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

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

Acharya, Sandipta ORCID: 0000-0003-2521-9968, Barman, Jharna, Cheruku, Pradeep, Chatterjee, Subhrangsu, Acharya, Parag ORCID: 0000-0003-2521-9968, Isaksson, Johan and Chattopadhyaya, Jyoti (2004) Significant pKa perturbation of nucleobases is an intrinsic property of the sequence context in DNA and RNA. Journal of the American Chemical Society, 126 (28). pp. 8674-8681. ISSN 0002-7863 (Print), 1520-5126 (Online) (doi:https://doi.org/10.1021/ja048484c)

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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 (ΔpKa = 0.67 ± 0.03) and ssRNAs (ΔpKa = 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 to the electronically coupled nature of the constituent nucleobases across the single strand, which demonstrates the unique chemical basis of the sequence context specificity of DNA or RNA in dictating the biological interaction, recognition, and function with any specific ligand.

Item Type: Article
Uncontrolled Keywords: nucleobase, electrostatics, oligomerization, genetics, molecular mechanism
Subjects: Q Science > QD Chemistry
Faculty / Department / Research Group: Faculty of Engineering & Science
Faculty of Engineering & Science > Natural Resources Institute
Faculty of Engineering & Science > Natural Resources Institute > Food & Markets Department
Last Modified: 10 Jul 2020 13:00
Selected for GREAT 2016: None
Selected for GREAT 2017: None
Selected for GREAT 2018: None
Selected for GREAT 2019: None
Selected for REF2021: None
URI: http://gala.gre.ac.uk/id/eprint/28722

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