PDBsum entry 4zkk

DNA

PDB id: 4zkk

Contents

DNA/RNA

Ligands

_CO ×3

Waters ×26

PDB id:

4zkk

Name:

DNA

Title:

The novel double-fold structure of d(gcatgcatgc)

Structure:

DNA (5'-d( Gp Cp Ap Tp Gp Cp Ap Tp Gp C)-3'). Chain: a. Engineered: yes

Source:

Synthetic: yes. Synthetic construct. Organism_taxid: 32630

Resolution:

1.80Å R-factor: 0.231 R-free: 0.246

Authors:

A.Thirugnanasambandam,S.Karthik,P.K.Mandal,N.Gautham

Key ref:

A.Thirugnanasambandam et al. (2015). The novel double-folded structure of d(GCATGCATGC): a possible model for triplet-repeat sequences. Acta Crystallogr D Biol Crystallogr, 71, 2119-2126. PubMed id: 26457435 DOI: 10.1107/S1399004715013930

Date:

30-Apr-15 Release date: 14-Oct-15

DNA/RNA chain

G-C-A-T-G-C-A-T-G-C 10 bases

DOI no: 10.1107/S1399004715013930

Acta Crystallogr D Biol Crystallogr 71:2119-2126 (2015)

PubMed id: 26457435

The novel double-folded structure of d(GCATGCATGC): a possible model for triplet-repeat sequences.

A.Thirugnanasambandam, S.Karthik, P.K.Mandal, N.Gautham.

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.