Conformational analysis of a dinucleotide photodimer with the aid of the genetic algorithm

✍ Scribed by Marcel J. J. Blommers; Carlos B. Lucasius; Gerrit Kateman; Robert Kaptein

• Publisher: Wiley (John Wiley & Sons)
• Year: 1992
• Tongue: English
• Weight: 593 KB
• Volume: 32
• Category: Article
• ISSN: 0006-3525
• DOI: 10.1002/bip.360320107

✦ Synopsis

SYNOPSIS

The solution structure of the photodimer cis,syn-dUp [ ] d T is derived with the aid of the genetic algorithm. The conformational space available for the molecule is sampled efficiently using the computer program DENISE and tested against a set of constraints available from nmr experiments. The dominant conformation in solution found with this approach can be described by the following combinations of sugar-phosphate backbone torsion angles: c( t ) , <( t ) , a( +) , /3( -ac) , and y( t ) . The conformation of the sugars and glycosidic torsion angles are S type and syn, respectively. The cyclobutane ring and pyrimidines are puckered. In addition, other conformations that exist in equilibrium with the first are found. It is concluded that the cyclobutane-pyrimidine system is rigid, whereas the sugar-phosphate backbone is flexible. The solution structures are compared with the crystal structure of the strongly related cyano-ethyl ester of cis,syn-dTp [ ] dT.