TY - JOUR
T1 - Evaluating the effects of the nonplanarity of nucleic acid bases on NMR, IR, and vibrational circular dichroism spectra: a density functional theory computational study
AU - Vokáčová, Z.
AU - Trantirek, L.
AU - Sychrovský, V.
PY - 2010
Y1 - 2010
N2 - The pyramidalizations of N9/1 glycosidic nitrogens in DNA and RNA nucleosides, recently discovered and
analyzed in their ultrahigh-resolution X-ray crystal structures (Sychrovsky´; et al. Nucleic Acid Res. 2009, 37,
7321.), were found to have significant effects on the structural interpretation of the 3J(C4/2-H1′) and 3J(C8/
6-H1′) NMR scalar couplings in purine/pyrimidine nucleosides. The calculated effects on IR and vibrational
circular dichroism (VCD) spectra were only minor. The calculated structural deformations in nucleosides,
depending on sugar-to-base orientation, gave rise to corrections in the phase shift of the Karplus equations
for the 3J(C8/6-H1′) and 3J(C4/2-H1′) couplings ranging from -26° to +25° and from -5.7° to +2.0°,
respectively. The sign alternation of this correction in syn and anti nucleosides arises from the stereoinversion
of the N9/1 glycosidic nitrogen occurring upon reorientation of the glycosidic torsion. The effect was calculated
consistently in the dG, dA, dC, dT, rA, and rG nucleosides. Utilization of the calculated phase-shift corrections
in the design of Karplus equations for the 3J couplings was suggested, and the effects on structural interpretation
of the experimental couplings were evaluated.
AB - The pyramidalizations of N9/1 glycosidic nitrogens in DNA and RNA nucleosides, recently discovered and
analyzed in their ultrahigh-resolution X-ray crystal structures (Sychrovsky´; et al. Nucleic Acid Res. 2009, 37,
7321.), were found to have significant effects on the structural interpretation of the 3J(C4/2-H1′) and 3J(C8/
6-H1′) NMR scalar couplings in purine/pyrimidine nucleosides. The calculated effects on IR and vibrational
circular dichroism (VCD) spectra were only minor. The calculated structural deformations in nucleosides,
depending on sugar-to-base orientation, gave rise to corrections in the phase shift of the Karplus equations
for the 3J(C8/6-H1′) and 3J(C4/2-H1′) couplings ranging from -26° to +25° and from -5.7° to +2.0°,
respectively. The sign alternation of this correction in syn and anti nucleosides arises from the stereoinversion
of the N9/1 glycosidic nitrogen occurring upon reorientation of the glycosidic torsion. The effect was calculated
consistently in the dG, dA, dC, dT, rA, and rG nucleosides. Utilization of the calculated phase-shift corrections
in the design of Karplus equations for the 3J couplings was suggested, and the effects on structural interpretation
of the experimental couplings were evaluated.
U2 - 10.1021/jp102329t
DO - 10.1021/jp102329t
M3 - Article
SN - 1089-5639
VL - 114
SP - 10202
EP - 10208
JO - Journal of Physical Chemistry A
JF - Journal of Physical Chemistry A
IS - 37
ER -