Literature DB >> 28471357

Crystal structure of d(CCGGGGTACCCCGG)2 at 1.4 Å resolution.

Selvam Karthik1, Arunachalam Thirugnanasambandam1, Pradeep Kumar Mandal2, Namasivayam Gautham1.   

Abstract

The X-ray crystal structure of the DNA tetradecamer sequence d(CCGGGGTACCCCGG)2 is reported at 1.4 Å resolution in the tetragonal space group P41212. The sequence was designed to fold as a four-way junction. However, it forms an A-type double helix in the presence of barium chloride. The metal ion could not be identified in the electron-density map. The crystallographic asymmetric unit consists of one A-type double helix with 12 base pairs per turn, in contrast to 11 base pairs per turn for canonical A-DNA. A large number of solvent molecules have been identified in both the grooves of the duplex and around the backbone phosphate groups.

Entities:  

Keywords:  A-DNA duplex; X-ray crystallography; d(CCGGGGTACCCCGG)2; tetragonal space group

Mesh:

Substances:

Year:  2017        PMID: 28471357      PMCID: PMC5417315          DOI: 10.1107/S2053230X17004770

Source DB:  PubMed          Journal:  Acta Crystallogr F Struct Biol Commun        ISSN: 2053-230X            Impact factor:   1.056


  22 in total

1.  The Holliday junction in an inverted repeat DNA sequence: sequence effects on the structure of four-way junctions.

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