Synthesis and physical characterization of DNA fragments containing N4-methylcytosine and 5-methylcytosine

Abstract

The synthesis of N4-methyl-2'-deoxycytidine and its fully protected mononucleotide, suitable for the oligonucleotide synthesis by phosphotriester method is described. A set of octanucleotides - d(CGCGCGCG), d(CG5mCGCGCG), d(CG4mCGCGCG) and dodecanucleotides - d(GGACCCGGGTCC), d(GGA5mCCCGGGTCC), d(GGA4mCCCGGGTCC) has been synthesized in a solution. Physical characterization of the oligonucleotide duplexes by means of UV and CD spectrometry provides the evidence that 4mC similarly to 5mC favours the B--greater than Z transition, although both of these methylated cytosines inhibit the B--greater than A conformational change. N4-Methylcytosine in contrast to 5-methylcytosine reduces the DNA double helix thermal stability.

Origins of Sequence Selectivity in Homologous Genetic Recombination: Insights from Rapid Kinetic Probing of RecA-mediated DNA Strand Exchange

“…As first observed in polymer studies, 26-29 the addition of methyl groups to the C5 position of pyrimidine bases in duplex DNAs comprised of oligonucleotides increases the thermal stability of the dsDNA. [30][31][32][33][34] In agreement with these studies, cursory thermal denaturation studies revealed that the intrinsic thermal stabilities of the dsDNA substrates increase in the following order: D17 < D0 < D16. The placement of the base substitutions on the O-strand was designed to maximize any potential impact by changing the relative stabilities of both the substrate (C·O) and Three A·T bp were replaced by G·T bp or three G·C bp were replaced by I·C bp to create dsDNA substrates D18 and D19, respectively (see Figure 3).…”

“…Substitution of 5-methylcytosine for cytosine has been shown to increase the stability of duplex DNA. 26,[28][29][30][31][32][33] Likewise, thymine (5-methyluracil) stabilizes duplexes relative to uracil. 27,32,34 Indeed, Wang and Kool noted that, in sequence contexts similar to those utilized here, addition of pyrimdine C5-methyl substituents always results in increased thermal stability.…”

Epigenetic Modifications of Cytosine: Biophysical Properties, Regulation, and Function in Mammalian DNA

“…Although the anti conformer of N 4‐methylcytosine would also not disrupt base‐pairing, the syn conformer would. Interconversion between these states would therefore significantly lower the thermal stability of its base pair with guanine, as has been observed . b) Models of B‐ and A‐DNA, the two major conformational classes of DNA that are known to be biologically relevant.…”

Triplex- and Duplex-Forming Abilities of Oligonucleotides Containing 2′-Deoxy-5-trifluoromethyluridine and 2′-Deoxy-5-trifluoromethylcytidine

“…The stabilization results from hydrophobic effects generated by a release of hydrating water molecules from the double helix to the bulk. Duplex stability is also enhanced by m C due to an increase in hydrophobic interactions with the neighboring bases 5,7,8) (Fig. 1).…”