EP1268492A1 - Monomeres reactifs pour la synthese d'oligonucleotides et de polynucleotides, oligonucleotides et polynucleotides modifies et leur procede de production - Google Patents

Monomeres reactifs pour la synthese d'oligonucleotides et de polynucleotides, oligonucleotides et polynucleotides modifies et leur procede de production

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Publication number
EP1268492A1
EP1268492A1 EP01927675A EP01927675A EP1268492A1 EP 1268492 A1 EP1268492 A1 EP 1268492A1 EP 01927675 A EP01927675 A EP 01927675A EP 01927675 A EP01927675 A EP 01927675A EP 1268492 A1 EP1268492 A1 EP 1268492A1
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European Patent Office
Prior art keywords
oligo
polynucleotides
mono
rna
dna
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EP01927675A
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German (de)
English (en)
Inventor
Markus Schweitzer
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Nanogen Recognomics GmbH
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Nanogen Recognomics GmbH
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Publication of EP1268492A1 publication Critical patent/EP1268492A1/fr
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07F—ACYCLIC, CARBOCYCLIC OR HETEROCYCLIC COMPOUNDS CONTAINING ELEMENTS OTHER THAN CARBON, HYDROGEN, HALOGEN, OXYGEN, NITROGEN, SULFUR, SELENIUM OR TELLURIUM
    • C07F9/00—Compounds containing elements of Groups 5 or 15 of the Periodic Table
    • C07F9/02—Phosphorus compounds
    • C07F9/06—Phosphorus compounds without P—C bonds
    • C07F9/22—Amides of acids of phosphorus
    • C07F9/24—Esteramides
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H21/00—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D317/00—Heterocyclic compounds containing five-membered rings having two oxygen atoms as the only ring hetero atoms
    • C07D317/08—Heterocyclic compounds containing five-membered rings having two oxygen atoms as the only ring hetero atoms having the hetero atoms in positions 1 and 3
    • C07D317/10—Heterocyclic compounds containing five-membered rings having two oxygen atoms as the only ring hetero atoms having the hetero atoms in positions 1 and 3 not condensed with other rings
    • C07D317/14—Heterocyclic compounds containing five-membered rings having two oxygen atoms as the only ring hetero atoms having the hetero atoms in positions 1 and 3 not condensed with other rings with substituted hydrocarbon radicals attached to ring carbon atoms
    • C07D317/18—Radicals substituted by singly bound oxygen or sulfur atoms
    • C07D317/22—Radicals substituted by singly bound oxygen or sulfur atoms etherified
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D317/00—Heterocyclic compounds containing five-membered rings having two oxygen atoms as the only ring hetero atoms
    • C07D317/08—Heterocyclic compounds containing five-membered rings having two oxygen atoms as the only ring hetero atoms having the hetero atoms in positions 1 and 3
    • C07D317/10—Heterocyclic compounds containing five-membered rings having two oxygen atoms as the only ring hetero atoms having the hetero atoms in positions 1 and 3 not condensed with other rings
    • C07D317/14—Heterocyclic compounds containing five-membered rings having two oxygen atoms as the only ring hetero atoms having the hetero atoms in positions 1 and 3 not condensed with other rings with substituted hydrocarbon radicals attached to ring carbon atoms
    • C07D317/28—Radicals substituted by nitrogen atoms
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07F—ACYCLIC, CARBOCYCLIC OR HETEROCYCLIC COMPOUNDS CONTAINING ELEMENTS OTHER THAN CARBON, HYDROGEN, HALOGEN, OXYGEN, NITROGEN, SULFUR, SELENIUM OR TELLURIUM
    • C07F9/00—Compounds containing elements of Groups 5 or 15 of the Periodic Table
    • C07F9/02—Phosphorus compounds
    • C07F9/06—Phosphorus compounds without P—C bonds
    • C07F9/22—Amides of acids of phosphorus
    • C07F9/24—Esteramides
    • C07F9/2404—Esteramides the ester moiety containing a substituent or a structure which is considered as characteristic
    • C07F9/2408—Esteramides the ester moiety containing a substituent or a structure which is considered as characteristic of hydroxyalkyl compounds
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07F—ACYCLIC, CARBOCYCLIC OR HETEROCYCLIC COMPOUNDS CONTAINING ELEMENTS OTHER THAN CARBON, HYDROGEN, HALOGEN, OXYGEN, NITROGEN, SULFUR, SELENIUM OR TELLURIUM
    • C07F9/00—Compounds containing elements of Groups 5 or 15 of the Periodic Table
    • C07F9/02—Phosphorus compounds
    • C07F9/06—Phosphorus compounds without P—C bonds
    • C07F9/22—Amides of acids of phosphorus
    • C07F9/24—Esteramides
    • C07F9/2404—Esteramides the ester moiety containing a substituent or a structure which is considered as characteristic
    • C07F9/2429—Esteramides the ester moiety containing a substituent or a structure which is considered as characteristic of arylalkanols
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07F—ACYCLIC, CARBOCYCLIC OR HETEROCYCLIC COMPOUNDS CONTAINING ELEMENTS OTHER THAN CARBON, HYDROGEN, HALOGEN, OXYGEN, NITROGEN, SULFUR, SELENIUM OR TELLURIUM
    • C07F9/00—Compounds containing elements of Groups 5 or 15 of the Periodic Table
    • C07F9/02—Phosphorus compounds
    • C07F9/547—Heterocyclic compounds, e.g. containing phosphorus as a ring hetero atom
    • C07F9/655—Heterocyclic compounds, e.g. containing phosphorus as a ring hetero atom having oxygen atoms, with or without sulfur, selenium, or tellurium atoms, as the only ring hetero atoms
    • C07F9/65515—Heterocyclic compounds, e.g. containing phosphorus as a ring hetero atom having oxygen atoms, with or without sulfur, selenium, or tellurium atoms, as the only ring hetero atoms the oxygen atom being part of a five-membered ring

Definitions

  • Reactive monomers for oligonucleotide and polynucleotide synthesis, modified oligonucleotides and polynucleotides and a process for their preparation Reactive monomers for oligonucleotide and polynucleotide synthesis, modified oligonucleotides and polynucleotides and a process for their preparation
  • the invention relates to oligonucleotides and polynucleotides which are modified with at least one acetal or aldehyde group, as well as a method for producing such modified oligonucleotides and polynucleotides and the novel monomeric building blocks required for this.
  • Aldehydes are reactive groups which are used for the conjugation of biomolecules with e.g. B. fluorophores, reporter groups, proteins, nucleic acids and other biomolecules, small molecules (such as biotin) but also for the immobilization of biomolecules on surfaces (for example: Hermanson, GT; Bioconjugate Techniques, Academic Press, San Diego 1996; Timofeev, EN;
  • aldehydes into oligonucleotides, all of which are based on an oxidation of a vicinal diol with sodium periodate to the aldehyde or to a bis-aldehyde.
  • This aldehyde then forms cyclic adducts (morpholine structure) with amines or hydrazides, which can be used for conjugation.
  • the decisive disadvantage of this method is that a nucleotide of the 3 ' end of an oligonucleotide must always be sacrificed for the conjugation.
  • this approach does not offer the possibility of changing the distance of the oligonucleotide from the conjugation partner.
  • the second possibility is to couple a phosphoramidite of a protected vicinal diol to the 5 'end of an oligonucleotide (Lemaitre, M .; Bayard, B .; Lebleu, B., Proc. Natl. Acad. Sci. USA 84 (1987) 648 ).
  • a specially manufactured building block which carries a masked vicinal diol group is coupled to the 5 'end of an oligonucleotide.
  • a vicinal diol group is then present which is also oxidized to the aldehyde with periodate.
  • aldehydes as reactive species are not stable in storage for an unlimited period.
  • the spontaneous oxidation in air in particular leads to its decomposition. It is therefore advisable to prepare aldehydes only immediately before they are used.
  • the simplest possible method for their production would be advantageous, which can be carried out easily and without great effort from storage-stable starting materials.
  • the task is solved by novel monomeric acetals and acetal-modified oligonucleotides and polynucleotides, which are very easy to store and offer easy access to aldehyde-modified oligo- and polynucleotides.
  • the monomeric acetals according to the invention, as well as the acetal-modified oligonucleotides and polynucleotides are stable with respect to the conditions of the standard methods for oligo- and polynucleotide synthesis or duplication, such as, for. B. the phosphoramidite method or PCR, and the reaction conditions for the introduction and removal of common protective groups.
  • an object of the present invention is a reactive monomer of formula (I), wherein I, v independently of one another are 0 or 1 and a is an integer between 1 and 5, preferably 1 to 3
  • X is a reactive phosphorus-containing group for oligonucleotide synthesis such.
  • B a phosphoramidite (II) or as a phosphonate (III)
  • V is a branching unit with at least three binding partners, for example an atom or an atomic group, preferably a nitrogen atom,
  • Y and Z independently of one another the same or different branched or unbranched, saturated or unsaturated, optionally cyclic, C1 to C 18 hydrocarbons, preferably methyl, ethyl, n-propyl, isopropyl, n-butyl, 2-butyl, tert-butyl , particularly preferably ethyl, represent, or wherein Y and Z together represent a radical of structure (V) or (VI) wherein R4 independently of one another, the same or different, H, methyl, phenyl, a branched or unbranched saturated or unsaturated, optionally cyclic Ci to C ⁇ 8 hydrocarbon or a radical of structure (VII), with R5 being the same or different, is H, methyl, alkyl, O-methyl, O-alkyl, or alkyl, where alkyl is a branched or unbranched, saturated or unsaturated, optionally cyclic Ci to C 18 hydrocarbon
  • L are linkers which are suitable for linking X with A or for linking X with V and V with A, for example branched or unbranched, saturated or unsaturated, optionally cyclic C 1 to C 6 Hydrocarbons such as alkyl - (C n H 2 n) - with n equal to an integer from 0 to 18, preferably 3 to 8, or equal to a polyether - (CH2) k - [O- (CH 2 ) m] o-0 - (CH2) p- with k, m, p independently of one another equal to an integer from 0 to 4, preferably 2, and o equal to an integer from 0 to 8, preferably 2 to 4, or equal to an amine - (CH 2 ) w-NH- (CH 2 ) u- with w and u independently of one another equal to a whole
  • the linkers L can be linked to the branching unit V via oxygen atoms.
  • the invention further relates to mono-, oligo- and polynucleotides of any sequence which are modified with at least one acetal group.
  • Mono-, oligo- and polynucleotides which are obtainable using at least one reactive monomer of the formula (I) according to the invention are particularly preferred.
  • U is O or S
  • W is OH, SH or H
  • Q is O or NH and z is greater than or equal to 1 and I, v, a, L, V and A have the meaning given above.
  • the reactive monomer of formula (I) can be specifically added at the end.
  • z depends on the degree of branching of the nucleotide chain, z is preferably between 1 and 10, particularly preferably z is 1 or 2.
  • Another advantage of the invention is the possibility of a reactive monomer selectively at the 3 and / or 5 " end of a DNA or RNA oligonucleotide or polynucleotide or at the ⁇ "and / or 4 - end of a p-DNA or p-RNA oligonucleotide or polynucleotide attach. In contrast, free diol groups are completely oxidized in the reaction with periodate.
  • Oligonucleotides or polynucleotides are all naturally occurring but also synthetically produced polymers that have the capability of being molecular
  • non-natural oligonucleotides and polynucleotides are the chemically modified derivatives of DNA, cDNA and RNA such as e.g. B. their phosphorothioates, phosphorodithioates, methylphosphonates, 2'-0-methyl-RNA, 2 " -0-allyl-RNA, 2'-fluoro-RNA, LNA or those molecules which, like PNA, can pair with DNA and RNA (Sanghivi, YS, Cook, DP, Carbohydrate Modification in Antisense Research, American Chemical Society,
  • the chain length is preferably sufficient, including a monomeric unit according to
  • Claim 1 from 2 to 10,000 monomer units, chain lengths of 5 to 30 monomer units are particularly preferred.
  • the monomer units that can be used to prepare the oligo- or polynucleotides are, above all, naturally occurring nucleotides, such as
  • Synthetic nucleotides are 2'-deoxyribofuranosyl nucleotides, ribofuranoslynucleosides, 2'-deoxy-2'-flouro ribofuranosyl nucleosides, 2'-0-methyl-ribofuranosylnuceosides, pentopyranosylnucleotides, 3'-deoxypentopyranosylnucleotides.
  • the heterocyclic bases for these nucleotides include:
  • Oligo- and polynucleotides in the sense of this invention also include such
  • Molecules which, in addition to the units required for molecular recognition, contain further molecular parts which serve for other purposes, such as, for example, detection, conjugation with other molecular units, immobilization on surfaces or on other polymers, spacing or branching of the nucleotide chain.
  • this includes the covalent or stable noncovalent conjugates of oligonucleotides with fluorescent dyes, chemiluminescent molecules, peptides, proteins, antibodies, aptamers, organic and inorganic molecules as well as conjugates from two or more pairing systems which have different pairing modes such as p-RNA conjugated with DNA or their chemically modified derivatives, p-RNA conjugated to RNA or their chemically modified derivatives, p-DNA conjugated to DNA or their chemically modified derivatives, p-DNA conjugated to RNA or their chemically modified derivatives, CNA conjugated to DNA or their chemically modified derivatives , CNA conjugated to RNA or its chemically modified derivatives. But also the immobilization on support surfaces, such as. B.
  • the surfaces can in turn have one or more layers of coatings polymer coatings, such as poly-lysine, agarose or polyacrylamide, are preferred.
  • the coating can contain several staggered layers or even disordered layers.
  • the individual layers can be designed in the form of monomolecular layers.
  • conjugation is understood to mean the covalent or non-covalent linkage of components such as molecules, oligo- or polynucleotides, supramolecular complexes or polymers with one or more other different or identical components, so that these are one under the conditions necessary for their use stable
  • conjugation does not necessarily have to be covalent, it can also take place via supramolecular forces, such as van der Waals interactions, dipole interactions, in particular hydrogen bonds, or ionic interactions.
  • conjugates with organic or inorganic molecules that have a biological activity.
  • drugs are radioactive
  • Isotopes steroids, phosphates, triphosphates, nucleoside triphosphates, derivatives of lead structures, transition state analogs, lipids, heterocycles, in particular nitrogen heterocycles, saccharides, branched or unbranched oligo- or polysaccharides, glycoproteins, glycopeptides, receptors or functional parts thereof such as the extracellular domain membrane-bound receptor,
  • Metabolites messenger substances, substances that are produced in the human or animal body in the event of pathological changes, antibodies or functional parts thereof, such as Fv fragments, single-chain Fv fragments, or Fab fragments, enzymes, filament components, viruses, virus components such as capsids , Viroids, and their derivatives such.
  • Substance libraries such as ensembles of structurally different compounds, preferably oligomeric or polymeric peptides, peptidoids, saccharides, nucleic acids, esters, acetals or monomers such as heterocycles, lipids, Steroids or attack structures of pharmaceuticals, preferably drug receptors, ion channels, in particular voltage-dependent ion channels, transporters, enzymes or biosynthetic units of microorganisms worth mentioning.
  • the invention also relates to the light from the respective acetal, for. B. by means of aqueous acids or photochemically producible aldehyde-modified p-RNA and p-DNA oligo- and polynucleotides.
  • Formula (I) assumed.
  • conventional phosphoramidites bearing one or more acetal groups can be used. These can be integrated into the oligo- or polynucleotides using the standard methods of solid-phase synthesis (schematic illustration in FIG. 2).
  • corresponding hydroxy acetals can be prepared from their halides by the Finkelstein reaction or by acetalization from a hydroxy
  • oligonucleotide solid-phase synthesis Beaucage, SL; lyer, RP, Tetrahederon 49 (1993) 6123; Caruthers, MH, Barone, AD; Beaucage, S. L; Dodds, DR; Fisher , EF; McBride, LJ; Matteucci, M .; Stabinsky, Z .; Tang, JY, Methods Enzymol. 154 (1987) 287; Caruthers MH; Beaton, G .; Wu, JV; Wiesler, W.,
  • Acetals are inert to all reaction conditions of the common oligonucleotide synthesis methods such as the phosphoramidite method. So the acetals are e.g. B. inert to activation with tetrazole,
  • acetals are stable against the basic reaction conditions in oligonucleotide deprotection. They survive the concentrated aqueous ammonia solution (55 ° C, 2-10 h) undamaged and are not damaged by alternative reagents such as those used in special cases (ethylenediamine, methylamine, hydrazine) (Hogrefe, R.I .; Vghefi, M. M .;
  • the aldehyde functionality is released from the acetals (as in Examples 8-11, for example) easily by treating the acetal oligonucleotides with aqueous acids (acetic acid, trifluoroacetic acid, hydrochloric acid etc.) or by irradiation with light (see see also the schematic representation in Figure 2). In either case, it is not necessary to separate the aldehyde oligonucleotide from reagents such as sodium periodate. It is enough, but not always necessary, to neutralize the acid. Should the salt content caused by the neutralization of the acid interfere with the conversion of the aldehyde, it can also be carried out using common processes, such as. B. gel filtration, dialysis, reverse phase extraction can be removed.
  • aldehyde oligo- or polynucleotides obtained in this way can be found for all in the literature (e.g. in Hermanson, GT, Bioconjugate Techniques, Academic Press, San Diego 1996; Timofeev, EN; Kochetkova, SV; Mirzabekov, AD; Florentiev, VL , Nucleic Acids Res. 24 (1996) 3142).
  • Of particular interest are the conjugation of oligo- or polynucleotides with proteins and peptides, fluorescent dyes, other oligonucleotides and the immobilization of oligo- or polynucleotides on surfaces and on other polymers.
  • Aldehyde-modified oligo- or polynucleotides furthermore offer the possibility of using the reaction shown in FIG. 1C for conjugation with peptides, proteins or other organic or inorganic molecules which carry a cysteine at their N-terminus.
  • a thiazolidine derivative is formed which, given the constitution of the aldehyde, can still rearrange (Lemieux, G.A .; Bertozzi, C.R., Trends in Biotechnology 16 (1998) 506; Liu, C.-F .;
  • acetals as protective groups for aldehydes also allows a particularly simple method for conjugating oligo- or polynucleotides:
  • the fully or partially protected acetal oligo- or polynucleotide which is still immobilized on the support material of the oligonucleotide solid-phase synthesis, is converted into the corresponding aldehyde oligo or polynucleotide. It is important that this reaction, which is possible by aqueous acids or by irradiation with light, does not lead to the oligo- or polynucleotide being split off from the support material.
  • the carrier-bound aldehyde nucleotide chain is then reacted with a corresponding reaction partner (for example, FIG. 1).
  • the oligo- or polynucleotide conjugate is then cleaved from the carrier by aqueous ammonia or alternative reagents (e.g. ethylenediamine, methylamine, hydrazine) and from the remaining protective groups, for DNA, for example, the benzoyl and isobutyryl protective groups on the exocyclic amino groups of the bases, freed.
  • aqueous ammonia or alternative reagents e.g. ethylenediamine, methylamine, hydrazine
  • protective groups for DNA, for example, the benzoyl and isobutyryl protective groups on the exocyclic amino groups of the bases, freed.
  • the prerequisite is that the conjugation
  • the linkage formed is stable against these deprotection conditions, which is the case with the products described by way of example in FIG. 1.
  • the advantage of this conjugation of carrier-bound oligo- or polynucleotides is that the excess of the components to be conjugated and other rea
  • Oligonucleotides were produced on an Expedite 8905 from PE Biosystems using the phosphoramidite method. Acetal phosphoramidites as well as the DNA amidites were used as a 0.1 M solution in dry acetonitrile. The coupling was done with tetrazole as an activator. The synthesis conditions previously described were used for p-RNA oligonucleotides (DE19741715) electrospray
  • the numbering of the individual substances given relates to the numbers used in FIGS. 3 to 5.
  • FIG. 3 exemplifies the synthesis of acetal phosphoramidites
  • FIG. 4 shows examples of DNA acetals and DNA aldehydes
  • FIG. 4 shows examples of p-RNA acetals and p-RNA aldehydes.
  • N- (2,2-dimethoxyethyl) -6-hydroxyhexamide 3a are mixed with 5.17 g (40 mmol, 4 eq., [129.25]) N-ethyl-diisopropylamine (Hünigs Base) in 40 ml of dry dichloromethane dissolved.
  • 2.6 g (11 mmol, 1.1 eq., [236.68]) phosphorous acid mono- (2-cyanoethyl ester) -diisopropylamide chloride 4 are added dropwise over 15 min. After 1 hour the TLC (ethyl acetate / n-heptane 2: 1) shows complete conversion.
  • Example 2 N- (2,2-Diethoxyethyl) -6-0 - [(2-cyanoethyl) -N, N- diisopropylamidophosphoramiditj-hexamide 5b: 2.47 g (10 mmol, [247.34]) N- (2,2- Diethoxyethyl) -6-hydroxyhexamide 3b is dissolved with 5.17 g (40 mmol, 4 eq., [129.25]) N-ethyl-diisopropylamine (Hünigs base) in 40 ml dry dichloromethane.
  • N- (2,2-diethoxybutyl) -6-hydroxyhexamide 7 are mixed with 1.64 g (12.7 mmol, 4 eq., [129.25]) N-ethyl-diisopropylamine (Hünigs Base) in 30 ml of dry dichloromethane dissolved. 1.65 g (6.99 mmol, 1.1 eq., [236.68])
  • Phosphorous acid mono (2-cyanoethyl ester) diisopropylamide chloride 4 dissolved in 2 ml dichloromethane are added dropwise over 40 min. After a further 30 min the TLC (ethyl acetate / n-heptane 10: 1) shows the complete consumption of the starting material. It is stopped with methynol and the solvent is removed on a rotary evaporator, the residue is applied directly to a chromatography column.
  • aldehydes via acetals will affect both DNA and p-RNA
  • Oligonucleotides shown. The sequences of the example oligonucleotides are shown in FIGS. 4 and 5.
  • Example 4 DNA acetal 9 from diethylacetal 5b (K3194 / 3196 04) The oligonucleotide synthesis is carried out according to the instructions given by the device manufacturer
  • TEAA pH 7.0 in water
  • B 0.1 M
  • TEAA pH 7.0 in acetonitrile / water (95: 5);
  • Example 5 DNA acetal 11 from diethylacetal 8 (K3208 / 3214/3218 016)
  • Example 6 p-RNA Acetal 13 from Diethylacetal 5b (K3168 016) The oligonucleotide synthesis is carried out as described in Example 4.
  • p-RNA Acetal 13 from Diethylacetal 5b K3168 016
  • the oligonucleotide synthesis is carried out as described in Example 4.
  • RNA was used with a longer coupling time and pyridinium hydrochloride as an activator.
  • the acetal phosphoramidites are also coupled with pyridinium hydrochloride as an activator.
  • a 1.5% (w / v) solution of diethylamine in dichloromethane is first added to the support and the mixture is shaken at RT over night (15 h) with exclusion of light. The solution is discarded and the support is washed with 3 portions of the following solvents: CH 2 Cl 2 , acetone, water.
  • the p-RNA is then treated with 24% aqueous hydrazine hydrate for elimination from the CPG support and for deprotection at 4 ° C. for 18 h. Hydrazine is removed by solid phase extraction with Sep-Pak C18 cartridges (0.5 g Waters, No. 20515;
  • Example 4 described. Retention time DNA acetal 13: 22.0 min; MS: calc .: [2719], obs. [2718]
  • Example 7 p-RNA Acetal 15 from Diethylacetal 8 (K3208 / 3214/3218 016) The oligonucleotide synthesis and workup is carried out as described in Example 6. Retention time p-RNA acetal 15: 24.0 min; MS: calc .: [2747], obs .: [2747]
  • the acetal oligonucleotide is dissolved in water and an excess of aqueous acid (for example HCl) is added.
  • aqueous acid for example HCl
  • the oligonucleotide concentration in the reaction solution thus obtained is usually between 20 and 60 ⁇ M, a large excess of acid is used (up to 5 ⁇ 10 4 molar equivalents).
  • the solution is incubated at room temperature and the progress of the reaction is monitored by HPLC. After the acetal oligonucleotide has reacted completely, the mixture is neutralized with aqueous NaOH.
  • the solution of the aldehyde oligonucleotide thus obtained can be used directly for
  • Conjugation reactions are used or desalted using the usual methods such as gel filtration or solid phase extraction (see Example 6).
  • Example 8 DNA aldehyde 10 from DNA acetal 9 26 nmol acetal 10 are mixed with 1 ml of 1 M aqueous HCl and incubated at RT for 6.5 h. The course of the reaction can be followed by RP-HPLC under the conditions given in Example 4. The acid is neutralized by adding 1N aqueous NaOH. The solution of DNA aldehyde obtained in this way can be used directly for conjugations or can be purified by RP-HPLC. Retention time DNA aldehyde 10: 20.6 min.
  • Example 10 p-RNA aldehyde 14 from DNA acetal 13 16 nmol acetal 13 are reacted with 400 ⁇ l of 0.5 M aqueous HCl as described in Example 8 to form DNA aldehyde 14. Retention time: 19.2 min; MS: calc .: [2645], obs .: [2645]
  • Moleqiuvalenten NaCNBH 4 are added. If necessary, dilute with acetate buffer pH 5. After 2 hours at RT, the mixture is desalted by gel filtration and the conjugate is purified by HPLC.
  • an acetal oligonucleotide is prepared by solid phase synthesis.
  • the carrier-bound oligonucleotide is then first mixed with a 1.5% (w / v) solution of diethylamine in dichloromethane and shaken at RT over night (15 h). The solution is discarded and the support is washed with 3 portions of the following solvents: CH 2 Cl 2 , acetone, water.
  • the carrier is rinsed for 2 h at RT with a 0.1 to 1 M aqueous acid solution (for example HCl) treated.

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Abstract

L'invention concerne la production d'oligonucléotides modifiés et leur utilisation pour des réactions de conjugaison. Elle concerne également des réactifs et des procédés pour produire des oligonucléotides modifiés par de l'aldéhyde, lesdits oligonucléotides contenant comme acétals des aldéhydes protégés (masqués). Après incorporation des acétals dans les oligonucléotides, ces derniers sont convertis en aldéhydes et utilisés pour la réaction de conjugaison. Cette réaction peut s'effectuer avec l'oligonucléotide libre ou avec l'oligonucléotide encore lié au substrat.
EP01927675A 2000-03-18 2001-02-19 Monomeres reactifs pour la synthese d'oligonucleotides et de polynucleotides, oligonucleotides et polynucleotides modifies et leur procede de production Withdrawn EP1268492A1 (fr)

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DE10013600A DE10013600A1 (de) 2000-03-18 2000-03-18 Reaktive Monomere für die Oligonucleotid- und Polynucleotidsynthese, modifizierte Oligonucleotide und Polynucleotiden und ein Verfahren zu deren Herstellung
DE10013600 2000-03-18
PCT/EP2001/001799 WO2001070751A1 (fr) 2000-03-18 2001-02-19 Monomeres reactifs pour la synthese d'oligonucleotides et de polynucleotides, oligonucleotides et polynucleotides modifies et leur procede de production

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WO2001070751A1 (fr) 2001-09-27
CA2402822A1 (fr) 2002-09-17
AU2001254648A1 (en) 2001-10-03
KR20020087092A (ko) 2002-11-21
DE10013600A1 (de) 2002-01-10
JP2004500403A (ja) 2004-01-08
US20030171570A1 (en) 2003-09-11

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