Detailed Information on Publication Record
2002
Exploring the Structure of a DNA Hairpin with the Help of NMR Spin-spin Coupling Constants: An Experimental and Quantum Chemical Investigation
SYCHROVSKÝ, Vladimír, Jaroslav VACEK, Pavel HOBZA, Lukáš ŽÍDEK, Vladimír SKLENÁŘ et. al.Basic information
Original name
Exploring the Structure of a DNA Hairpin with the Help of NMR Spin-spin Coupling Constants: An Experimental and Quantum Chemical Investigation
Authors
SYCHROVSKÝ, Vladimír (203 Czech Republic), Jaroslav VACEK (203 Czech Republic), Pavel HOBZA (203 Czech Republic), Lukáš ŽÍDEK (203 Czech Republic, belonging to the institution), Vladimír SKLENÁŘ (203 Czech Republic, guarantor, belonging to the institution) and Dieter CREMER (752 Sweden)
Edition
Journal of Physical Chemistry B, USA, The American Chemical Society, 2002, 1089-5639
Other information
Language
English
Type of outcome
Článek v odborném periodiku
Field of Study
10403 Physical chemistry
Country of publisher
United States of America
Confidentiality degree
není předmětem státního či obchodního tajemství
Impact factor
Impact factor: 2.765
RIV identification code
RIV/00216224:14310/02:00006454
Organization unit
Faculty of Science
UT WoS
000178273500038
Keywords in English
NMR; coupling constants; DNA hairpin DFT
Tags
Změněno: 9/3/2015 05:41, prof. Mgr. Lukáš Žídek, Ph.D.
Abstract
V originále
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.
Links
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