Interaction between the Z-Type DNA Duplex and 1,3-Propanediamine: Crystal Structure of d(CACGTG)2 at 1.2 Å Resolution
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- 作者：Narendra Narayana ; N. Shamala ; Krishna N. Ganesh ; and M. A. Viswamitra
- 刊名：Biochemistry
- 出版年：2006
- 出版时间：January 31, 2006
- 年：2006
- 卷：45
- 期：4
- 页码：1200 - 1211
- 全文大小：664K
- 年卷期：v.45,no.4(January 31, 2006)
- ISSN：1520-4995
文摘
The crystal structure of a hexamer duplex d(CACGTG)2 has been determined and refined toan R-factor of 18.3% using X-ray data up to 1.2 Å resolution. The sequence crystallizes as a left-handedZ-form double helix with Watson-Crick base pairing. There is one hexamer duplex, a spermine molecule,71 water molecules, and an unexpected diamine (Z-5, 1,3-propanediamine, C3H10N2) in the asymmetricunit. This is the high-resolution non-disordered structure of a Z-DNA hexamer containing two AT basepairs in the interior of a duplex with no modifications such as bromination or methylation on cytosinebases. This structure does not possess multivalent cations such as cobalt hexaammine that are known tostabilize Z-DNA. The overall duplex structure and its crystal interactions are similar to those of the pure-spermine form of the d(CGCGCG)2 structure. The spine of hydration in the minor groove is intact exceptin the vicinity of the T5A8 base pair. The binding of the Z-5 molecule in the minor grove of thed(CACGTG)2 duplex appears to have a profound effect in conferring stability to a Z-DNA conformationvia electrostatic complementarity and hydrogen bonding interactions. The successive base stacking geometryin d(CACGTG)2 is similar to the corresponding steps in d(CG)3. These results suggest that specificpolyamines such as Z-5 could serve as powerful inducers of Z-type conformation in unmodified DNAsequences with AT base pairs. This structure provides a molecular basis for stabilizing AT base pairsincorporated into an alternating d(CG) sequence.