Classifications

• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07D—HETEROCYCLIC COMPOUNDS
  • C07D473/00—Heterocyclic compounds containing purine ring systems
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07D—HETEROCYCLIC COMPOUNDS
  • C07D403/00—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group C07D401/00
  • C07D403/02—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group C07D401/00 containing two hetero rings
  • C07D403/04—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group C07D401/00 containing two hetero rings directly linked by a ring-member-to-ring-member bond
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07D—HETEROCYCLIC COMPOUNDS
  • C07D473/00—Heterocyclic compounds containing purine ring systems
  • C07D473/26—Heterocyclic compounds containing purine ring systems with an oxygen, sulphur, or nitrogen atom directly attached in position 2 or 6, but not in both
  • C07D473/28—Oxygen atom
  • C07D473/30—Oxygen atom attached in position 6, e.g. hypoxanthine
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07D—HETEROCYCLIC COMPOUNDS
  • C07D473/00—Heterocyclic compounds containing purine ring systems
  • C07D473/26—Heterocyclic compounds containing purine ring systems with an oxygen, sulphur, or nitrogen atom directly attached in position 2 or 6, but not in both
  • C07D473/32—Nitrogen atom
  • C07D473/34—Nitrogen atom attached in position 6, e.g. adenine
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
  • C07H19/00—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof
  • C07H19/02—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof sharing nitrogen
  • C07H19/04—Heterocyclic radicals containing only nitrogen atoms as ring hetero atom
  • C07H19/06—Pyrimidine radicals
  • C07H19/10—Pyrimidine radicals with the saccharide radical esterified by phosphoric or polyphosphoric acids
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
  • C07H19/00—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof
  • C07H19/02—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof sharing nitrogen
  • C07H19/04—Heterocyclic radicals containing only nitrogen atoms as ring hetero atom
  • C07H19/16—Purine radicals
  • C07H19/20—Purine radicals with the saccharide radical esterified by phosphoric or polyphosphoric acids

Definitions

• the present invention relates to fluorescent structural analogs of the non-fluorescent nucleobases (amine bases, nitrogenous bases) and nucleosides commonly found in DNA and RNA, methods of their derivatization and subsequent use thereof use in the chemical or enzymatic synthesis of fluorescent oligonucleotides (polynucleotides), and to their new and useful application as probes in hybridization and sequencing reactions and the like. Additionally, the present invention relates to applications in which fluorescent structural analogs are substituted for specific non- fluorescent nucleosides in prescribed DNA or RNA sequences and to methods of using fluorescent oligonucleotides as hybridization reagents and probes for diagnostic and therapeutic purposes and as diagnostic and therapeutic research tools.
• the present invention relates to maleimide derivatives of pyrimidines such as uridine and cytidine at their C-5 position, and to maleimide derivatives of purines such as adenine and guanine at their 8-position and to methods of their synthesis and the structure and synthesis of nucleoside tri-phosphates and phosphoramidites, etc., incorporating these derivatives.
• N-nucleosides which predominate in the composition of DNA and RNA from all sources have the structures:
• R ⁇ is H for inosine and NH 2 for guanosine
• R 9 is H for uridine and CH 3 for thymidine.
• R 12 , R 14 OH for ribonucleotides
• R 12 OH
• R 14 H for 2'-deoxy nucleotides
• R )2 H
• R 14 OH for 3'-deoxy nucleotides
• R ]2 , R j4 H in dideoxy nucleotides.
• the six commonly occurring nucleotides do not absorb light at wavelengths >290 nm and are effectively non-fluorescent under physiological conditions.
• Derivatives of the commonly occurring N- nucleotides for a variety of synthetic, diagnostic, and therapeutic purposes are common, including substitutions on both the heterocyclic base and the furanose ring. These substitutions can be made at the loci shown in:
• R R 2 , and R 3 can be a H, OH, alkyl, acyl, amide, thioether, or disulfide);
• R 5 is H or part of an etheno linkage with R 4 ;
• R 9 is hydrogen, methyl, bromine, fluorine, or iodine, or an alkyl or aromatic substituent, or an optional linking moiety including an amide, thioether, or disulfide linkage or a combination thereof such as R r (CH2) X - 2 , or R,-R 2 -(CH 2 ) X -R 3 -, where x is an integer in the range of 1 and 25 inclusive;
• R 10 is hydrogen, or an acid-sensitive base stable blocking group, or a phosphorous derivative,
• R 12 is hydrogen, OH, or a phosphorous derivative;
• N and C in the N-nucleosides and C- nucleosides designate the atom at which the glycosidic covalent bond connects the sugar and the heterocyclic base.
• the bases are either adenine, guanine, cytosine, inosine, uracil, or thymine.
• the bases are attached to a furanose sugar, a general structure of which is shown hereinunder.
• the sugar substituents for the fluorescent analogs share the same numbering system for all R groups, but the numbering system for some of the heterocycle analogs may differ.
• Nucleotide sequences are commonly utilized in a variety of applications including diagnostic and therapeutic probes which hybridize target DNA and RNA and amplification of target sequences. It is often necessary, or useful, to label nucleotide sequences.
• Hybridization of specific DNA or RNA sequences typically involves annealing oligonucleotides of lengths which range from as little as 5 bases to more than 10,000 bases (10 kb).
• the majority of oligonucleotide probes is currently in research use are radioactively labeled; however, because of (i) the short half lives of the isotopes in common usage, (ii) the safety requirements, and (iii) the costs of handling and disposal of radioactive probes, convenient and sensitive non-isotopic methods of detection are required for hybridization diagnostic methods to achieve widespread acceptance and application. Non-isotopic methods of labeling oligonucleotide probes.
• PNAS 85:8790-8794 synthesizing modified nucleosides containing (a) protected reactive groups, such as NH 2 , SH, CHO, or COOH, (b) activatable monofunctional linkers, such as NHS esters, aldehydes, or hydrazides, or (c) affinity binding groups, such as biotin, attached to either the heterocyclic base or the furanose moiety. Modifications have been made on intact oligonucleotides or to monomeric nucleosides which have subsequently been inco ⁇ orated into oligonucleotides during chemical synthesis via terminal transferase or "nick translation" (see, e.g., Brumbaugh et al.
• non-nucleoside linkers and labels have been attached to the 3' or 5' end of existing oligonucleotides by either enzymatic or chemical methods. Modification of nucleoside residues internal to the sequence of a DNA or RNA strand has proven to be a difficult procedure, since the reaction conditions must be mild enough to leave the RNA or DNA oligomers intact and still yield reaction products which can participate in normal Watson-Crick base pairing and stacking interactions.
• DNA probes have been amino modified and subsequently derivatized to carry a hapten such as 2,4-dinitrophenol (DNP) to which enzyme-conjugated anti-hapten antibodies bind which subsequently can be processed using a calorimetric substrate as a label (Keller et al. [1988] Analytical Biochemistry 170:441-450).
• DNP 2,4-dinitrophenol
• Patent No. 4,910,300 covering pyrimidine derivatives on which the 6-amino group at C4 had been modified.
• 3' and 5' amino modifying phosphoramidites have been widely used in chemical synthesis or derivatized oligonucleotides and are commercially available
• nucleoside 5'-triphosphates or 3'-0- phosphoramidites were modified with a biotin moiety conjugated to an aliphatic amino group at the 5-position of uracil (Langer et al. [1981] PNAS 78:6633-6637; Saiki et al. [1985] Science 230: 1350-1354).
• the nucleotide triphosphate derivatives are effectively inco ⁇ orated into double stranded DNA by standard techniques of "nick translation". Once in an oligonucleotide, the residue may be bound by avidin, streptavidin, or anti- biotin antibody which can then be used for detection by fluorescence, chemiluminescence, or enzymatic processing.
• Immunofluorescent detection can be done using monoclonal Fab' fragments which are specific for RNA:DNA hybrids in which the probe has been derivatized with, e.g., biotin-11-UTP
• (x) Acridinium ester labeling.
• a single phenyl ester of methyl acridinium is attached at a central position on an RNA or DNA probe. Hydrolysis of the ester releases an acridone, C0 2 , and light. Because the ester on unhybridized probes hydrolyses more quickly than the ester on probes which have hybridized to target RNA or DNA, the chemiluminescence of the hybridized probes can be distinguished from that of free probes and is used in a "hybridization protection assay" (Weeks et al. [1983] Clin. Chem. 29: 1474-1479).
• Internucleotide linkage reporter groups (i) Internucleotide linkage reporter groups (Ri p site). Phosphorothioate esters have been used to provide a binding site for fluorophores such as monobromobimane (Conway et al. [1989] Nucl. Acids Res. Symposium Series 21 :43-44). Agrawal and Zamecnik ([1990] Nucl. Acids Res.
• Fluorescent N-nucleosides an fluorescent structural analogs.
• Formycin A (generally referred to as Formycin), the prototypical fluorescent nucleoside analog, was originally isolated as an antitumor antibiotic from the culture filtrates of Nocardia interforma (Hori et al. [1966] J. Antibiotics, Ser. A 17:96-99) and its structure identified as 7- amino-3-b-D-ribofuranosyl (lH-pyrazolo-[4,3d] pyrimidine).
• This antibiotic which has also been isolated from culture broths of Streptomyces lavendulae (Aizawa et al. [1965] Agr. Biol. Chem. 29:375-376), and Streptomyces gummaensis (Japanese Patent No.
• Formycin, formycin B, and oxoformycin B are pyrazolopyrimidine nucleosides and are structural analogs of adenosine, inosine, and hypoxanthine, respectively; a pyrazopyrimidine structural analog of guanosine obtained from natural sources has not been reported in the literature. A thorough review of the biosynthesis of these compounds is available in Ochi et al. (1974) J. Antibiotics xxiv:909-916.
• N-nucleosides Physical properties of the N-nucleosides. Because several of the N- nucleosides were known to be active as antibiotic, antiviral, or anti-tumor compounds, their chemical derivatization and physical properties have been extensively studied and compared to the structures and syntheses of the N- nucleosides commonly found in DNA and RNA. In the late 1960s, several structural analogs of the six commonly occurring N-nucleosides were found to be fluorescent under physiological conditions; fluorescence in the analogs results from a molecular rigidity of the heterocycle structure itself; not all the structural analogs of a given type, e.g., the C-nucleosides, are fluorescent, nor is fluorescence an exclusive or inherent property of any particular class of structural analogs.
• Nucleic acid hybridizations are now commonly used in genetic research, biomedical research and clinical diagnostics.
• a single stranded nucleic acid (either deoxyribonucleic acid, DNA, or ribonucleic acid, RNA) is hybridized to a labeled nucleic acid probe and the resulting labeled duplexes are detected.
• Chemical methods for inco ⁇ orating modified nucleotides are described hereinabove and in PCT application WO 84/03285.
• the synthetic polynucleotides containing the modified nucleotides usually referred as a "linker arm nucleotide"
• linker arm nucleotide can subsequently be derivatized with a fluorescent moiety.
• nucleosides were labeled using a linker arm. No work has been described in which increasing the fluorescence of, for example, uridine and cytidine is effected by extending the conjugation of the base moieties thereof by addition of an unsaturated moiety, as further detailed hereunder.
• Fluorescent dyes have many uses and are known to be particularly suitable for biological applications in which the high detectability of fluorescence is desirable.
• fluorescent dyes have many uses and are known to be particularly suitable for biological applications in which the high detectability of fluorescence is desirable.
• Stokes shift that is, a large separation between the wavelengths for maximum excitation (EX) and the wavelength of maximal emission (EM), e.g., EM-EX > 100 nm); (ii) a high quantum yield (e.g., QY > 0.5); (iii) a high extinction coeffient (e.g., EC > 30,000); and (iv) an excitation maximum close to a laser line (e.g., 442 nm of Helium-Cadmium laser or
• EX 495 nm
• EM 525 nm
• QY 0.5
• the subject invention pertains to nucleobases and nucleoside structural analogs which are fluorescent.
• the fluorescent nucleoside structural analogs of the present invention are useful as monomers in synthesizing and labelling nucleoside sequences (oligonucleotides, polynucleotides).
• the fluorescence of such nucleoside sequences can be used as a research or diagnostic tool to detect and identify specific genetic sequences.
• This methodology is distinct from other non-radioactive methods of probe detection in that it does not utilize nucleosides which have been coupled to enzymes or other reactive proteins and does not require post-hybridization processing for the detection of hybridization.
• the fluorescent nucleoside structural analogs of the present invention are useful as fluorescent chain elongation terminators in DNA sequencing reactions.
• nucleoside analogs according to the present invention can be used as (i) specific substitutes for a given non-fluorescent nucleoside in an oligonucleotide or polynucleotide probe, (ii) as labels for the identification and detection of specific sequences of a template; and (iii) for nucleic acid sequencing.
• B is selected from the group consisting of derivatives of naturally occurring nitrogenous bases having a C-H group at positions 5 or 8, and derivatives of nitrogenous base-analogs having a C-H group at positions 5 or 8;
• D is at least one derivatizing group, including hydrogen; and M is a maleimide derivative.
• B is selected from the group consisting of adenine derivative, guanine derivative, uracil derivative, cytosine derivative and inosine derivative.
• B is selected from the group consisting of purine derivative and pyrimidine derivative.
• D includes a chemical functionality group attached to a linker arm. According to still further features in the described preferred embodiments D includes a ribose derivative.
• D further includes one to three phosphate groups attached at a 5' position on the ribose derivative. According to still further features in the described preferred embodiments D further includes a phosphoramidite derivative attached at a 3' position on the ribose derivative. According to still further features in the described preferred embodiments D includes a deoxyribose derivative.
• D further includes one to three phosphate groups attached at a 5' position on the deoxyribose derivative.
• D further includes a phosphoramidite derivative attached at a 3 ' or 5' position on the deoxyribose derivative.
• D is a polymer
• the polymer includes nucleoside derivatives.
• the polymer includes amino acid derivatives. According to still further features in the described preferred embodiments the polymer is a polynucleotide.
• the polymer is a polypeptide.
• the polymer is a protein-nucleic acid polymer.
• Ri , R 2 , R 3 , R and R 5 are each independently a derivatizing group, including hydrogen. According to still further features in the described preferred embodiments R j is terminating with a reactive group having a general structure of:
• P is selected from the group consisting of alkyl, branched alkyl, aromatic group, derivatized aromatic group and combinations thereof; n is an integer in a range of 1 to 100; and A is an active chemical moiety.
• n is an integer in a range of 2-50.
• n is an integer in a range of 3-7.
• A is capable of reacting with a nucleophile.
• the nucleophile is selected from the group consisting of amino and hydroxy groups.
• A is designed to form a chemical bond with the nucleophile, the bond is selected from the group consisting of ether bond, ester bond, amide bond, phosphonate bond, carbamate bond, and sulfone bond.
• A is an active ester
• the active ester is selected from the group consisting of N- hydroxy succinimido, halogenoacyl, vinylsulfone, isothiocyanate, cyanate, chloromethyl ketone, iodoacetamidyl, iodoalkyl, bromoalkyl and active phosphate group.
• Z is selected from the group consisting of hydrogen, hydroxyl, amine, amide, nitro, an electron withdrawing group, an electron attracting groups and an aromatic group terminating with the hydrogen, hydroxyl, amine, amide, nitro, an electron attracting groups.
• R 4 is selected from the group consisting of alkyl and aromatic group.
• R 5 is selected from the group consisting of hydrogen and amino protecting group useful in a protection of amino acids in peptide synthesis.
• the amino protecting group is selected from the group consisting of trifluoroacetyl, acetyl, benzoyl, 9- fluorenylmethyloxycarbonyl, allyloxycarbonyl, 4- toluenesulfonylethyloxycarbonyl, methylsulfonylethyloxycarbonyl, 2- cyano-t-butyloxycarbonyl, chloroacetyl, acetoacetyl and 2,2,2- trichloroethyloxycarbonyl.
• R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , R 8 and R 12 are each independently a derivatizing group.
• R ⁇ is a chemical functionality group.
• the chemical functionality group is selected from the group consisting of hydroxylic group OR 9 and amino group NR 10 .
• R 9 is an acid labile protecting group.
• the acid labile protecting group is selected from the group consisting of triphenylmethyl, p-anisyldiphenylmethyl, di-p- anisyldiphenylmefhyl, p-dimethoxy trityltrityl, formyl, t-butyloxycarbonyl, benzyloxycarbonyl, 2-chlorobenzyloxycarbonyl, 4- chlorobenzoyloxycarbonyl, 2,4-dichlorobenzyloxycarbonyl, furfurylcarbonyl, t-amyloxycarbonyl, adamantyloxycarbonyl, 2- phenylpropyl-(2)-oxycarbonyl, 2-(4-biphenyl)propyl-(2)-oxycarbonyl, 2- nitrophenylsulfenyl and diphenylphosphinyl.
• R 9 is a base labile protecting group.
• the base labile protecting group is selected from the group consisting of trifluoroacetyl, 9-fluorenylmethyloxycarbonyl, allyloxycarbonyl, 4-toluenesulfonylethyloxycarbonyl, methylsulfonylethyloxycarbonyl, 2-cyano-t-butyloxycarbonyl, silyl ethers, and ,2,2,2-trichloroethylcarbonate.
• R 10 is a nitrogen protecting group.
• the nitrogen protecting group is selected from the group consisting of trifluoroacetyl, 9-fluorenylmethyloxycarbonyl, allyloxycarbonyl 4-toluenesulfonylethyloxycarbonyl, methylsulfonylethyloxycarbonyl, and 2-cyano-t-butyloxycarbonyl, chloroacetyl, acetoacetyl, and 2,2,2-trichloroethyloxycarbonyl.
• R 5 is a chemical functionality group.
• the chemical functionality group is an amino group NR 10 .
• R ]0 is an acid labile protecting group.
• the acid labile protecting group is selected from the group consisting of triphenylmethyl, p-anisyldiphenylmethyl, di-p- anisyldiphenylmethyl, p-dimethoxytrityl, formyl, t-butyloxycarbonyl, benzyloxycarbonyl, 2-chlorobenzyloxycarbonyl, 4- chlorobenzoyloxycarbonyl, 2,4-dichlorobenzyloxycarbonyl, furfurylcarbonyl, t-amyloxycarbonyl, adamantyloxycarbonyl, 2- phenylpropyl-(2)-oxycarbonyl, 2-(4-biphenyl)propyl-(2)-oxycarbonyl, di-p- anisyldiphenylmethyl, 2-nitrophenylsulfenyl and diphenyl
• the base labile protecting group is selected from the group consisting of trifluoroacetyl, 9-fluorenylmethyloxycarbonyl, 4- toluenesulfonylethyloxycarbonyl, methylsulfonylethyloxycarbonyl and 2- cyano-t-butyloxycarbonyl.
• R 7 is selected from the group consisting of hydrogen and OR n , wherein R ⁇ is a chemical protecting group.
• the Ri j protecting group is selected from the group consisting of lower aryl and alkylether.
• the R j i protecting group is selected from the group consisting of, triphenylmethyl, acetal, tetrahydropyranyl, silyl ether, trimethylsilyl and t-butyl-dimethylsilyl .
• the Ri i protecting group is selected from the group consisting of hydroxylic and amino groups
• R 8 is selected from the group consisting of lower and heterocyclic alkyl.
• R 8 is selected from the group consisting of methyl, isopropyl, mo ⁇ holino, pyrrolidino and 2,2,6,6-tetramethylpyrrolidino.
• R 12 is a phosphate protecting group.
• the phosphate protecting group is selected from the group consisting of trichloroethyl, allyl, cyanoethyl and sulfonyl ethyl. Further according to the present invention there is provided a compound selected from the group consisting of:
• TPO is a triphosphate group
• R 2 , R 3 and R 4 are each independently a derivatizing group, including hydrogen
• R 7 and R 13 are each independently selected from the group consisting of hydrogen and hydroxyl group.
• Z is selected from the group consisting of hydrogen, hydroxyl, amine, amide, nitro, an electron withdrawing group, an electron attracting groups and an aromatic group.
• R 4 is selected from the group consisting of alkyl and aromatic group.
• B is selected from the group consisting of derivatives of naturally occurring nitrogenous bases having a C-H group at positions 5 or 8, and derivatives of nitrogenous base-analogs having a C-H group at positions 5 or 8;
• D is at least one derivatizing group, including hydrogen; and M is a maleimide derivative;
• the method comprising the steps of the method comprising the steps of contacting a derivatized base DB with mercuric acetate and condensing with N-alkylmaleimide.
• R j , R 2 , R 3 , R 4 and R5 are each independently a derivatizing group, including hydrogen; the method comprising the steps of contacting a derivatized base with mercuric acetate and condensing with N- alkylmaleimide.
• R 2 , R 3 , R 4 , R 5 , R ⁇ , R 7 , R 8 and R 12 are each independently a derivatizing group
• the method comprising the steps of (a) contacting a nucleoside with mercuric salt, followed condensation with N-alkylmaleimide; (b) protecting amino groups of the nucleoside with a protecting group (e.g., allyloxycarbamate); (c) protecting 5' hydroxyl of the nucleoside with an acid labile group (e.g., dimethoxytrityl); and (d) condensing with allylic phosphoramidate reagent.
• a protecting group e.g., allyloxycarbamate
• an acid labile group e.g., dimethoxytrityl
• condensing with allylic phosphoramidate reagent e.g., dimethoxytrityl
• TPO is a triphosphate group
• R 2 , R 3 and R 4 are each independently a derivatizing group, including hydrogen
• R7 and R 13 are each independently selected from the group consisting of hydrogen and hydroxyl group
• the method comprising the steps of contacting a 5' triphosphate nucleoside with mercuric salt and condensing with N- alkylmaleimide.
• a method of hybridizing a target nucleic acid with a nucleic acid probe comprising the steps of contacting a sample including the target nucleic acid with the nucleic acid probe under hybridization conditions, wherein the nucleic acid probe includes at least one fluorescent derivative of a nucleobase, the fluorescent derivative includes a maleimide derivative attached at a C5 or C8 position of the nucleobase.
• a method of detecting a sequence of target nucleic acid comprising the steps of (a) providing the target nucleic acid in a single stranded form; (b) contacting, under hybridization conditions, the single stranded form of the target nucleic acid with a sequencing primer, such that a sequence dependent primer-target nucleic acid duplex is formed; and (c) contacting under polymerization conditions the duplex with deoxynucleoside-tri-phosphates and at least one dideoxynucleoside-tri-phosphate and with a DNA polymerase; wherein at least one of the sequencing primer, deoxynucleoside-tri-phosphates or the dideoxynucleoside-tri -phosphate includes a fluorescent derivative of a nucleobase, the fluorescent derivative includes a maleimide derivative attached at a C5 or C8 position of the nucleobase.
• a method of synthesizing a polynucleotide comprising the steps of using a solid phase synthesis protocol to sequentially, following a predetermined order, add nucleoside derivatives present initially in their phosphoramidite form to a growing chain of the polynucleotide in a 3' to 5' direction, wherein at least one of the nucleoside derivatives includes a fluorescent derivative of a nucleobase, the fluorescent derivative includes a maleimide derivative attached at a C5 or C8 position of the nucleobase.
• a method of synthesizing a polynucleotide comprising the steps of (a) providing the template nucleic acid in a single stranded form; (b) contacting, under hybridization conditions, the single stranded form of the template nucleic acid with at least one primer, such that a sequence dependent primer-target nucleic acid duplex is formed; and (c) contacting under polymerization conditions the duplex with deoxynucleoside-tri-phosphates and with a DNA polymerase; wherein at least one of the primers or the deoxynucleoside-tri- phosphates includes a fluorescent derivative of a nucleobase, the fluorescent derivative includes a maleimide derivative attached at a C5 or C8 position of the nucleobase.
• a method of target dependent chemical ligation of probes comprising the steps of (a) providing a first probe including a fluorescence moiety including a protected moiety being bound to the fluorescence moiety; (b) providing a second probe including a nucleophile moiety, the nucleophile moiety is selected such that when in appropriate proximity and orientation with respect to the protected moiety, the nucleophile moiety releases the protected moiety to yield a fluorescent moiety fluorescing or chemiluminescing differently than the fluorescence moiety; wherein the first and second probes are selected such that by hybridizing to the target the appropriate proximity and orientation are obtained.
• the present invention successfully addresses the shortcomings of the presently known configurations by providing novel nucleobases and nucleoside structural analogs featuring improved spectral qualities by conjugating a maleimide derivative at C5 or C8 positions of pyrimidine nucleobases or purine nucleobases, respectively.
• FIG. 1 is a plot showing the excitation (dotted line, Ex) and emission (solid line, Em) spectra of 2'-Deoxy-5-N-ethylmaleimidouridine dissolved in methanol (10 ⁇ g/ml) according to the present invention
• FIG. 2 is a photograph showing the fluorescence of a solution held in a tube containing an oligonucleotide in which a single structural analog according to the present invention is inco ⁇ orated when irradiated at 360 nm using the GelDoc UV fluorescent gel documentation system by Bio-Rad
• FIGs. 3a-d are X-ray diffraction derived three dimensional models of 2'-Deoxy-5-N-butylmaleimidouridine and lattice dimmers thereof according to the present invention. DESCRIPTION OF THE PREFERRED EMBODIMENTS
• the present invention provides derivatives of pyrimidine and/or purine analogs of the commonly occurring nucleoside bases, which are fluorescent in different organic solvents and in aqueous buffers or in a mixture of organic and water solvents.
• the present invention is based upon increasing the conjugation of double bonds at C-5 position of pyrimidines such as uridine and cytidine, and at C-8 position of purines of adenine and guanine.
• pyrimidines such as uridine and cytidine
• purines of adenine and guanine In general, as the degree of conjugation in hydrocarbon compounds increases, the intensity of fluorescence often increases and a bathochromic shift is observed.
• the fluorescent nucleoside or nucleotide analogs according to the present invention are useful as monomers in synthesizing and labeling nucleotide sequences and proteins.
• the invention further concerns the use of these fluorescent nucleotides which can be substituted for naturally occurring nucleotides in the synthesis of oligonucleotide and polynucleotide probes.
• the fluorescence of such oligonucleotides or polynucleotides can be used as a diagnostic tool to detect and identify specific genetic sequences.
• This methodology is distinct from other non- radioactive methods of probe detection in that it does not utilize nucleotides which have been coupled via a linker arm to fluorescent dyes, but serves as hybridization sites and as a fluorescent dyes at the same time.
• the present invention provides novel fluorescent nucleoside analogs and the novel triphosphate and phosphoramidite forms thereof, which are useful in the synthesis of labeled polynucleotide probes, in branched DNA, in fluorescence in situ hybridization technology and in DNA sequencing.
• the present invention provides a structure according to the formula:
• D-B-M wherein B can be a derivative of a naturally occurring nitrogenous base having a C-H group at positions 5 or 8, derivative of nitrogenous base analog having a C-H group at positions 5 or 8, preferably a purine nitrogenous base derivative or a pyrimidine nitrogenous base derivative, such as, but not limited to, an adenine derivative, guanine derivative, uracil derivative and an inosine derivative; wherein D can be a chemical functionality group attached to a linker arm, preferably a ribose derivative, preferably derivatized with one to three phosphate groups attached at a 5 ' position on the ribose derivative or with a phosphoramidite derivative attached at a 3' position of the ribose derivative, a deoxyribose derivative, preferably derivatized with one to three phosphate groups attached at a 5' position on the deoxyribose derivative or with a phosphoramidite derivative attached at a 3' or 5' position of the
• fluorescent structural analogs Q, R, S, T, U of the commonly occurring nucleosides and their derivatives are provided having the structural formula of:
• the present invention provides novel fluorescent phosphoramidite forms of nucleosides and analogs thereof, which are useful in the synthesis of fluorescently labeled polynucleotide probes.
• Their structures are V, W, X, Y and Z and they contain R 2 , R 3 , R 4 , R 5 , R , R 7 , R 8 and R 12 derivatizing groups.
• R 6 is a chemical functionality group, preferably hydroxylic group OR 9 or amino group NR 10 ; wherein R 9 is an acid labile protecting group, preferably triphenylmethyl, p-anisyldiphenylmethyl, di-p-anisyldiphenylmethyl, p- dimethoxy trityltrityl, formyl, t-butyloxycarbonyl, benzyloxycarbonyl, 2- chlorobenzyloxycarbonyl, 4-chlorobenzoyloxycarbonyl, 2,4- dichlorobenzyloxycarbonyl, furfurylcarbonyl, t-amyloxycarbonyl, adamantyloxycarbonyl, 2-phenylpropyl-(2)-oxycarbonyl, 2-(4- biphenyl)propyl-(2)-oxycarbonyl, 2-nitrophenylsulfenyl or diphenylphosphinyl; wherein R 9 is an acid labile protecting group, preferably
• R 5 is a chemical functionality group, preferably an amino group NR 10 , such as, but not limited to, triphenylmethyl, p- anisyldiphenylme hyl, di-p-anisyldiphenylmethyl, p-dimethoxytrityl, formyl, t-butyloxycarbonyl, benzyloxycarbonyl, 2- chlorobenzyloxycarbonyl, 4-chlorobenzoyloxycarbonyl, 2,4- dichlorobenzyloxycarbonyl, furfurylcarbonyl, t
• the present invention provides fluorescent structural analogs of the commonly occurring and analog nucleosides and their derivatives.
• the compounds of these structures, F, G, H, I and J contain a triphosphate group (TPO), R 2 , R 3 and R 4 derivatizing groups and R 7 and R 13 , which can be hydrogen or hydroxyl groups.
• TPO triphosphate group
• R 2 , R 3 and R 4 derivatizing groups
• R 7 and R 13 which can be hydrogen or hydroxyl groups.
• R 2 and R 3 can be hydrogen, methyl, halogen, or an unsaturated moiety having a formula:
• B is selected from the group consisting of 9 of naturally occurring nitrogenous bases having a C-H group at positions 5 or 8, and derivatives of nitrogenous base-analogs having a C-H group at positions 5 or 8;
• D is at least one derivatizing group, including hydrogen;
• M is a maleimide derivative
• the method is effected by executing the following method steps, in which in a first step a derivatized base DB is contacted with mercuric acetate and in a second step the product is condensed with N- alkylmaleimide, as follows:
• R b R 2 , R 3 , R and R 5 are each independently a derivatizing group, including hydrogen;
• the method is effected by executing the following method steps, in which in a first step a derivatized base is contacted with mercuric acetate and in a second step the product is condensed with N-alkylmaleimide, as follows:
• the method is effected by executing the following method steps, in which in a first step a nucleoside is contacted with mercuric salt, followed condensation with N-alkylmaleimide. In a second step, amino groups of the nucleoside are protected with a protecting group (e.g., allyloxycarbamate). In a third step 5' hydroxyl of the nucleoside is protected with an acid labile group (e.g., dimethoxytrityl). Whereas in a final step, the product is condensed with allylic phosphoramidate reagent. All as follows:
• the method is effected by executing the following method steps, in which in a first step a 5' triphosphate nucleoside is contacted with mercuric salt and in a second step the product is condensed with N-alkylmaleimide, as follows:
• a method of hybridizing a target nucleic acid with a nucleic acid probe can be used in liquid as well as surface hybridization reactions.
• Hybridization according to the present invention can be performed in liquid (e.g., while performing a PCR or sequencing reaction) or on a surface.
• a surface hybridization according to the present invention includes processes such as, but not limited to, in situ hybridization, filter hybridization and solid phase (e.g., particulates) hybridization. These processes are well known in the art and therefore are not further elaborated herein. Protocols and uses for such processes can be found in, for example, Sambrook, J., Fritsch, E.F., Maniatis, T. (1989) Molecular Cloning. A Laboratory Manual. Cold Spring Harbor Laboratory Press, New York.
• the method is performed by executing the following method step in which a sample including the target nucleic acid is contacted with a nucleic acid probe under hybridization conditions.
• the nucleic acid probe includes at least one fluorescent derivative of a nucleobase which includes a maleimide derivative attached at a C5 or C8 position of the nucleobase, as further detailed hereinabove.
• a method of determining a sequence of target nucleic acid is effected by executing the following method steps, in which, in a first step the target nucleic acid is provided in a single stranded form (i.e., if it is double stranded, it is denatured). In a second step of the method, the single stranded form of the target nucleic acid is contacted, under hybridization conditions, with a sequencing primer (i.e., a primer hybridizable 5' to the region of the target to be sequenced), such that a sequence dependent primer-target nucleic acid duplex is formed.
• a sequencing primer i.e., a primer hybridizable 5' to the region of the target to be sequenced
• the duplex is contacted, under polymerization conditions, with deoxynucleoside-tri- phosphates (four types), with at least one dideoxynucleoside-tri-phosphate and with a DNA polymerase.
• at least one of the sequencing primer, deoxynucleoside-tri-phosphates or the dideoxynucleoside-tri-phosphate includes a fluorescent derivative of a nucleobase which includes a maleimide derivative attached at a C5 or C8 position of the nucleobase.
• the sequencing primer or one or more of the includes the deoxynucleoside-tri-phosphates
• four independent reactions are individually performed each with a different dideoxynucleoside-tri-phosphate, wherein reading the sequence following electrophoresis is dependent upon migration/lane.
• the different dideoxynucleoside-tri-phosphates are labeled with four distinctive fluorescent moieties, at least one is a fluorescent derivative of a nucleobase which includes a maleimide derivative attached at a C5 or C8 position of the nucleobase, then the different reactions can be performed in a single reaction tube, wherein reading the sequence following electrophoresis is based on migration/spectra.
• a method of synthesizing a polynucleotide is effected by executing the following method step, in which, a solid phase synthesis protocol is used to sequentially, following a predetermined order, add nucleoside derivatives present initially in their phosphoramidite form to a growing chain of the polynucleotide in a 3' to 5' direction, wherein at least one of the nucleoside derivatives includes a fluorescent derivative of a nucleobase, the fluorescent derivative includes a maleimide derivative attached at a C5 or C8 position of the nucleobase.
• a method of synthesizing a polynucleotide is effected by executing the following method steps, in which, in a first step, the template nucleic acid is provided in a single stranded form. In a second step of the method, the single stranded form of the template nucleic acid is contacted under hybridization conditions with at least one primer, such that a sequence dependent primer- target nucleic acid duplex is formed.
• the duplex is contacted under polymerization conditions with deoxynucleoside-tri-phosphates and with a DNA polymerase, wherein at least one of the primers or the deoxynucleoside-tri-phosphates includes a fluorescent derivative of a nucleobase, the fluorescent derivative includes a maleimide derivative attached at a C5 or C8 position of the nucleobase.
• a method of target dependent chemical ligation of probes is effected by executing the following method steps, in which, in a first step, a first probe including a fluorescence moiety including a protected moiety being bound to the fluorescence moiety is provided.
• a second probe including a nucleophile moiety the nucleophile moiety is selected such that when in appropriate proximity and orientation with respect to the protected moiety, the nucleophile moiety is allowed to react with the fluorescent moiety by addition reaction and consequently quench the fluorescence and release the protected moiety to yield a new fluorescent moiety fluorescing or chemiluminescing differently than the first fluorescence moiety.
• the first and second probes are selected such that by hybridizing to the target the appropriate proximity and orientation are obtained.
• the present invention uses the novel fluorescent compounds as a key part in chemical amplification technology.
• This embodiment comprises a method of preparing fluorescent derivatives of uridine, cytidine, adenine and guanine, which are chemically attached to an oligonucleotide probe to form a fluorescent moiety which . includes a protected moiety, which is bound to the fluorescence moiety.
• This moiety is not fluorescent, but upon reacting with a nucleophile, the fluorescence of the first fluorescence moiety is quenched and hydrolysis of the first fluorescence moiety takes place. The protected moiety is thus released to yield a new and different fluorescence or a chemiluminescence in different wavelength than the first moiety, as follows:
• B is a base from naturally occurring nucleotides and M-is a chemical moiety, such as maleimide and its derivatives, which upon conjugation with B forms a first fluorescent moiety (B-M).
• A is another chemical moiety which is fluorescent by itself, but when it is bound to M as (M-A), becomes a non- fluorescent moiety.
• M becomes M', which facilitates hydrolysis of M and subsequently releases A as A' wherein A' is a new fluorescent moiety.
• This embodiment of the present invention is thus useful, for example, in monitoring non-enzymatic (i.e., chemical) amplification reactions, such as the reactions disclosed in PCT/US94/06690 and in U.S. Pat. application No. 08/431,527, both are inco ⁇ orated by reference as if fully set forth herein, wherein the nucleophile is, for example, attached to an end of a second and juxtaposed oligonucleotide:
• Example 11 An example of structures operative according to this embodiment are described in Example 11 hereinunder.
• novel fluorescent nucleobases and nucleosides and methods of use of the fluorescent nucleosides in, for example, nucleic acid probes, for labeling proteins, hormones, steroids etc.
• novel fluorescent nucleoside analogs dyes of the present invention are derivatives of uracyl, cytidine and other pyrimidine derivatives at their C5-position, and of adenine and guanine and other purine derivatives at their 8-position.
• Derivatization at these sites according to the present invention is to form a conjugation of extended double-bonds which results in forming novel fluorescent moieties.
• One preferred embodiment is the use of these inherently fluorescent nucleoside analogs in the chemical and enzymatic synthesis of DNA hybridization probes including solid phase synthesis, template directed enzymatic polymerization and amplification, for use in various hybridization based reactions as fluorescent nucleic acid probes.
• the fluorescent nucleic acid probes according to the present invention are capable of specific Watson-Crick base pairing with prescribed sequences of target DNA or RNA.
• This methodology is distinct from other non-radioactive methods of target DNA or RNA detection in that, the fluorescent nucleotide analogs serves as a part of the oligonucleotide hybridization probes and as fluorescent labels.
• Another embodiment of the present invention relates to the use of the novel fluorescent nucleoside analogs in DNA sequencing.
• the coated silica was added on the top of a silica column (5 x 60 cm) using a solution of 10 % methanol in dichloromethane as eluent and the resulting appropriate residue was evaporated to dryness. Rf: 0.41. Yield : 947 mg. (27 %). mass spectrum m/e: 352 (molecular ion), 236 (uracyl - N- ethylmaleimide), 197, 179, 152, 126, 117 (deoxyribose).
• the reagent (allyloxy)bis(diisopropylamino)phosphine is prepared according to Hayakawa et al. in J. Am. Chem. Soc. (1990), 112: 1691.
• the coated silica was added on the top of a silica column (5x60 cm) using a solution of 10% methanol in dichloromethane as eluent and the resulting fluorescent product was collected and the solvent was evaporated to dryness.
• the coated silica was added on the top of a silica column (5 x 60 cm) using a solution of 10 % methanol in dichloromethane as eluent and the resulting appropriate residue was evaporated to dryness. Rf: 0.41. Yield : 947 mg. (27 %). mass spectrum m/e: 380 (molecular ion), 236 (uracyl - N- butylmaleimide), 197, 179, 152, 126, 117 (deoxyribose).
• Tables 1-3 below provide crystallography data.
• Figures 3a-d provide
• U(eq) is defined as one third of the trace of the orthogonalized Uij tensor.
• Enzymatic syntheses converts the monophosphate to the triphosphate analog with e.g., polynucleotide kinase using established procedures, as described by Schobert B. (1995) Analytical Biochemistry 226:288, which is inco ⁇ orated by reference as if fully set forth herein.
• the 5'-monophosphates are prepared chemically by POCL 2 ad described in Lin and Brown (1989) Nucl. Acids Res. 17: 10373; Yoshikawa et al. (1967) Tetrahedron Lett. 5095, which are inco ⁇ orated by reference as if fully set forth herein.
• the corresponding triphosphates can be chemically synthesized according to the same authors or by Hoard and Ott (1965) J. Am. Chem. Soc. 87: 1785, and Michelson (1964) Biochim. Biophys. Ada 91 : 1.
• the monophosphates are treated with 1,1'- carbonildiimidazole followed with tributylammonium pyrophosphate in dimefhylformamide under anhydrous conditions to give the triphosphorylated form.
• A is, for example, N-Acridinylmaleimide, as described by M. Machida et al. in Chem. Pharm. Bull. (1978), Vol 26, 596 as follows:

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