[A synthetic zinc chelating peptide competes for DNA binding sites with antibiotics, adsorbed in a minor DNA groove]. / Sinteticheskii tsinkkhelatiruiushchii peptid konkuriruet za sviazyvaiushchie mesta na DNK s antibiotikami, adsorbiruiushchimisia v uzkoi borozdke DNK.

Effects of sibiromicyn, distamicyn A and its analogs on binding to DNA and to poly(dA).poly(dT) are reported for a 23-amino acid synthetic zinc-binding peptide, a part of the DNA-binding domain of the transcriptional activator GAL-4. Circular dichroism and fluorometry have shown that the synthetic peptide and two distamicyn A analogs compete for binding sites on DNA and on poly(dA).poly(dT). Antibiotic sibiromycin which forms a covalent bond with a guanine 2-amino group in the minor DNA groove can displace the peptide from a 19 bp self-complementary oligonucleotide serving as a specific target site for Gal-4 protein. The peptide is shown to bind to a glucosylated phage T2 DNA, but its affinity to T2 DNA is weaker than to calf thymus DNA under the same conditions. A method to estimate binding constant and size of the binding site for the synthetic peptide and poly(dA).poly(dT) is proposed based on the binding isotherms of distamycin analogs in the absence and in the presence of the peptide. Using isotherms of binding to poly(dA).poly(dT) for two distamycin analogs with binding constants differing 60-fold, the binding constant of the peptide in the presence of 0.1 M NaCl is estimated as 1.4.10(7)-1.8.10(7) M-1.

[Design of de novo specific DNA-binding peptides, using the motif beta-chain-turn-beta-chain for recognizing a nucleotide sequence in DNA]. / Konstruirovanie de novo spetsifichnykh DNK-sviazyvaiushchikh peptidov, ispol'zuiushchikh motiv beta-tsep'-povorot-beta-tsep' dlia uznavaniia nukleotidnoi posledovatel'nosti na DNK.

De novo design and synthesis by a solid phase technique of linear and cyclic 26-residues peptides are reported. The peptides use beta-strand-turn-beta -strand motif for sequence recognition on DNA. Amino acid sequences in the two peptides are identical, but the structure of the cyclic peptide is constrained by S-S bridge between two cysteine residues. A 28-residue peptide containing at the N-terminus a copper-chelating peptide Gly-Gly-His is also synthesized which can be used as a potential DNA-cleaving reagent. Binding of these peptides to various natural and synthetic DNAs and DNA fragment with a known base pair sequence has been studied by CD spectroscopy, fluorescence methods and DNAse I footprinting technique. By means of CD spectroscopy it is shown that 26-residue linear and cyclic peptides are partially in disordered and beta-conformations in aqueous solution in absence and in presence of 20% trifluoroethanol (TFE), but assume partially an alpha-helix conformation in the presence of 50% TFE. It is shown that linear and cyclic peptides bind to DNA. The binding approaches saturation level when one peptide molecule is bound approximately per three or four DNA base pairs. We found that antibiotic distamycin A, binding in the minor DNA groove, competes effectively with the 26-residue linear and cyclic peptides for binding to poly(dA).poly (dT). According to the CD spectroscopy data the linear and cyclic peptides undergo conformation changes upon binding to DNA, whereas the DNA structure is not markedly altered. Difference CD spectra obtained by subtracting the spectrum of the free DNA from the spectrum of the peptide-DNA mixture differ from the spectrum of the free peptide. The shapes of difference CD spectra are consistent with a conformation transition from a disordered conformation into a beta-like conformation upon binding of peptide to DNA. DNAase I footprinting diagrams show that there is a specific protection by linear and cyclic peptides of the nucleotide sequences on two ends of operators OR1, OR2 and OR3 and pseudooperators within the cro gene of 434 phage.

[Interaction of a synthetic zinc-binding peptide with DNA]. / Vzaimodeistvie s DNK sinteticheskogo tsinksviazyvaiushchego peptida.

Synthesis, DNA- and zinc ion-binding activities of the synthetic 23-residue peptide, forming a part of the DNA-binding domain of yeast transcription activator GAL-4, are reported. In presence of zinc ions considerable changes in the shapes of the fluorescence and CD spectra of the peptide are observed. It is shown that the peptide forms complexes with zinc ions containing one metal ion per peptide molecule with association constants on the order of (1-2) x 10(6) M-1. Using gel filtration on a TSK-gel column we have shown that in aqueous solution at concentrations of 10(-4)-10(-6) M the peptide exists predominantly in the dimeric form. Dimerization constants were found to be 5 x 10(6) M-1 and 1.7 x 10(7) M-1 in the absence and in the presence of zinc ions, respectively. It is shown that the peptide binds to DNA. The binding approaches saturation when one peptide molecule is bound approximately to five base pairs of DNA. The shapes of the titration curves obtained from binding of the peptide to DNA show that the peptide can bind to DNA both in the monomeric and self-associated forms (dimer or tetramer). Increasing DNA concentration and decreasing the peptide/DNA molar ratio lead to a shift in the equilibria between self-associated peptide species and monomers toward the formation of monomer peptide complexes.