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@article{314191, author = {Trantírek, Lukáš and Štefl, Richard and Vorlíčková, Michalea and Koča, Jaroslav and Sklenář, Vladimír and Kypr, Jaroslav}, article_location = {USA}, article_number = {4}, keywords = {DNA; A-type double helix; B-type deoxyribose pucker; buckled CG step; minor group widening}, language = {eng}, issn = {0022-2836}, journal = {Journal of Molecular Biology}, title = {An A-type Double Helix of DNA Having B-type Puckering of the Deoxyribose Rings}, volume = {297}, year = {2000} }
TY - JOUR ID - 314191 AU - Trantírek, Lukáš - Štefl, Richard - Vorlíčková, Michalea - Koča, Jaroslav - Sklenář, Vladimír - Kypr, Jaroslav PY - 2000 TI - An A-type Double Helix of DNA Having B-type Puckering of the Deoxyribose Rings JF - Journal of Molecular Biology VL - 297 IS - 4 SP - 907 EP - 907 PB - Academic Press SN - 00222836 KW - DNA KW - A-type double helix KW - B-type deoxyribose pucker KW - buckled CG step KW - minor group widening N2 - 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. ER -
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. \textit{Journal of Molecular Biology}. USA: Academic Press, 2000, roč.~297, č.~4, s.~907-922. ISSN~0022-2836.
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