TRANTÍREK, Lukáš, Richard ŠTEFL, Michalea VORLÍČKOVÁ, Jaroslav KOČA, Vladimír SKLENÁŘ a 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, roč. 297, č. 4, s. 907-922. ISSN 0022-2836.
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Základní údaje
Originální název An A-type Double Helix of DNA Having B-type Puckering of the Deoxyribose Rings
Autoři TRANTÍREK, Lukáš (203 Česká republika), Richard ŠTEFL (203 Česká republika), Michalea VORLÍČKOVÁ, Jaroslav KOČA (203 Česká republika), Vladimír SKLENÁŘ (203 Česká republika, garant) a Jaroslav KYPR.
Vydání Journal of Molecular Biology, USA, Academic Press, 2000, 0022-2836.
Další údaje
Originální jazyk angličtina
Typ výsledku Článek v odborném periodiku
Obor 10600 1.6 Biological sciences
Stát vydavatele Spojené státy
Utajení není předmětem státního či obchodního tajemství
Impakt faktor Impact factor: 5.388
Kód RIV RIV/00216224:14310/00:00000057
Organizační jednotka Přírodovědecká fakulta
UT WoS 000086345700006
Klíčová slova anglicky DNA; A-type double helix; B-type deoxyribose pucker; buckled CG step; minor group widening
Štítky A-type double helix, B-type deoxyribose pucker, buckled CG step, DNA, minor group widening
Změnil Změnil: doc. Mgr. Richard Štefl, Ph.D., učo 19362. Změněno: 26. 1. 2007 17:24.
Anotace
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.
Anotace česky
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.
Návaznosti
VS96095, projekt VaVNázev: Laboratoř struktury a dynamiky biomolekul
Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Posílení výzkumu na vysokých školách
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