The sub-nanomolar binding of DNA-RNA hybrids by the single-chain Fv fragment of antibody S9.6

J Mol Recognit. 2013 Aug;26(8):376-81. doi: 10.1002/jmr.2284.


The monoclonal antibody S9.6 binds DNA-RNA hybrids with high affinity, making it useful in research and diagnostic applications, such as in microarrays and in the detection of R-loops. A single-chain variable fragment (scFv) of S9.6 was produced, and its affinities for various synthetic nucleic acid hybrids were measured by surface plasmon resonance (SPR). S9.6 exhibits dissociation constants of approximately 0.6 nM for DNA-RNA and, surprisingly, 2.7 nM for RNA-RNA hybrids that are AU-rich. The affinity of the S9.6 scFv did not appear to be strongly influenced by various buffer conditions or by ionic strength below 500 mM NaCl. The smallest epitope that was strongly bound by the S9.6 scFv contained six base pairs of DNA-RNA hybrid. Published 2013. This article is a U.S. Government work and is in the public domain in the USA.

Publication types

  • Research Support, N.I.H., Intramural

MeSH terms

  • Amino Acid Sequence
  • Antibodies, Monoclonal / isolation & purification
  • Antibodies, Monoclonal / metabolism*
  • Antibody Affinity
  • Antibody Specificity
  • Buffers
  • Cations, Divalent / chemistry
  • DNA / chemistry
  • DNA / metabolism*
  • Epitopes / chemistry
  • Epitopes / metabolism
  • Hydrogen-Ion Concentration
  • Kinetics
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Nucleic Acid Heteroduplexes / chemistry
  • Nucleic Acid Heteroduplexes / metabolism*
  • Osmolar Concentration
  • RNA / chemistry
  • RNA / metabolism*
  • Single-Chain Antibodies / isolation & purification
  • Single-Chain Antibodies / metabolism*
  • Surface Plasmon Resonance


  • Antibodies, Monoclonal
  • Buffers
  • Cations, Divalent
  • Epitopes
  • Nucleic Acid Heteroduplexes
  • Single-Chain Antibodies
  • RNA
  • DNA