Synthetic antibodies for specific recognition and crystallization of structured RNA

Proc Natl Acad Sci U S A. 2008 Jan 8;105(1):82-7. doi: 10.1073/pnas.0709082105. Epub 2007 Dec 27.


Antibodies that bind protein antigens are indispensable in biochemical research and modern medicine. However, knowledge of RNA-binding antibodies and their application in the ever-growing RNA field is lacking. Here we have developed a robust approach using a synthetic phage-display library to select specific antigen-binding fragments (Fabs) targeting a large functional RNA. We have solved the crystal structure of the first Fab-RNA complex at 1.95 A. Capability in phasing and crystal contact formation suggests that the Fab provides a potentially valuable crystal chaperone for RNA. The crystal structure reveals that the Fab achieves specific RNA binding on a shallow surface with complementarity-determining region (CDR) sequence diversity, length variability, and main-chain conformational plasticity. The Fab-RNA interface also differs significantly from Fab-protein interfaces in amino acid composition and light-chain participation. These findings yield valuable insights for engineering of Fabs as RNA-binding modules and facilitate further development of Fabs as possible therapeutic drugs and biochemical tools to explore RNA biology.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Antibodies / chemistry
  • Antigens / chemistry
  • Base Sequence
  • Biochemistry / methods*
  • Computational Biology / methods
  • Crystallization
  • Crystallography, X-Ray / methods
  • Kinetics
  • Magnesium / chemistry
  • Molecular Conformation
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Peptide Library
  • RNA / chemistry*
  • Sequence Homology, Amino Acid
  • Tetrahymena / metabolism


  • Antibodies
  • Antigens
  • Peptide Library
  • RNA
  • Magnesium

Associated data

  • PDB/2R8S