may be further modified after polymerization, such as by conjugation with a labeling component.

As used herein, when referring to modification of a nucleic acid, the term "at least one nucleotide" refers to one, a few, or all nucleotides in a nucleic acid, thereby indicating that any or all occurrences of A, C, T, G or U in the nucleic acid may be modified or not modified.

As used herein, "nucleic acid ligand," "aptamer," "SOMAmer," and "clone" are used interchangeably to refer to a non-naturally occurring nucleic acid that has a desired effect on a target molecule. Desirable effects include, but are not limited to, binding to a target, catalytically altering a target, reacting with a target in a manner that modifies or alters the functional activity of the target or target, covalently attaching to a target (as in a suicide inhibitor), and facilitating a reaction between the target and another molecule. In some embodiments, the effect is specific binding affinity for a target molecule that is bound to a three-dimensional chemical structure other than a polynucleotide of an aptamer through a mechanism unrelated to Watson/Crick (Watson/Crick) base pairing or triple helix formation, wherein the aptamer is not a nucleic acid of known physiological function being bound by the target molecule. An aptamer to a given target comprises a nucleic acid identified from a mixture of candidate nucleic acids by a method comprising: (a) Contacting the candidate mixture with the target, wherein nucleic acids having increased affinity for the target relative to other nucleic acids in the candidate mixture can be partitioned from the remainder of the candidate mixture; (b) Partitioning the affinity-enhanced nucleic acid from the remainder of the candidate mixture; and (c) amplifying the affinity-enhanced nucleic acids to produce a ligand-enriched nucleic acid mixture, thereby identifying an aptamer to the target molecule. It should be appreciated that affinity interactions are a matter of extent; however, in the present context, "specific binding affinity" of an aptamer to its target means that the aptamer typically binds its target with a much higher degree of affinity than it binds to a mixture or other non-target component in the sample. An "aptamer," "SOMAmer," or "nucleic acid ligand" is a set of copies of a type or class of nucleic acid molecule having a particular nucleotide sequence. The aptamer may comprise any suitable number of nucleotides. "aptamer" refers to more than one group of such molecules. Different aptamers may have the same or different numbers of nucleotides. The aptamer may be DNA or RNA, and may be single-stranded, double-stranded, or contain double-stranded or triple-stranded regions. In some embodiments, the SELEX method described herein or known in the art is used to prepare the aptamer.

As used herein, "SOMAmer" or slow off-rate modified aptamer refers to an aptamer having improved off-rate characteristics. The modified SELEX method described in U.S. patent No. 7,947,447, entitled "Method for Generating Aptamers with Improved Off-Rates," can be used to generate somamers.

As used herein, an aptamer comprising two different types of 5-position modified pyrimidines or C-5 modified pyrimidines may be referred to as a "double modified aptamer", an aptamer having "two modified bases (two modified bases)", an aptamer having "two base modifications" or "two modified bases (two bases modified)", an aptamer having "double modified bases", all of which are used interchangeably. The same terminology may also be used for a library of aptamers (A library of aptamers) or aptamer library (aptamer library). Thus, in some embodiments, the aptamer comprises two different 5-position modified pyrimidines selected from BPEdU (or 2 'modified versions thereof, such as 2' -OMe-BPE-U) and BPEdC (or 2 'modified versions thereof, such as 2' -OMe-BPE-C), BPEdU (or 2 'modified versions thereof, such as 2' -OMe-BPE-U) and PBndC (or 2 'modified versions thereof, such as 2' -OMe-PBn-C), BPEdU (or 2 'modified versions thereof, such as 2' -OMe-BPE-U) and POPdC (or 2 'modified versions thereof, such as 2' -OMe-POP-C), BPEdU (or 2 'modified versions thereof, such as 2' -OMe-BPE-U) and DPPdC (or 2 'modified versions thereof, such as 2' -OMe-DPP-C), BPEdU (or 2 'modified versions thereof, such as 2' -OMe-BPE-U and PBdU (or 2 'modified versions thereof, such as 2' -OMe-BPE-U) and PBE-C), BPEdU (or 2 'modified versions thereof, such as 2' -OMe-POdC), BPE (or 2 'modified versions thereof, such as 2' -OMe-POE-U) and BPdC (or 2 'modified versions thereof, such as 2' -OMe-POE-BPE-U) and DPdC (or 2 'modified versions thereof, such as 2' -OMe-BPE-U-C), BPE-C) and DPdC (or 2 'modified versions thereof, such as 2' -OMe-BPE-C, such as 2' -OMe-PBn-U) and PBndC (or 2' modified versions thereof, such as 2' -OMe-PBn-C), PBndU (or 2' modified versions thereof, such as 2' -OMe-PBn-U) and POPdC (or 2' modified versions thereof, such as 2' -OMe-POP-C), PBndU (or 2' modified versions thereof, such as 2' -OMe-PBn-U) and DPPdC (or 2' modified versions thereof, such as 2' -OMe-DPP-C), POPdU (or 2' modified versions thereof, such as 2' -OMe-POP-U) and BPEdC (or 2' modified versions thereof, such as 2' -OMe-BPE-C), POdU (or 2' modified versions thereof), such as 2' -OMe-POP-U) and PBndC (or 2' modified versions thereof, such as 2' -OMe-PBn-C), POPdU (or 2' modified versions thereof, such as 2' -OMe-POP-U) and POPdC (or 2' modified versions thereof, such as 2' -OMe-POP-C), POPdU (or 2' modified versions thereof, such as 2' -OMe-POP-U) and DPPdC (or 2' modified versions thereof, such as 2' -OMe-DPP-C), DPPdU (or 2' modified versions thereof, such as 2' -OMe-DPP-U) and BPEdC (or 2' modified versions thereof, such as 2' -OMe-BPE-C), DPPdU (or 2 'modified versions thereof, such as 2' -OMe-DPP-U) and PBndC (or 2 'modified versions thereof, such as 2' -OMe-PBn-C), DPPdU (or 2 'modified versions thereof, such as 2' -OMe-DPP-U) and POPdC (or 2 'modified versions thereof, such as 2' -OMe-POP-C), DPPdU (or 2 'modified versions thereof, such as 2' -OMe-DPP-U) and DPPdC (or 2 'modified versions thereof, such as 2' -OMe-DPP-C), DBM dU (or 2 'modified versions thereof, such as 2' -OMe-DBM-U) and BPEdC (or 2 'modified versions thereof, such as 2' -OMe-BPE-C), DBM dU (or 2 'modified versions thereof, such as 2' -OMe-DBM-U) and PBndC (or 2 'modified versions thereof, such as 2' -OMe-PBn-C), DBMdU (or 2 'modified versions thereof, such as 2' -OMe-DBM-U) and POPdC (or 2 'modified versions thereof, such as 2' -OMe-POP-C), DBMdU (or 2 'modified versions thereof, such as 2' -OMe-DBM-U) and DPPdC (or 2 'modified versions thereof, such as 2' -OMe-DPP-C), DBMdU (or 2 'modified versions thereof, such as 2' -OMe-DBM-U) and DBMdC (or 2 'modified versions thereof, such as 2' -OMe-DBM-C), DBM dU (or 2' modified versions thereof, such as 2' -OMe-DBM-U) and BHdC (or 2' modified versions thereof, such as 2' -OMe-BH-C), BHdU (or 2' modified versions thereof, such as 2' -OMe-BH-U) and BPEdC (or 2' modified versions thereof, such as 2' -OMe-BPE-C), BHdU (or 2' modified versions thereof, such as 2' -OMe-BH-U) and PBndC (or 2' modified versions thereof, such as 2' -OMe-PBn-C), BHdU (or 2' modified versions thereof, such as 2' -OMe-BH-U) and POPdC (or 2' modified versions thereof, such as 2' -OMe-POP-C), BHdU (or 2' modified versions thereof, such as 2' -OMe-POP-U), DPdC (or 2' modified versions thereof, such as 2' -OMe-DPP-C), BHU (or 2' modified versions thereof, such as 2' -OMe-BH-U) and DBM-C (or 2' modified versions thereof), BHdU (or 2' modified versions thereof, such as 2' -OMe-POP-C), BHdC (or 2' modified versions thereof, such as 2' -OMe-POP-C). In some embodiments, the aptamer comprises two different 5-position modified pyrimidines, wherein the first 5-position modified pyrimidine is selected from BPEdU (or a 2' modified version thereof, such as 2' -OMe-BPE-U), PBndU (or a 2' modified version thereof, such as 2' -OMe-PBn-U), POPdU (or a 2' modified version thereof, such as 2' -OMe-POP-U), DPPdU (or a 2' modified version thereof, such as 2' -OMe-DPP-U), BPEdC (or a 2' modified version thereof, such as 2' -OMe-BPE-C), PBndC (or a 2' modified version thereof, such as 2' -OMe-PBn-C), POPdC (or a 2' modified version thereof, such as 2' -OMe-POP-C), DPPdC (or a 2' modified version thereof, such as 2' -OMe-DPP-C), and wherein the second 5-position modified pyrimidine is a different 5-position modified pyrimidine is selected from the group consisting of 2' -OMe-POdU (or a 2' modified version thereof, such as 2' -OMe-BPE-C), PBdC (or a 2' modified version thereof, such as 2' -OMe-PBE-C), POPdC (or a 2' modified version thereof, such as 2' -OMe-POdC), or a 2' -modified version thereof, such as 2' -OMe-POdC (or a 2' -modified version thereof, such as 2' -OMe-PdP-C), DPP-C) or a 2, such as 2' -OMe-Thr-U), PPdC (or a 2' modified version thereof, such as 2' -OMe-PP-C), 2NapdU (or a 2' modified version thereof, such as 2' -OMe-2 Nap-U), trpdU (or a 2' modified version thereof, such as 2' -OMe-Trp-U), 2NapdC (or a 2' modified version thereof, such as 2' -OMe-2 Nap-C), tyrdC (or a 2' modified version thereof, such as 2' -OMe-Tyr-C). In some embodiments, the aptamer comprises at least one first modified uridine and/or thymidine or at least one first modified cytidine, wherein the at least one first modified uridine and/or thymidine or at least one first modified cytidine is modified at the 5-position with a moiety comprising two phenyl groups covalently linked to each other. In some embodiments, the aptamer comprises at least one second modified uridine and/or thymidine and at least one second modified cytidine, wherein the at least one second modified uridine and/or thymidine is modified at the 5-position by a moiety selected from the group consisting of a naphthyl moiety, a benzyl moiety, a fluorobenzyl moiety, a tyrosyl moiety, an indole moiety, a morpholino moiety, an isobutyl moiety, a 3, 4-methylenedioxybenzyl moiety, a benzothienyl moiety, and a benzofuranyl moiety, and wherein the at least one second modified cytidine is modified at the 5-position by a moiety selected from the group consisting of a naphthyl moiety, a tyrosyl moiety, and a benzyl moiety. In certain embodiments, the moiety is covalently attached to the 5-position of the base via a linker comprising a group selected from the group consisting of an amide linker, a carbonyl linker, an ester linker, a urea linker, a urethane linker, a guanidine linker, an amidine linker, a sulfoxide linker, and a sulfone linker.

As used herein, an aptamer comprising a single type of 5-position modified pyrimidine or C-5 modified pyrimidine may be referred to as a "single modified aptamer", an aptamer having a "single modified base (single modified base)", an aptamer having a "single base modification" or a "single modified base (single bases modified)", all of which are used interchangeably. The same terminology may also be used for a library of aptamers (Alibrary of aptamers) or aptamer library (aptamer library). As used herein, "protein" is used synonymously with "peptide", "polypeptide" or "peptide fragment". A "purified" polypeptide, protein, peptide or peptide fragment is substantially free of cellular material or other contaminating proteins from the cell, tissue or cell-free source from which the amino acid sequence was obtained, or substantially free of chemical precursors or other chemicals upon chemical synthesis.

In certain embodiments, at least 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% of the uracils of the aptamer are modified at the 5-position. In certain embodiments, at least 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% of the cytosines of the aptamer are modified at the 5-position.

Modified nucleotides

In certain embodiments, the present disclosure provides oligonucleotides, such as aptamers, comprising a pyrimidine modified at the 5-position.

In some embodiments, the present disclosure provides a compound comprising a pyrimidine nucleoside modified at the 5-position, or a salt thereof, wherein the pyrimidine modified at the 5-position is substituted with a moiety comprising two phenyl groups covalently linked to each other through a first linker, and wherein the moiety is covalently linked to the 5-position of the pyrimidine through a second linker.

In some embodiments, the first linker comprises at least one atom selected from carbon and oxygen or is a bond.

In some embodiments, the 5-position modified pyrimidine comprises a moiety at the 5-position selected from the group consisting of a phenylbenzyl moiety, a phenoxybenzyl moiety, and a diphenylmethyl moiety.

In some embodiments, the second linker comprises a group selected from the group consisting of an amide linker, a carbonyl linker, a propynyl linker, an alkyne linker, an ester linker, a urea linker, a carbamate linker, a guanidine linker, an amidine linker, a sulfoxide linker, and a sulfone linker. In some embodiments, the second linker comprises an amide linker. In some embodiments, the amide linker further comprises one or more carbon atoms or 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 carbon atoms.

In some embodiments, the compound comprises a uridine modified in the 5-position.

In some embodiments, the compound comprises a cytidine modified at the 5-position.

In some embodiments, the present disclosure provides an oligonucleotide comprising a structure of formula IA or formula IB:

or a salt of any of these.

In some embodiments, each L is independently- (CH) ₂ ) _n -, whereinn is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10.

In some embodiments, each R ₁ Independently selected from the group consisting of:

wherein is R ₁ The point of attachment of the group to the L group.

In some embodiments, each X is independently selected from the group consisting of: -H, -OH, -OMe, -O-allyl, -O-ethyl, -O-propyl, -OCH ₂ CH ₂ OCH ₃ -fluoro, -t-butyldimethylsilyloxy, -NH ₂ And-azido.

In some embodiments, each R ₂ Is independently selected from the group consisting of-OH, -acetyl, -OBz, -OP (N (CH) ₂ CH ₃ ) ₂ )(OCH ₂ CH ₂ CN)、-OP(N(R _x ) ₂ )(OCH ₂ CH ₂ CN), wherein each R _x Independently is (C) _1-6 ) Alkyl, t-butyldimethylsilyloxy, -O-ss, -OR, -SR, -ZP (Z') (Z ") -O-R; wherein ss is a solid support, Z, Z 'and Z' are each independently selected from O and S, and R is an adjacent nucleotide.

In some embodiments, each R ₃ Independently selected from the group consisting of-OH, -O-trityl-O-4, 4' -dimethoxytrityl, -O-triphosphate, -OR, -SR, -NH ₂ -NHR and-Z-P (Z ') (Z ") O-R, wherein Z, Z' and Z" are each independently selected from O and S, and R is an adjacent nucleotide.

In some embodiments, n is 1, 2, or 3.

In some embodiments, X is-H or-OMe.

in some embodiments, the 5-position modified pyrimidine is selected from the group consisting of BPEdU, 2'-OMe-BPE-U, 2' -F-BPE-U, PBndU, 2'-OMe-PBn-U, 2' -F-PBn-U, POPdU, 2'-OMe-POP-U, 2' -F-POP-U, DPPdU, 2'-OMe-DPP-U, 2' -F-DPP-U, DBMdU, 2'-OMe-DBM-U, 2' -F-DBM-U, BHdU, 2'-OMe-BH-U, 2' -F-BH-U, BPEdC, 2'-OMe-BPE-C, 2' -F-BPE-C, PBndC, 2'-OMe-PBn-C, 2' -F-PBn-C, POPdC, 2'-OMe-POP-C, 2' -OMe-POP-C, DPPdC, 2'-F-DPP-C, DBMdC, 2' -OMe-DBM-C, 2 '-F-C, BHdC, 2' -OMe-DBM-C, 2'-OMe-PBn-C, POPdC, and 2' -BH-C.

In some embodiments, the present disclosure provides compounds comprising a structure of formula IIA or formula IIB:

Or a salt of any of these.

In some embodiments, each L is independently- (CH) ₂ ) _n -wherein n is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10.

wherein is R ₁ The point of attachment of the group to the L group.

In some embodiments, n is 1, 2, or 3.

In some embodiments, X is-H or-OMe.

In some embodiments of the present invention, in some embodiments,each R ₁ Independently selected from the group consisting of:

in some embodiments, the oligonucleotide comprises at least one modified pyrimidine as shown in FIG. 3 or FIG. 4, wherein each X is independently selected from the group consisting of-H, -OH, -OMe-O-allyl, -F, -OEt, -OPr, -OCH ₂ CH ₂ OCH ₃ 、NH ₂ And-azido.

In some embodiments, the present disclosure provides a compound selected from the group consisting of:

/>

or a salt of any of these.

In some embodiments, each X is independently selected from the group consisting of: -H, -OH, -O-methyl, -O-allyl, -O-ethyl, -O-propyl, -OCH ₂ CH ₂ OCH ₃ -fluoro, -t-butyldimethylsilyloxy, -NH ₂ And-azido.

In some embodiments, X is-H or-OMe.

In some embodiments, a compound is provided comprising a structure of formula III, formula IV, or formula V:

or a salt of any of these.

wherein is R ₁ The point of attachment of the group to the L group.

In some embodiments, n is 1, 2, or 3.

In some embodiments, X is-H or-OMe.

in any of the embodiments described herein, the oligonucleotide may be an aptamer. In some such embodiments, the oligonucleotide is an aptamer that specifically binds to a target polypeptide.

Preparation of oligonucleotides

The automated synthesis of oligodeoxynucleosides is a common practice in many laboratories (see e.g., matteuci, m.d. and Caruthers, m.h. (1990) j.am. Chem. Soc.,1033185-3191, the contents of which are hereby incorporated by reference in their entirety). OligoribonucleosidesSynthesis is also well known (see e.g. Scaringe, s.a., et al, (1990) Nucleic Acids Res).185433-5441, the contents of which are hereby incorporated by reference in their entirety). As described herein, phosphoramidites can be used to incorporate modified nucleosides into oligonucleotides by chemical synthesis, and triphosphates can be used to incorporate modified nucleosides into oligonucleotides by enzymatic synthesis. (see, e.g., vaught, J.D. et al (2004) J.am.chem.Soc.,12611231-11237; vaugh, J.V., et al (2010) J.am.chem.Soc.1324141-4151; gait, m.j. "Oligonucleotide Synthesis a practical approach" (1984) IRL Press (Oxford, UK); herdiewijn, p. "Oligonucleotide Synthesis" (2005) (Humana Press, totowa, n.j. (each of which is incorporated herein by reference in its entirety).

In some embodiments, the compounds provided herein can be used in standard phosphoramidite oligonucleotide synthesis methods, including automated methods using commercially available synthesizers.

In some embodiments, the use of a compound provided herein in oligonucleotide synthesis increases the yield of a desired oligonucleotide product.

SELEX process

The terms "SELEX" and "SELEX process" are used interchangeably herein and generally refer to a combination of (1) selecting a nucleic acid that interacts with a target molecule in a desired manner (e.g., binds to a protein with high affinity), and (2) amplifying the selected nucleic acid. The SELEX process can be used to identify aptamers that have high affinity for a particular target molecule or biomarker.

SELEX generally comprises: preparing a candidate mixture of nucleic acids; binding the candidate mixture to a desired target molecule to form an affinity complex; separating the affinity complex from unbound candidate nucleic acids; separating and isolating the nucleic acid from the affinity complex; purifying the nucleic acid; and identifying the specific aptamer sequence. The process may include multiple cycles to further increase the affinity of the selected aptamer. The process may include an amplification step at one or more points in the process. See, for example, U.S. Pat. No. 5,475,096 entitled "Nucleic Acid Ligands". The SELEX process can be used to generate aptamers that bind covalently to their targets as well as aptamers that bind non-covalently to their targets. See, for example, U.S. Pat. No. 5,705,337 entitled "Systematic Evolution of Nucleic Acid Ligands by Exponential Enrichment: chemi-SELEX".

The SELEX process can be used to identify high affinity aptamers containing modified nucleotides that impart improved characteristics to the aptamer, such as, for example, improved in vivo stability or improved delivery characteristics. Examples of such modifications include chemical substitutions at ribose and/or phosphate and/or base positions. Aptamers containing modified nucleotides identified by the SELEX process are described in U.S. patent No. 5,660,985, entitled "High Affinity Nucleic Acid Ligands Containing Modified Nucleotides," which describes oligonucleotides containing nucleotide derivatives chemically modified at the 5 '-and 2' -positions of a pyrimidine. U.S. Pat. No. 5,580,737 describes high specificity aptamers containing a peptide sequence consisting of 2 '-amino (2' -NH) ₂ ) One or more nucleotides modified by 2 '-fluoro (2' -F) and/or 2 '-O-methyl (2' -OMe). See also U.S. patent application publication No. 20090998549, entitled "SELEX and PHOTOSELEX," which describes nucleic acid libraries with extended physical and chemical properties and their use in SELEX and photoSELEX.

SELEX can also be used to identify aptamers with desirable off-rate characteristics. See U.S. patent No. 7,947,447, entitled "Method for Generating Aptamers with Improved Off-Rates," which is incorporated by reference herein in its entirety, describing an improved SELEX method for producing aptamers that can bind to target molecules. Methods for producing aptamers and photoaptamers are described, which dissociate at a slower rate from their respective target molecules. The method involves contacting a candidate mixture with a target molecule, allowing nucleic acid-target complexes to form, and performing a slow off-rate enrichment process in which nucleic acid-target complexes having a fast off-rate will dissociate and not re-form, while complexes having a slow off-rate remain intact. Additionally, the method includes using modified nucleotides in generating a candidate nucleic acid mixture to generate an aptamer with improved off-rate properties (see U.S. patent No. 8,409,795, entitled "SELEX and PhotoSELEX"). (see also, U.S. patent No. 7,855,054 and U.S. patent publication No. 20070166740). Each of these applications is incorporated by reference herein in its entirety.

"target" or "target molecule" or "target" herein refers to any compound upon which a nucleic acid can act in a desired manner. The target molecule may be, but is not limited to, a protein, peptide, nucleic acid, carbohydrate, lipid, polysaccharide, glycoprotein, hormone, receptor, antigen, antibody, virus, pathogen, toxic substance, substrate, metabolite, transitional analogue, cofactor, inhibitor, drug, dye, nutrient, growth factor, cell, tissue, any portion or fragment of any of the foregoing, and the like. Essentially any chemical or biological effector may be a suitable target. Molecules of any size can serve as targets. The target may also be modified in some manner to enhance the likelihood or strength of interaction between the target and the nucleic acid. The target may also include any minor change in a particular compound or molecule, such as in the case of a protein, e.g., minor changes in amino acid sequence, disulfide bond formation, glycosylation, lipidation, acetylation, phosphorylation, or any other manipulation or modification, such as conjugation with a labeling component that does not substantially alter the identity of the molecule. A "target molecule" or "target" is a set of copies of a molecular or multi-molecular structure of a type or class that is capable of binding to an aptamer. "target molecule" or "target" refers to more than one set of such molecules. An embodiment of the SELEX method in which the target is a peptide is described in U.S. patent No. 6,376,190 entitled "Modified SELEX Processes Without Purified Protein". In some embodiments, the target is a protein.

As used herein, "competitor molecule" and "competitor" are used interchangeably to refer to any molecule that can form a non-specific complex with a non-target molecule. In this context, a non-target molecule includes a free aptamer, wherein e.g. a competitor may be used to inhibit non-specific binding (re-binding) of the aptamer to another non-target molecule. A "competitor molecule" or "competitor" is a set of copies of a type or class of molecule. "competitor molecule" or "competitor" refers to more than one set of such molecules. Competitor molecules include, but are not limited to, oligonucleotides, polyanions (e.g., heparin, herring sperm DNA, salmon sperm DNA, tRNA, dextran sulfate, polydextrose, non-alkaline phosphodiester polymers, dntps, and pyrophosphates). In various embodiments, a combination of one or more competitors may be used.

As used herein, "non-specific complex" refers to a non-covalent association between two or more molecules other than an aptamer and its target molecule. The non-specific complexes represent interactions between molecular classes. Nonspecific complexes include complexes formed between an aptamer and a non-target molecule, a competitor and a target molecule, and a target molecule and a non-target molecule.

As used herein, the term "slow off-rate enrichment process" refers to a process that alters the relative concentration of certain components of a candidate mixture such that the relative concentration of aptamer affinity complexes having a slow off-rate increases relative to the concentration of aptamer affinity complexes having a faster, less desirable off-rate. In some embodiments, the slow off-rate enrichment process is a slow off-rate enrichment process based on a solution. Thus, the slow off-rate enrichment process based on a solution is performed in a solution such that neither the target nor the nucleic acid in the mixture that forms the aptamer affinity complex is immobilized on the solid support during the slow off-rate enrichment process. In various embodiments, the slow off-rate enrichment process can include one or more steps including adding and incubating with the competitor molecule, diluting the mixture, or a combination of these (e.g., diluting the mixture in the presence of the competitor molecule). Because the effect of the slow off-rate enrichment process is generally dependent on the different off-rates of the different aptamer affinity complexes (i.e., the aptamer affinity complexes formed between the target molecule and the different nucleic acids in the candidate mixture), the duration of the slow off-rate enrichment process is selected so as to preserve a high proportion of the aptamer affinity complexes with a slow off-rate while significantly reducing the number of aptamer affinity complexes with a fast off-rate. The slow off-rate enrichment process may be used in one or more cycles during the SELEX process. When the dilution and addition of competitors are used in combination, they may be performed simultaneously or sequentially in any order. When the total target (protein) concentration in the mixture is low, a slow off-rate enrichment process can be used. In some embodiments, when the slow off-rate enrichment process includes dilution, the mixture may be diluted as much as possible, bearing in mind that aptamer-retained nucleic acids are recovered in subsequent rounds in the SELEX process. In some embodiments, the slow off-rate enrichment process includes the use of competitors as well as dilution, allowing the mixture to be diluted below what may be required without the use of competitors.

In some embodiments, the slow off-rate enrichment process includes adding a competitor, and the competitor is a polyanion (e.g., heparin or dextran sulfate (dextran)). In previous SELEX selections, heparin or dextran has been used to identify specific aptamers. However, in such methods, heparin or dextran is present during the equilibration step of the target and aptamer binding to form a complex. In such methods, as the concentration of heparin or dextran increases, the ratio of high affinity target/aptamer complex to low affinity target/aptamer complex increases. However, due to competition for target binding between nucleic acid and competitor, high concentrations of heparin or dextran can reduce the number of high affinity target/aptamer complexes at equilibrium. In contrast, in some embodiments, the method adds competitors after allowing the target/aptamer complex to form, thus not affecting the number of complexes formed. The addition of competitors after equilibrium binding between target and aptamer creates an unbalanced state that evolves in time to a new equilibrium with less target/aptamer complex. Trapping the target/aptamer complex before a new equilibrium is reached can enrich the sample for slow off-rate aptamers, as fast off-rate complexes will dissociate first.

In other embodiments, a polyanionic competitor (e.g., dextran sulfate or another polyanionic material) is used during the slow off-rate enrichment process to facilitate identification of an aptamer that is difficult to present with a polyanion. In this context, a "polyanionic intolerant aptamer (polyanionic refractory aptamer)" is an aptamer that is capable of forming an aptamer/target complex that is less likely to dissociate in a solution that also contains a polyanionic intolerant material than an aptamer/target complex that contains a non-polyanionic intolerant aptamer. In this way, polyanionic intolerant aptamers can be used to perform analytical methods to detect the presence, amount, or concentration of a target in a sample, where the detection method includes the use of polyanionic materials (e.g., dextran sulfate) for which the aptamer is intolerant.

Thus, in some embodiments, a method for producing a polyanionic intolerant aptamer is provided. After contacting the candidate mixture of nucleic acids with the target, the nucleic acids in the target and candidate mixture are allowed to equilibrate. Polyanionic competitors were introduced and incubated in solution for a sufficient period of time to ensure that most of the rapid off-rate aptamers in the candidate mixture were dissociated from the target molecule. In addition, aptamers in the candidate mixture that are likely to dissociate in the presence of polyanionic competitors will be released from the target molecule. The mixture is partitioned to separate high affinity, slow off-rate aptamers that remain associated with the target molecule and any uncomplexed material is removed from the solution. The aptamer may then be released and isolated from the target molecule. The isolated aptamer may also be amplified and additional selection rounds applied to enhance the overall performance of the selected aptamer. This approach can also be used with minimal incubation times if it is not necessary to select a slow off-rate aptamer for a particular application.

Thus, in some embodiments, an improved SELEX method is provided for identifying or producing an aptamer having a slow (long) off-rate, wherein a target molecule and a candidate mixture are contacted and incubated together for a period of time sufficient for equilibrium binding to occur between the target molecule and the nucleic acid contained in the candidate mixture. After equilibration binding, an excess of competitor molecule, e.g., a polyanionic competitor, is added to the mixture and the mixture is incubated with the excess of competitor molecule for a predetermined period of time. A substantial portion of the aptamer having a rate of dissociation less than the predetermined incubation period will dissociate from the target within the predetermined incubation period. Because excess competitor molecules can bind non-specifically to the target and occupy the target binding site, re-association of these "rapid" off-rate aptamers with the target is minimized. A significant portion of the aptamer with a longer off-rate will remain complexed with the target for a predetermined incubation period. At the end of the incubation period, the nucleic acid-target complex is separated from the remainder of the mixture, allowing the slow off-rate aptamer population to separate from the aptamer population with the fast off-rate. The dissociation step can be used to dissociate the slow off-rate aptamer from its target and allow for the separation, identification, sequencing, synthesis and amplification of slow off-rate aptamers (single aptamer or a group of slow off-rate aptamers) with high affinity and specificity for the target molecule. As with conventional SELEX, the aptamer sequences identified from a round of modified SELEX procedure can be used to synthesize new candidate mixtures, so that the steps of contacting, equilibrating binding, adding competitor molecules, incubating with competitor molecules, and separating slow off-rate aptamers can be iterated/repeated as many times as desired.

The combination of allowing equilibrium binding of the candidate mixture to the target, followed by addition of excess competitor and incubation with the competitor for a predetermined period of time allows selection of populations of aptamers having much higher dissociation rates than those previously achieved.

To achieve equilibrium binding, the candidate mixture may be incubated with the target for at least about 5 minutes, or at least about 15 minutes, about 30 minutes, about 45 minutes, about 1 hour, about 2 hours, about 3 hours, about 4 hours, about 5 hours, or about 6 hours.

The predetermined incubation period of the competitor molecule with the candidate mixture and the mixture of target molecules may be selected as desired, taking into account factors such as the nature of the target and the known rate of dissociation (if any) of the known aptamer for the target. The predetermined incubation period may be selected from: at least about 5 minutes, at least about 10 minutes, at least about 20 minutes, at least about 30 minutes, at least about 45 minutes, at least about 1 hour, at least about 2 hours, at least about 3 hours, at least about 4 hours, at least about 5 hours, at least about 6 hours.

In other embodiments, dilution is used as the dissociation rate enhancement process, and incubation of the diluted candidate mixture, target molecule/aptamer complex, may be performed for a predetermined period of time, which may be selected from the group consisting of: at least about 5 minutes, at least about 10 minutes, at least about 20 minutes, at least about 30 minutes, at least about 45 minutes, at least about 1 hour, at least about 2 hours, at least about 3 hours, at least about 4 hours, at least about 5 hours, at least about 6 hours.

Some embodiments of the present disclosure relate to the identification, generation, synthesis, and use of slow off-rate aptamers. These are the dissociation rates (t _1/2 ) Higher than that normally obtained by conventional SELEX. For mixtures of non-covalent complexes containing aptamer and target, t _1/2 Represents the time taken for half of the aptamer to dissociate from the aptamer-target complex. T of slow off-rate aptamer according to the present disclosure _1/2 Selected from one of the following: greater than or equal to about 30 minutes; about 30 minutes to about 240 minutes; about 30 minutes to about 60 minutes; about 60 minutes to about 90 minutes, about 90 minutes to about 120 minutes; about 120 minutes to about 150 minutes; about 150 minutes to about 180 minutes; about 180 minutes to about 210 minutes; about 210 minutes to about 240 minutes.

The characteristic feature of an aptamer identified by the SELEX procedure is its high affinity for its target. The aptamer will have a dissociation constant (k) for its target selected from one of _d ): less than about 1 μM, less than about 100nM, less than about 10nM, less than about 1nM, less than about 100pM, less than about 10pM, less than about 1pM.

Oligonucleotide library

In some embodiments, a library of oligonucleotides comprising random sequences is provided. In some embodiments, such libraries may be used to perform SELEX. In some embodiments, each oligonucleotide in the library of oligonucleotides comprises a plurality of randomized positions, such as at least 20, 25, 30, 35, 40, 45, or 50, or 20-100, 20-80, 20-70, 20-60, 20-50, 20-40, or 30-40 randomized positions. In some embodiments, each oligonucleotide in the library of oligonucleotides comprises an immobilized sequence flanking the randomized position. Such fixed flanking sequences may be identical or different from each other (i.e., the 5 'flanking sequence and the 3' flanking sequence may be identical or different), and in some embodiments may be identical for all members of the library (i.e., all members of the library may have identical 5 'flanking sequences, and/or all members of the library may have identical 3' flanking sequences).

In some embodiments, the randomized positions can be comprised of four or more different nucleotide bases, wherein one or more of the nucleotide bases are modified. In some embodiments, all one type of nucleotide base is modified or unmodified (e.g., all cytidine in the randomized region is modified, or all unmodified). In some embodiments, one type of nucleotide base in the randomized region exists in a modified form and an unmodified form. In some such embodiments, the randomized positions consist of two modified nucleotide bases and two unmodified nucleotide bases. In some such embodiments, the randomized positions consist of adenine, guanine, C5-modified cytidine, and C5-modified uridine. Non-limiting exemplary C5-modified cytidine and C5-modified uridine are shown in FIGS. 2-6. For example, oligonucleotide libraries and methods of making the same are further described in the examples herein.

Exemplary aptamers

In some embodiments, aptamers that bind to a target molecule are provided. In some embodiments, the target molecule is a target protein.

In some embodiments, provided with IL-33 binding aptamer.

In some embodiments, the aptamer that binds IL-33 is 15 to 100, or 15 to 90, or 15 to 80, or 15 to 70, or 15 to 60, or 15 to 50, 20 to 100, or 20 to 90, or 20 to 80, or 20 to 70, or 20 to 60, or 20 to 50, or 30 to 100, or 30 to 90, or 30 to 80, or 30 to 70, or 30 to 60, or 30 to 50, or 40 to 100, or 40 to 90, or 40 to 80, or 40 to 70, or 40 to 60, or 40 to 50 nucleotides in length.

In some embodiments, an aptamer that binds XIAP is provided.

In some embodiments, the XIAP-binding aptamer is 15 to 100, or 15 to 90, or 15 to 80, or 15 to 70, or 15 to 60, or 15 to 50, 20 to 100, or 20 to 90, or 20 to 80, or 20 to 70, or 20 to 60, or 20 to 50, or 30 to 100, or 30 to 90, or 30 to 80, or 30 to 70, or 30 to 60, or 30 to 50, or 40 to 100, or 40 to 90, or 40 to 80, or 40 to 70, or 40 to 60, or 40 to 50 nucleotides in length.

In some embodiments, provides binding to K-Ras aptamer.

In some embodiments, the length of the aptamer that binds K-Ras is 15 to 100, or 15 to 90, or 15 to 80, or 15 to 70, or 15 to 60, or 15 to 50, 20 to 100, or 20 to 90, or 20 to 80, or 20 to 70, or 20 to 60, or 20 to 50, or 30 to 100, or 30 to 90, or 30 to 80, or 30 to 70, or 30 to 60, or 30 to 50, or 40 to 100, or 40 to 90, or 40 to 80, or 40 to 70, or 40 to 60, or 40 to 50 nucleotides.

In some embodiments, aptamers that bind TNF-alpha are provided.

In some embodiments, the aptamer that binds TNF- α is 15 to 100, or 15 to 90, or 15 to 80, or 15 to 70, or 15 to 60, or 15 to 50, 20 to 100, or 20 to 90, or 20 to 80, or 20 to 70, or 20 to 60, or 20 to 50, or 30 to 100, or 30 to 90, or 30 to 80, or 30 to 70, or 30 to 60, or 30 to 50, or 40 to 100, or 40 to 90, or 40 to 80, or 40 to 70, or 40 to 60, or 40 to 50 nucleotides in length.

In some embodiments, an aptamer that binds a target molecule (e.g., any of IL-33, XIAP, K-Ras, TNF- α) comprises a region of at least 10, at least 15, at least 20, at least 25, or at least 30 nucleotides in length, or 5 to 30, 10 to 30, 15 to 30, 5 to 20, or 10 to 20 nucleotides in length, at the 5 'end of the aptamer, wherein the region at the 5' end of the aptamer lacks a 5-position modified pyrimidine.

In some embodiments, an aptamer that binds a target molecule (e.g., any of IL-33, XIAP, K-Ras, TNF- α) comprises a region of at least 10, at least 15, at least 20, at least 25, or at least 30 nucleotides in length, or 5 to 30, 10 to 30, 15 to 30, 5 to 20, or 10 to 20 nucleotides in length at the 3 'end of the aptamer, wherein the region at the 3' end of the aptamer lacks a 5-position modified pyrimidine.

In some embodiments, a method of treating or preventing Traumatic Brain Injury (TBI) or rheumatoid arthritis is provided, comprising administering an aptamer provided herein to a subject in need thereof.

Salt

The corresponding salts of the compounds, e.g., pharmaceutically acceptable salts, may be conveniently or desirably prepared, purified and/or processed. Examples of pharmaceutically acceptable salts are shown in Berge et al (1977) "Pharmaceutically Acceptable Salts" J.Pharm.Sci.661-19.

For example, if the compound is anionic or has a functional group that can be anionic (e.g., -COOH can be-COO) ^- ) The salt may be formed with a suitable cation. Examples of suitable inorganic cations include, but are not limited to, alkali metal ions, such as Na ⁺ And K ⁺ The method comprises the steps of carrying out a first treatment on the surface of the Alkaline earth metal cations, e.g. Ca ²⁺ And Mg (magnesium) ²⁺ The method comprises the steps of carrying out a first treatment on the surface of the Other cations, e.g. Al ⁺³ . Examples of suitable organic cations include, but are not limited to, ammonium ions (i.e., NH ₄ ⁺ ) And substituted ammonium ions (e.g., NH ₃ R ^X+ 、NH ₂ R ^X ₂ ⁺ 、NHR ^X ₃ ⁺ 、NR ^X ₄ ⁺ ). Examples of some suitable substituted ammonium ions are those derived from: ethylamine, diethylamine, dicyclohexylamine, triethylamine, butylamine, ethylenediamine, ethanolamine, diethanolamine, piperazine, benzylamine, phenylbenzylamine, choline, meglumine and tromethamine, and amino acids such as lysine and arginine. Examples of common quaternary ammonium ions are N (CH ₃ ) ₄ ⁺ 。

If the compound is cationic or has a functional group that can be cationic (e.g., -NH) ₂ Can be-NH ₃ ⁺ ) Salt thenMay be formed with a suitable anion. Examples of suitable inorganic anions include, but are not limited to, those derived from the following inorganic acids: hydrochloric acid, hydrobromic acid, hydroiodic acid, sulfuric acid, sulfurous acid, nitric acid, nitrous acid, phosphoric acid, and phosphorous acid.

Examples of suitable organic anions include, but are not limited to, those derived from the following organic acids: 2-acetoxybenzoic acid, acetic acid, ascorbic acid, aspartic acid, benzoic acid, camphorsulfonic acid, cinnamic acid, citric acid, edetic acid, ethanedisulfonic acid, ethanesulfonic acid, fumaric acid, glucoheptonic acid, gluconic acid, glutamic acid, glycolic acid, oxaloacetic acid, hydroxynaphthalene carboxylic acid, hydroxyethanesulfonic acid, lactic acid, lactonic acid, lauric acid, maleic acid, malic acid, methanesulfonic acid, mucic acid, oleic acid, oxalic acid, palmitic acid, pamoic acid, pantothenic acid, phenylacetic acid, phenylsulfonic acid, propionic acid, pyruvic acid, salicylic acid, stearic acid, succinic acid, sulfanilic acid, tartaric acid, toluenesulfonic acid, and valeric acid. Examples of suitable polymeric organic anions include, but are not limited to, those derived from the following polymeric acids: tannic acid and carboxymethyl cellulose.

Unless otherwise specified, references to a particular compound also include salt forms thereof.

Kit comprising an aptamer

The present disclosure provides kits comprising any of the aptamers described herein. Such kits may comprise, for example, at least one aptamer; and the components may optionally include at least one of, for example: (a) A pharmaceutically acceptable carrier, such as a solvent or solution; (b) Pharmaceutically acceptable excipients, such as stabilizers or buffers; (c) At least one container, vial or device for holding and/or mixing the kit components; and (d) a delivery device. The kit may optionally further comprise one or more of the following: (e) A labeling agent useful for detecting a target molecule bound to an aptamer; (f) a solid support, such as a microarray or bead; and (g) reagents related to the quantification of the polymerase chain reaction products, such as intercalating fluorescent dyes or fluorescent DNA probes.

Examples

The following examples are presented in order to more fully illustrate some embodiments of the invention. However, these examples should in no way be construed as limiting the broad scope of the invention. One of ordinary skill in the art can readily devise various compounds that employ the basic principles of the present discovery without departing from the spirit of the invention.

General procedure for purification of nucleoside triphosphates by anion exchange HPLC.

The nucleoside triphosphates were purified via anion exchange chromatography using an HPLC column loaded with Source Q resin (GE Healthcare), which was mounted on a preparative HPLC system and detected at 278 nm. The linear elution gradient was run from low buffer B content to high buffer B content at ambient temperature during elution using two buffers (buffer A:10mM triethylammonium bicarbonate/10% acetonitrile, and buffer B:1M triethylammonium bicarbonate/10% acetonitrile). The desired product is typically the final material eluted from the column and is observed as a broad peak spanning about ten to twelve minutes of retention time (early eluting products include a variety of reaction byproducts, most importantly nucleoside bisphosphates). Several fractions were collected during product elution. Fractions were analyzed by reverse phase HPLC on a Waters 2795HPLC with a Waters Symmetry column (PN: WAT 054215). The pure product containing fractions (typically > 90%) were evaporated in a Genevac HT-12 evaporator to give a colorless to light brown resin.

General procedure for reversed phase HPLC purification of nucleoside triphosphates.

The nucleoside triphosphates were purified via reverse phase chromatography using a Waters Novapak C8,30mm by 300mm column (PN: 186002473) mounted on a Waters preparative HPLC system, detection at 278 nm. The linear elution gradient used two buffers (buffer A:100mM triethylammonium bicarbonate and buffer B:100% acetonitrile) and the gradient was run from low buffer B content to high buffer B at ambient temperature during elution. The desired product is typically the final material eluted from the column and is observed as a broad peak spanning about five to twelve minutes of retention time (early eluting product includes a variety of reaction byproducts). Several fractions were collected during product elution. Fractions were analyzed by reverse phase HPLC on a Waters 2795HPLC with a Waters Symmetry column (PN: WAT 054215). The pure product containing fractions (typically > 90%) were evaporated in a Genevac HT-12 evaporator to give a colorless to light brown resin.

Fractions were reconstituted in deionized water and pooled for final analysis. Product quantification was performed by analysis using a Hewlett Packard 8452A diode array spectrophotometer at 278 nm. The product yield was calculated via equation a=epsilon CL, where a is the uv absorbance, epsilon is the estimated extinction coefficient and L is the path length (1 cm).

Example 1: preparation of modified deoxycytidine

Step 1: synthesis of 5- (N-carboxamide) -2' -deoxycytidine derivatives (scheme 1, product 2):

commercially available 5-iodo-2' -deoxycytidine (scheme 1, product 1) was charged into a round bottom flask and dissolved in anhydrous N, N-Dimethylformamide (DMF). By using the essential aromatic primary amine (RCH ₂ NH ₂ 4-8 equivalent weight) of CO</(=1 atm) and (Ph) ₃ P) ₄ Pd (2 mol%) was treated at room temperature for 24-48 hours to convert the starting material to the corresponding N-substituted carboxamide. The progress of the reaction was monitored by thin layer chromatography (silica gel, eluent: 8-12% methanol/dichloromethane) or reverse phase HPLC (Waters 2795HPLC with 2489 detector and using Waters Symmetry column, buffer A:100mM triethylammonium acetate, buffer B: acetonitrile, gradient: 30% -70% buffer B over 30 min). The resulting crude reaction mixture was filtered through a celite bed to remove excess catalyst and solid byproducts. The filtrate was then diluted in dichloromethane and washed with deionized water to remove excess DMF, resulting in the formation of a white to off-white crystalline solid in the dichloromethane layer. The organic layer containing the solid material was collected in a schottky bottle and stirred at room temperature for several hours to overnight, then filtered and the solid was washed with dichloromethane. The filter cake is dried in vacuo and the resulting white to off-white solid, 5-modified cytidine carboxamide, is recovered in about 50% -70% yield.

Step 2: synthesis of 4-N-acetyl-5- (N-carboxamide) -2' -deoxycytidine derivative (scheme 1, product 3):

the product of step 1 was charged to a round bottom flask, dissolved in anhydrous N, N-Dimethylformamide (DMF) and treated with the appropriate anhydride (acetic anhydride or propionic anhydride, 2 equivalents) and the mixture was stirred at room temperature to 40 ℃ under argon for at least 18 hours. The progress of the reaction was monitored by HPLC (Waters 2795HPLC with 2489 detector and using Waters Symmetry column, buffer A:100mM triethylammonium acetate, buffer B: acetonitrile, gradient: 30% -70% buffer B, over 30 min). After the reaction was completed, the crude mixture was diluted in ethyl acetate, transferred to a separatory funnel and washed with 2% sodium bicarbonate solution (1X), deionized water (1X) and brine (1X). The organic layer was collected in a schottky bottle and stirred at room temperature for several hours to overnight during which time a white to off-white crystalline solid formed. The mixture was filtered and the solids and glassware were washed with ethyl acetate. The filter cake is dried in vacuo and the resulting white to off-white solid, 4-N-acetyl-5-modified cytidine carboxamide, is recovered in about 50% -70% yield.

Step 3: synthesis of 5' -O- (4, 4' -dimethoxytrityl) -4-N-acetyl-5- (N-carboxamide) -2' -deoxycytidine derivative (scheme 1, product 4):

The product of step 2 was dissolved in anhydrous pyridine under argon in a round bottom flask with magnetic stirring. 4,4' -Dimethoxytrityl chloride (1.1 eq.) was added to the stirred mixture in four to five portions over one hour. The reaction was stirred for an additional hour, then quenched with ethanol (6 eq) and the reaction mixture evaporated to a viscous residue. The crude material was dissolved in ethyl acetate and washed with 2% sodium bicarbonate (1×), dried over sodium sulfate, filtered and evaporated to an orange yellow foam. The crude material was purified by flash column chromatography (silica gel pretreated with 1% triethylamine/99% ethyl acetate; product eluted with 75% ethyl acetate/25% hexane). The product-containing fractions were concentrated to provide white to off-white foam in 70% -80% yield.

Step 4: synthesis of 5'-O- (4, 4' -dimethoxytrityl) -4-N-acetyl-5- (N-carboxamide) -2 '-deoxycytidine-3' -O- (N, N-diisopropyl-O-2-cyanoethyl phosphoramidite) derivative (scheme 1, product 5):

in a round bottom flask with magnetic stirring in argonThe product of step 3 was dissolved under gas in anhydrous dichloromethane. To the reaction mixture was added 2-cyanoethyl-N, N' -tetraisopropylphosphine (1.5 eq) followed by pyridine trifluoroacetate (1.7 eq). The reaction was stirred for 30-60 minutes and then analyzed by thin layer chromatography (silica gel, eluent: 50-60% ethyl acetate/hexanes) to show completion of the reaction. The crude mixture was applied to a silica gel flash column preconditioned with 1% triethylamine/99% ethyl acetate and equilibrated with 60% ethyl acetate/40% hexane. Eluting the product with the same mobile phase, cooling to 0 ^℃ And purged with argon and collected in an argon purged bottle. The product-containing fractions were concentrated to provide white to off-white foam in 70% -80% yield.

Scheme 1

To prepare the 2-cyanoethyl phosphoramidite reagent (CEP reagent), the 5- (N-carboxamide) -2 '-deoxycytidine derivative is optionally N-protected, then 5' o-protected as (4, 4 '-dimethoxytrityl) -derivative (4) by reaction with 4,4' -dimethoxytrityl chloride in pyridine (see, e.g., ross et al, nucleotides & Nucleic Acids,25,765-770 (2006)). The synthesis of CEP reagent (5) of high purity (> 98%) is accomplished by pyridinium trifluoroacetate catalyzing the condensation of 3 '-alcohol with 2-cyanoethyl-N, N' -tetraisopropylphosphine (see, e.g., sanghvi et al, organic Process Research & Development,4,175-181 (2000)) and final purification by silica gel flash chromatography with a degassing solvent (see, e.g., still et al, j. Org. Chem.,43,2923-2925 (1978)).

To prepare the 5 '-triphosphate reagent (TPP reagent, scheme 2), the 5' o-DMT protected nucleoside (scheme 1 or scheme 2, product 4) was acetylated with acetic anhydride in pyridine followed by cleavage of the DMT and 4-N-acetyl protecting groups with 1,3, -hexafluoro-2-propanol (scheme 2, product 6) (see, e.g., leonard and Neelima, tetrahedron Letters,36 (43), 7833-7836 (1995)). The resulting crystalline 3 '-O-acetylated nucleoside was converted to crude 5' -O-triphosphate by the Ludwig-Eckstein method (Ludwig, J. And Eckstein, F.J. org. Chem.,1989, 54:631) (scheme 2, product 7). These chemically modified nucleotides typically require a two-stage purification process: anion exchange chromatography (AEX) followed by reverse phase preparative HPLC in order to obtain high purity (> 90%).

Example 1-1: preparation of 5- [ (N- (3, 3-diphenylpropyl) carboxamide ] -2' -deoxycytidine (DPPdC) derivatives

5- [ N- (3, 3-diphenylpropyl) carboxamide]-synthesis of 2' -deoxycytidine nucleosides (scheme 1, product 2): commercially available 5-iodo-2' -deoxycytidine (scheme 1, product 1, 20g,56.8 mmol) was charged into a round bottom flask and dissolved in anhydrous N, N-dimethylformamide (DMF, 137 mL). By using the necessary aromatic primary amine (3, 3-diphenylpropylamine, (51.6 g,244mmol,4.3 eq.) and CO</(1 atm), bis (dibenzylideneacetone) palladium (0) (1.14 g,2mmol,0.035 eq.) and triphenylphosphine (2.34 g,8.5mmol,0.15 eq.) were treated at room temperature for 24-48 hours to convert the starting materials to the corresponding N-substituted carboxamides. The progress of the reaction was monitored by thin layer chromatography (silica gel, eluent: 8-12% methanol/dichloromethane) or reverse phase HPLC (Waters 2795HPLC with 2489 detector and using Waters Symmetry column, buffer A:100mM triethylammonium acetate, buffer B: acetonitrile, gradient: 30% -70% buffer B over 30 min). The resulting crude reaction mixture was filtered through a celite bed to remove excess catalyst and solid byproducts. The filtrate was then diluted in dichloromethane and washed with deionized water to remove excess DMF, resulting in the formation of a white to off-white crystalline solid in the dichloromethane layer. The organic layer containing the solid material was collected in a schottky bottle and stirred at room temperature for several hours to overnight, then filtered and the solid was washed with dichloromethane. The filter cake was dried in vacuo and the resulting white to off-white solid, 5-modified cytidine carboxamide (14.65 g,56% yield) was recovered. ¹ H-NMR(300mHz,DMSO-d ₆ ):δ＝8.37(s,1H),8.14(t,J＝5.3Hz,1H),7.99(bs,1H),7.69(bs,1H),7.24-7.33(m,8H),7.13-7.21(m,2H),6.12(t,J＝6.3Hz,1H),5.24(d,J＝4.2Hz,1H),5.09(t,J＝5.6Hz),4.22-4.30(m,1H),4.03(t,J＝7.8Hz,1H),3.83(t,J _A ＝7.5,J _B ＝3.9Hz,1H),3.55-3.72(m,2H),3.08(dd,J _A ＝13.5,J _B ＝6.0Hz,2H),2.10-2.32(m,4H). ¹³ C-NMR(100mHz,DMSO-d ₆ ):δ＝170.53(1C),165.72(1C),163.98(1C),153.93(1C),145.19(2C),145.14(2C),144.13(1C),128.91(4C),128.09(2C),128.07(2C),126.59(2C),99.74(1C),86.44(1C),85.59(1C),75.07(1C),61.68(1C),48.52(1C),38.37(1C),37.93(1C),34.67(1C),21.32(1C)。C ₂₅ H ₂₈ N ₄ O ₅ MS (m/z) calculated value of (c): 464.52, found: 463.2[ M-H ]] ^- (ESI ^- )。

4-N-acetyl-5- [3, 3-diphenylpropyl ] carboxamide]-synthesis of 2' -deoxycytidine nucleosides (scheme 1, product 3): the product of the previous step (scheme 1, product 2, 14.5g,31.2 mmol)) was charged to a round bottom flask, dissolved in anhydrous N, N-dimethylformamide (DMF, 284 mL) and treated with acetic anhydride (5.9 mL,62mmol,2 eq.) and the mixture stirred under argon at room temperature to 40℃for about 5.5 hours. The progress of the reaction was monitored by HPLC (Waters 2795HPLC with 2489 detector and using Waters Symmetry column, buffer A:100mM triethylammonium acetate, buffer B: acetonitrile, gradient: 30% -70% buffer B, over 30 min). After the reaction was completed, the crude mixture was diluted in ethyl acetate, transferred to a separatory funnel and washed with 2% sodium bicarbonate solution (1X), deionized water (1X) and brine (1X). The organic layer was collected in a schottky bottle and stirred at room temperature for several hours to overnight during which time a fine crystalline solid formed. The mixture was filtered and the solids and glassware were washed with ethyl acetate. The filter cake was dried in vacuo and the resulting white to off-white solid product (12.04 g,76% yield) was recovered. ¹ H-NMR(300mHz,DMSO-d ₆ ):δ＝11.32(s,1H),8.70(s,1H),8.36-8.45(m,1H),7.23-7.36(m,8H),7.11-7.20(m,2H),6.09(t,J＝5.7Hz,1H),5.24-5.31(m,1H),4.22-4.32(m,1H),3.88-3.94(m,1H),3.57-3.75(m,2H),3.05-3.16(m,2H),2.36-2.41(bs,3H),2.14-2.36(m,4H). ¹³ C-NMR(100mHz,DMSO-d ₆ ):δ＝170.63(1C),164.80(1C),159.17(1C),152.64(1C),145.45(1C),144.58/144.56(2C),144.56(1C),128.36(4C),127.52(4C),126.03(2C),99.94(1C),88.09(1C),86.89(1C),69.35(1C),60.55(1C),47.92(1C),40.51(1C),37.98(1C),33.91(1C),26.10(1C)。C ₂₇ H ₃₀ N ₄ O ₆ MS (m/z) calculated value of (c): 506.56, found: 505.3[ M-H ]] ^- (ESI ^- )。

5'-O- (4, 4' -Dimethoxytrityl) -4-N-acetyl-5- [ N- (3, 3-diphenylpropyl) carboxamide]-synthesis of 2' -deoxycytidine (scheme 1, product 4): the product of the previous step (scheme 1, product 3, 12.2g,24.1 mmol) was dissolved in anhydrous pyridine (80 mL) under argon in a round bottom flask with magnetic stirring. 4,4' -Dimethoxytrityl chloride (9.2 g,27.0mmol,1.1 eq.) was added to the stirred mixture in four portions over the course of one hour. The reaction was stirred for an additional hour, then quenched with ethanol (9.5 mL,163mmol,6.8 eq.) and the reaction mixture evaporated to a viscous residue. The crude material was dissolved in ethyl acetate, transferred to a separatory funnel and washed with 2% sodium bicarbonate (1X). The organic layer was collected and dried over sodium sulfate, filtered and evaporated to an orange yellow foam. The crude material was purified by flash column chromatography (silica gel pretreated with 1% triethylamine/99% ethyl acetate; product eluted with 80% -90% ethyl acetate 20% -10% hexane). The product containing fractions were concentrated to provide a white to off-white foam (15.27 g,78% yield). ¹ H-NMR(300mHz,DMSO-d ₆ ):δ＝11.36(s,1H),8.57(t,J＝4.5Hz,1H),8.37(s,1H),7.09-7.39(m,19H),6.72-6.87(d,4H),6.10(t,J＝6.0Hz,1H),5.15(d,J＝4.5Hz,1H),4.35(dt,J _A ＝9.9,J _B ＝4.5Hz 1H),4.08-3.98(m,1H),3.92(t,J＝7.5Hz,1H),3.68(d,J＝2.4Hz,6H),3.17-3.31(m,2H),2.78-3.02(m,2H),2.33-2.46(m,4H),2.17-2.29(m,1H),1.92-2.11(m,2H). ¹³ C-NMR(100mHz,DMSO-d ₆ ):δ＝170.61(1C),164.61(1C),159.26(1C),157.93/157.90(2C),152.54(1C),144.97(1C),144.65(1C),144.23(2C),135.40/135.35(2C),129.57(1C),129.49(1C),128.34(4C),127.66 1C),127.54(1C),127.41/127.40(4C),126.51(1C),126.04(2C),113.00(4C),99.94(1C),87.39(1C),86.32(1C),85.60(1C),69.90(1C),59.66(1C),54.85/54.82(2C),48.27(1C),40.37(1C),38.16(1C),33.73(1C),26.13(1C)。C ₄₈ H ₄₈ N ₄ O ₈ MS (m/z) calculated value of (c): 808.93, found: 807.3[ M-H ] ] ^- (ESI ^- )。

5'-O- (4, 4' -Dimethoxytrityl) -4-N-acetyl-5- [ N- (3, 3-diphenylpropyl) carboxamide]-synthesis of 2 '-deoxycytidine-3' -O- (N, N-diisopropyl-O-2-cyanoethyl phosphoramidite) (scheme 1, product 5): the product of the previous step (scheme 1, product 4, 14.0g,17.3 mmol) was dissolved in anhydrous dichloromethane (43 mL) under argon in a round bottom flask with magnetic stirring. To the reaction mixture was added 2-cyanoethyl-N, N, N ', N' -tetraisopropylphosphine (8.2 mL,26mmol,1.5 eq.) followed by pyridinium trifluoroacetate (5.4 g,28.2mmol,1.6 eq.). The reaction was stirred for 30 minutes and then analyzed by thin layer chromatography (silica gel, eluent: 60% ethyl acetate/40% hexane) and analysis showed completion of the reaction. The crude mixture was applied to a silica gel flash column preconditioned with 1% triethylamine/99% ethyl acetate and equilibrated with 60% ethyl acetate/40% hexane. Eluting the product with the same mobile phase, cooling to 0 ^℃ And purged with argon and collected in an argon purged bottle. The product containing fractions were concentrated to provide a white to off-white foam (13.85 g,79% yield). ¹ H-NMR(300mHz,DMSO-d ₆ ):δ＝11.36(s,1H),8.56(bt,1H),8.41-8.47(d,1H),7.11-7.37(m,19H),6.74-6.83(d,4H),6.03-6.10(m,1H),4.30-4.44(m,1H),4.12-4.22(m,1H),3.91(dd,J _A ＝14.1,J _B ＝7.5Hz,1H),3.63-3.78(m,7H),3.43-3.62(m,3H),3.22-3.37(m,2H),2.79-3.02(m,2H),2.75(t,J＝6.0Hz,1H),2.64(t,J＝6.0,Hz,1H),2.33-2.45(m,5H),1.94-2.08(m,2H),1.11(dd,J _A ＝12.3,J _B ＝6.6Hz 12H),0.97(d,J＝6.6Hz,3H). ³¹ P-NMR(300mHz,DMSO-d ₆ ):δ＝147.56/147.56(s,1P)。C ₅₇ H ₆₅ N ₆ O ₉ MS (m/z) calculated value of P: 1009.15, found: 1007.3[ M-H ]] ^- (ESI ^- )。

5- [ N- (3, 3-diphenylpropyl) carboxamide ]-synthesis of 3 '-O-acetyl-2' -deoxycytidine nucleoside (scheme 2, product 6): in a round bottom flask with magnetic stirring, the starting material (scheme 2, product 4,1.26g,1.56 mmol) was dissolved in anhydrous pyridine (10 mL) under argon. Acetic anhydride (1 mL,10.5mmol,6.7 eq.) was added dropwise to the stirred mixture. The reaction was stirred for 29 hours and detected by HPLC (with 2489Waters 2795HPLC using a Waters Symmetry column, buffer A:100mM triethylammonium acetate, buffer B: acetonitrile, gradient: 75% buffer B, isocratic over 30 minutes) monitors the progress of the reaction. The crude mixture was evaporated, and acetone was co-evaporated twice to recover a pale yellow foam. The residue was dissolved in 1, 3-hexafluoro-2-propanol (10 mL,95 mmol)) and heated at about 50℃for 16 hours (Leonard, N.J. tetrahedron Letters,1995, 36:7833). Complete cleavage of the DMT group was confirmed by TLC (5% methanol/dichloromethane). The red solution was quenched by pouring into well-stirred methanol (approximately 75 mL). The resulting yellow solution was concentrated in vacuo and the residue was dissolved in hot ethyl acetate (20 mL). After cooling the product crystallized and the resulting slurry was stirred at 0 ℃, then filtered and washed with ethyl acetate. 3' -O-acetyl-nucleoside (product 6) was isolated as a white solid (0.55 g,70% yield). ¹ H-NMR(300mHz,DMSO-d ₆ ):δ＝8.38(s,1H),8.26(bt,J＝4.8Hz,1H),8.04(bs,1H),7.77(bs,1H),7.24-7.41(m,8H),7.12-7.23(m,2H),6.17(t,J＝6.9Hz,1H),5.23-5.30(m,1H),5.18(t,J＝5.3Hz,1H),3.98-4.14(m,2H),3.62-3.77(m,2H),3.10(dd,J _A ＝12.3,J _B ＝6.6Hz,2H),2.35-2.48(m,2H),2.22-2.35(m,2H),2.08(s,3H). ¹³ C-NMR(100mHz,DMSO-d ₆ ):δ＝170.53(1C),165.72(1C),163.98(1C),153.93(1C),145.19(2C),145.14(2C),144.13(1C),128.91(4C),128.09(2C),128.07(2C),126.59(2C),99.74(1C),86.44(1C),85.59(1C),75.07(1C),61.68(1C),48.52(1C),38.37(1C),37.93(1C),34.67(1C),21.32(1C)。C ₂₇ H ₃₀ N ₄ O ₆ MS (m/z) calculated value of (c): 506.56, found: 506.2[ M-H ]] ^- (ESI ^- )。

5- [ N- (3, 3-diphenylpropyl) carboxamide]-synthesis of 2 '-deoxycytidine-5' -O-triphosphate (tri-triethylammonium salt) (7): the triphosphate (7) was synthesized from 3' -O-acetyl-nucleoside (6) by the procedure of Ludwig and Eckstein (Ludwig, J. And Eckstein, F.J. org. Chem.1989, 54:631) on a 500. Mu. Mol scale (5X). After ammonolysis and evaporation, the crude triphosphate product was purified by anion exchange chromatography and reverse phase chromatography as described in general procedure (above). [ epsilon ] _est. 13.700cm ^-1 M ^-1 ]The isolated purified product was 59.8. Mu. Mol (productRate 12%). ¹ H-NMR(300mHz,D ₂ O):δ＝7.95(s,1H),7.22-7.28(m,4H),7.11-7.19(m,4H),6.97-7.05(m,2H),6.05(t,J＝6.8Hz,1H),4.51(quintet,J＝3.0Hz,1H),4.10-4.17(m,3H),3.92(t,J＝7.5Hz,1H),3.29-3.40(m,1H),3.18.-3.29(m,1H),3.00(q,J＝7.5Hz,19H),2.25-2.37(m,3H),2.11-2.22(m,1H),1.11(t,J＝7.2Hz,29H). ¹³ C-NMR(80mHz,DMSO-d ₆ ):δ＝165.52(1C),163.55(1C),155.78(1C),145.35/145.38(2C),142.70(1C),128.81(4C),127.45(4C),126.18/126.20(2C),100.74(1C),86.84(1C),85.86/85.98(1C),70.70(1C),65.27/65.34(1C),49.60(1C),46.50(3C),39.76(1C),39.01(1C),33.50(1C),8.17(3C). ³¹ P-NMR(100mHz,D ₂ O):δ＝-9.94(d,J＝16.7Hz,1P),-11.60(d,J＝17.0Hz,1P),-23.30(t,J＝17Hz,1P)。C ₂₅ H ₃₀ N ₄ O ₁₄ P ₃ MS (m/z) calculated value of (c): 703.45, found: 703.1[ M-H] ^- (ESI ^- )。

Examples 1-2: preparation of 5- [ N- (4-phenylbenzyl) carboxamide ] -2' -deoxycytidine (PBndC) derivatives

5- [ N- (4-phenylbenzyl) carboxamide]-synthesis of 2' -deoxycytidine nucleosides (scheme 1, product 2): commercially available 5-iodo-2' -deoxycytidine (scheme 1, product 1, 20.87g,69.1 mmol) was charged into a round bottom flask and dissolved in anhydrous N, N-dimethylformamide (DMF, 150 mL). By using 4-phenylbenzylamine (47.83 g,261mmol,4.2 eq.) and carbon monoxide</(1 atm), bis (dibenzylideneacetone) palladium (0) (1.25 g,2.17mmol,0.035 eq.) and triphenylphosphine (2.54 g,9.7mmol,0.15 eq.) were treated at room temperature for 24-48 hours to convert the starting materials to the corresponding N-substituted carboxamides. The progress of the reaction was monitored by thin layer chromatography (silica gel, eluent: 8-12% methanol/dichloromethane) or reverse phase HPLC (Waters 2795HPLC with 2489 detector and using Waters Symmetry column, buffer A:100mM triethylammonium acetate, buffer B: acetonitrile, gradient: 30% -70% buffer B over 30 min). The resulting crude reaction mixture was filtered through a celite bed to remove excess catalyst and solid byproducts. The filtrate was then diluted in dichloromethane and washed with deionized water to remove excess DMF, resulting in a water layer and a dichloromethane layer A white to off-white crystalline solid formed. Each layer containing the solid material was collected separately in its own schottky bottle and stirred at room temperature for several hours to overnight, then filtered and the solid was washed with dichloromethane. The filter cake was dried in vacuo and the resulting white to off-white solid, 5-modified cytidine carboxamide (17.00 g,63% yield) was recovered. ¹ H-NMR(300mHz,DMSO-d ₆ ):δ＝8.85(t,J＝5.6Hz,1H),8.49(s,1H),7.62-7.73(m,4H),7.36-7.52(m,5H),6.20(t,J＝6.4Hz,1H),5.30(d,J＝4.4Hz,1H),5.12(t,J＝5.4,1H),4.43-4.56(m,2H),4.28-4.34(1H),3.88(dd,J _A ＝7.8,J _B ＝4.2Hz),3.60-3.73(d,J＝4.2Hz,2H),2.24(t,J＝6.0,1H). ¹³ C-NMR(100mHz,DMSO-d ₆ ):δ＝166.70(1C),164.75(1C),154.77(1C),145.08(1C),141.20(1C),140.04(1C),139.70(1C),130.18(2C),129.03(2C),128.59(2C),127.92(2C),127.82(2C),99.98(1C),88.88(1C),87.07(1C),71.24(1C),62.28(1C),43.24(1C),41.41(1C)。C ₂₃ H ₂₄ N ₄ O ₅ MS (m/z) calculated value of (c): 436.47, found: 435.2[ M-H ]] ^- (ESI ^- )。

4-N-propionyl-5- [ (4-phenylbenzyl) carboxamide]-synthesis of 2' -deoxycytidine nucleoside (scheme 1, product 3): the product of the previous step (scheme 1, product 2, 16.83g,38.62 mmol) was charged to a round bottom flask, dissolved in anhydrous N, N-dimethylformamide (DMF, 350 mL) and treated with propionic anhydride (10 mL,80mmol,2 eq.) and the mixture stirred under argon at 40℃for about 6 hours. The progress of the reaction was monitored by HPLC (Waters 2795HPLC with 2489 detector and using Waters Symmetry column, buffer A:100mM triethylammonium acetate, buffer B: acetonitrile, gradient: 30% -70% buffer B, over 30 min). After the reaction was completed, the crude mixture was diluted in dichloromethane, transferred to a separatory funnel and washed with deionized water (1×). The organic and aqueous layers were collected in separate schottky flasks and stirred at room temperature for several hours to overnight during which time a fine crystalline solid formed. The resulting mixture was filtered and the solids and glassware were washed with ethyl acetate. The filter cake was dried in vacuo and the resulting white to off-white solid product (12.74 g,767% yield) was recovered. ¹ H-NMR(300mHz,DMSO-d ₆ ):δ＝11.39(s,1H),9.03(t,J＝5.7Hz,1H),8.76(s,1H),7.62-7.69(m,4H),7.41-7.50(m,4H),7.33-7.40(m,1H),6.12(t,J＝6.2Hz,1H),5.30(d,J＝4.2Hz,1H),5.13(t,J＝5.3,1H),4.40-4.58(m,2H),4.23-4.34(1H),3.93(dd,J _A ＝7.8,J _B ＝3.9Hz,1H),3.58-3.76(d,J＝4.2Hz,2H),2.81(dd,J _A ＝14.7,J _B ＝7.2Hz,2H),2.31-2.48(m,1H),2.18-2.29(m,1H),1.06(t,J＝7.4Hz,3H). ¹³ C-NMR(80mHz,DMSO-d ₆ ):δ＝174.58(1C),165.58(1C),159.75(1C),153.28(1C),146.18(1C),140.42(1C),139.38(1C),138.46(1C),129.39(2C),128.41(2C),127.83(1C),127.14(2C),127.06(2C),100.49(1C),88.69(1C),87.49(1C),70.15(1C),61.22(1C),42.75(1C),40.98(1C),31.74(1C),9.04(1C)。C ₂₆ H ₂₈ N ₄ O ₆ MS (m/z) calculated value of (c): 492.53, found: 491.2[ M-H ]] ^- (ESI ^- )。

5'-O- (4, 4' -Dimethoxytrityl) -4-N-acetyl-5- [ N- (4-phenylbenzyl) carboxamide]-synthesis of 2' -deoxycytidine derivatives (scheme 1, product 4): the product of the previous step (16.01 g,32.5 mmol) was dissolved in anhydrous pyridine (108 mL) under argon in a round bottom flask with magnetic stirring. 4,4' -Dimethoxytrityl chloride (13.13 g,38.8mmol,1.1 eq.) was added to the stirred mixture in five portions over the course of one hour. The reaction was stirred for an additional fifteen minutes, then quenched with ethanol (11.5 mL,195mmol,6 eq.) and the reaction mixture evaporated to a viscous residue. The crude material was dissolved in warm dichloromethane, transferred to a separatory funnel and washed with 2% sodium bicarbonate (1X). The organic layer was collected and dried over sodium sulfate, filtered and evaporated to an orange yellow foam. The crude material was purified by flash column chromatography (silica gel pretreated with 1% triethylamine/99% ethyl acetate; product eluted with 80% -90% ethyl acetate 20% -10% hexane). The product containing fractions were concentrated to provide a white to off-white foam (15.27 g,78% yield). ¹ H-NMR(300mHz,DMSO-d ₆ ):δ＝11.49(s,1H),9.13(t,J＝5.3Hz,1H),8.49(s,1H),7.59-7.68(m,2H),7.52-7.59(m,2H),7.42-7.51(m,2H),6.12(t,J＝6.0Hz,1H),5.33(d,J＝4.5Hz,1H),4.26(d,J＝5.1Hz,2H),4.13-4.22(m,1H),4.00-4.09(m,1H),3.71(bs,6H),3.19-3.33(m,2H),2.83(dd,J _A ＝14.4,J _B ＝7.2,2H),2.35-2.46(m,1H),2.21-2.33(m,1H),1.07(t,J＝7.4Hz,3H). ¹³ C-NMR(100mHz,DMSO-d ₆ ):δ＝174.59(1C),165.47(1C),159.84(1C),158.53(1C),153.15(1C),146.06(1C),145.28(1C),140.35(1C),139.41(1C),138.13(1C),136.00(1C),130.17(1C),130.11(1C),129.39(2C),128.49(2C),128.13(1C),127.85(1C),127.14(1C),127.07(2C),127.04(2C),113.61(4C),100.48(1C),87.98(1C),86.19(1C),70.70(1C),64.41(1C),55.41(2C),42.79(1C),40.73(1C),31.83(1C),9.04(1C)。C ₄₇ H ₄₆ N ₄ O ₈ MS (m/z) calculated value of (c): 794.90, found: 793.3[ M-H ] ] ^- (ESI ^- )。

5'-O- (4, 4' -Dimethoxytrityl) -4-N-acetyl-5- [ N- (4-phenylbenzyl) carboxamide]-synthesis of 2 '-deoxycytidine-3' -O- (N, N-diisopropyl-O-2-cyanoethyl phosphoramidite) (scheme 1, product 5): the product of step 3 (scheme 1, product 4, 11.88g,14.9 mmol) was dissolved in anhydrous dichloromethane (38 mL) under argon in a round bottom flask with magnetic stirring. To the reaction mixture was added 2-cyanoethyl-N, N, N ', N' -tetraisopropylphosphine (8 mL,25.2mmol,1.5 eq.) followed by pyridine trifluoroacetate (4.75 g,24.6mmol,2.1 eq.). The reaction was stirred for 30 minutes and then analyzed by thin layer chromatography (silica gel, eluent: 60% ethyl acetate/40% hexane) and analysis showed completion of the reaction. The crude mixture was applied to a silica gel flash column preconditioned with 1% triethylamine/99% ethyl acetate and equilibrated with 60% ethyl acetate/40% hexane. Eluting the product with the same mobile phase, cooling to 0 ^℃ And purged with argon and collected in an argon purged bottle. The product containing fractions were concentrated to provide a white to off-white foam (12.04 g,81% yield). ¹ H-NMR(300mHz,DMSO-d ₆ ):δ＝11.48(s,1H),9.12(t,J＝4.7Hz,1H),8.54/8.57(s,1H),7.59-7.66(m,2H),7.51-7.58(m,2H),7.43-7.50(m,2H),7.18-7.40(m,12H).6.77-6.89(m,4H),6.03-6.13(m,1H),4.12-4.47(m,4H),3.70(s,6H),3.43-3.780(m,4H),3.22-3.36(m,2H),2.82(dd,J _A ＝14.9,J _B ＝7.4Hz,2H),2.76(t,J＝5.9Hz,1H),2.64(t,J＝5.9Hz,1H),2.36-2.46(m,2H),1.02-1.17(m,12H),0.98(d,J＝6.9Hz,2H). ³¹ P-NMR(100mHz,DMSO-d ₆ ):δ＝147.55/147.35(s,1P)。C ₅₆ H ₆₃ N ₆ O ₉ MS (m/z) calculated value of P: 995.13, found: 993.4[ M-H ]] ^- (ESI ^- )。

5- [ N- (4-phenylbenzyl) carboxamide ]-synthesis of 3 '-O-acetyl-2' -deoxycytidine nucleoside (scheme 2, product 6): in a round bottom flask with magnetic stirring, the starting material (scheme 2, product 4,1.26g,1.56 mmol) was dissolved in anhydrous pyridine (10 mL) under argon. Acetic anhydride (1 mL,10.5mmol,6.7 eq.) was added dropwise to the stirred mixture. The reaction was stirred for 16.5 hours and the progress of the reaction was monitored by TLC (8% methanol/dichloromethane). The crude mixture was evaporated to recover a pale yellow foam. The residue was dissolved in 1, 3-hexafluoro-2-propanol (10 mL,95 mmol)) and heated at about 50℃for 22.25 hours (Leonard, N.J. tetrahedron Letters,1995, 36:7833). Complete cleavage of the DMT group was confirmed by TLC (8% methanol/dichloromethane). The red solution was quenched by pouring into well-stirred methanol (approximately 75 mL). The resulting yellow solution was concentrated in vacuo and the residue was dissolved in hot ethyl acetate (20 mL). After cooling the product crystallized and the resulting slurry was stirred at 0 ℃, then filtered and washed with ethyl acetate. 3' -O-acetyl-nucleoside (6) was isolated as a white solid (0.45 g,56% yield). ¹ H-NMR(300mHz,DMSO-d ₆ ):δ＝8.86(t,J＝5.7Hz,1H),8.44(s,1H),7.99-8.18(bs,1H),7.75-7.88(bs,1H),7.60-7.68(m,4H),7.32-7.51(m,5H),6.16(dd,J _A ＝8.1,J _B ＝6.0Hz,1H),5.20-5.27(m,1H),5.14(t,J＝5.7Hz,1H),4.38-4.53(m,2H),4.06(dd,J _A ＝5.7,J _B ＝3.9Hz,1H),3.59-3.72(m,2H),2.28-2.47(m,2H),2.07(s,3H). ¹³ C-NMR(80mHz,DMSO-d ₆ ):δ＝170.52(1C),165.85(1C),164.00(1C),153.88(1C),144.44(1C),140.43(1C),139.29(1C),138.56(1C),129.40(2C),128.28(2C),127.82(1C),127.154(2C),127.05(2C),99.52(1C),86.44(1C),85.55(1C),75.11(1C),61.67(1C),42.50(1C),37.79(1C),21.33(1C)。C ₂₅ H ₂₆ N ₄ O ₆ MS (m/z) calculated value of (c): 478.51, found: 477.2[ M-H ]] ^- (ESI ^- )。

5- [ N- (4-phenylbenzyl) formyl Amines]-2 '-deoxyuridine-5' -O-triphosphate (tri-triethylammonium salt) (scheme 2, product 7): the triphosphate (7) was synthesized from 3' -O-acetyl-nucleoside (6) by the procedure of Ludwig and Eckstein (Ludwig, J. And Eckstein, F.J. org. Chem.1989, 54:631) on a 500. Mu. Mol scale (5X). After ammonolysis and evaporation, the crude triphosphate product was purified by anion exchange chromatography and reverse phase chromatography as described in general procedure (above). [ epsilon ] _est .13,700cm ^-1 M ^-1 ]The isolated purified product was 275. Mu. Mol (55% yield). ¹ H-NMR(300mHz,D ₂ O):δ＝8.40(s,1H),7.51-7.60(m,4H),7.32-7.43(m,4H),7.25-7.33(m,1H),6.09(t,J＝6.5Hz,1H),4.57(quintet,J＝3.6mHz,1H),4.43(q,J＝15.3Hz,2H),4.11-4.23(m,3H),3.00(q,J＝7.5Hz,19H),2.31-2.42(m,1H),2.16-2.90(m,1H),1.135(t,J＝7.2Hz,31H). ¹³ C-NMR(75Hz,D ₂ O):δ＝166.29(1C),163.67(1C),155.92(1C),143.40(1C),140.04(1C),139.14(1C),138.02(1C),129.07(2C),128.00(2C),86.89(1C),86.07/85.96(1C),70.50(1C),65.23/65.16(1C),41.01(3C),42.95(1C),39.88(1C),8.16(3C). ³¹ P-NMR(100mHz,D ₂ O):δ＝8.60(d,J＝16.9Hz,1P),-11.40(d,J＝16.8Hz,1P),-23.00(t,J＝17.0Hz,1P)。C ₂₅ H ₂₆ N ₄ O ₁₄ P ₃ MS (m/z) calculated value of (c): 675.40, found: 675.1[ M-H ]] ^- (ESI ^- )。

Scheme 2

Example 2: preparation of modified deoxyuridine

Step 1: synthesis of 5' -O- (4, 4' -dimethoxytrityl) -5- (N-carboxamide) -2' -deoxyuridine derivative (scheme 3, product 9):

the starting material 5 '-O-dimethoxytrityl-5-trifluoroethoxycarbonyl-2' -deoxyuridine (scheme 3, product 8) was prepared by the procedure of Matsuda et al (Noruma, Y.; ueno, Y.; matsuda, A.nucleic Acids Research 1997,25:2784-2791；Ito,T.；Ueno,Y.；Matsuda,A.Nucleic Acid Research 2003,31:2514-2523). Will be(8) Essential aromatic primary amines (RCH ₂ NH ₂ (1.3 eq), triethylamine (2 eq) and anhydrous acetonitrile under inert atmosphere at 40-50 ℃ for 18-24 hours. Quantitative conversion of (8) to amide (9) was confirmed by thin layer chromatography (silica gel, 5% methanol/dichloromethane) or HPLC. The reaction mixture was concentrated in vacuo and purified by flash chromatography on silica gel (Still, w.c.; kahn, m.; mitra, a.j. Org. Chem.1978, 432923) the residue was purified using 0-3% methanol in 1% triethylamine/ethyl acetate as eluent. Fractions containing pure product were combined and evaporated to give (9) as a white foam in 80% -90% yield.

Step 2: synthesis of 5'-O- (4, 4' -dimethoxytrityl) -5- (N-carboxamide) -2 '-deoxyuridine-3' -CE phosphoramidite derivative (scheme 3, product 10):

DMT-protected nucleoside (9) was dissolved in anhydrous dichloromethane under argon in a round bottom flask with magnetic stirring. To the reaction mixture was added 2-cyanoethyl-N, N' -tetraisopropylphosphine (1.05 eq) followed by pyridinium trifluoroacetate (1.1 eq). The reaction was stirred for 30-60 minutes and then analyzed by thin layer chromatography (silica gel, eluent: 5% methanol/95% dichloromethane) and analysis showed completion of the reaction. The crude mixture was applied to a silica flash column equilibrated with 1% triethylamine/20% hexane/79% ethyl acetate and the product eluted with the same mobile phase, cooled to 0 ℃ and purged with argon and collected in an argon purged bottle. The product-containing fractions were concentrated to provide white to off-white foam in 80% -90% yield.

Scheme 3

To prepare the 5 '-triphosphate reagent (TPP reagent, scheme 3, product 12), the 5' o-DMT protected nucleoside (scheme 3, product 9) was acetylated with acetic anhydride in pyridine followed by cleavage of DMT with 1,3, -hexafluoro-2-propanol (HFIP, scheme 3, product 11) (see, e.g., leonard and Neelima, 1995). The resulting crystalline 3' -O-acetylated nucleoside was purified by Ludwig-Ecks tein (Ludwig, J. And Eckstein, F.J. org.chem.,1989,54631) process to crude 5' -O-triphosphate (scheme 3, product 12). These chemically modified nucleotides typically require a two-stage purification process: anion exchange chromatography (AEX) followed by reverse phase preparative HPLC to obtain high purity [ ]>90%) of the desired product.

Example 2-1: preparation of 5- [ N- (3, 3-diphenylpropyl) carboxamide ] -2' -deoxyuridine (DPPdU) derivatives (scheme 3)

5'-O- (4, 4' -Dimethoxytrityl) -5- [ N- (3, 3-diphenylpropyl) carboxamide]-synthesis of 2' -deoxyuridine (scheme 3, product 9): the starting material 5 '-O-dimethoxytrityl-5-trifluoroethoxycarbonyl-2' -deoxyuridine (scheme 3, product 8, 10.55g,16.6 mmol)) was charged to a dry, argon purged round bottom flask. Anhydrous acetonitrile (22 mL) and 3, 3-diphenylpropylamine (4.38 g,20.7mmol,1.25 eq.) were added to the flask and the mixture stirred to dissolve the solids. Triethylamine (4.6 mL,33.2mmol,2 eq.) was added to the stirred mixture, and the mixture was transferred to a water bath and heated at 40℃under an inert atmosphere. The progress of the reaction was monitored by reverse phase HPLC (Waters 2795HPLC with 2489 detector and using Waters Symmetry column, buffer A:100mM triethylammonium acetate, buffer B: acetonitrile, gradient: 70% buffer B, isocratic within 30 minutes). After stirring for about 6.5 hours, analysis showed the reaction was complete. The mixture was stirred at room temperature for another 16 hours, at which time stirring was stopped and the solvent evaporated to recover a pale yellow foam. The crude mixture was applied to a silica gel flash column equilibrated with 1% triethylamine/79% ethyl acetate/20% hexane. The product was initially eluted with the same mobile phase, with the mobile phase changed to 99% ethyl acetate/1% triethylamine followed by 2% methanol/97% ethyl acetate/1% triethylamine to complete the elution. The product containing fractions were concentrated to provide a white to off-white foam (11.58 g,91% yield). ¹ H-NMR(300mHz,CD ₃ CN):δ＝8.65(t,J＝5.9Hz,1H),8.54(s,1H),7.43-7.48(m,2H),7.26-7.383(m,14H),7.16-7.23(m,3H),6.87(dd,J _A ＝9.0,J _B ＝2.1Hz,4H),6.12(t,J＝6.6Hz,1H),4.29(td,J _A ＝10.1,J _B ＝3.8Hz,1H),3.98-4.05(m,2H),3.75(d,J＝0.6,6H),3.29(d,J＝4.2Hz,2H),3.19-3.27(m,2H),2.19-2.44(m,4H). ¹³ C-NMR(100mHz,CD ₃ CN):δ＝163.24(1C),7.43-7.48(m,2H),7.26-7.383(m,14H),7.16-7.23(m,3H),6.87(dd,JA＝9.0,JB＝2.1Hz,4H),6.12(t,J＝6.6Hz,1H),4.29(td,J _A ＝10.1,J _B ＝3.8Hz,1H),3.98-4.05(m,2H),3.75(d,J＝0.6,6H),3.29(d,J＝4.2Hz,2H),3.19-3.27(m,2H),2.19-2.44(m,4H).)。C ₄₆ H ₄₅ N ₃ O ₈ MS (m/z) calculated value of (c): 767.88, found: 766.2[ M-H ]] ^- (ESI ^- )。

5'-O- (4, 4' -Dimethoxytrityl) -4-N-acetyl-5- [ N- (3, 3-diphenylpropyl) carboxamide]-synthesis of 2 '-deoxyuridine-3' -O- (N, N-diisopropyl-O-2-cyanoethyl phosphoramidite) (scheme 3, product 10): the product of the previous step (scheme 3, product 9, 10.36g,13.5 mmol) was dissolved in anhydrous dichloromethane (34 mL) under argon in a round bottom flask with magnetic stirring. To the reaction mixture was added 2-cyanoethyl-N, N, N ', N' -tetraisopropylphosphine (4.5 mL,14.2mmol,1.05 eq.) followed by pyridine trifluoroacetate (2.98 g,14.9mmol,1.1 eq.). The reaction was stirred for 1.25 hours and then analyzed by thin layer chromatography (silica gel, eluent: 60% ethyl acetate/40% hexane) and analysis showed completion of the reaction. The crude mixture was applied to a silica gel flash column equilibrated with 50% ethyl acetate/49% hexane/1% triethylamine and product elution was achieved using increasing concentrations of ethyl acetate, the final fraction eluting with 59% ethyl acetate/40% hexane/1% triethylamine. All mobile phases were cooled to 0 ℃ and purged with argon and the product was collected in an argon purged bottle. The product containing fractions were concentrated to provide a white to off-white foam (8.97 g,69% yield). ¹ H-NMR(300mHz,DMSO-d ₆ ):δ＝12.93(s,1H),8.70(t,J＝5.7Hz,1H),8.47/8.46(s,1H),7.12-7.40(m,19H),6.86(dd,J _A ＝9.0,J _B ＝2.4Hz,4H),6.04-6.13(m,1H),4.28-4.40(m,1H),4.03-4.12(m,1H),3.92-4.01(m,1H),3.69/3.68(s,6H),3.64-3.76(m,1H),3.40-3.62(m,4H),3.11-3.31(m,4H),2.75(t,J＝5.9Hz,1H),2.64(td,J _A ＝6.0,J _B ＝0.8Hz,1H),2.36-2.47(m,2H),2.26(dd,J _A ＝14.4,J _B ＝7.2Hz 2H),1.10(dd,J _A ＝12.3,J _B ＝6.6Hz 9H),0.95(d,J＝9.3Hz,3H). ³¹ P-NMR(300mHz,DMSO-d ₆ ):δ＝147.22/147.58(s,1P)。C ₅₅ H ₆₂ N ₅ O ₉ MS (m/z) calculated value of P: 968.10, found: 966.3[ M-H ]] ^- (ESI ^- )。

5- [ N- (3, 3-diphenylpropyl) carboxamide]-synthesis of 3 '-O-acetyl-2' -deoxyuridine (scheme 3, product 11): in a round bottom flask with magnetic stirring, the starting material (scheme 3, product 9,0.953g,1.24 mmol) was dissolved in anhydrous pyridine (10 mL) under argon. Acetic anhydride (1 mL,10.5mmol,8.5 eq.) was added dropwise to the stirred mixture. The reaction mixture was stirred at room temperature for 25 hours and the reaction was verified to be complete by thin layer chromatography (TLC, 80% ethyl acetate/20% hexane). The crude mixture was evaporated, co-evaporated with toluene to recover a pale yellow to tan foam. The residue was dissolved in 1, 3-hexafluoro-2-propanol (HFIP, 10mL,95 mmol)), the residue was purified (Leonard, N.J. tetrahedron Letters,1995,367833) and heated at about 50 c for 18 hours. Complete cleavage of the DMT group was confirmed by TLC (5% methanol/dichloromethane). The red solution was quenched by pouring into well-stirred methanol (approximately 50-75 mL). The resulting yellow solution was concentrated in vacuo and the residue was dissolved in hot ethyl acetate (10-20 mL). After cooling the product crystallized and the resulting slurry was stirred at 0 ℃, then filtered and washed with ethyl acetate. 3' -O-acetyl-nucleoside (product 11) was isolated as a white solid (0.40 g,64% yield). ¹ H-NMR(400mHz,DMSO-d ₆ ):δ＝11.94(s,1H),8.77(bt,J＝5.8Hz,1H),8.72(s,1H),7.22-7.35(m,8H),7.16(t,J＝6.8Hz,2H),6.14(t,J＝6.8Hz,1H),5.22-5.26(m,1H),5.19(t,J＝4.4Hz,1H),4.63(d,J＝5.6Hz,2H),4.10(dd,J _A ＝5.2,J _B ＝3.2Hz,1H),3.58-3.67(m,2H),2.31-2.41(m,2H),2.26(dd,J _A ＝14.0,J _B ＝7.2Hz,2H),2.06(s,3H). ¹³ C-NMR(100mHz,DMSO-d ₆ ):δ＝170.46(1C),163.69(1C),161.81(1C),150.07(1C),146.15(1C),144.99(2C),128.93(4C),128.02(4C),126.61(2C),106.14(1C),85.85(1C),85.77(1C),75.23(1C),61.65(1C),48.70(1C),38.05(1C),37.84(1C),34.97(1C),21.30(1C)。C ₂₇ H ₂₉ N ₃ O ₇ MS (m/z) calculated value of (c): 507.54, found: 506.1[ M-H ]] ^- (ESI ^- )。

5- [ N- (3, 3-diphenylpropyl) carboxamide]-synthesis of 2 '-deoxyuridine 5' -O-triphosphate (tri-triethylammonium salt) (scheme 3, product 12): the triphosphate (12) was synthesized from 3' -O-acetyl-nucleoside (11) by the procedure of Ludwig and Eckstein (Ludwig, J. And Eckstein, F.J. org. Chem.1989, 54:631) on a 500. Mu. Mol scale (5X). After ammonolysis and evaporation, the crude triphosphate product was purified by anion exchange chromatography and reverse phase chromatography as described in general procedure (above). [ epsilon ] _est .13.700cm ^-1 M ^-1 ]The isolated purified product was 59.8. Mu. Mol (12% yield). ¹ H-NMR(300mHz,D ₂ O):δ＝7.95(s,1H),7.22-7.28(m,4H),7.11-7.19(m,4H),6.96-7.05(d,2H),6.05(t,J＝6.9Hz,1H),4.51(quintet,J＝3.0Hz,1H),4.10-4.18(m,3H),3.92(t,J＝7.5Hz,1H),3.17-3.40(m,2H),2.90(q,J＝7.5Hz,19H),2.25-2.38(m,3H),2.11-2.22(m,1H),1.11(t,J＝7.5Hz,29H). ³¹ P-NMR(100mHz,D ₂ O):δ＝-9.93(d,J＝20.3Hz,1P),-11.63(d,J＝20.9Hz,1P),-11.63(d,J＝20.9Hz,1P)。C ₂₅ H ₂₉ N ₃ O ₁₅ P ₃ MS (m/z) calculated value of (c): 704.43, found: 704.1M-H] ^- (ESI ^- )。

Example 2-1: preparation of 5- { N- [2- (4-biphenylethyl) carboxamide ] } -2' -deoxyuridine (BPEdU) derivative (scheme 3)

5'-O- (4, 4' -Dimethoxytrityl) -5- { N- [2- (4-biphenylethyl) carboxamide]Synthesis of 2' -deoxyuridine (scheme 3, product 9): the starting material 5 '-O-dimethoxytrityl-5-trifluoroethoxycarbonyl-2' -deoxyuridine (scheme 3, product 8, 10.45g,15.9 mmol)) was charged to a dry, argon purged round bottom flask. Anhydrous acetonitrile (20 mL) and 2- (4-biphenylyl) ethylamine (3.81 g,19.1mmol,1.2 eq.) were added to the flask and the mixture stirred to dissolve the solids. Triethylamine (4.4 mL,31.8mmol,2 eq.) was added to the stirred mixture, and the mixture was transferred to a water bath and heated at 40℃under an inert atmosphere. By thin layer chromatography (silica gel, eluent: 8% methanol/dichloromethane) ) And reverse phase HPLC (Waters 2795HPLC with 2489 detector and using Waters Symmetry column, buffer a:100mM triethylammonium acetate, buffer B: acetonitrile, gradient: 70% buffer B, isocratic over 30 min) was monitored for reaction progress. After stirring for about 6 hours, analysis showed that the reaction was still incomplete. The mixture was stirred at room temperature for an additional 16 hours, re-analyzed and confirmed to be complete. Agitation was stopped and the solvent evaporated to recover a pale yellow foam. The crude mixture was applied to a silica gel flash column equilibrated with 1% triethylamine/79% ethyl acetate/20% hexane. The product was initially eluted with the same mobile phase, which was changed to 0-2% methanol/1% triethylamine/ethyl acetate as the elution proceeded to complete the elution. The product containing fractions were concentrated to provide a white to off-white foam (10.89 g,91% yield). ¹ H-NMR(300mHz,CD ₃ CN):δ＝8.69(t,J＝5.6Hz,1H),8.57(s,1H),7.57-7.67(m,4H),7.44-7.50(m,4H),7.29-7.40(m,8H),7.20-7.26(m,1H),6.86-6.92(m,4H),6.11(t,J＝6.4Hz,1H),4.28(dt,J _A ＝7.5,J _B ＝3.9Hz,1H),4.01(dd,JA＝8.3,JB＝4.3Hz,1H),3.61(q,J＝6.6Hz,2H),3.30(d,J＝4.2Hz,2H),2.90(t,J＝7.1Hz,2H),2.33-2.43(m,1H),2.19-2.29(m,1H). ¹³ C-NMR(100mHz,CD ₃ CN):δ＝163.02(1C),161.59(1C),158.65(1C),149.45(1C),145.53(1C),145.08(1C),140.61(1C),138.94(1C),138.83(1C),135.88(1C),135.87(1C),130.09(1C),130.08(1C),129.32(2C),128.88(2C),128.04(2C),127.88(2C),127.26(1C),126.95(2C),126.79(2C),126.75(1C),113.13(2C),113.11(2C),105.75(1C),86.42(1C),86.37(1C),86.31(1C),71.03(1C),63.55(1C),54.89(2C),40.34(1C),40.25(1C),34.92(1C)。C ₄₅ H ₄₃ N ₃ O ₈ MS (m/z) calculated value of (c): 753.85, found: 745.2[ M-H ]] ^- (ESI ^- )。

5'-O- (4, 4' -Dimethoxytrityl) -5- { N- [2- (4-biphenylethyl) carboxamide]Synthesis of 2 '-deoxyuridine-3' -O- (N, N-diisopropyl-O-2-cyanoethyl phosphoramidite) (scheme 3, product 10): the product of the previous step (scheme 3, product 9, 18.76g,24.9 mmol) was dissolved in anhydrous dichloromethane (62 mL) under argon in a round bottom flask with magnetic stirring. Addition of 2-cyanoethyl-N, N, N 'to the reaction mixture' Tetraisopropylphosphine (8.3 mL,26.1mmol,1.05 eq.) followed by pyridine trifluoroacetate (5.40 g,14.9mmol,1.1 eq.) was added. The reaction was stirred for 30 minutes and then analyzed by thin layer chromatography (silica gel, eluent: 5% methanol/dichloromethane) and analysis showed completion of the reaction. The crude mixture was applied to a silica gel flash column equilibrated with 69% ethyl acetate/30% hexane/1% triethylamine and product elution was achieved using increasing concentrations of ethyl acetate, the final fraction eluting with 79% ethyl acetate/20% hexane/1% triethylamine. All mobile phases were cooled to 0 ℃ and purged with argon and the product was collected in an argon purged bottle. The product containing fractions were concentrated to provide a white to off-white foam (20.97 g,88% yield). ¹ H-NMR(400mHz,DMSO-d ₆ ):δ＝11.93(s,1H),8.78(t,J＝5.7Hz,1H),8.52/8.50(s,1H),7.55-7.68(m,4H),7.11-7.49(m,16H),6.84-6.92(m,4H),6.03-6.13(m,1H),4.29-4.41(m,1H),4.07-4.13(m,1H),3.73(s,6H),3.42-3.70(m,6H),3.18-3.31(m,2H),2.83(t,J＝7.2Hz,2H),2.75(t,J＝5.9Hz,2H),2.64(td,J _A ＝6.0,J _B ＝0.9Hz,1.5H),2.36-2.46(m,2H),1.10(dd,J _A ＝12.3,J _B ＝6.6Hz,12H),0.96(d,J＝6.9Hz,2H). ³¹ P-NMR(400mHz,DMSO-d ₆ ):δ＝147.32/147.66(s,1P)。C ₅₄ H ₆₀ N ₅ O ₉ MS (m/z) calculated value of P: 954.07, found: 952.6[ M-H ]] ^- (ESI ^- )。

5'-O- (4, 4' -Dimethoxytrityl) -5- { N- [2- (4-biphenylyl) ethylcarboxamide]Synthesis of 3 '-O-acetyl-2' -deoxyuridine (scheme 3, product 11): in a round bottom flask with magnetic stirring, the starting material (scheme 3, product 9,0.98g,1.30 mmol) was dissolved in anhydrous pyridine (10 mL) under argon. Acetic anhydride (1 mL,10.5mmol,8.1 eq.) was added dropwise to the stirred mixture. The reaction mixture was stirred at room temperature for 25 hours and the reaction was verified to be complete by thin layer chromatography (TLC, 80% ethyl acetate/20% hexane). The crude mixture was evaporated to recover a pale yellow to tan foam. The residue was dissolved in 1, 3-hexafluoro-2-propanol (10 mL,95 mmol)), the residue was purified (Leonard, N.J. tetrahedron Letters,1995, 367833) and heated at about 50 c for 17 hours. Through TLC (5% methanol/dichloromethane) confirmed complete cleavage of DMT groups. The red solution was quenched by pouring into well-stirred methanol (approximately 25-30 mL). Almost immediately, the formation of solids begins; the mixture was stirred for about 18 hours, at which time the product was recovered by filtration through a filter cake washed with cold isopropyl ether. 3' -O-acetyl-nucleoside (product 11) was isolated as a white solid (0.680 g, 100% yield). ¹ H-NMR(500mHz,DMSO-d ₆ ):δ＝11.99(s,1H),8.80(t,J＝5.5Hz,1H),8.76(s,1H),7.64(d,J＝7.5Hz,2H),7.60(d,J＝8.0Hz,2H),7.45(t,J＝7.8Hz,2H),7.31-7.37(m,4H),6.14(t,J＝6.8Hz,1H),5.22-5.26(m,1H),5.19(t,J＝4.5Hz,1H),4.09(d,J＝1.5Hz,1H),3.62(dd,J _A ＝7.5,J _B ＝4.0Hz,2H),3.62(dd,J _A ＝7.5,J _B ＝4.0Hz,2H),2.84(t,J＝7.0Hz,2H),2.30-2.40(m,2H),2.06(s,3H). ¹³ C-NMR(100mHz,CD ₃ CN):δ＝170.50(1C),165.59(1C),161.85(1C),150.03(1C),146.30(1C),140.42(1C),139.05(1C),138.54(1C),129.72(2C),129.37(1C),127.70(1C),127.14(2C),126.96(2C),106.03(1C),85.87(1C),85.80(1C),75.25(1C),61.65(1C),40.57(1C),38.10(1C),35.33(1C),21.30(1C)。C ₂₆ H ₂₇ N ₃ O ₇ MS (m/z) calculated value of (c): 493.52, found: 492.1[ M-H ]] ^- (ESI ^- )。

5'-O- (4, 4' -Dimethoxytrityl) -5- { N- [2- (4-biphenylethyl) carboxamide]Synthesis of 2 '-deoxyuridine-5' -O-triphosphate (tri-triethylammonium salt) (scheme 3, product 12): the triphosphate (12) was synthesized from 3' -O-acetyl-nucleoside (11) by the procedure of Ludwig and Eckstein (Ludwig, J. And Eckstein, F.J. org. Chem.1989, 54:631) on a 500. Mu. Mol scale (5X). After ammonolysis and evaporation, the crude triphosphate product was purified by anion exchange chromatography and reverse phase chromatography as described in general procedure (above). [ epsilon ] _est. 13.700cm ^-1 M ^-1 ]The isolated purified product was 182. Mu. Mol (35.9% yield). ¹ H-NMR(300mHz,D ₂ O):δ＝8.38(s,1H),7.55-7.61(m,5H),7.40-7.46(m,2H),7.32-7.37(m,3H),6.11(t,J＝6.8Hz,1H),4.53(quintet,J＝3.2Hz,1H),4.16-4.21(m,1H),4.09-4.15(m,2H),3.60(t,J＝6.8Hz,2H),3.14(q,J＝7.2Hz,24H),2.89(t,J＝6.8Hz,2H),2.25-2.40(m,2H),2.26(m,1H),1.22(t,J＝7.2Hz,36H). ³¹ P-NMR(100mHz,D ₂ O):δ＝-10.91(d,J＝19.8Hz,1P),-11.41(d,J＝19.9Hz,1P),-23.32(t,J＝19.8Hz,1P)。C ₂₄ H ₂₇ N ₃ O ₁₅ P ₃ MS (m/z) calculated value of (c): 690.41, found: 690.1[ M-H ]] ^- (ESI ^- )。

Examples 2-3.5 preparation of- [ N- (4-phenoxyphenylmethyl) formamide ] -2' -deoxyuridine (POPdU) derivatives (scheme 3)

5'-O- (4, 4' -Dimethoxytrityl) -5- [ N- (4-phenoxyphenylmethyl) carboxamide]-synthesis of 2' -deoxyuridine (scheme 3, product 9): the starting material 5 '-O-dimethoxytrityl-5-trifluoroethoxycarbonyl-2' -deoxyuridine (scheme 3, product 8, 28.47g,43.4 mmol)) was charged to a dry, argon purged round bottom flask. Anhydrous acetonitrile (54 mL) and 4-phenoxyphenylmethylamine (10.38 g,52.1mmol,1.2 eq) were added to the flask and the mixture stirred to dissolve the solids. Triethylamine (12 mL,86.8mmol,2 eq.) was added to the stirred mixture. The reaction was stirred at room temperature under an inert atmosphere for 22 hours. At this point, the progress of the reaction was assessed by reverse phase HPLC (Waters 2795HPLC with 2489 detector and using Waters Symmetry column, buffer A:100mM triethylammonium acetate, buffer B: acetonitrile, gradient: 70% buffer B, isocratic within 30 minutes) and found complete. Agitation was stopped and the solvent evaporated to recover a pale yellow foam. The crude mixture was applied to a silica gel flash column equilibrated with 99% ethyl acetate/1% triethylamine. The product was initially eluted with the same mobile phase, which was changed to 0-1.5% methanol/1% triethylamine/ethyl acetate as the elution proceeded to complete the elution. The product containing fractions were concentrated to provide a white to off-white foam (28.89 g,88% yield). ¹ H-NMR(400mHz,DMSO-d ₆ ):δ＝9.25(t,J＝6.0Hz,1H),8.48(s,1H),7.40-7.22(m,15H),7.15-7.19(m,1H),7.08-7.17(m,1H),6.92-7.00(m,6H),6.84-6.90(m,4H),6.10(t,J＝6.4Hz,1H),4.40-4.52(m,2H),4.11(dt,J _A ＝10.4,J _B ＝4.0Hz,1H),3.95(dd,J _A ＝8.6,J _B ＝4.4Hz,1H),3.70(d,J＝1.6,6H),3.19(d,J＝4.4Hz,2H),2.25-2.33(m,1H),2.16-2.24(m,1H). ¹³ C-NMR(100mHz,DMSO-d ₆ ):δ＝163.39(1C),161.21(1C),158.49(1C),158.47(1C),157.31(1C),155.88(1C),150.42(1C),145.83(1C),145.34(1C),135.93(1C),135.81(1C),134.98(1C),130.45(2C),130.26(2C),130.15(2C),129.54(2C),123.63(1C),118.74(2C),118.69(2C),113.68/113.67(4C),105.56(1C),86.38(1C),86.31(1C),86.20(1C),70.88(1C),64.09(1C),55.41/55.40(2C),44.85(1C),40.56(1C)。C ₄₄ H ₄₁ N ₃ O ₉ MS (m/z) calculated value of (c): 755.82, found: 754.2[ M-H ]] ^- (ESI ^- )。

5'-O- (4, 4' -Dimethoxytrityl) -5- [ N- (4-phenoxyphenylmethyl) carboxamide]-synthesis of 2 '-deoxyuridine-3' -O- (N, N-diisopropyl-O-2-cyanoethyl phosphoramidite) (scheme 3, product 10): the product of the previous step (scheme 3, product 9, 29.14g,38.6 mmol) was dissolved in anhydrous dichloromethane (100 mL) under argon in a round bottom flask with magnetic stirring. To the reaction mixture was added 2-cyanoethyl-N, N, N ', N' -tetraisopropylphosphine (12 mL,40.5mmol,1.05 eq.) followed by pyridine trifluoroacetate (8.30 g,43.0mmol,1.1 eq.). The reaction was stirred for 3 hours and then analyzed by thin layer chromatography (silica gel, eluent: 55% ethyl acetate/45% hexane) and analysis showed the reaction to be complete. The crude mixture was applied to a silica gel flash column equilibrated with 59% ethylacetate amine/40% hexane/1% triethylamine and the product eluted with the same mobile phase, which was cooled to 0 ℃ and purged with argon and the product collected in an argon purged bottle. The product containing fractions were concentrated to provide a white to off-white foam (30.25 g,82% yield). ¹ H-NMR(300mHz,DMSO-d ₆ ):δ＝11.98(s,1H),9.09(t,J＝6.6Hz,1H),8.53 8.52(s,1H),7.08-7.40(m,14H),6.91-7.00(m,4H),6.82-6.87(m,4H),6.04-6.13(m,1H),4.29-4.55(m,3H),4.05-4.14(m,1H),3.71(bs,6H),3.46-3.70(m,4H),3.18-3.31(m,2H),2.75(t,J＝6.0,1H),2.64(td,J _A ＝6.0,J _B ＝0.3Hz,1H),2.37-2.48(t,J＝5.9Hz,2H),0.97(d,J＝6.9Hz,2H). ³¹ P-NMR(300mHz,DMSO-d ₆ ):δ＝147.32/147.65(s,1P)。C ₅₃ H ₅₈ N ₃ O ₁₀ MS (m/z) calculated value of P: 956.05, found: 954.3[ M-H ] ] ^- (ESI ^- )。

5'-O- (4, 4' -Dimethoxytrityl) -5- [ N- (4-phenoxyphenylmethyl) carboxamide]-synthesis of 2' -deoxyuridine (scheme 3, product 11): in a round bottom flask with magnetic stirring, the starting material (scheme 3, product 9,0.79g,1.05 mmol) was dissolved in anhydrous pyridine (10 mL) under argon. Acetic anhydride (1 mL,10.5mmol,10 eq.) was added dropwise to the stirred mixture. The reaction mixture was stirred at room temperature for 20 hours and the reaction was verified to be complete by thin layer chromatography (TLC, 80% ethyl acetate/20% hexane). The crude mixture was evaporated, toluene co-evaporated to recover a pale yellow to tan foam. The residue was dissolved in 1, 3-hexafluoro-2-propanol (HFIP, 10mL,95 mmol)), the residue was purified (Leonard, N.J. tetrahedron Letters,1995,367833) and heated at about 50 c for 16 hours. Complete cleavage of the DMT group was confirmed by TLC (5% methanol/dichloromethane). The red solution was quenched by pouring into well-stirred methanol (approximately 20-30 mL). Almost immediately, some solids began to form. The volume of the mixture was reduced by about 50% by evaporation and the mixture was stirred for about one hour. At this point the mixture had become viscous and contained solids and the product was recovered by washing the filter cake with cold isopropyl ether. 3' -O-acetyl-nucleoside (product 11) was isolated as a white solid (0.36 g,69% yield). ¹ H-NMR(400mHz,DMSO-d ₆ ):δ＝11.94(s,1H),9.12(t,J＝6.0Hz,1H),8.79(s,1H),7.27-7.41(m,2H),7.32(t,J＝7.4Hz,2H),7.12(t,J＝7.4Hz,1H),6.92-7.02(m,4H),6.15(t,J＝7.2Hz,1H),5.24(bt,J＝2.4Hz,1H),5.19(bt,J＝4.4Hz,1H),4.46(d,J＝6.0Hz,2H),4.10(bdd,J _A ＝5.0,J _B ＝3.4Hz,1H),3.58-3.68(m,2H),2.29-2.42(m,2H),2.06(s,3H).). ¹³ C-NMR(100mHz,DMSO-d ₆ ):δ＝170.48(1C),163.63(1C),161.96(1C),157.32(1C),155.91(1C),155.91(1C),146.49(1C),134.78(1C),130.47(2C),129.60(2C),123.75(1C),119.20(2C),118.83(2C),106.10(1C),85.91(1C),85.81(1C),75.22(1C),61.65(1C),48.04(1C),38.12(1C),37.84(1C),34.97(1C),21.30(1C)。C ₂₅ H ₂₅ N ₃ O ₈ MS (m/z) calculated value of (c): 495.49, found: 494.1[ M-H ]] ^- (ESI ^- )。

5’-O- (4, 4' -dimethoxytrityl) -5- { N- [2- (4-biphenylethyl) carboxamide]Synthesis of 2 '-deoxyuridine-5' -O-triphosphate (tri-triethylammonium salt) (scheme 3, product 12): the triphosphate (12) was synthesized from 3' -O-acetyl-nucleoside (11) by the procedure of Ludwig and Eckstein (Ludwig, J. And Eckstein, F.J. org. Chem.1989, 54:631) on a 500. Mu. Mol scale (5X). After ammonolysis and evaporation, the crude triphosphate product was purified by anion exchange chromatography and reverse phase chromatography as described in general procedure (above). [ epsilon ] _est .13.700cm ^-1 M ^-1 ]The isolated purified product was 192. Mu. Mol (38.2% yield). ¹ H-NMR(300mHz,D ₂ O):δ＝8.38(s,1H),7.14-7.26(m,4H),7.05(t,J＝7.5Hz,1H),6.76-6.82(m,4H),6.09(t,J＝6.6Hz,1H),4.5(quintet,J＝3.3Hz,1H),4.39(q,J＝15.3Hz,2H),4.60(dd,J _A ＝15.1,J _B ＝3.4Hz,1H),4.05-4.17(m,3H),3.08(q,J＝7.5Hz,23H),2.26-2.37(m,2H),1.16(t,J＝7.5Hz,35H). ¹³ C-NMR(100mHz,D ₂ O):δ＝163.49(1C),156.60(1C),155.82(1C),150.38(1C),146.45(1C),133.41(1C),130.01(2C),129.04(2C),123.76(1C),118.87(2C),118.60(2C),105.70(1C),101.53(1C),86.91(1C),85.92/85.81(1C),70.86(1C),65.49(1C),46.59(8C),42.28(1C),38.74(1C),22.74(1C),8.19(8C)。C ₂₅ H ₂₅ N ₃ O ₁₆ P ₃ MS (m/z) calculated value of (c): 692.38; actual measurement value: 692.0[ M-H ]] ^- (ESI ^- )。

Example 3: selection of aptamers with pyrimidine nucleotides modified at the 5-position

This example provides a representative method for selecting and generating DNA aptamers using direct comparison of biphenyl modified dU libraries with monophenyl modified nucleotide libraries.

Preparation of candidate mixtures

Candidate mixtures of partially randomized ssDNA oligonucleotides were prepared by polymerase extension by annealing DNA primers to biotinylated ssDNA templates (as shown in table 1 below). The candidate mixture contains a 40 nucleotide random cassette containing dATP, dGTP, dCTP and 5- (N-3-phenylpropyl formamide) -2 '-deoxyuridine triphosphate (PP-dUTP), 5- [ N- (4-phenylbenzyl) formamide ] -2' -deoxyuridine triphosphate (PBn-dUTP), 5- [ N- (4-phenoxybenzyl) formamide ] -2 '-deoxyuridine triphosphate (POP-dUTP), 5- { N- [ (1, 1' -biphenyl) -4-yl) ethyl ] formamide } -2 '-deoxyuridine triphosphate (BPE-dUTP) or 5- [ N- (3, 3-diphenylpropyl) formamide ] -2' -deoxyuridine triphosphate (DPP-dUTP)).

TABLE 1 sequence of templates and primers

B' =biotin

9200 microliters of a 50% slurry of streptavidin Plus UltraLink resin (PIERCE) was washed three times with 40mL of 16mM NaCl at a time. The resin was resuspended in 16mM NaCl at a final volume of 8.5 mL. 352 nanomolar was performed with two biotin residues (designated B' in the sequence) and 40 randomized positions (designated N in the sequence ₄₀ ) Is added to the washed UltraLink SA beads and is spun at 37℃for 30 minutes. The beads were then washed three times with 16mM NaCl. Between each wash, the beads were recovered by centrifugation. The beads containing the capture templates were now suspended in 1.125mL of extension reaction buffer containing 18nmol of primer 1 (SEQ ID NO: 2), 1XSQ20 buffer (120 mM Tris-HCl (pH 7.8), 10mM KCl, 7mM MgSO ₄ 、6mM(NH ₄ ) ₂ SO ₄ 0.001% BSA and 0.1% Triton X-100), 112 units KOD XL DNA polymerase (EMD MILLIPORE), and 1mM each of dATP, dGTP, dCTP and one of PP-dUTP, PBn-dUTP, POP-dUTP, BPE-dUTP or DPP-dUTP. The beads were incubated at 68℃for 2 hours. The beads were then washed three times with 16mM NaCl. The aptamer library was eluted from the beads with 2mL of 20mM NaOH. The eluted library was immediately neutralized with 52. Mu.L of 1N HCl and 100. Mu.L of HEPES pH 7.5 and 2. Mu.L of 10% TWEEN-20. The library was concentrated to about 0.32mL-0.52mL using a AMICON Ultracel YM-3 filter and the library concentration was determined by UV absorption spectroscopy.

Immobilization of target proteins

The following protein targets used in SELEX were purchased from commercial suppliers: interleukin-33 (IL-33) protein, novoprotein catalog number C233; XIAP protein, R & DSystems catalog No. 895-XB-050; TNF-alpha protein, acro Biosystems catalog number TNA-5228; KRAS (K-Ras) protein, sino Biological catalog number 12259-H07E. The resulting His-tagged target protein was immobilized on His-tagged Dynabead (Thermo Fisher) paramagnetic beads (MyOne SA, invitrogen, or His beads hereinafter) for SELEX (round 1 to 7). Beads (40 mg) were prepared by washing three times with 20mL of SB18T0.01 buffer consisting of 40mM HEPES (4- (2-hydroxyethyl) piperazine-1-ethanesulfonic acid) buffer, 102mM NaCl, 5mM KCl, 5mM MgCl2 and 0.01% TWEEN 20 adjusted to pH 7.5 with NaOH. Finally, the beads were suspended in SB18T0.01 at 2.5mg/mL and stored at 4 ℃ until use.

Selection of aptamers by slow off-rate enrichment process

Seven rounds of SELEX procedure were completed in total and selected for affinity and slow off rate. Reverse selection is performed prior to each round to reduce background and reduce the likelihood of obtaining an aptamer that binds non-specifically to the protein. The reverse selection proceeds as follows.

For round 1, a 100 μldna candidate mixture containing approximately 1 nanomolar DNA in SB18T0.01 was heated at 95 ℃ for 5 minutes, then cooled to 70 ℃ for 5 minutes, then cooled to 48 ℃ for 5 minutes, then transferred to 37 ℃ for 5 minutes of blocking. The samples were then combined with 10 μl of protein competitor mixture (0.1% HSA, 10 μΜ casein and 10 μΜ prothrombin in SB18T0.01) and 0.025mg (10 μl) of the HEXA-His coated His beads (Anaspec, cat. 24420) and incubated for 10 min at 37 ℃. Beads were removed by magnetic separation.

For rounds 2-7, 65. Mu.L aliquots of the DNA candidate mixture obtained from the previous round (65% of the eDNA obtained from the previous round) were mixed with 16. Mu.L of 5x SB18T0.01. The sample was heated to 95 ℃ for 3 minutes and cooled to 37 ℃ at a rate of 0.1 ℃/sec. The samples were then combined with 9 μl of protein competitor mixture (0.1% HSA, 10 μΜ casein and 10 μΜ prothrombin in SB18T0.01) and 0.025mg (10 uL) His beads and incubated for 10 min at 37 ℃ with mixing. Beads were removed by magnetic separation.

After the first counter-selection, the target protein was pre-immobilized on His beads for round 1 selection procedure. To achieve this, 0.125mg of protein His beads were mixed with 50 picomoles of target protein and incubated for 30 minutes at 37 ℃. Unbound target was removed by washing the beads with SB18T0.01. The reverse selected DNA candidate mixture (100. Mu.L) was added to the beads and incubated for 60 minutes with mixing at 37 ℃. The slow off-rate enrichment procedure was not used in the first round and the beads were washed 5 times with 100 μl SB18T0.01 only. After washing, bound aptamers were eluted from the beads by adding 170 μl of 2mM NaOH and incubating for 5 min with mixing at 37 ℃. After magnetic separation of the beads, the aptamer-containing eluate (170. Mu.L) was transferred to a new tube and the solution was neutralized by adding 40. Mu.L of neutralization buffer (500 mM Tris-HCl pH 7.5, 8mM HCl).

For rounds 2-7, selection was performed with the DNA candidate mixture and the target protein as described below, while the same selection was performed with the DNA candidate mixture in parallel but without the target protein. Comparison of Ct values obtained from PCR of samples with target protein (signal S) and samples without target protein (background B) can be used as a guideline for the next round of target concentration reduction. If the ΔCt value is greater than 4 but less than 8, the target protein is reduced by three times in the next round. If the Δct value is greater than 8, the next round of targets is reduced by a factor of 10.

For round 2, the labeled target protein (5 picomoles, 10 μl) was mixed with 40 μl of the reverse-selected DNA candidate mixture and incubated for 15 minutes at 37 ℃. The slow off-rate enrichment procedure was started by adding 50 μl of 10mM dextran sulfate followed immediately by 0.0125mg His beads. This was allowed to incubate at 37℃for 15 minutes with mixing. The beads were then washed 5 times with 100 μl SB18T0.01. The aptamer chains were eluted from the beads by adding 100 μl sodium perchlorate and incubating for 10 min with mixing at 37 ℃. Beads were removed by magnetic separation and 100 μl of aptamer eluate was transferred to a new tube.

Rounds 3 to 7 were performed as described for round 2, except that the amount of target protein was reduced as needed based on the delta Ct value for each target and library combination. Dextran sulfate was added 15 minutes (rounds 3 and 4), 30 minutes (rounds 5 and 6), 45 minutes (round 7) before the His beads were added.

For rounds 2 to 7, after perchlorate elution, 100. Mu.L of the aptamer eluate was captured with 0.0625mg (25. Mu.L) of SA beads (hereinafter referred to as primer beads) previously bound to primer 2 (SEQ ID NO: 3) and incubated at 50℃for 10 minutes while shaking, followed by 10 minutes while shaking at 25 ℃. The beads were washed 2 times with 100 μl SB18T0.01 and 1 time with 16mM NaCl. Bound aptamer was eluted with 120 μl water and incubated at 75 ℃ for 2 min. Beads were removed by magnetic separation and 120 μl of aptamer eluate was transferred to a new tube. Primer beads were prepared by suspending 15mg SA beads (1.5 mL of 10mg/mL SA beads washed once with 2mL of 20mM NaOH, twice with 2mL of SB18T 0.01) in 0.5mL of 1M NaCl, 0.01% tween-20 and adding 7 nanomoles of primer 2 (SEQ ID NO: 3). The mixture was incubated at 37℃for 1 hour. After incubation, the beads were washed 2 times with 1mL of SB18T0.01 and 2 times with 1mL of 16mM NaCl. The beads were resuspended in 5M NaCl, 0.01% tween-20 to 2.5mg/ml.

Aptamer amplification and purification

The selected aptamer DNA was amplified and quantified by QPCR for each round. 48 μL of LDNA was added to 12 μL of QPCR mix (10 XKOD DNA polymerase buffer; novagen #71157, diluted to 5 X25 mM MgCl2, 5 μM forward PCR primer (primer 1, SEQ ID NO: 2), 5 μM biotinylated reverse PCR primer (primer 2, SEQ ID NO: 3), 5 XSYBR Green I, 0.075U/. Mu.L KOD XL DNA polymerase and 1mM dATP, dCTP, dGTP and dTTP each) and thermally cycled in a Bio-Rad MyIQ QPCR instrument using the following protocol: 1 cycle, 96 ℃ for 15 seconds and 68 ℃ for 30 minutes; followed by 25 cycles at 96℃for 15 seconds and 68℃for 1 minute. Quantification was performed using instrument software and the copy numbers of the selected DNA (with and without target protein) were compared to determine the signal/background ratio.

After amplification, the PCR products were captured on SA beads via the biotinylated antisense strand. 25mL of SA beads (10 mg/mL) were washed once with 25mL of 20mM NaOH, twice with 25mL of SB18T0.01, resuspended in 25mL of SB18T0.01, and stored at 4 ℃. mu.L of SA beads (10 mg/mL in SB18T0.01) was added to 50. Mu.L of double stranded QPCR product and incubated for 5 min at 25℃with mixing. The "sense" strand was eluted from the beads by adding 100. Mu.L of 20mM NaOH and incubating for 1 min at 25℃with mixing. The eluted strand was discarded and the beads were washed 2 times with SB18T0.01 and once with 16mM NaCl.

The aptamer sense strand containing PP-dUTP, PBn-dUTP, POP-dUTP, BPE-dUTP or DPP-dUTP is prepared by primer extension from the immobilized antisense strand. The beads were suspended in 40. Mu.L of primer extension reaction mixture (1 Xprimer extension buffer (120 mM Tris-HCl pH 7.8, 10mM KCl, 7mM MgSO4, 6mM (NH 4) 2SO4, 0.1% TRITON X-100 and 0.001% bovine serum albumin), 4. Mu.M forward primer (primer 1, SEQ ID NO: 2), 0.5mM each dATP, dCTP, dGTP and PP-dUTP, PBn-dUTP, POP-dUTP, BPE-dUTP or DPP-dUTP, and 0.075U/. Mu.L KOD XL DNA polymerase) and incubated at 68℃for 45 minutes with mixing. The beads were washed 2 times with SB18T0.01, 1 time with 16mM NaCl, and the aptamer chains were eluted from the beads by adding 85. Mu.L of 20mM NaOH and incubating for 2 minutes with mixing at 37 ℃. After magnetic separation 83. Mu.L of the aptamer eluate was transferred to a new tube, neutralized with 20. Mu.L of 80mM HCl and buffered with 5. Mu. L0.1M HEPES (pH 7.5).

Selection stringency and feedback

The relative target protein concentration for each selection step decreases with QPCR signal (Δct), following the following rules:

if ΔCt <4, [ P ] (i+1) = [ P ] (i)

If 4.ltoreq.ΔCt <8, [ P ] (i+1) = [ P ] (i)/3.2

If ΔCt is greater than or equal to 8, [ P ] (i+1) = [ P ] (i)/10

Where [ P ] = protein concentration and i = current round number.

After each round of selection, the convergence status of the enriched DNA mixture was determined. mu.L of double stranded QPCR product was diluted to 200. Mu.L with 4mM MgCl2 containing 1XSYBR Green I. Samples were subjected to a convergent analysis using a C0t assay that measures the hybridization time of a complex mixture of double-stranded oligonucleotides. The samples were thermally cycled using the following protocol: 3 cycles, 98℃for 1 minute and 85℃for 1 minute; 2 cycles, 98℃for 1 minute and then 85℃for 30 minutes. Fluorescence images were measured at 5 second intervals during 30 minutes at 85 ℃. Fluorescence intensity was plotted as a function of time log and an increase in SELEX hybridization rate was observed per round, indicating sequence convergence.

Example 4: enrichment of the equilibrium binding constant (Kd) of SELEX pool to protein targets

This example provides the methods used herein to measure SELEX library-protein binding affinity and determine Kd.

Binding affinities of the enriched round 7 SELEX library shown in table 2 below were determined. Briefly, the binding constants (Kd values) of the enriched SELEX library to recombinant XIAP, IL-33, TNF- α and K-Ras proteins were determined by a filter binding assay. The Kd values of the enriched SELEX pool in SB18T buffer were measured. The 5' end-labelling of the enriched SELEX library of round 7 was performed using T4 polynucleotide kinase (New England Biolabs) and gamma- [32P ] ATP (Perkin-Elmer). Radiolabeled aptamer (20,000-40,000CPM, -0.03 nM) was mixed with target protein at a concentration ranging from 10-7M to 10-12M and incubated for 40 min at 37 ℃.

After incubation, the reaction was mixed with an equal volume of 10mM dextran sulfate and 0.014mg His-tagged Dynabeads (Invitrogen) and incubated for 5 minutes at 37 ℃. Bound complexes were captured on a Durapore filter plate (EMD Millipore) and bound aptamer fractions were quantified using a phosphorescence imager (Typhoon FLA 9500, GE) and the data analyzed in ImageQuant (GE).

To determine binding affinity, the data were fitted using the following equation:

y= (max-min) (protein)/(K) _d +protein) +min

And plotted using GraphPad Prism version 7.00, or the data was fitted using a four parameter sigmoidal dose response model. All data were plotted using GraphPad Prism version 7.00. The results are shown in Table 2 of FIGS. 1A-1I.

Table 2.

Target(s)	SELEX 7 th round library	Kd(M)
			XIAP	dATP、dGTP、dCTP、PP-dUTP	>1.0x10 ^-6
XIAP	dATP、dGTP、dCTP、DPP-dUTP	1.7x10 ^-8
			XIAP	dATP、dGTP、dCTP、PBn-dUTP	1.0x10 ^-8
IL-33	dATP、dGTP、dCTP、PP-dUTP	>1.0x10 ^-6
			IL-33	dATP、dGTP、dCTP、PBn-dUTP	9.3x10 ^-9
K-Ras	dATP、dGTP、dCTP、PP-dUTP	1.7x10 ^-9
			K-Ras	dATP、dGTP、dCTP、POP-dUTP	2.8x10 ^-10
K-Ras	dATP、dGTP、dCTP、DPP-dUTP	1.2x10 ^-10
			K-Ras	dATP、dGTP、dCTP、PBn-dUTP	1.4x10 ^-10
K-Ras	dATP、dGTP、dCTP、BPE-dUTP	1.8x10 ^-10
			TNF-α	dATP、dGTP、dCTP、PP-dUTP	1.4x10 ^-9
TNF-α	dATP、dGTP、dCTP、POP-dUTP	7.2x10 ^-11

Example 5: selection of aptamers with biphenyl modified nucleotides

This example provides a representative method for selecting and generating DNA aptamers using direct comparison of biphenyl modified dC libraries with monophenyl modified nucleotide libraries.

Preparation of candidate mixtures

Candidate mixtures of partially randomized ssDNA oligonucleotides were prepared by polymerase extension by annealing DNA primers to biotinylated ssDNA templates (as shown in table 3 below). The candidate mixture contains a 40 nucleotide random cassette containing dATP, dGTP, dUTP and one of PP-dCTP, bn-dCTP, DPP-dCTP, PBn-dCTP or POP-dCTP.

TABLE 3 sequence of templates and primers

B' =biotin

4900 microliters of a 50% slurry of streptavidin Plus UltraLink resin (PIERCE) was washed once with 1XSB18T buffer and three times with 16mM NaCl. The resin was aliquoted into six branches and 28 nanomoles were made with two biotin residues (designated B' in the sequence) and 40 randomized positions (designated N in the sequence) ₄₀ ) Is added to the washed UltraLink SA beads and is spun at 37℃for 30 minutes. The beads were then washed three times with 16mM NaCl. Between each wash, the beads were recovered by centrifugation. The beads now containing captured template were suspended in 1.67mL of extension reaction buffer [ containing 56nmol of primer 1 (SEQ ID NO: 5), 1 XSQ 20 buffer (120 mM Tris-HCl (pH 7.8), 10mM KCl, 7mM MgSO ] ₄ 、6mM(NH ₄ ) ₂ SO ₄ 0.001% BSA and 0.1% Triton X-100), 112 units KOD XL DNA polymerase (EMD MILLIPORE), and 1mM each of dATP, dGTP, dUTP and one of Bn-dCTP, PP-dCTP, PBn-dCTP, POP-dCTP or DPP-dCTP. The beads were incubated at 71℃for 2 hours. The beads were then washed three times with 16mM NaCl. The aptamer library was eluted from the beads with 1mL of 20mM NaOH. The eluted library was immediately neutralized with 15. Mu.L of 1N HCl and 10. Mu.L of HEPES pH 7.5 and 1. Mu.L of 10% TWEEN-20. The concentration of each library was determined by ultraviolet absorption spectroscopy.

Immobilization of target proteins

The following protein targets used in SELEX were purchased from commercial suppliers: TNFaAcro Biosystems catalog number TNA-5228; B7-H4, R & D Systems catalog number 6576-B7-050; sL-selectin, R & D Systems catalog number 728-LS-100. The resulting His-tagged target protein was immobilized on His-tagged Dynabead (Thermo Fisher) paramagnetic beads (MyOne SA, invitrogen, or His beads hereinafter) for SELEX (round 1 to 7). Beads (40 mg) were prepared by washing three times with 20mL of SB18T0.01. Finally, the beads were suspended in SB18T0.01 at 2.5mg/mL and stored at 4 ℃ until use.

Selection of aptamers by slow off-rate enrichment process

A total of eight rounds of SELEX procedure were completed and selected for affinity and slow off-rate. Reverse selection is performed prior to each round to reduce background and reduce the likelihood of obtaining an aptamer that binds non-specifically to the protein. The reverse selection proceeds as follows.

For rounds 2-8, 65. Mu.L aliquots of the DNA candidate mixture obtained from the previous round (65% of the eDNA obtained from the previous round) were mixed with 16. Mu.L of 5x SB18T0.01. The sample was heated to 95 ℃ for 3 minutes and cooled to 37 ℃ at a rate of 0.1 ℃/sec. The samples were then combined with 9 μl of protein competitor mixture (0.1% HSA, 10 μΜ casein and 10 μΜ prothrombin in SB18T0.01) and 0.025mg (10 uL) His beads and incubated for 10 min at 37 ℃ with mixing. Beads were removed by magnetic separation.

For rounds 2-8, selection was performed with the DNA candidate mixture and the target protein as described below, while the same selection was performed with the DNA candidate mixture in parallel but without the target protein. Comparison of Ct values obtained from PCR of samples with target protein (signal S) and samples without target protein (background B) can be used as a guideline for the next round of target concentration reduction. If the ΔCt value is greater than 4 but less than 8, the target protein is reduced by three times in the next round. If the Δct value is greater than 8, the next round of targets is reduced by a factor of 10.

Rounds 3 to 8 were performed as described for round 2, except that the amount of target protein was reduced as needed based on the delta Ct value for each target and library combination. Dextran sulfate was added 15 minutes (rounds 3 and 4), 30 minutes (rounds 5 and 6), 45 minutes (rounds 7 and 8) before the His beads were added.

For rounds 2 to 8, after perchlorate elution, 100. Mu.L of the aptamer eluate was captured with 0.0625mg (25. Mu.L) of SA beads (hereinafter referred to as primer beads) previously bound to primer 2 (SEQ ID NO: 6), and incubated at 50℃for 10 minutes while shaking, followed by 25℃for 10 minutes while shaking. The beads were washed 2 times with 100 μl SB18T0.01 and 1 time with 16mM NaCl. Bound aptamer was eluted with 120 μl water and incubated at 75 ℃ for 2 min. Beads were removed by magnetic separation and 120 μl of aptamer eluate was transferred to a new tube. Primer beads were prepared by suspending 120mg SA beads (1.5 mL of 10mg/mL SA beads washed once with 2mL of 20mM NaOH, twice with 2mL of SB18T 0.01) in 0.5mL of 1M NaCl, 0.01% tween-20 and adding 14 nanomoles of primer 2 (SEQ ID NO: 6). The mixture was incubated at 37℃for 1 hour. After incubation, the beads were washed 2 times with 1mL of SB18T0.01 and 2 times with 1mL of 16mM NaCl. The beads were resuspended in 5M NaCl, 0.01% tween-20 to 2.5mg/ml.

Aptamer amplification and purification

The selected aptamer DNA was amplified and quantified by QPCR for each round. 48 μL of LDNA was added to 12 μL of QPCR mix (10 XKOD DNA polymerase buffer; novagen #71157, diluted to 5 X25 mM MgCl2, 5 μM forward PCR primer (primer 1, SEQ ID NO: 5), 5 μM biotinylated reverse PCR primer (primer 2, SEQ ID NO: 6), 5 XSYBR Green I, 0.075U/. Mu.L KOD XL DNA polymerase and each 1mM dATP, dCTP, dGTP and dTTP) and thermally cycled in a Bio-Rad MyIQ QPCR instrument with the following protocol: 1 cycle, 96 ℃ for 15 seconds and 71 ℃ for 30 minutes; followed by 25 cycles of 96℃for 15 seconds and 71℃for 1 minute. Quantification was performed using instrument software and the copy numbers of the selected DNA (with and without target protein) were compared to determine the signal/background ratio.

The aptamer sense strand containing Bn-dCTP, PP-dCTP, PBn-dCTP, POP-dCTP or DPP-dCTP is prepared by primer extension from the immobilized antisense strand. The beads were suspended in 40. Mu.L of primer extension reaction mixture (1 Xprimer extension buffer (120 mM Tris-HCl pH 7.8, 10mM KCl, 7mM MgSO4, 6mM (NH 4) 2SO4, 0.1% TRITON X-100 and 0.001% bovine serum albumin), 4. Mu.M forward primer (primer 1, SEQ ID NO: 5), 0.5mM each dATP, dUTP, dGTP and Bn-dCTP, PP-dCTP, PBn-dCTP, POP-dCTP or DPP-dCTP, and 0.075U/. Mu.L KOD XL DNA polymerase) and incubated at 71℃for 45 minutes with mixing. The beads were washed 2 times with SB18T0.01, 1 time with 16mM NaCl, and the aptamer chains were eluted from the beads by adding 85. Mu.L of 20mM NaOH and incubating for 2 minutes with mixing at 37 ℃. After magnetic separation 83. Mu.L of the aptamer eluate was transferred to a new tube, neutralized with 20. Mu.L of 80mM HCl and buffered with 5. Mu. L0.1M HEPES (pH 7.5).

Selection stringency and feedback

if ΔCt <4, [ P ] (i+1) = [ P ] (i)

If 4.ltoreq.ΔCt <8, [ P ] (i+1) = [ P ] (i)/3.2

If ΔCt is greater than or equal to 8, [ P ] (i+1) = [ P ] (i)/10

Where [ P ] = protein concentration and i = current round number.

Example 6: enrichment of the equilibrium binding constant (Kd) of SELEX pool to protein targets

SELEX library-protein binding affinities were measured and Kd determined using the following method.

The binding affinities of enriched round 6 or round 8 SELEX libraries shown in table 4 below were determined. Briefly, the binding constants (Kd values) of the enriched SELEX library to recombinant tnfα and B7-H4 proteins were determined by a filter binding assay. The Kd values of the enriched SELEX pool in SB18T buffer were measured. The 5' end-labeling was performed on round 6 or round 8 enriched SELEX libraries using T4 polynucleotide kinase (New England Biolabs) and gamma- [32P ] ATP (Perkin-Elmer). Radiolabeled aptamer (20,000-40,000CPM, -0.03 nM) was mixed with target protein at a concentration ranging from 10-7M to 10-12M and incubated for 40 min at 37 ℃. After incubation, the reaction was mixed with an equal volume of 10mM dextran sulfate and 0.014mg His-tagged Dynabeads (Invitrogen) and incubated for 5 minutes (TNF. Alpha. And sL-selectin) at 37 ℃. For the B7-H4 protein, 2.2mg of Zorbax resin (Agilent Technologies) was added to each reaction. Bound complexes were captured on a Durapore filter plate (EMD Millipore) and bound aptamer fractions were quantified using a phosphorescence imager (Typhoon FLA 9500, GE) and the data analyzed in ImageQuant (GE).

y= (max-min) (protein)/(K) _d + protein) +min and plotted using GraphPad prism version 7.00, or the data was fitted using a four parameter sigmoidal dose response model. All data were plotted using GraphPad Prism version 7.00. The results are shown in FIGS. 7A-7F and Table 4.

Table 4.

Target(s)	SELEX round 6 or 8 library	Kd(M)
			TNFα	dATP、dGTP、dUTP、PP-dCTP	>1.0x10 ^-6
TNFα	dATP、dGTP、dUTP、Bn-dCTP	>1.0x10 ^-6
			TNFα	dATP、dGTP、dUTP、DPP-dCTP	1.3x10 ^-9
TNFα	dATP、dGTP、dUTP、PBn-dCTP	1.1x10 ^-9
			TNFα	dATP、dGTP、dUTP、POP-dCTP	3.7x10 ^-10
B7-H4	dATP、dGTP、dUTP、Bn-dCTP	>1.0x10 ^-6
			B7-H4	dATP、dGTP、dUTP、PBn-dCTP	8.0x10 ^-9
sL-selectin	dATP、dGTP、dUTP、PP-dCTP	4.5x10 ^-9
			sL-selectin	dATP、dGTP、dUTP、PBn-dCTP	6.1x10 ^-10
sL-selectin	dATP、dGTP、dUTP、POP-dCTP	2.4x10 ^-10

Results

After the eighth round of SELEX was completed, the affinity enriched libraries of the sixth and eighth rounds were analyzed in the filter binding assay to identify those libraries containing high affinity binding sequences and to evaluate the value of biphenyl dC modification (DPP-dC, PBn-dC, POP-dC) compared to mono benzene ring dC modification (Bn-dC, PP-dC) in SELEX. We found that biphenyl dC modifications of DPP-dC, PBn-dC and POP-dC showed improved results in SELEX library affinity binding. TNF alpha protein was found to be up to 1.0x10 in the eighth round of SELEX library modified with Bn-dC and PP-dC ^-7 There is no measurable binding affinity at the protein concentration of M. However, high affinity binding was measured for the eighth round of DPP-dC, PBn-dC and POP-dC libraries (table 4), indicating that these modified libraries were successful at SELEX. Similarly, the sixth round pool of B7-H4 protein had no measurable binding affinity for Bn-dC, whereas the PBn-dC modified pool had 8.0x10 ^-9 High affinity of M. The sL-selectin protein has moderate PP-dC binding affinity for round 8 pool (4.5x10 ^-9 M), whereas the biphenyl libraries of PBn-dC and POP-dC have significantly improved affinities (6.1x10, respectively) ^-10 M and 2.4x10 ^-10 M). These results indicate that the biphenyl library is enriched for higher affinity sequences than the monophenyl PP-dC library. Overall, these results show that biphenyl modified dC libraries produced improved results in SELEX.

Claims

1. A compound comprising a pyrimidine nucleoside modified at the 5-position or a salt thereof,

wherein the 5-position modified pyrimidine is substituted with a moiety comprising two phenyl groups covalently linked to each other through a first linker, and wherein the moiety is covalently linked to the 5-position of the pyrimidine through a second linker.

2. The compound of claim 1, wherein the first linker comprises at least one atom selected from carbon and oxygen or is a bond.

3. The compound of any one of claims 1-2, wherein the pyrimidine modified at the 5-position comprises a moiety at the 5-position selected from the group consisting of a phenylbenzyl moiety, a phenoxybenzyl moiety, and a diphenylmethyl moiety.

4. The compound of any one of claims 1-3, wherein the second linker comprises a group selected from an amide linker, a carbonyl linker, a propynyl linker, an alkyne linker, an ester linker, a urea linker, a carbamate linker, a guanidine linker, an amidine linker, a sulfoxide linker, and a sulfone linker.

5. The compound of any one of claims 1-3, wherein the second linker comprises an amide linker.

6. The compound of claim 5, wherein the amide linker further comprises one or more carbon atoms or 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 carbon atoms.

7. The compound of any one of claims 1-6, comprising a uridine modified in the 5-position.

8. The compound of any one of claims 1-7, comprising a cytidine modified at the 5-position.

9. A compound comprising a structure of formula IA or formula IB:

or a salt of any of these,

wherein the method comprises the steps of

each R ₁ Independently selected from:

each X is independently selected from the group consisting of-H, -OH, -OMe-O-allyl, -O-ethyl, -O-propyl, -OCH ₂ CH ₂ OCH ₃ -fluoro, -t-butyldimethylsilyloxy, -NH ₂ And-azido;

each R ₂ Independently selected from-OH, -acetyl, -OBz, -OP (N (CH) ₂ CH ₃ ) ₂ )(OCH ₂ CH ₂ CN)、-OP(N(R _x ) ₂ )(OCH ₂ CH ₂ CN), wherein each R _x Independently is (C) _1-6 ) Alkyl, t-butyldimethylsilyloxy, -O-ss, -OR, -SR, -ZP (Z') (Z ") -O-R; wherein ss is a solid support, Z, Z' and Z "are each independently selected from O and S, and R is an adjacent nucleotide;

Each R ₃ Independently selected from the group consisting of-OH, -O-trityl, -O-4,4' -dimethoxytrityl-O-triphosphate, -OR, -SR, -NH ₂ -NHR and-Z-P (Z ') (Z ") O-R, wherein Z, Z' and Z" are each independently selected from O and S, and R is an adjacent nucleotide.

10. The compound of claim 9, wherein n is 1, 2 or 3.

11. The compound of any one of claims 9-10, wherein X is-H.

12. The compound of any one of claims 9-10, wherein X is-OMe.

13. The compound of any one of claims 9-12, wherein each R ₁ Independently selected from

14. The compound of any one of claims 1-13, wherein the 5-position modified pyrimidine is selected from the group consisting of BPEdU, 2' -OMe-BPE-U, 2' -F-BPE-U, PBndU, 2' -OMe-PBn-U, 2' -F-PBn-U, POPdU, 2' -OMe-POP-U, 2' -F-POP-U, DPPdU, 2' -OMe-DPP-U, 2' -F-DPP-U, DBMdU, 2' -OMe-DBM-U, 2' -F-DBM-U, BHdU, 2' -OMe-BH-U, 2' -F-BH-U, BPEdC, 2' -OMe-BPE-C, 2' -F-BPE-C, PBndC, 2' -OMe-PBn-C, 2' -F-PBn-C, POPdC, 2' -OMe-POP-C, 2' -F-POP-C, DPPdC, 2' -OMe-DPP-C, DBMdC, 2' -OMe-C, 2' -OMe-F-DBM-C, 82 ' -OMe-C, and 2' -BH-C.

15. A compound comprising a structure of formula IIA or formula IIB:

or a salt of any of these,

wherein the method comprises the steps of

each R ₁ Independently selected from:

16. The compound of claim 15, wherein n is 1, 2, or 3.

17. The compound of any one of claims 15-16, wherein X is-H.

18. The compound of any one of claims 15-16, wherein X is-OMe.

19. The compound of any one of claims 15-18, wherein each R ₁ Independently selected from:

20. a compound comprising the structure:

or a salt of any of these;

wherein each X is independently selected from the group consisting of-H, -OH, -O-methyl-O-allyl, -O-ethyl, -O-propyl, -OCH ₂ CH ₂ OCH ₃ -fluoro, -t-butyldimethylsilyloxy, -NH ₂ And-azido.

21. The compound of claim 20, wherein X is-H.

22. The compound of claim 20, wherein X is-OMe.

23. An oligonucleotide comprising a compound of any of claims 1-14.

24. The oligonucleotide of claim 23, comprising RNA, DNA, or a combination thereof.

25. The oligonucleotide of any one of claims 23-24, which is 15 to 100, or 15 to 90, or 15 to 80, or 15 to 70, or 15 to 60, or 15 to 50, or 20 to 100, or 20 to 90, or 20 to 80, or 20 to 70, or 20 to 60, or 20 to 50, or 30 to 100, or 30 to 90, or 30 to 80, or 30 to 70, or 30 to 60, or 30 to 50, or 40 to 100, or 40 to 90, or 40 to 80, or 40 to 70, or 40 to 60, or 40 to 50 nucleotides in length.

26. The oligonucleotide of any one of claims 23-25, which is an aptamer that binds to a target.

27. An aptamer comprising a compound of any one of claims 1-14.

28. The aptamer of any one of claims 26-27, wherein the aptamer is 15 to 100, or 15 to 90, or 15 to 80, or 15 to 70, or 15 to 60, or 15 to 50, or 20 to 100, or 20 to 90, or 20 to 80, or 20 to 70, or 20 to 60, or 20 to 50, or 30 to 100, or 30 to 90, or 30 to 80, or 30 to 70, or 30 to 60, or 30 to 50, or 40 to 100, or 40 to 90, or 40 to 80, or 40 to 70, or 40 to 60, or 40 to 50 nucleotides in length.

29. The aptamer of any one of claims 26-28, comprising a 5-modified pyrimidine selected from the group consisting of: BPEdU, 2'-OMe-BPE-U, 2' -F-BPE-U, PBndU, 2'-OMe-PBn-U, 2' -F-PBn-U, POPdU, 2'-OMe-POP-U, 2' -F-POP-U, DPPdU, 2'-OMe-DPP-U, 2' -F-DPP-U, DBMdU, 2'-OMe-DBM-U, 2' -F-DBM-U, BHdU, 2'-OMe-BH-U, 2' -F-BH-U, BPEdC, 2'-OMe-BPE-C, 2' -F-BPE-C, PBndC, 2'-OMe-PBn-C, 2' -F-PBn-C, POPdC, 2'-OMe-POP-C, DPPdC, 2' -OMe-DPP-C, 2'-F-DPP-C, DBMdC, 2' -OMe-DBM-C, BHdC, 2'-OMe-BH-C and 2' -F-BH-C.

30. The aptamer of any one of claims 26-29, comprising at least one 5-position modified uridine selected from the group consisting of: BPEdU, 2'-OMe-BPE-U, 2' -F-BPE-U, PBndU, 2'-OMe-PBn-U, 2' -F-PBn-U, POPdU, 2'-OMe-POP-U, 2' -F-POP-U, DPPdU, 2'-OMe-DPP-U, 2' -F-DPP-U, DBMdU, 2'-OMe-DBM-U, 2' -F-DBM-U, BHdU, 2'-OMe-BH-U, 2' -F-BH-U, and at least one 5-position modified cytidine selected from the group consisting of: BPEdc, 2'-OMe-BPE-C, 2' -F-BPE-C, PBndC, 2'-OMe-PBn-C, 2' -F-PBn-C, POPdC, 2'-OMe-POP-C, 2' -F-POP-C, DPPdC, 2'-OMe-DPP-C, 2' -F-DPP-C, DBMdC, 2'-OMe-DBM-C, 2' -F-DBM-C, BHdC, 2'-OMe-BH-C and 2' -F-BH-C.

31. The aptamer of any one of claims 26-30, wherein the aptamer comprises a region of at least 10, at least 15, at least 20, at least 25, or at least 30 nucleotides in length, or 5 to 30, 10 to 30, 15 to 30, 5 to 20, or 10 to 20 nucleotides in length, at the 5 'end of the aptamer, wherein the region at the 5' end of the aptamer lacks a 5-modified pyrimidine.

32. The aptamer of any one of claims 26-31, wherein the aptamer comprises a region of at least 10, at least 15, at least 20, at least 25, or at least 30 nucleotides in length, or 5 to 30, 10 to 30, 15 to 30, 5 to 20, or 10 to 20 nucleotides in length at the 3 'end of the aptamer, wherein the region at the 3' end of the aptamer lacks a 5-modified pyrimidine.

33. An aptamer comprising at least one first 5-position modified pyrimidine and at least one second 5-position modified pyrimidine, wherein the first 5-position modified pyrimidine and the second 5-position modified pyrimidine are different 5-position modified pyrimidines, and wherein the at least one first 5-position modified pyrimidine is a compound according to any one of claims 1-14.

34. The aptamer of claim 33, wherein the at least one second 5-position modified pyrimidine is selected from the group consisting of BndC, 2'-OMe-Bn-C, PEdC, 2' -OMe-PE-C, PPdC, 2'-OMe-PP-C, napdC, 2' -OMe-Nap-C, 2NapdC, 2'-OMe-2Nap-C, NEdC, 2' -OMe-NE-C, 2NEdC, 2'-OMe-2NE-C, tyrdC, 2' -OMe-Tyr-C, bndU, 2'-OMe-Bn-U, napdU, 2' -OMe-Nap-U, PEdU, 2'-OMe-PE-U, ibdU, 2' -OMe-Ib-U, FBndU, 2'-OMe-FBn-U, 2' -Nap-U, NEdU, 2'-OMe-NE-U, MBndU, 2' -OMe-MBn-U, BFdU, 2 '-OMe-BF-95, 2' -OMe-PP-U, PPdU, 2 '-OMe-3872, and 2' -OMe-49.

35. The aptamer of any one of claims 33-34, wherein the at least one second 5-position modified pyrimidine is selected from the group consisting of NapdC, 2'-OMe-Nap-C, 2NapdC, 2' -OMe-2Nap-C, tyrdC, 2'-OMe-Tyr-C, PPdC, 2' -OMe-PP-C, napdU, 2'-OMe-Nap-U, PPdU, 2' -OMe-PP-U, MOEdU, 2'-OMe-MOE-U, tyrdU, 2' -OMe-Tyr-U, trpdU, 2'-OMe-Trp-U, thrdU, and 2' -OMe-Thr-U.

36. The aptamer of any one of claims 26-35, wherein the aptamer has improved nuclease stability and/or a longer half-life in human serum and/or improved affinity and/or improved dissociation rate compared to an aptamer having the same length and comprising a nucleobase sequence of an unmodified pyrimidine instead of the 5-position modified pyrimidine.

37. A composition comprising a plurality of the aptamers of any one of claims 26-36.

38. The composition of claim 37, wherein each aptamer comprises a random region.

39. The composition of claim 38, wherein the random region is 20 to 100, or 20 to 90, or 20 to 80, or 20 to 70, or 20 to 60, or 20 to 50, or 20 to 40, or 30 to 100, or 30 to 90, or 30 to 70, or 30 to 60, or 30 to 50, or 30 to 40 nucleotides in length.

40. A composition comprising an aptamer and a target, wherein the aptamer and the target are capable of forming a complex, and wherein the aptamer is the aptamer of any one of claims 26-35.

41. A composition comprising a first aptamer, a second aptamer, and a target,

wherein the first aptamer, the second aptamer, and the target are capable of forming a trimeric complex; and is also provided with

Wherein the first aptamer is an aptamer comprising a compound of any one of claims 1-14; and is also provided with

Wherein the second aptamer comprises at least one second 5-position modified pyrimidine.

42. The composition of claim 41, wherein the target is selected from the group consisting of a protein, a peptide, a carbohydrate, a small molecule, a cell, and a tissue.

43. The composition of any one of claims 41-42, wherein the target is a target protein selected from the group consisting of IL-33, XIAP, K-Ras, and TNF-alpha.

44. A pharmaceutical composition comprising at least one aptamer of any one of claims 26-35, or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable carrier.

45. The pharmaceutical composition of claim 44, for use in treating or preventing a disease or disorder mediated by a protein selected from the group consisting of IL-33, XIAP, K-Ras, and TNF-alpha.

46. A method of treating or preventing a disease or disorder in a subject comprising administering to a subject in need thereof the aptamer of any one of claims 26-35 or the pharmaceutical composition of any one of claims 44-45.

47. The method of claim 46, wherein the disease or disorder is mediated by a protein selected from the group consisting of IL-33, XIAP, K-Ras, and TNF-alpha.

48. The method of any one of claims 46-47, wherein the disease or disorder is Traumatic Brain Injury (TBI) or rheumatoid arthritis.

49. A method, comprising:

(a) Contacting an aptamer capable of binding to a target molecule with a sample;

(b) Incubating the aptamer with the sample to allow aptamer-target complex formation;

(c) Enriching the aptamer-target complex in the sample; and

(d) Detecting the presence of the aptamer, the aptamer-target complex, or the target molecule, wherein detection of the aptamer, the aptamer-target complex, or the target molecule indicates the presence of the target molecule in the sample, and wherein no detection of the aptamer, the aptamer-target complex, or the target molecule indicates the absence of the target molecule in the sample;

wherein the aptamer comprises the compound of any one of claims 1-14 or is the aptamer of any one of claims 26-35.

50. The method of claim 49, wherein the method comprises at least one additional step selected from the group consisting of: adding a competitor molecule to the sample; capturing the aptamer-target complex on a solid support; and adding a competitor molecule and diluting the sample; wherein the at least one additional step is performed after step (a) or step (b).

51. The method of claim 50, wherein the competitor molecule is selected from polyanionic competitors.

52. The method of claim 51, wherein the polyanionic competitor is selected from the group consisting of an oligonucleotide, a polyglucan, DNA, heparin, and dNTP.

53. The method of claim 52, wherein the polyglucan is dextran sulfate; and the DNA is herring sperm DNA or salmon sperm DNA.

54. The method of any one of claims 49-53, wherein the target molecule is selected from the group consisting of a protein, a peptide, a carbohydrate, a small molecule, a cell, and a tissue.

55. The method of any one of claims 49-54, wherein the sample is selected from the group consisting of whole blood, leukocytes, peripheral blood mononuclear cells, plasma, serum, sputum, breath, urine, semen, saliva, meningeal fluid, amniotic fluid, glandular fluid, lymph fluid, nipple aspirate, bronchial aspirate, synovial fluid, joint aspirate, cells, cell extracts, stool, tissue biopsies, and cerebral spinal fluid.

56. A method for detecting a target in a sample, comprising:

(a) Contacting the sample with a first aptamer to form a mixture, wherein the first aptamer is capable of binding to the target to form a first complex;

(b) Incubating the mixture under conditions allowing the first complex to form;

(c) Contacting the mixture with a second aptamer, wherein the second aptamer is capable of binding to the first complex to form a second complex;

(d) Incubating the mixture under conditions allowing the second complex to form;

(e) Detecting the presence or absence of the first aptamer, the second aptamer, the target, the first complex, or the second complex in the mixture, wherein the presence of the first aptamer, the second aptamer, the target, the first complex, or the second complex is indicative of the presence of the target in the sample;

wherein the first aptamer comprises a compound of any one of claims 1-14; and is also provided with

Wherein the second aptamer comprises at least one second 5-position modified pyrimidine;

wherein the first aptamer, the second aptamer, and the target are capable of forming a trimeric complex.

57. The method of claim 56, wherein said target molecule is selected from the group consisting of a protein, a peptide, a carbohydrate, a small molecule, a cell, and a tissue.

58. The method of any one of claims 56-57, wherein said first aptamer, said second aptamer, and said target are capable of forming a trimeric complex.

59. The method of any one of claims 56-58, wherein the second aptamer comprises at least one second 5-position modified pyrimidine selected from the group consisting of: bndC, 2'-OMe-Bn-C, PEdC, 2' -OMe-PE-C, PPdC, 2'-OMe-PP-C, napdC, 2' -OMe-Nap-C, 2Napdc, 2'-OMe-2Nap-C, NEdC, 2' -OMe-NE-C, 2NEdC, 2'-OMe-2NE-C, tyrdC, 2' -OMe-Tyr-C, bndU, 2'-OMe-Bn-U, napdU, 2' -OMe-Nap-U, PEdU, 2'-OMe-PE-U, ibdU, 2' -OMe-Ib-U, FBndU, 2'-OMe-FBn-U, 2NapdU, 2' -OMe-2Nap-U, NEdU, 2'-OMe-NE-U, MBndU, 2' -OMe-MBn-U, BFdU, 2'-OMe-BF-U, BTdU, 2' -OMe-BT-U, PPdU, 2'-OMe-PP-U, MOEdU, 2' -OMe-MOE-U, tyrdU, 2'-OMe-Ib-U, FBndU, 2' -OMe-FBn-U, 2 '-OMe-52, 2' -OMe-35 and Tre-4535.

60. The method of any one of claims 56-59, wherein said second aptamer comprises at least one second 5-position modified pyrimidine selected from the group consisting of: napdc, 2'-OMe-Nap-C, 2Napdc, 2' -OMe-2Nap-C, tyrdC, 2'-OMe-Tyr-C, PPdC, 2' -OMe-PP-C, napdU, 2'-OMe-Nap-U, PPdU, 2' -OMe-PP-U, MOEdU, 2'-OMe-MOE-U, tyrdU, 2' -OMe-Tyr-U, trpdU, 2'-OMe-Trp-U, thrdU and 2' -OMe-Thr-U.

61. A method for identifying one or more aptamers capable of binding to a target molecule, comprising:

(a) Contacting a library of aptamers with the target molecule to form a mixture, and allowing formation of aptamer-target complexes, wherein the aptamer-target complexes are formed when the aptamers have affinity for the target molecule;

(b) Separating the aptamer-target complex from the remainder of the mixture (or enriching the aptamer-target complex);

(c) Dissociating the aptamer-target complex; and

(d) Identifying the one or more aptamers capable of binding to the target molecule;

wherein the aptamer library comprises a plurality of polynucleotides and the aptamer library is the composition of any one of claims 37-43.

62. The method of claim 61, wherein each polynucleotide comprises an immobilization region at the 5' end of the polynucleotide.

63. The method of claim 62, wherein the immobilization region at the 5' end of each polynucleotide is at least 10, at least 15, at least 20, at least 25, or at least 30 nucleotides in length, or 5 to 30, 10 to 30, 15 to 30, 5 to 20, or 10 to 20 nucleotides in length.

64. The method of any one of claims 61-63, wherein each polynucleotide comprises an immobilization region at the 3' end of the polynucleotide.

65. The method of claim 64, wherein the immobilization region at the 3' end of the polynucleotide is at least 10, at least 15, at least 20, at least 25, or at least 30 nucleotides in length, or 5 to 30, 10 to 30, 15 to 30, 5 to 20, or 10 to 20 nucleotides in length.

66. The method of any one of claims 61-65, wherein each polynucleotide comprises a random region.

67. The method of claim 66, wherein the random region is 20 to 100, or 20 to 90, or 20 to 80, or 20 to 70, or 20 to 60, or 20 to 50, or 20 to 40, or 30 to 100, or 30 to 90, or 30 to 70, or 30 to 60, or 30 to 50, or 30 to 40 nucleotides in length.

68. The method of any one of claims 61-67, wherein each polynucleotide is 15 to 100, or 15 to 90, or 15 to 80, or 15 to 70, or 15 to 60, or 15 to 50, or 20 to 100, or 20 to 90, or 20 to 80, or 20 to 70, or 20 to 60, or 20 to 50, or 30 to 100, or 30 to 90, or 30 to 80, or 30 to 70, or 30 to 60, or 30 to 50, or 40 to 100, or 40 to 90, or 40 to 80, or 40 to 70, or 40 to 60, or 40 to 50 nucleotides in length.

69. The method of any one of claims 61-68, wherein each polynucleotide is an aptamer that binds to a target, and wherein the library comprises at least 1000 aptamers, wherein each aptamer comprises a different nucleotide sequence.

70. The method of any one of claims 61-69, wherein steps (a), (b), and/or (c) are repeated at least once, twice, three times, four times, five times, six times, seven times, eight times, nine times, or ten times.

71. The method of any one of claims 61-70, wherein the one or more aptamers capable of binding to the target molecule are amplified.

72. The method of any one of claims 61-71, wherein the mixture comprises a polyanionic competitor molecule.

73. The method of claim 72, wherein the polyanionic competitor is selected from the group consisting of an oligonucleotide, a polyglucan, DNA, heparin, and dNTP.

74. The method of claim 73, wherein the polyglucan is dextran sulfate; and the DNA is herring sperm DNA or salmon sperm DNA.

75. The method of any one of claims 61-74, wherein the target molecule is selected from the group consisting of a protein, a peptide, a carbohydrate, a small molecule, a cell, and a tissue.

76. The compound of any one of claims 1-14, the aptamer of any one of claims 26-35, the composition of any one of claims 37-45, or the method of any one of claims 46-75, wherein the pyrimidine modified at the 5-position is capable of being incorporated by a polymerase.

77. A kit comprising a compound of any one of claims 1-14, a compound of any one of claims 15-22, an oligonucleotide of any one of claims 23-25, an aptamer of any one of claims 26-35, a composition of any one of claims 37-43, and optionally one or more of the following: (a) A pharmaceutically acceptable carrier, such as a solvent or solution; (b) Pharmaceutically acceptable excipients, such as stabilizers or buffers; (c) At least one container, vial or device for holding and/or mixing the kit components; and (d) a delivery device.

78. The kit of claim 77, optionally further comprising one or more of: (e) A labeling agent useful for detecting a target molecule bound to an aptamer; (f) a solid support, such as a microarray or bead; and (g) reagents related to the quantification of the polymerase chain reaction products, such as intercalating fluorescent dyes or fluorescent DNA probes.

79. A compound comprising a structure of formula III, formula IV or formula V:

or a salt of any of these, wherein:

each R ₁ Independently selected from:

80. The compound of claim 79, wherein n is 1, 2, or 3.

81. The compound of any one of claims 79-80, wherein X is-H.

82. The compound of any one of claims 79-80, wherein X is-OMe.

83. The compound of any one of claims 79-82, wherein R ₁ Selected from the group consisting of

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