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

doi:10.1016/j.bpj.2009.06.045

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

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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 language	English (US)
Pages (from-to)	1804-1807
Number of pages	4
Journal	Biophysical journal
Volume	97
Issue number	6
DOIs	https://doi.org/10.1016/j.bpj.2009.06.045
State	Published - Sep 16 2009

ASJC Scopus subject areas

Biophysics

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title = "Recognition imaging of acetylated chromatin using a DNA aptamer",

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.",

author = "Liyun Lin and Qiang Fu and Williams, {Berea A R} and Azzaz, {Abdelhamid M.} and Shogren-Knaak, {Michael A.} and Chaput, {John C.} and Stuart Lindsay",

note = "Funding Information: This study was supported by grants from the Agilent Foundation to S.M.L., the National Cancer Institutes (R21 CA125510) to J.C.C. and S.M.L., and the National Institutes of Health (GM79663) to M.S.K.",

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AU - Lin, Liyun

AU - Fu, Qiang

AU - Williams, Berea A R

AU - Azzaz, Abdelhamid M.

AU - Shogren-Knaak, Michael A.

AU - Chaput, John C.

AU - Lindsay, Stuart

N1 - Funding Information: This study was supported by grants from the Agilent Foundation to S.M.L., the National Cancer Institutes (R21 CA125510) to J.C.C. and S.M.L., and the National Institutes of Health (GM79663) to M.S.K.

PY - 2009/9/16

Y1 - 2009/9/16

N2 - 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.

AB - 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.

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Recognition imaging of acetylated chromatin using a DNA aptamer

Abstract

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