Electron Microscopic and Physico-Chemical Studies of DNA Complexes with Synthetic Oligopeptides: Binding Specificity and DNA Compact Structures

It has been shown by the equilibrium dialysis that at a polyU concentration above the "critical" one, the complete polymer saturation with trivaline reaches approximately 0.7 trivaline molecules per one phosphate group. i.e. at these conditions peptide dimer occupies on polyU a site of three bases (phosphates) in length. The trivaline complex with polyU at a concentration lower than the "critical" one does not reveal any noticeable fluorescence, but has rather significant positive linear dichroism at 265 and 330 nm. The trivaline-nucleic acids complex has a significant fluorescence at any dsDNA concentration while with polyU it is only so at a concentration above the "critical" one. Electron microscopy has shown that at a rather high concentration of dsDNA molecules in solution a "biduplex" structure undergoes an additional stage of compaction, during which the extended particles more than 30 nm in diameter are formed.

Section: Dgtv: Dsdna Complexes At the Extremely Low And High Dsdna Cosupporting

confidence: 74%

Section: Dgtv: Dsdna Complexes At the Extremely Low And High Dsdna Comentioning

confidence: 97%

Homology in Trivaline Complex Formation with dsDNA and ssRNA

Streltsov¹,

Semenov

Moroz

1993

“…Previous studies on binding of small ~ structure-forming peptides to DNA show that these peptides usually exist in a disordered conformation in aqueous solution, but assume a ~-like conformation upon binding DNA (20,39,41 ). A similar situation may take place when carboxyterminal residues oflambda cro interact with DNA.…”

Section: Spectra Of Complexes Between Cro Protein and Dna In The Fmentioning

confidence: 95%

Interaction of Lambda cro Repressor with Synthetic Operator 0_R3 Studied by Competition Binding with Minor Groove Binders

Gursky

Surovaya

Kurochkin

et al. 1992

Self Cite

In the present work, we employ a combination of CD spectroscopy and gel retardation technique to characterize thermodynamically the binding of lambda phage cro repressor to a 17 base pair operator OR3. We have found that three minor groove-binding antibiotics, distamycin A, netropsin and sibiromycin, compete effectively with the cro for binding to the operator OR3. Among these antibiotics, sibiromycin binds covalently to DNA in the minor groove at the NH2 of guanine, whereas distamycin A and netropsin interact preferentially with runs of AT base pairs and avoid DNA regions containing guanine bases in the two polynucleotide strands. Only subtle DNA conformation changes are known to take place upon binding of these antibiotics. Both the CD spectral profiles and the results of the gel retardation experiments indicate that distamycin A and netropsin can displace cro repressor from the operator OR3. The binding of cro repressor to the OR3 is accompanied by considerable changes in CD in the far-UV region which appear to be attributed to a DNA-dependent structural transition in the protein. Spectral changes are also induced in the wavelength region of 270-290 nm. The CD spectral profile of the cro-OR3 mixture in the presence of distamycin A can be represented as a sum of the CD spectrum of the repressor-operator complex and spectrum of distamycin-DNA complex at the appropriate molar ratio of the bound antibiotic to the operator DNA (r). When r tends to the saturation level of binding the CD spectrum in the region of 270-360 nm approaches a CD pattern typical of complexes of the antibiotic with the free DNA oligomer. This suggests that simultaneous binding of cro repressor and distamycin A to the same DNA oligomer is not possible and that distamycin A and netropsin can be used to determine the equilibrium affinity constant of cro repressor to the synthetic operator from competition-type experiments. The binding constant of cro repressor to the OR3 is found to be (6 +/- 1).10(6)M-1 at 20 degrees C in 10 mM sodium cacodylate buffer (pH 7.0) in the presence of 0.1 M NH4F.

“…In our previous work (26)(27)(28)(29)(30) we have shown that certain small peptides with inert amino acid side chains (such as trivaline) bind, in a ~-associated form, more tightly to poly(dG)•poly(dC) than to poly(dA)•poly(dT). Attachment of trivaline to the amino terminus of a netropsin analogue alters its binding specificity (30).…”

Section: Niko/aev Et A/mentioning

confidence: 98%

Design of Sequence-Specific DNA Binding Ligands That Use a Two-Stranded Peptide Motif for DNA Sequence Recognition

et al. 1996

Self Cite

The design and DNA binding activity of beta-structure-forming peptides and netropsin-peptide conjugates are reported. It is found that a pair of peptides-S,S'-bis(Lys-Gly-Val-Cys-Val-NH-NH-Dns)-bridged by an S-S bond binds at least 10 times more strongly to poly(dG).poly(dC) than to poly(dA).poly(dT). This peptide can also discriminate between 5'-GpG-3' and 5'-GpC-3' steps in the DNA minor groove. Based on these observations, new synthetic ligands, bis-netropsins, were constructed in which two netropsin-like fragments were attached by means of short linkers to a pair of peptides-Gly-Cys-Gly- or Val-Cys-Val-bridged by S-S bonds. These compounds possess a composite binding specificity: the peptide chains recognize 5'-GpG-3' steps on DNA, whereas the netropsin-like fragments bind preferentially to runs of 4 AT base pairs. Our data indicate that combining the AT-base-pair specific properties of the netropsin-type structure with the 5'-GpG-3'-specific properties of certain oligopeptides offers a new approach to the synthesis of ligands capable of recognizing mixed sequences of AT- and GC-base pairs in the DNA minor groove. These compounds are potential models for DNA-binding domains in proteins which specifically recognize base pair sequences in the minor groove of DNA.