Poly-2′-deoxy-2′-fluoro-cytidylic acid: enzymatic synthesis, spectroscopic characterization and interaction with poly-inosinic acid

Abstract

The polymerization of 2'deoxy-2'-fluoro-cytidine-diphosphate (dCflDP) by polynucleotide phosphorylase is barely detectable in the presence of Mg++ under usual experimental conditions for polymerization of nucleoside diphosphates. High concentrations of enzyme have to be used to accomplish the synthesis. Mn++ is a better activator than Mg++ for the reaction. cCflDP inhibits the polymerization of CDP and has a Km=8.8X10-3M, six times higher than CDP.- The polymer, poly (dCfl), ressembles in many respects poly(C), but not poly(dC): the acid selfstructure forms at similar pK's; interaction with poly(I) yields a 1:1 complex the CD spectrum of which is similar to that of poly(I).poly(C). Finally, the Tm's of poly(I).poly(dCfl) are comparable to those of poly(I).poly(C).

CD Spectral Comparisons of the Acid-Induced Structures of Poly[d(A)]Poly[r(A)], Poly[d(C)], and Poly[r(C)]

“…The same increase in Na + had only a marginal, if any, effect on the p~ values of the DNA polymers. Our data were in reasonable agreement with those published by Guschlbauer and his collaborators for poly[r(C)], poly[r(A)], and poly[d(C)] (22,54). Moreover, poly[d(C)] had a pKa for the coil-helix transition that was the farthest from its monomerpKa, while poly[d(A)] was the only polymer whose p~ was essentially identical with that of its monomer.…”

“…Others have shown that protonation of poly[r(C)] increases as the pH is reduced to 3 (15), causing denaturation of the acid self-complex to form a fully protonated single-strand (15,23). We found, in agreement with previous work ( 15,22), that the fully protonated polymer was hyperchromic and had a much reduced long wavelength CD band, compared with the duplex form ( Figure 7).…”

“…The CD spectrum of single-stranded poly[d(C)] at pH 8.5 ( Figure 6A) had a band at 277 nm that was considerably smaller than the 276 nm band of single-stranded poly[r(C)] at pH 7.0 (Figure 7 A), as found by others (22). Calculated spectra of these Downloaded by [Rutgers University] at 12:38 13 April 2015 single-stranded polymers in B-DNA and A-RNA geometries also show a large difference in magnitude (52).…”

Post-SELEX Chemical Optimization of a Trypanosome-Specific RNA Aptamer

“…C2modifications are known to affect the sugar puckering of nucleic acids [33,34]. The introduction of fluorine, the most electronegative element, leads to an almost pure C3 -endo conformation [36,37]. Heteroatom modifications like 2amino-groups favour a C2 -endo pucker, which is one of the main determinants of the "DNA-like" B-helix.…”

Principles of Nucleic Acid Structure

“…..... --.,... drogen bonding in some instances (87) (Figure 4-11a). However, O2, methylation (238)(239)(240) or replacement of O2, by chlorine (241), fluorine (242)(243)(244), or the azido group (245) does not markedly reduce the conformational stability of synthetic RNAs and therefore the 02,-H···04, hydrogen bond cannot be a crucial, structure-stabilizing factor. More recent NMR data suggest a water-mediated hydrogen-bonded bridge between 02,H and 3' -phosphate which could well account for at least part of the conformation rigidity of RNAs (246,247) (Figure 4-11b).…”