7-Deaza-2′-Deoxyxanthosine: Nucleobase Protection and Base Pairing of Oligonucleotides (original) (raw)
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The Journal of Organic Chemistry, 1995
The preparation of oligonucleotides containing 2-aza-2'-deoxyinosine is described. Protection of the 2-azahypoxanthine moiety with the photolabile 2-nitrobenzyl group enabled us to obtain the phosphoramidite derivative and oligonucleotides containing protected 2-aza-2'-deoxyinosine. After purification, photolysis of the oligonucleotides containing the protected analogue provided the desired oligonucleotides in good yields. Melting curves of duplexes containing 2-azahypoxanthine paired with the four natural bases at pH 6 and pH 8 proved that 2-azahypoxanthine base pairs were less stable than perfectly matched duplexes but showed little variation among different bases. Synthetic oligonucleotide probes have proven to be very useful in the detection of cloned DNA sequences. When a partial protein sequence is available, the design of oligonucleotide probes is complicated by the degeneracy of the genetic code. To circumvent this problem, a sustained effort has been devoted to the design of base analogues that can potentially base pair with any of the four natural bases. 2'-Deoxyinosine was the first compound studied and it is the most used.' Its ribonucleoside derivative, inosine, was found in &RNA at the third position of the anticodon, capable of pairing with the A, C, and U bases of the codon. Abasic and phenyl analogues have been prepared but base pairing was significantly less stable than the normal Watson-Crick base pairing.2 The preparation of oligonucleotides containing 2'-deoxyinosine derivatives: allopurinol 2'-deoxyriboside and 7-deaza-2'-deoxyinosine have also been de~cribed.~ Oligonucleotides containing 5-fluorouracil have been reported to form stable base pairs with adenine and guanine.4 Similarly, it has been shown that oligonucleotides containing pyrimidine analogues that have an amino-imino tautomeric constant near unity, pair equally well with A and G. The same holds for a purine analogue that is able to form strong base pairs with T and C.5 Very recently, oligonucleotides containing 3-nitropyrrole 2'-deoxyriboside at several sites have been used as primers for sequencing and polymerase chain reaction + Centro de Investigaci6n y Desarrolo.
Synthesis, oligonucleotide incorporation and base pair stability of 7-methyl-8-oxo-2′-deoxyguanosine
Org. Biomol. Chem., 2006
Fluorescent base analogues (FBAs) have emerged as a powerful class of molecular reporters of location and environment for nucleic acids. In our overall mission to develop bright and useful FBAs for all natural nucleobases, herein we describe the synthesis and thorough characterization of bicyclic thymidine (bT), both as a monomer and when incorporated into DNA. We have developed a robust synthetic route for the preparation of the bT DNA monomer and the corresponding protected phosphoramidite for solidphase DNA synthesis. The bT deoxyribonucleoside has a brightness value of 790 M −1 cm −1 in water, which is comparable or higher than most fluorescent thymine analogues reported. When incorporated into DNA, bT pairs selectively with adenine without perturbing the B-form structure, keeping the melting thermodynamics of the B-form duplex DNA virtually unchanged. As for most fluorescent base analogues, the emission of bT is reduced inside DNA (4.5-and 13-fold in single-and double-stranded DNA, respectively). Overall, these properties make bT an interesting thymine analogue for studying DNA and an excellent starting point for the development of brighter bT derivatives.
Nucleic Acids Research, 1986
3-Methoxy-4-phenoxybenzoyl group has been used for the protection of exocyclic amino group of nucleosides. In case of 2'deoxycytidine it has been found to be highly selective under controlled conditions. The N-protected derivatives of 2'-deoxyadenosine and 2 '-deoxyguanosine have been found to be suf ficiently stable towards acids minimising depurination under conditions of synthesis of oligodeoxyribonucleotide on solid support via phosphotriester approach. The high lipophilicity of the group and milder deprotection conditions are additional advantages.
Nucleic Acids Research, 1999
Theoretical calculations on double and triple helices containing 8-amino-2′-deoxyadenosine were made to analyze the possible differences in base pairing properties between 8-aminoadenine and adenine. These calculations indicate a strong preferential stabilization of the triplex over the duplex when adenine is replaced by 8-aminoadenine. In addition, a protected phosphoramidite derivative of 8-amino-2′deoxyadenosine was prepared for the introduction of 8-aminoadenine into synthetic oligonucleotides using the phosphite-triester approach. DNA triple helical structures are normally observed at acidic pH. However, when oligonucleotides carrying 8-aminoadenine are used, very stable triple helical structures can be observed even at neutral pH. Biological applications of triple helices could benefit from the use of 8-aminoadenine derivatives.
Advanced method for oligonucleotide deprotection
Nucleic Acids Research, 2000
A new procedure for rapid deprotection of synthetic oligodeoxynucleotides has been developed. While all known deprotection methods require purification to remove the residual protective groups (e.g. benzamide) and insoluble silicates, the new procedure based on the use of an ammonia-free reagent mixture allows one to avoid the additional purification steps. The method can be applied to deprotect the oligodeoxynucleotides synthesized by using the standard protected nucleoside phosphoramidites dG iBu , dC Bz and dA Bz .
A study of 7-deaza-2'-deoxyguanosine 2'-deoxycytidine base pairing in DNA
Nucleic Acids Research, 2007
The incorporation of 7-deazaguanine modifications into DNA is frequently used to probe protein recognition of H-bonding information in the major groove of DNA. While it is generally assumed that 7-deazaguanine forms a normal Watson-Crick base pair with cytosine, detailed thermodynamic and structural analyses of this modification have not been reported. The replacement of the 7-N atom on guanine with a C-H, alters the electronic properties of the heterocycle and eliminates a major groove cation-binding site that could affect the organization of salts and water in the major groove. We report herein the characterization of synthetic DNA oligomers containing 7-deazaguanine using a variety of complementary approaches: UV thermal melting, differential scanning calorimetry (DSC), circular dichroism (CD), chemical probing and NMR. The results indicate that the incorporation of a 7-deazaguanine modification has a significant effect on the dynamic structure of the DNA at the flanking residue. This appears to be mediated by changes in hydration and cation organization.