Significant pKa perturbation of nucleobases is an intrinsic property of the sequence context in DNA and RNA

Journal of the American Chemical Society
Sandipta AcharyaJyoti Chattopadhyaya

Abstract

The pH titration and NMR studies (pH 6.6-12.5) in the heptameric isosequential ssDNA and ssRNA molecules, [d/r(5'-CAQ1GQ2AC-3', with variable Q1/Q2)], show that the pKa of the central G residue within the heptameric ssDNAs (DeltapKa = 0.67 +/- 0.03) and ssRNAs (DeltapKa = 0.49 +/- 0.02) is sequence-dependent. This variable pKa of the G clearly shows that its pseudoaromatic character, hence, its chemical reactivity, is strongly modulated and tuned by its sequence context. In contradistinction to the ssDNAs, the electrostatic transmission of the pKa of the G moiety to the neighboring A or C residues in the heptameric ssRNAs (as observed by the response of the aromatic marker protons of As or Cs) is found to be uniquely dependent upon the sequence composition. This demonstrates that the neighboring As or Cs in ssRNAs have variable electrostatic efficiency to interact with the central G/G-, which is owing to the variable pseudoaromatic characters (giving variable chemical reactivities) of the flanking As or Cs compared to those of the isosequential ssDNAs. The sequence-dependent variation of pKa of the central G and the modulation of its pKa transmission through the nearest-neighbors by variable electrostatic interaction is owing t...Continue Reading

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Citations

Mar 29, 2007·Nucleic Acids Research·N L MironovaM A Zenkova
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Nov 18, 2011·Chemical Communications : Chem Comm·Lorenzo FranceschiniGiovanni Maglia
Dec 4, 2008·The Journal of Physical Chemistry. C, Nanomaterials and Interfaces·Bidisha SenguptaJeffrey Petty

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