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.
authors.affiliation: Biodesign Institute, Arizona State University, Tempe, Arizona, USA.
authors.forename: Liyun
authors.initials: L
authors.lastname: Lin
authors.forename: Qiang
authors.initials: Q
authors.lastname: Fu
authors.forename: Berea A R
authors.initials: BA
authors.lastname: Williams
authors.forename: Abdelhamid M
authors.initials: AM
authors.lastname: Azzaz
authors.forename: Michael A
authors.initials: MA
authors.lastname: Shogren-Knaak
authors.forename: John C
authors.initials: JC
authors.lastname: Chaput
authors.forename: Stuart
authors.initials: S
authors.lastname: Lindsay
mesh_terms: D000107:Acetylation; D000595:Amino Acid Sequence; D000818:Animals; D052157:Aptamers, Nucleotide / Q000235:genetics / Q000378:metabolism*; D001483:Base Sequence; D002843:Chromatin / Q000737:chemistry / Q000378:metabolism*; D006657:Histones / Q000032:analysis / Q000737:chemistry / Q000378:metabolism; D008024:Ligands; D008324:Mammary Tumor Virus, Mouse / Q000235:genetics; D018625:Microscopy, Atomic Force; D015336:Molecular Probe Techniques; D008969:Molecular Sequence Data; D011485:Protein Binding; D029867:Xenopus Proteins / Q000737:chemistry / Q000378:metabolism; D014982:Xenopus laevis
chemical_list: D052157:Aptamers, Nucleotide; D002843:Chromatin; D006657:Histones; D008024:Ligands; D029867:Xenopus Proteins