Quantitative estimation of the contribution of pyrrolcarboxamide groups of the antibiotic distamycin A into specificity of its binding to DNA AT pairs

Abstract

Interaction of DNA with the analogs of the antibiotic distamycin A having different numbers of pyrrolcarboxamide groups and labeled with dansyl was studied. The binding isoterms of the analogs to synthetic polydeoxyribonucleotides were obtained. Analysis of the experimental data leads to the following conclusions: (1) the free energy of binding of the analogs to poly(dA).poly(dT) depends linearly on the number of amide groups in the molecule of the analog whereas attachment of each pyrrolcarboxamide group produces changes of 2 kcal/mole in the free energy; (2) attachment of a pyrrolcarboxamide unit to the GC pair results in the free energy change of 0.95 kcal/mole; (3) the binding of analogs to poly(dA).poly(dT) is a cooperative process, presumbly, dependent on conformational changes induced by the binding of analogs to DNA.

Sequence-specific recognition of B-DNA by oligo(N-methylpyrrolecarboxamide)s.

“…The general rule of n amides affording binding site sizes of n + 1 base pairs is consistent with the oligopeptides binding in the minor groove of righthanded DNA with the amide NH groups forming bridges be- Sequence Specificity. The literature characterizes netropsin and distamycin as molecules that bind preferably to A Trich regions of DNA (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11). It is known from equilibrium binding studies of distamycin analogues that homopolymer dA-dT sequences are preferred over alternating d(A-T) d(A-T) copolymer sequences (6, 7).…”

“…It is known from equilibrium binding studies of distamycin analogues that homopolymer dA-dT sequences are preferred over alternating d(A-T) d(A-T) copolymer sequences (6, 7). The question arises whether G-C base pairs are permissible in the preferred binding sites of netropsin, distamycin, or higher oligo(N-methylpyrrolecarboxamide) homologs on DNA (6,7,23). P4E binds (5'-3') G-A-A-A-T-T, P5E binds A-G-A-A-A-T-T, and P6E binds T-A-G-A-A-A-T-T on the 381-bp fragment (Fig.…”

“…These di-and tripeptides show a marked preference for DNA rich in adenine (A) and thymine (T) and have binding sites four to six base pairs in size (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11). From a recent x-ray analysis of the complex of netropsin with the B-DNA dodecamer of sequence C-G-C-G-A-A-T-T-C-G-C-G, Dickerson and coworkers provide a molecular basis for the sequence-specific recognition of DNA by netropsin, and by extension, distamycin (12).…”

Sequence-specific double-strand cleavage of DNA by penta-N-methylpyrrolecarboxamide-EDTA X Fe(II).

“…P5E.Fe(II)/dithiothreitol cleaves supercoiled pBR322 DNA (10 ,uM in base pairs) at 2 orders of magnitude lower concentrations than does DE.Fe(II)/dithiothreitol. This higher efficiency presumably results from increased DNA binding affinity and specificity arising from additional hydrogen bonding interactions associated with the pentapeptide P5E.Fe(II) versus the tripeptide DEFe(II) (12)(13)(14)(15).…”

“…The natural product distamycin A is a tripeptide containing three N-methylpyrrolecarboxamides that binds in the minor groove of double-helical DNA with a strong preference for A+T-rich regions (6)(7)(8)(9)(10)(11). The sequence specificity of distamycin binding presumably results from hydrogen bonding between the amide NHs of the antibiotic and the 0-2 of thymine or the N-3 of adenine (12)(13)(14)(15) (4,5). The question arises whether a DNA-binding molecule with increased specific base-pair interactions would efficiently cleave DNA on opposite strands.…”