TY - JOUR
T1 - Residue interactions affecting the deprotonation of internal guanine moieties in oligodeoxyribonucleotides, calculated by FMO methods
AU - González-Olvera, Julio C.
AU - Zamorano-Carrillo, Absalom
AU - Arreola-Jardón, Gerardo
AU - Pless, Reynaldo C.
N1 - Publisher Copyright:
© 2022, The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.
PY - 2022/2
Y1 - 2022/2
N2 - 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.
AB - 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.
KW - DNA oligonucleotides
KW - Deprotonated guanine
KW - Intrinsic acidity
KW - PIEDA
KW - Quantum descriptors
UR - http://www.scopus.com/inward/record.url?scp=85123795701&partnerID=8YFLogxK
U2 - 10.1007/s00894-022-05033-x
DO - 10.1007/s00894-022-05033-x
M3 - Artículo
C2 - 35079869
AN - SCOPUS:85123795701
SN - 1610-2940
VL - 28
JO - Journal of Molecular Modeling
JF - Journal of Molecular Modeling
IS - 2
M1 - 43
ER -