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The Crystal Structure of d(CCCCGGGG): A New A-Form Variant with an Extended Backbone Conformation

1987; Taylor & Francis; Volume: 5; Issue: 2 Linguagem: Inglês

10.1080/07391102.1987.10506390

1538-0254

Tali E. Haran, Zippora Shakked, A. H.-J. Wang, Alexander Rich,

Bacterial Genetics and Biotechnology

Abstract The crystal structure of d(CCCCGGGG) has been determined at a resolution of 2.25Å. The oligomers crystallize as A-DNA duplexes occupying crystallographic two-fold axes. The backbone conformation is, in general, similar to that observed in previously reported crystal structures of A-DNA fragments, except for the central linkage, where it adopts an extended structure resulting from all trans conformation at the P-05′-C5′-C4′ bonds. This type of conformation facilitates interstrand stacking between the guanines at the C-G site. The local helix twist at this step is very small (25°) compared to an overall average of 33.5°. The unique structure of the C-G base-pair step, namely the extended backbone and the distinct stacking geometry, may be an important feature in the recognition mechanism between double- stranded DNA molecules and restriction endonucleases such as Msp I, which cuts the sequence CCGG very specifically with a rate unaffected by neighboring base pairs.