Ab initio comprehensive conformational analysis of 2'-deoxyuridine, the biologically significant DNA minor nucleoside, and reconstruction of its low-temperature matrix infrared spectrum.
A comprehensive conformational analysis of isolated 2'-deoxyuridine (dU), a minor DNA nucleoside, has been performed by means of ab initio calculations at the MP2/6-311++G (d,p)//DFT B3LYP/6-31G (d,p) level of theory. At 298.15 and 420 K, all 94 allowed conformers of dU are within 8.96 and 7.91 kcal/mol Gibbs energy ranges, respectively. Syn orientation for the base and South (S) conformers for the sugar dominate at 298.15 K: syn/anti=62.3%:37.7% and S/N=77.2%:22.8%. At 420 K in the majority of conformers, the base is anti oriented and the population of North (N) sugars increases: syn/anti=39.3%:60.7% and S/N=63.0%:37.0%. Values of all conformational parameters and correlations between them, as well as their correlations with valence bonds, and also correlations between valence bonds and angles were estimated. In general, 14 types of intramolecular H-bonds were detected (1-3 H-bonds per conformer, the total number 175), namely, C1'H...O2 (16 H-bonds), C2'H1...O5' (9), C2'H2...O2 (21), C3'H...O2 (21), C5'H1...O2 (14), C5'H2...O2 (11), C6H...O4' (37), C6H...O5' (22), C3'H...HC6 (4), O5'H...HC6 (2), O3'H...O5' (5), O5'H...O4' (1), O5'H...O3' (4), and O5'H...O2 (8). Geometric, vibrational, structural-topological, and energetic features of the OH...O intramolecular H-bonds in dU conformers were determined. The close similarity between energetic and geometric characteristics of dU and thymidine DNA-like conformers in anti and relevant syn conformations and their transition states of the anti-->syn interconversion implies that mismatch DNA glycosylase discriminates between the two nucleosides, mainly because of the difference in the shapes of their bases. Convolution of calculated IR spectra of all the dU conformers within the limits 3400-3700 cm(-1) appears to be consistent with its low-temperature matrix IR spectrum (Ivanov et al. Spectrochim. Acta, Part A 2003, 59, 1959), wavenumber discrepancy not exceeding 1%. It was concluded that, for a reliable reproduction of the experimental spectrum, the whole set of conformers should be taken into consideration. The suggested method makes reconstruction of the isolated nucleoside IR spectrum at a physiological interval of temperature reasonably possible.
Yurenko
Yevgen P
YP
Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, vul. Zabolotnoho 150, 03143, Kyiv, Ukraine.
Zhurakivsky
Roman O
RO
Ghomi
Mahmoud
M
Samijlenko
Svitlana P
SP
Hovorun
Dmytro M
DM
D019295:Computational Biology; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry*; D003857:Deoxyuridine / Q000737:chemistry*; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008968:Molecular Conformation; D010100:Oxygen / Q000737:chemistry; D013055:Spectrophotometry, Infrared; D013696:Temperature; D014732:Vibration; D014867:Water / Q000737:chemistry
D014867:Water; D004247:DNA; D010100:Oxygen; D003857:Deoxyuridine