Recognition imaging of acetylated chromatin using a DNA aptamer

Liyun Lin, Qiang Fu, Berea A R Williams, Abdelhamid M. Azzaz, Michael A. Shogren-Knaak, John C. Chaput, Stuart Lindsay

Research output: Contribution to journalArticlepeer-review

14 Scopus citations

Abstract

Histone acetylation plays an important role in the regulation of gene expression. A DNA aptamer generated by in vitro selection to be highly specific for histone H4 protein acetylated at lysine 16 was used as a recognition element for atomic force microscopy-based recognition imaging of synthetic nucleosomal arrays with precisely controlled acetylation. The aptamer proved to be reasonably specific at recognizing acetylated histones, with recognition efficiencies of 60% on-target and 12% off-target. Though this selectivity is much poorer than the >2000:1 equilibrium specificity of the aptamer, it is a large improvement on the performance of a ChIP-quality antibody, which is not selective at all in this application, and it should permit high-fidelity recognition with repeated imaging. The ability to image the precise location of posttranslational modifications may permit nanometer-scale investigation of their effect on chromatin structure.

Original languageEnglish (US)
Pages (from-to)1804-1807
Number of pages4
JournalBiophysical journal
Volume97
Issue number6
DOIs
StatePublished - Sep 16 2009

ASJC Scopus subject areas

  • Biophysics

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