Minor Groove Hydration of DNA in Solution: Dependence on Base Composition and Sequence
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- 作者：Haukur Jó ; hannesson and Bertil Halle
- 刊名：Journal of the American Chemical Society
- 出版年：1998
- 出版时间：July 22, 1998
- 年：1998
- 卷：120
- 期：28
- 页码：6859 - 6870
- 全文大小：206K
- 年卷期：v.120,no.28(July 22, 1998)
- ISSN：1520-5126
文摘
The hydration of six B-DNA dodecamers with A-tracts of variable length and sequence has beeninvestigated via the nuclear magnetic relaxation dispersion (NMRD) of the water 2H and 17O resonances. Bysubdividing the aqueous DNA solution into microscopic emulsion droplets, NMRD measurements could beperformed at -20 
C, thereby greatly enhancing the sensitivity of the method. The NMRD profiles show thatall six dodecamers contain long-lived water molecules. These water molecules are displaced by netropsin andmust therefore be located in the minor groove. The number of long-lived water molecules is correlated withthe width of the minor groove as seen in crystal structures. The NMRD data are consistent with a single fileof 3-9 long-lived water molecules located at the base pair steps and extending 1-2 steps on either side of theA-tract. Dodecamers with central A-tracts of sequence A4T4, T4A4, and (AT)4 are found to contain seven ornine long-lived water molecules, challenging the common view that T-A steps widen the minor groove anddisrupt the hydration structure. The long-lived water molecules observed here are highly ordered with anentropy comparable to that of water molecules in ice, but most of them undergo a symmetric flip motionwhile residing in the groove. The mean water residence time is essentially the same, 10-15 ns at -20 C, forall investigated dodecamers, suggesting that water exchange occurs from an open state with a uniformly wideminor groove. From the temperature dependence of the water residence time, an activation enthalpy of 53 kJmol-1 is obtained for this process.
C, thereby greatly enhancing the sensitivity of the method. The NMRD profiles show thatall six dodecamers contain long-lived water molecules. These water molecules are displaced by netropsin andmust therefore be located in the minor groove. The number of long-lived water molecules is correlated withthe width of the minor groove as seen in crystal structures. The NMRD data are consistent with a single fileof 3-9 long-lived water molecules located at the base pair steps and extending 1-2 steps on either side of theA-tract. Dodecamers with central A-tracts of sequence A4T4, T4A4, and (AT)4 are found to contain seven ornine long-lived water molecules, challenging the common view that T-A steps widen the minor groove anddisrupt the hydration structure. The long-lived water molecules observed here are highly ordered with anentropy comparable to that of water molecules in ice, but most of them undergo a symmetric flip motionwhile residing in the groove. The mean water residence time is essentially the same, 10-15 ns at -20 C, forall investigated dodecamers, suggesting that water exchange occurs from an open state with a uniformly wideminor groove. From the temperature dependence of the water residence time, an activation enthalpy of 53 kJmol-1 is obtained for this process.