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Residue interactions affecting the deprotonation of internal guanine moieties in oligodeoxyribonucleotides, calculated by FMO methods

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Abstract

The effect of vicinal molecular groups on the intrinsic acidity of a central guanine residue in short single-stranded DNA models and the potentials exerted by the backbone and the nucleobases on the leaving proton were determined by the fragment molecular orbital (FMO) method, in terms of quantum descriptors (QDs) and pair interaction interfragment decomposition analysis (PIEDA). The acidity of the central guanine moiety decreased with increasing oligonucleotide length, in response to changes by less than 1 eV in the ionization potential, global softness, electrophilicity index, and electronegativity descriptors. The differences in these descriptors were majorly interpreted in terms of the electrostatic influence of the negative charges residing on the backbone of the molecule. Additionally, this electric-field effect was determined explicitly for the displacement of the test hydronium ion to a distance of 250 Å from its original position, resulting in good agreement with calculations of the variation in Gibbs free energies, obtained from physical experiments conducted on the identical oligonucleotide sequences. The reported results are useful for biophysical applications of deoxyriboligonucleotides containing guanine residues in order to induce local negative charges at specific positions in the DNA chain.

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Data Availability

All raw data are available from the authors upon request.

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Code availability

All the codes used in the calculations are available from the authors upon request.

Funding

JCGO received support from a Graduate student stipend from CONACYT. The stipend number is 37678. This work is part of CONACYT Basic Science Project No. 61322.

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Authors and Affiliations

  1. Universidad Politécnica de Santa Rosa Jáuregui, 76220, Queretaro, Mexico

    Julio C. González-Olvera & Gerardo Arreola-Jardón

  2. Laboratorio de Biofísica Computacional, SEPI-ENMH, Instituto Politécnico Nacional, 07360 Zacatenco, CDMX, Mexico

    Absalom Zamorano-Carrillo

  3. Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Instituto Politécnico Nacional, 76090, Queretaro, Mexico

    Reynaldo C. Pless

Authors
  1. Julio C. González-Olvera
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  2. Absalom Zamorano-Carrillo
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  3. Gerardo Arreola-Jardón
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  4. Reynaldo C. Pless
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All authors designed the project. JCGO and RCP performed the calculations. All authors contribute to writing of the manuscript.

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Correspondence to Julio C. González-Olvera.

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González-Olvera, J.C., Zamorano-Carrillo, A., Arreola-Jardón, G. et al. Residue interactions affecting the deprotonation of internal guanine moieties in oligodeoxyribonucleotides, calculated by FMO methods. J Mol Model 28, 43 (2022). https://doi.org/10.1007/s00894-022-05033-x

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