Genome-wide analysis of a G-quadruplex-specific single-chain antibody that regulates gene expression

Nucleic Acids Res. 2009 Nov;37(20):6716-22. doi: 10.1093/nar/gkp740. Epub 2009 Sep 10.


G-quadruplex nucleic acids have been proposed to play a role in a number of fundamental biological processes that include transcription and translation. We have developed a single-chain antibody that is selective for G-quadruplex DNA over double-stranded DNA, and here show that when it is expressed in human cells, it significantly affects the expression of a wide variety of genes, in a manner that correlates with the presence of predicted G-quadruplexes. We observe cases where gene expression is increased or decreased, and that there are apparent interactions with G-quadruplex motifs at the beginning and end of the genes, and on either strand. The outcomes of this genome-wide study demonstrate that G-quadruplex recognition by the antibody has physiological consequences, and provides insights into some of the complexity associated with G-quadruplex-based regulation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Line, Tumor
  • DNA / immunology
  • DNA / metabolism
  • G-Quadruplexes*
  • Gene Expression Regulation*
  • Genome, Human
  • Humans
  • Promoter Regions, Genetic
  • Single-Chain Antibodies / genetics
  • Single-Chain Antibodies / metabolism*
  • Transcription Initiation Site
  • Transcription, Genetic


  • Single-Chain Antibodies
  • DNA