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Structure of the Deoxytetranucleotide d-pApTpApT and a Sequence-Dependent Model for Poly(dA-dT)

Viswamitra, MA and Shakked, Zippora and Jones, PG and Sheldrick, GM and Salisbury, SA and Kennard, Olga (1982) Structure of the Deoxytetranucleotide d-pApTpApT and a Sequence-Dependent Model for Poly(dA-dT). In: Biopolymers, 21 (3). pp. 513-533.


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The x-ray structure of the hydrated ammonium salt of the deoxytetranucleotide d-pApTpApT was determined by Patterson and direct methods at a resolution of 1 . The crystal structure contains right-handed double-helical segments formed by complementary Watson-Crick-type hydrogen bonding between the adenine and thymine bases of neighboring molecules. The minihelix contains two base pairs. The chains are antiparallel. The A-T and T-A sequences have different phosphodiester conformations. The deoxyribose-pucker and the sugar-base orientation alternate along the chain depending on the nature of the base ($3^\prime$ -endo for purine and $2^\prime$ -endo for pyrimidine). The extended structure is stabilized by base-base, base-sugar, and hydrogen-bond interactions. The minihelix of two base pairs provides starting coordinates for model-building studies of the dA-dT polymer. A B-DNA-type polymer structure is described, which has sequence-dependent alternations of both the deoxyribose pucker and the phosphate diester bridge conformation. Such sequence-dependent DNA structures, if present locally in regions such as operator sequences, could facilitate sequence-specific interactions. The crystal study also suggests possible geometrical parameters for the replication fork.

Item Type: Journal Article
Publication: Biopolymers
Publisher: John Wiley & Sons, Inc.
Additional Information: The copyright belongs to John Wiley & Sons, Inc.
Department/Centre: Division of Physical & Mathematical Sciences > Physics
Date Deposited: 07 Dec 2005
Last Modified: 19 Sep 2010 04:21
URI: http://eprints.iisc.ac.in/id/eprint/4268

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