Resolution and characterization of the structural polymorphism of a single quadruplex-forming sequence

Magdalena M. Dailey, M. Clarke Miller, Paula J. Bates, Andrew N. Lane, John O. Trent

Research output: Contribution to journalArticlepeer-review

109 Scopus citations

Abstract

The remarkable structural polymorphism of quadruplex-forming sequences has been a considerable impediment in the elucidation of quadruplex folds. Sequence modifications have commonly been used to perturb and purportedly select a particular form out of the ensemble of folds for nuclear magnetic resonance (NMR) or X-ray crystallographic analysis. Here we report a simple chromatographic technique that separates the individual folds without need for sequence modification. The sequence d(GGTGGTGGTGGTTGTGGTGGTGGTGG) forms a compact quadruplex according to a variety of common biophysical techniques. However, NMR and chromatography showed that this oligonucleotide produces at least eight monomeric quadruplex species that interconvert very slowly at room temperature. We have used a combination of spectroscopic, hydrodynamic and thermodynamic techniques to evaluate the physicochemical properties of the mixture and the individual species. These species have almost identical thermodynamic, hydrodynamic and electrophoretic properties, but significantly different NMR and circular dichroism (CD) spectra, as well as kinetic stability. These results demonstrate that simple standard low-resolution techniques cannot always be used for quadruplex fold determination or quality control purposes, and that simple thermodynamic analysis does not directly provide interpretable thermodynamic parameters.

Original languageEnglish
Article numbergkq166
Pages (from-to)4877-4888
Number of pages12
JournalNucleic Acids Research
Volume38
Issue number14
DOIs
StatePublished - Mar 25 2010

Bibliographical note

Funding Information:
National Institutes of Health (CA113735-01 to J.O.T.), National Institutes of Health Grant Number P20RR018733 from the National Center for Research Resources, and the Kentucky Challenge for Excellence. Funding for open access charge: National Institutes of Health (CA113735-01), NCI grant.

ASJC Scopus subject areas

  • Genetics

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