PDBsum entry 2kqh

DNA

PDB id: 2kqh

Contents

DNA/RNA

Metals

__K ×2

PDB id:

2kqh

Name:

DNA

Title:

A g-rich sequence within thE C-kit oncogene promoter forms a parallel g-quadruplex having asymmetric g-tetrad dynamics

Structure:

5'-d( Cp Gp Gp Gp Cp Gp Gp Gp Cp Gp Cp Gp Ap Gp Gp Gp Ap Gp Gp Gp T)-3'. Chain: a. Engineered: yes

Source:

Synthetic: yes

NMR struc:

10 models

Authors:

S.-T.D.Hsu,P.Varnai,A.Bugaut,A.P.Reszka,S.Neidle,S.Balasubramanian

Key ref:

S.T.Hsu et al. (2009). A G-rich sequence within the c-kit oncogene promoter forms a parallel G-quadruplex having asymmetric G-tetrad dynamics. J Am Chem Soc, 131, 13399-13409. PubMed id: 19705869

Date:

05-Nov-09 Release date: 24-Nov-09

Supersedes:

2kj2

DNA/RNA chain

C-G-G-G-C-G-G-G-C-G-C-G-A-G-G-G-A-G-G-G-T 21 bases

J Am Chem Soc 131:13399-13409 (2009)

PubMed id: 19705869

A G-rich sequence within the c-kit oncogene promoter forms a parallel G-quadruplex having asymmetric G-tetrad dynamics.

S.T.Hsu, P.Varnai, A.Bugaut, A.P.Reszka, S.Neidle, S.Balasubramanian.

ABSTRACT

Guanine-rich DNA sequences with the ability to form quadruplex structures are enriched in the promoter regions of protein-coding genes, particularly those of proto-oncogenes. G-quadruplexes are structurally polymorphic and their folding topologies can depend on the sample conditions. We report here on a structural study using solution state NMR spectroscopy of a second G-quadruplex-forming motif (c-kit2) that has been recently identified in the promoter region of the c-kit oncogene. In the presence of potassium ions, c-kit2 exists as an ensemble of structures that share the same parallel-stranded propeller-type conformations. Subtle differences in structural dynamics have been identified using hydrogen-deuterium exchange experiments by NMR spectroscopy, suggesting the coexistence of at least two structurally similar but dynamically distinct substates, which undergo slow interconversion on the NMR timescale.