Optimisation of a peptide library for screening specific RNA ligands by flow-injection NMR.
Flow-injection NMR is a very attractive technique for identifying weak but specific ligand-macromolecule interactions. The low-sensitivity of this method is, however, a major concern which hinders its widespread application to large-scale screening. Focussing on RNA-targeting ligands, we have shown in this report that it is possible to design a peptide library that will simultaneously satisfy a number of physico-chemical restraints and sample the sequence space in an "optimal" fashion. This library, which contains less than 200 peptides, covers most of the allowable tripeptide sequences in a non-redundant fashion. In addition, for almost any allowable tetrapeptide sequences, the library contains a close neighbor that will differ at the most by a single conservative replacement. A subset of this library was actually synthesised and used in a preliminary screen against human tRNA(Lys)(3), the primer of HIV-1 reverse transcriptase.
Tisné
Carine
C
Cristallographie RMN Biologiques, UMR 8015 CNRS, Faculté de Pharmacie, 4 avenue de l'Observatoire, Paris, 75006, France.
Dardel
Frédéric
F
D000465:Algorithms; D000818:Animals; D004353:Drug Evaluation, Preclinical / Q000295:instrumentation / Q000379:methods*; D006801:Humans; D008024:Ligands; D009682:Magnetic Resonance Spectroscopy / Q000379:methods; D019151:Peptide Library; D012313:RNA / Q000037:antagonists & inhibitors*
D008024:Ligands; D019151:Peptide Library; D012313:RNA