Energetics of interaction of oligopeptide (lac 53–57) with DNA base sequences and origin of sequence‐specific recognition

Abstract

Computer model building with a dynamic energy minimization procedure is used here to study the interaction of a pentapeptide sequence from the lac repressor headpiece (lac 53-57) with different base sequences of DNA. The peptide fragment for this purpose was considered in the classical j?-antiparallel as well as the P-associated conformation. The model of its interaction with DNA was optimised for various binding positions and base sequences. Partitioning of energy is analysed for different dielectric constant values and the main contributing factors to sequence-specific binding are discussed. DNA recognition lac 53-5 7 Energy partitioning

Computer simulation of zinc finger motifs from cellular nucleic acid binding protein and their interaction with consensus DNA sequences

“…Theoretical conformational considerations and X-ray crystallographic data [15,16] indicate that small oligonucleotide sequences exist in B-conformation. There were two reasons for choosing single-stranded over double-stranded DNA: (i) known affinity of CNBP an estrogen receptor (hER) for singlestranded DNA [ 1,17]; (ii) topological considerations.…”

Theoretical study on binding of Hoechst 33258 with oligonucleotides

“…We present here energy optimised models for the interaction of the dye with different oligonucleotic sequences. This technique has gained popularity in the recent past for the prediction of geometries of complexes of DNA with oligopeptides and nonintercalating antitumour antibiotics [14][15][16][17][18][19][20][21]. It is therefore desirable to elucidate the stereochemical and energetics details of these models.…”