TY - JOUR
T1 - Molecular mechanics of the interactions of spermine with DNA
T2 - DNA bending as a result of ligand binding
AU - Feuerstein, Burt G.
AU - Pattabiraman, Nagarajan
AU - Marton, Laurence J.
N1 - Funding Information:
We thank Robert Langridge for the use of the facilities of the Computer Graphics Laboratory and the Program MIDAS, Peter Kollman for use of the program AMBER and for his comments on the manuscipt, and Hirak S. Basu and Neil Buckley for comments on the manuscript. Supported in part by NTH Grants CA-41757 (B.G.F.), National Cooperative Drug Discovery Group Grant CA-37606 (L.J.M.), and Program Project Grant CA-13525 (L.J.M.). The Computer Graphics Laboratory is supported in part by NIH Grant RR-1081.
PY - 1990/3/11
Y1 - 1990/3/11
N2 - We used energy minimization of a molecular mechanical force field to evaluate spermine interactions with B-form DNA oligomers with either alternating purine/pyrimidine or homopolymeric sequences. Four different positions for spermine docking-within, along, and bridging the minor groove and bridging the major groove-were assessed for each sequence. Interaction at the major groove of alternating purine/pyrimidine sequences appears to be the most favorable of all models assessed, and are associated with significant bending of DNA. Interactions at the major groove of homopolymers were less favorable than those of heteropolymers and showed little or no bending. Interactions with the minor groove were most favorable for spermine positioned near the base of the groove, and became less favorable as spermine was moved toward the top of the groove. Association along the phosphate backbone alone was the least favorable of the interactions.
AB - We used energy minimization of a molecular mechanical force field to evaluate spermine interactions with B-form DNA oligomers with either alternating purine/pyrimidine or homopolymeric sequences. Four different positions for spermine docking-within, along, and bridging the minor groove and bridging the major groove-were assessed for each sequence. Interaction at the major groove of alternating purine/pyrimidine sequences appears to be the most favorable of all models assessed, and are associated with significant bending of DNA. Interactions at the major groove of homopolymers were less favorable than those of heteropolymers and showed little or no bending. Interactions with the minor groove were most favorable for spermine positioned near the base of the groove, and became less favorable as spermine was moved toward the top of the groove. Association along the phosphate backbone alone was the least favorable of the interactions.
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U2 - 10.1093/nar/18.5.1271
DO - 10.1093/nar/18.5.1271
M3 - Article
C2 - 2320418
AN - SCOPUS:0025253542
SN - 0305-1048
VL - 18
SP - 1271
EP - 1282
JO - Nucleic acids research
JF - Nucleic acids research
IS - 5
ER -