Conformational analysis of a dinucleotide photodimer with the aid of the genetic algorithm.
The solution structure of the photodimer cis,syn-dUp[]dT 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: epsilon(t), zeta(t), alpha(+), beta(-ac), and gamma(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.
Blommers
M J
MJ
Bijvoet Center, University of Utrecht, The Netherlands.
Lucasius
C B
CB
Kateman
G
G
Kaptein
R
R
D000465:Algorithms; D003503:Cyclobutanes / Q000737:chemistry; D008433:Mathematics; D008968:Molecular Conformation; D011740:Pyrimidine Dimers / Q000737:chemistry*; D011743:Pyrimidines / Q000737:chemistry; D012984:Software; D013237:Stereoisomerism; D014466:Ultraviolet Rays; D014961:X-Ray Diffraction
D003503:Cyclobutanes; D011740:Pyrimidine Dimers; D011743:Pyrimidines