4ZKK

The novel double-fold structure of d(GCATGCATGC)

Summary for 4ZKK

• Entry DOI: 10.2210/pdb4zkk/pdb
• Descriptor: DNA (5'-D(*GP*CP*AP*TP*GP*CP*AP*TP*GP*C)-3'), COBALT (II) ION (3 entities in total)
• Functional Keywords: folded, minor-groove tetrad, bi-loop, triplet, dna
• Biological source: synthetic construct
• Total number of polymer chains: 1
• Total formula weight: 3221.80

Authors

Thirugnanasambandam, A.,Karthik, S.,Mandal, P.K.,Gautham, N. (deposition date: 2015-04-30, release date: 2015-10-14, Last modification date: 2024-03-20)

Primary citation

Thirugnanasambandam, A.,Karthik, S.,Mandal, P.K.,Gautham, N.
The novel double-folded structure of d(GCATGCATGC): a possible model for triplet-repeat sequences
Acta Crystallogr.,Sect.D, 71:2119-2126, 2015

PubMed Abstract: The structure of the decadeoxyribonucleotide d(GCATGCATGC) is presented at a resolution of 1.8 Å. The decamer adopts a novel double-folded structure in which the direction of progression of the backbone changes at the two thymine residues. Intra-strand stacking interactions (including an interaction between the endocylic O atom of a ribose moiety and the adjacent purine base), hydrogen bonds and cobalt-ion interactions stabilize the double-folded structure of the single strand. Two such double-folded strands come together in the crystal to form a dimer. Inter-strand Watson-Crick hydrogen bonds form four base pairs. This portion of the decamer structure is similar to that observed in other previously reported oligonucleotide structures and has been dubbed a `bi-loop'. Both the double-folded single-strand structure, as well as the dimeric bi-loop structure, serve as starting points to construct models for triplet-repeat DNA sequences, which have been implicated in many human diseases.

PubMed: 26457435
DOI: 10.1107/S1399004715013930

Experimental method

X-RAY DIFFRACTION (1.801 Å)