TRANTÍREK, Lukáš, Richard ŠTEFL, Michalea VORLÍČKOVÁ, Jaroslav KOČA, Vladimír SKLENÁŘ and Jaroslav KYPR. An A-type Double Helix of DNA Having B-type Puckering of the Deoxyribose Rings. Journal of Molecular Biology. USA: Academic Press, 2000, vol. 297, No 4, p. 907-922. ISSN 0022-2836.
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Basic information
Original name An A-type Double Helix of DNA Having B-type Puckering of the Deoxyribose Rings
Authors TRANTÍREK, Lukáš (203 Czech Republic), Richard ŠTEFL (203 Czech Republic), Michalea VORLÍČKOVÁ, Jaroslav KOČA (203 Czech Republic), Vladimír SKLENÁŘ (203 Czech Republic, guarantor) and Jaroslav KYPR.
Edition Journal of Molecular Biology, USA, Academic Press, 2000, 0022-2836.
Other information
Original language English
Type of outcome Article in a journal
Field of Study 10600 1.6 Biological sciences
Country of publisher United States of America
Confidentiality degree is not subject to a state or trade secret
Impact factor Impact factor: 5.388
RIV identification code RIV/00216224:14310/00:00000057
Organization unit Faculty of Science
UT WoS 000086345700006
Keywords in English DNA; A-type double helix; B-type deoxyribose pucker; buckled CG step; minor group widening
Tags A-type double helix, B-type deoxyribose pucker, buckled CG step, DNA, minor group widening
Changed by Changed by: prof. Mgr. Richard Štefl, Ph.D., učo 19362. Changed: 26/1/2007 17:24.
Abstract
DNA usually adopts structure B in aqueous solution, while structure A is preferred in mixtures of trifluoroethanol (TFE) with water. However, the octamer d(CCCCGGGG) and other d(CnGn) fragments of DNA provide CD spectra that suggest that the base-pairs are stacked in an A-like fashion even in aqueous solution. Yet, d(CCCCGGGG) undergoes a cooperative TFE-induced transition into structure A, indicating that an important part of the aqueous duplex retains structure B. NMR spectroscopy shows that puckering of the deoxyribose rings is of the B-type. Hence, combination of the information provided by CD spectroscopy and NMR spectroscopy suggests an unprecedented double helix of DNA in which A-like base stacking is combined with B-type puckering of the deoxyribose rings. In order to determine whether this combination is possible, we used molecular dynamics to simulate the duplex of d(CCCCGGGG). Remarkably, the simulations, completely unrestrained by the experimental data, provided a very stable double helix of DNA, exhibiting just the intermediate B/A features described above. The double helix contained well-stacked guanine bases but almost unstacked cytosine bases. This generated a hole in the double helix center, which is a property characteristic for A-DNA, but absent from B-DNA. The minor groove was narrow at the double helix ends but wide at the central CG step where the Watson- Crick base-pairs were buckled in opposite directions. The base-pairs stacked tightly at the ends but stacking was loose in the duplex center. The present double helix, in which A-like base stacking is combined with B-type sugar puckering, is relevant to replication and transcription because both of these phenomena involve a local B-to-A transition.
Abstract (in Czech)
DNA usually adopts structure B in aqueous solution, while structure A is preferred in mixtures of trifluoroethanol (TFE) with water. However, the octamer d(CCCCGGGG) and other d(CnGn) fragments of DNA provide CD spectra that suggest that the base-pairs are stacked in an A-like fashion even in aqueous solution. Yet, d(CCCCGGGG) undergoes a cooperative TFE-induced transition into structure A, indicating that an important part of the aqueous duplex retains structure B. NMR spectroscopy shows that puckering of the deoxyribose rings is of the B-type. Hence, combination of the information provided by CD spectroscopy and NMR spectroscopy suggests an unprecedented double helix of DNA in which A-like base stacking is combined with B-type puckering of the deoxyribose rings. In order to determine whether this combination is possible, we used molecular dynamics to simulate the duplex of d(CCCCGGGG). Remarkably, the simulations, completely unrestrained by the experimental data, provided a very stable double helix of DNA, exhibiting just the intermediate B/A features described above. The double helix contained well-stacked guanine bases but almost unstacked cytosine bases. This generated a hole in the double helix center, which is a property characteristic for A-DNA, but absent from B-DNA. The minor groove was narrow at the double helix ends but wide at the central CG step where the Watson- Crick base-pairs were buckled in opposite directions. The base-pairs stacked tightly at the ends but stacking was loose in the duplex center. The present double helix, in which A-like base stacking is combined with B-type sugar puckering, is relevant to replication and transcription because both of these phenomena involve a local B-to-A transition.
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VS96095, research and development projectName: Laboratoř struktury a dynamiky biomolekul
Investor: Ministry of Education, Youth and Sports of the CR, Laboratory of Structure and Dynamics of Biomolecules
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