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Sequence-dependent B - A transition in DNA evaluated with dimeric and trimeric scalesстатья
Статья опубликована в высокорейтинговом журнале
Информация о цитировании статьи получена из
Web of Science
Статья опубликована в журнале из списка Web of Science и/или Scopus
Дата последнего поиска статьи во внешних источниках: 24 октября 2018 г.
- Авторы: Tolstorukov M.Y., Ivanov V.I., Malenkov G.G., Jernigan R.L., Zhurkin V.B.
- Журнал: Biophysical Journal
- Том: 81
- Номер: 12
- Год издания: 2001
- Издательство: Biophysical Society
- Местоположение издательства: United States
- Первая страница: 3409
- Последняя страница: 3421
- Аннотация: ABSTRACT Experimental data on the sequence-dependent B7A conformational transition in 24 oligo- and polymeric duplexes yield optimal dimeric and trimeric scales for this transition. The 10 sequence dimers and the 32 trimers of the DNA duplex were characterized by the free energy differences between the B and A forms in water solution. In general, the trimeric scale describes the sequence-dependent DNA conformational propensities more accurately than the dimeric scale, which is likely related to the trimeric model accounting for the two interfaces between adjacent base pairs on both sides (rather than only one interface in the dimeric model). The exceptional preference of the B form for the AA:TT dimers and AAN:N_TT trimers is consistent with the cooperative interactions in both grooves. In the minor groove, this is the hydration spine that stabilizes adenine runs in B form. In the major groove, these are hydrophobic interactions between the thymine methyls and the sugar methylene groups from the preceding nucleotides, occurring in B form. This interpretation is in accord with the key role played by hydration in the B7A transition in DNA. Importantly, our trimeric scale is consistent with the relative occurrences of the DNA trimers in A form in protein-DNA cocrystals. Thus, we suggest that the B/A scales developed here can be used for analyzing genome sequences in search for A-philic motifs, putatively operative in the protein-DNA recognition.
- Добавил в систему: Маленков Георгий Георгиевич
Прикрепленные файлы
| № | Имя | Описание | Имя файла | Размер | Добавлен |
|---|---|---|---|---|---|
| 1. | Полный текст | ba_atransition.pdf | 369,2 КБ | 23 февраля 2018 [malenkov] |