2KQH

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

Replaces:  2KJ2

Summary for 2KQH

• Entry DOI: 10.2210/pdb2kqh/pdb
• Related: 2KQG
• Descriptor: 5'-D(*CP*GP*GP*GP*CP*GP*GP*GP*CP*GP*CP*GP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3', POTASSIUM ION (2 entities in total)
• Functional Keywords: c-kit2, oncogene, promoter, g-quadruplex, dna
• Total number of polymer chains: 1
• Total formula weight: 6729.45

Authors

Hsu, S.-T.D.,Varnai, P.,Bugaut, A.,Reszka, A.P.,Neidle, S.,Balasubramanian, S. (deposition date: 2009-11-05, release date: 2009-11-24, Last modification date: 2024-05-01)

Primary citation

Hsu, S.-T.D.,Varnai, P.,Bugaut, A.,Reszka, A.P.,Neidle, S.,Balasubramanian, S.
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, 2009

PubMed 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.

PubMed: 19705869
DOI: 10.1021/ja904007p

Experimental method

SOLUTION NMR