caa a22 4500 477136265 CHVBK 20180405111718.0 cr unu---uuuuu 170330e19970101xx s 000 0 eng 10.1023/A:1018667416967 doi (NATIONALLICENCE)springer-10.1023/A:1018667416967 Application of a genetic algorithm in the conformational analysis of methylene-acetal-linked thymine dimers in DNA: Comparison with distance geometry calculations [Elektronische Daten] [Mischa Beckers, Lutgarde Buydens, Jeroen Pikkemaat, Cornelis Altona] The three-dimensional spatial structure of a methylene-acetal-linked thymine dimer presentin a 10 base-pair (bp) sense-antisense DNA duplex was studied with a geneticalgorithm designed to interpret NOE distance restraints. Trial solutions were represented bytorsion angles. This means that bond angles for the dimer trial structures are kept fixed duringthe genetic algorithm optimization. Bond angle values were extracted from a 10 bpsense-antisense duplex model that was subjected to energy minimization by means ofa modified AMBER force field. A set of 63 proton-proton distance restraints definingthe methylene-acetal-linked thymine dimer was available. The genetic algorithm minimizesthe difference between distances in the trial structures and distance restraints. A largeconformational search space could be covered in the genetic algorithm optimization byallowing a wide range of torsion angles. The genetic algorithm optimization in all cases ledto one family of structures. This family of the methylene-acetal-linked thymine dimer in theduplex differs from the family that was suggested from distance geometry calculations. It isdemonstrated that the bond angle geometry around the methylene-acetal linkage plays animportant role in the optimization. Kluwer Academic Publishers, 1997 Genetic algorithm nationallicence Distance geometry nationallicence Methylene-acetal linkage nationallicence Beckers Mischa Laboratory for Analytical Chemistry, Catholic, University of Nijmegen, Toernooiveld 1, 6525 ED, Nijmegen, The Netherlands aut Buydens Lutgarde Laboratory for Analytical Chemistry, Catholic, University of Nijmegen, Toernooiveld 1, 6525 ED, Nijmegen, The Netherlands aut Pikkemaat Jeroen Leiden Institute of Chemistry, Gorlaeus Laboratories, P.O. Box 9502, 2300 RA, Leiden, The Netherlands aut Altona Cornelis Laboratory for Analytical Chemistry, Catholic, University of Nijmegen, Toernooiveld 1, 6525 ED, Nijmegen, The Netherlands aut Journal of Biomolecular NMR Kluwer Academic Publishers 9/1(1997-01-01), 25-34 0925-2738 9:1<25 1997 9 10858 https://doi.org/10.1023/A:1018667416967 text/html Onlinezugriff via DOI 1 research-article jats NATIONALLICENCE 856 40 https://doi.org/10.1023/A:1018667416967 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Beckers Mischa Laboratory for Analytical Chemistry, Catholic, University of Nijmegen, Toernooiveld 1, 6525 ED, Nijmegen, The Netherlands aut NATIONALLICENCE 700 1- Buydens Lutgarde Laboratory for Analytical Chemistry, Catholic, University of Nijmegen, Toernooiveld 1, 6525 ED, Nijmegen, The Netherlands aut NATIONALLICENCE 700 1- Pikkemaat Jeroen Leiden Institute of Chemistry, Gorlaeus Laboratories, P.O. Box 9502, 2300 RA, Leiden, The Netherlands aut NATIONALLICENCE 700 1- Altona Cornelis Laboratory for Analytical Chemistry, Catholic, University of Nijmegen, Toernooiveld 1, 6525 ED, Nijmegen, The Netherlands aut NATIONALLICENCE 773 0- Journal of Biomolecular NMR Kluwer Academic Publishers 9/1(1997-01-01), 25-34 0925-2738 9:1<25 1997 9 10858 Metadata rights reserved Springer special CC-BY-NC licence nationallicence BK010053 XK010053 XK010000 NATIONALLICENCE NATIONALLICENCE NL-springer