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@article{405487,
author = {Sychrovský, Vladimír and Vacek, Jaroslav and Hobza, Pavel and Žídek, Lukáš and Sklenář, Vladimír and Cremer, Dieter},
article_location = {USA},
article_number = {29},
keywords = {NMR; coupling constants; DNA hairpin DFT},
language = {eng},
issn = {1089-5639},
journal = {Journal of Physical Chemistry B},
title = {Exploring the Structure of a DNA Hairpin with the Help of NMR Spin-spin Coupling Constants: An Experimental and Quantum Chemical Investigation},
volume = {106},
year = {2002}
}
TY - JOUR
ID - 405487
AU - Sychrovský, Vladimír - Vacek, Jaroslav - Hobza, Pavel - Žídek, Lukáš - Sklenář, Vladimír - Cremer, Dieter
PY - 2002
TI - Exploring the Structure of a DNA Hairpin with the Help of NMR Spin-spin Coupling Constants: An Experimental and Quantum Chemical Investigation
JF - Journal of Physical Chemistry B
VL - 106
IS - 29
SP - 10242
EP - 10242
PB - The American Chemical Society
SN - 10895639
KW - NMR
KW - coupling constants
KW - DNA hairpin DFT
N2 - A 13C, 15N-labeled DNA hairpin molecule of the sequence d(GCGAAGC) = d(G1C2G3A4A5G6C7) is investigated by NMR spectroscopy to determine one-bond and two-bond NMR spin-spin coupling constants 1J(X, H) (X= C, N), 1J(C, X) (X= C, N), and 2J(X,H) (X=C,N). Measured J values for the Watson-Crick (WC) base-pairs G1C7, G6C2, the mismatched base-pair G3A5 and the unpaired base A4 were compared with calculated J values to verify sign and magnitude. For the J-calculations, coupled perturbed density functional theory in connection with the B3LYP hybrid functional and basis sets (9s5p1d/5s,1p)[6s,4p,1d/3s,1p] as well as (11s,7p,2d/6s,2p)[7s,6p,2d/4s,2p] was employed to determine diamagnetic spin-orbit, paramagnetic spin-orbit, Fermi contact, and spin-dipolar contributions to the total isotropic coupling constant J. Coupling constants 1J(C,H) and 2J(N,H) turn out to be very sensitive to the position of C and N in the pyrimidine or purine rings and, therefore, can be used for rapid structure determination. Coupling constant 1J(N1,C6) in G of GC clearly reflects the impact of H-bonding by an increase from -6.5 to -10.6 Hz. The direct investigation of H-bonding via the 2J(N,N') coupling constants reveals that these parameters depend on the distance R(N-N'), the bending angle N-H..N', and the degree of planarity at the H-donor group. Different types of H-bonding were identified. H-bonding is weaker in AG and therefore, leads to smaller changes in the J values of the bases A and G upon pairing than in the case of the WC base-pair GC.
ER -
SYCHROVSKÝ, Vladimír, Jaroslav VACEK, Pavel HOBZA, Lukáš ŽÍDEK, Vladimír SKLENÁŘ and Dieter CREMER. Exploring the Structure of a DNA Hairpin with the Help of NMR Spin-spin Coupling Constants: An Experimental and Quantum Chemical Investigation. \textit{Journal of Physical Chemistry B}. USA: The American Chemical Society, 2002, vol.~106, No~29, p.~10242-10250. ISSN~1089-5639.
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