Switching DNA-binding specificity by unnatural amino acid substitution

Atanu Maiti, Siddhartha Roy

Research output: Contribution to journalArticle

3 Scopus citations


The specificity of protein-nucleic acid recognition is believed to originate largely from hydrogen bonding between protein polar atoms, primarily side-chain and polar atoms of nucleic acid bases. One way to design new nucleic acid binding proteins of novel specificity is by structure-guided alterations of the hydrogen bonding patterns of a nucleic acid-protein complex. We have used cI repressor of bacteriophage λ as a model system. In the λ-repressor-DNA complex, the ε-NH2 group (hydrogen bond donor) of lysine-4 of λ-repressor forms hydrogen bonds with the amide carbonyl atom of asparagine-55 (acceptor) and the O6 (acceptor) of CG6 of operator site OL1. Substitution of lysine-4 (two donors) by iso-steric S-(2-hydroxyethyl)-cysteine (one donor and one acceptor), by site-directed mutagenesis and chemical modification, leads to switch of binding specificity of λ-repressor from C:G to T:A at position 6 of OL1. This suggests that unnatural amino acid substitutions could be a simple way of generating nucleic acid binding proteins of altered specificity.

Original languageEnglish (US)
Pages (from-to)5896-5903
Number of pages8
JournalNucleic acids research
Issue number18
StatePublished - 2005

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