Exploring the Structure of a DNA Hairpin with the Help of NMR
Spin-spin Coupling Constants: An Experimental and Quantum
Chemical Investigation

J 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.

Základní údaje

Originální název

Exploring the Structure of a DNA Hairpin with the Help of NMR Spin-spin Coupling Constants: An Experimental and Quantum Chemical Investigation

Autoři

SYCHROVSKÝ, Vladimír; Jaroslav VACEK; Pavel HOBZA; Lukáš ŽÍDEK; Vladimír SKLENÁŘ a Dieter CREMER

Vydání

Journal of Physical Chemistry B, USA, The American Chemical Society, 2002, 1089-5639

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10403 Physical chemistry

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Impakt faktor

Impact factor: 2.765

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14310/02:00006454

Organizační jednotka

Přírodovědecká fakulta

UT WoS

000178273500038

Klíčová slova anglicky

NMR; coupling constants; DNA hairpin DFT

Štítky

coupling constants, DNA hairpin DFT, NMR

Změněno: 9. 3. 2015 05:41, prof. Mgr. Lukáš Žídek, Ph.D.

Anotace

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.

Návaznosti

LN00A016, projekt VaV

Název: BIOMOLEKULÁRNÍ CENTRUM

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Biomolekulární centrum

Citovat

SYCHROVSKÝ, Vladimír; Jaroslav VACEK; Pavel HOBZA; Lukáš ŽÍDEK; Vladimír SKLENÁŘ a Dieter CREMER. Exploring the Structure of a DNA Hairpin with the Help of NMR Spin-spin Coupling Constants: An Experimental and Quantum Chemical Investigation. Journal of Physical Chemistry B. USA: The American Chemical Society, 2002, roč. 106, č. 29, s. 10242-10250. ISSN 1089-5639.

@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 a 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, roč.~106, č.~29, s.~10242-10250. ISSN~1089-5639.

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