3qk4
Crystal structure of d(CGCGGGTACCCGCG)2 as A-DNA duplexCrystal structure of d(CGCGGGTACCCGCG)2 as A-DNA duplex
Structural highlights
Publication Abstract from PubMedWe report the 2.6A resolution crystal structure of the tetra-decamer d(CGCGGGTACCCGCG) in the tetragonal space group P4(3). This sequence contains the KpnI restriction site GGTACC in the centre which is flanked by alternating 'CG' sequences, and has a 'TA' step at the centre. These are features could favour the left-handed Z type helix. Despite this, overall the molecule has the A form. This is the first tetra-decamer crystallized in the A-DNA conformation, i.e. more than one full turn of the A helix. The crystallographic asymmetric unit consists of one tetra-decamer duplex. The helical twist and slide, as well as the base pair-base pair stacking interactions show alternations at the alternating pyrimidine-purine and purine-pyrimidine base steps. This variation is reminiscent of the dinucleotide repeat in left-handed Z-DNA helices. The crystal packing is unlike other A-DNA crystal structures, with each helix having a large number of contacts of many different types with symmetry-related neighbours. The structure of a full turn of an A-DNA duplex d(CGCGGGTACCCGCG)(2).,Venkadesh S, Mandal PK, Gautham N Biochem Biophys Res Commun. 2011 Apr 8;407(2):307-12. Epub 2011 Mar 21. PMID:21397589[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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