Synthesis and Biophysical and Biological Properties of Oligonucleotides Containing 2-Aza-2'-Deoxyinosine (original) (raw)
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Synthesis and properties of (2′ S)- and (2′ R)-2′-deoxy-2′- C-methyl oligonucleotides
Tetrahedron, 2001
AbstractÐThe synthesis of (2 0 S)-and (2 0 R)-2 0 -deoxy-2 0 -C-methyl-N 3 -(4-t-butylbenzoyl) uridine, (2 0 S)-2 0 -deoxy-2 0 -C-methyluridine and (2 0 S)-2 0 -deoxy-2 0 -C-methyl-N 4 -isobutyryl cytidine building blocks are here described. The preparation of oligonucleotides carrying these monomers in all positions but 3 0 -end is presented and the binding af®nity between these new fragments and the complementary DNA and RNA sequences is also assessed. (2 0 R) substituted oligonucleotides did not hybridize with either the complementary DNA or RNA sequences. However, the ®rst derivative of melting curves of hybrids containing (2 0 S) modi®ed oligonucleotides indicated melting transitions. q
Tetrahedron, 1998
From propyne and S-iodo-a,2deoxyuridine, obtained by glycosylation, 5-propynyla,2'deoxyuridine was synthesized following the proc&ue of Hobbs. One part was then transformed through displacement of its C4-triazolo derivative with ammonia into 5-propynyl-a,2'-deoxyqtidine derivative. Finally, the corresponding a. 5-propynyl nucleoside phosphoramidites were prepared, and 5-propynyla oligonucleotides (12-mer) with either phosphodiester and phosphorothioate were synthesized The melting temperatures showed that duplexes with complementary DNA are stabilized between 0.65 and 1.2Wmod, and duplexes with RNA are stabilized between 1.2 and 1.4Wmod.
Synthesis and Hybridization Properties of Modified Oligodeoxynucleotides Carrying Non-Natural Bases
Chemistry & Biodiversity, 2009
The impact of the presence of non-natural bases on the properties of oligodeoxynucleotides has been studied. First, oligodeoxynucleotides carrying 2'deoxyzebularine were prepared and the stability of duplexes carrying this analogue was determined by DNA melting experiments. Melting temperatures and thermodynamic data showed the preference of 2'-deoxyzebularine for 2'-deoxyguanosine, which behaves as a 2'-deoxycytidine analogue forming a less stable base pair due to the absence of the amino group at position 4. Moreover, the duplex-hairpin equilibrium of a self-complementary oligodeoxynucleotide carrying several natural and non-natural bases including 2'-deoxyzebularine as a central mispair, was studied. Depending of the base present in the middle of the sequence it is possible to affect the stability of the bimolecular duplex modulating the duplex-hairpin equilibrium. Magnesium ions were shown to stabilize preferentially the bimolecular duplex form. The results indicate the importance of the modifications and the role of cations in shifting the structural equilibrium.
Nucleic Acids Research, 1997
We have attempted to alleviate the pH dependency of triplex recognition of guanine by using intermolecular triplexes containing 2-amino-5-(2-deoxy-D-ribofuranosyl)pyridine (AP) as an analogue of 2′-deoxycytidine (dC). We find that for the β-anomer of AP, the complex between (AP) 6 T 6 and the target site G 6 A 6 •T 6 C 6 is stable, generating a clear DNase I footprint at oligonucleotide concentrations as low as 0.25 µM at pH 5.0, in contrast to 50 µM C 6 T 6 which has no effect on the cleavage pattern. This complex is still stable at pH 6.5 producing a footprint with 1 µM oligonucleotide. Oligonucleotides containing the α-anomer of AP are much less effective than the β-anomer, though in some instances they are more stable than the unmodified oligonucleotides. The results of molecular dynamics studies on a range of AP-containing triplexes has rationalized the observed stability behaviour in terms of hydrogen-bonding behaviour.
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.
Proceedings of the National Academy of Sciences, 1998
A universal base that is capable of substituting for any of the four natural bases in DNA would be of great utility in both mutagenesis and recombinant DNA experiments. This paper describes the properties of oligonucleotides incorporating two degenerate bases, the pyrimidine base 6H,8H-3,4dihydropyrimido[4,5-c][1,2]oxazin-7-one and the purine base N 6-methoxy-2,6-diaminopurine, designated P and K, respectively. An equimolar mixture of the analogues P and K (called M) acts, in primers, as a universal base. The thermal stability of oligonucleotide duplexes were only slightly reduced when natural bases were replaced by P or K. Templates containing the modified bases were copied by Taq polymerase; P behaved as thymine in 60% of copying events and as cytosine in 40%, whereas K behaved as if it were guanine (13%) or adenine (87%). The dUTPase gene of Caenorhabditis elegans, which we have found to contain three nonidentical homologous repeats, was used as a model system to test the use of these bases in primers for DNA synthesis. A pair of oligodeoxyribonucleotides, each 20 residues long and containing an equimolar mixture of P and K at six positions, primed with high specificity both T7 DNA polymerase in sequencing reactions and Taq polymerase in PCRs; no nonspecific amplification was obtained on genomic DNA of C. elegans. Use of P and K can significantly reduce the complexity of degenerate oligonucleotide mixtures, and when used together, P and K can act as a universal base. The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked ''advertisement'' in accordance with 18 U.S.C. §1734 solely to indicate this fact.