Biophysical approaches to study DNA base flipping

Abstract

The most dramatic yet localized enzyme-induced conformational deformation of the helical structure of DNA is base flipping, in which a nucleobase is unpaired, removed from the stack and further rotated out to assume a fully extrahelical position. Since its first demonstration in crystal structures of cytosine methyltransferase-DNA complexes numerous studies revealed that base flipping is a fundamental mechanism in DNA modification and repair, mediates sequence-specific recognition by restriction endonucle-ases, and is part of replication, transcription and recombination events. Here we discuss experimental and theoretical approaches used to study DNA base flipping in different systems. © 2009 Springer Netherlands.