Flexibility and structural conservation in a c-KIT G-quadruplex.

Dengguo Wei,Jarmila Husby,Stephen Neidle

doi:10.1093/nar/gku1282

Abstract

A quadruplex sequence from the promoter region of the c-KIT gene forms a stable quadruplex, as characterized by crystallographic and NMR methods. Two new crystal structures are reported here, together with molecular dynamics simulation studies on these quadruplex crystal structures and an NMR structure. The new crystal structures, each in a distinct space group and lattice packing arrangement, together with the existing structures, demonstrate that the c-KIT quadruplex fold does not change with differing environments, suggesting that quadruplex topological dynamism is not a general phenomenon. The single and dinucleotide loops in these structures show a high degree of conformational flexibility within the three crystal forms and the NMR ensemble, with no evidence of clustering to particular conformers. This is in accord with the findings of high loop flexibility from the molecular dynamics studies. It is suggested that intramolecular quadruplexes can be grouped into two broad classes (i) those with at least one single-nucleotide loop, often showing singular topologies even though loops are highly flexible, and (ii) with all loops comprising at least two nucleotides, leading to topological dynamism. The loops can have more stable and less dynamic base-stacked secondary structures.

Highlights

Quadruplex DNA and RNA structures are formed from repeats of guanine tracts that are interspersed by mixed sequences (‘loops’)
We further report on a series of molecular dynamics (MD) simulations, on a total of five distinct c-KIT quadruplex starting-points from the two highresolution crystal structures and the nuclear magnetic resonance (NMR) structure
No additional potassium or magnesium ions were observed in the grooves or loops of these quadruplexes. This contrasts with their location in the higher-resolution brominated uridine (BrU) form

Summary

Introduction

Quadruplex DNA and RNA structures are formed from repeats of guanine tracts that are interspersed by mixed sequences (‘loops’). Sequences encoding for quadruplex nucleic acids have been found in a variety of locations in the human [3,4] and other genomes [5], principally in eukaryotic telomeres [6,7], in promoter regions [8,9,10], in untranslated regions especially 5 and 3 -UTRs [11,12] and in a number of breakpoint regions [13,14,15,16]. Even though there is no definitive evidence to date of cause and effect in cells for a particular promoter quadruplex gene target, the attractiveness of the concept has led to its current emphasis as a novel drug discovery strategy

Methods

Results

Conclusion