Echinomycin is a peptide antibiotic which binds strongly to double-helical DNA up to a limit of approximately one molecule per five base-pairs. There is no detectable interaction with rRNA and only extremely feeble non-specific interaction with poly(rA)-poly(rU). Heat denaturation of DNA greatly decreases the binding, and similarly limited interaction is observed with naturally occurring single...

Aclacinomycin A was observed to effect the thermal denaturation of DNA and to increase Tm. The visible absorption spectrum of the antibiotic showed bathochromic and hypochromic shifts upon reaction with native and heat-denatured DNA. [14C]Aclacinomycin A was demonstrated by equilibrium dialysis to bind to DNA. Native calf thymus DNA appeared to possess one binding site per ca. 6 nucleotides for...

Sequence-specific binding to genomic-size DNA sequences by artificial agents is of major interest for the development of gene-targeting strategies, gene-diagnostic applications, and biotechnical tools. The binding of one such agent, peptide nucleic acid (PNA), to a randomized human genome has been modeled with statistical mass action calculations. With the length of the PNA probe, the average p...

We have purified and characterized a single-stranded DNA binding protein (N4 SSB) induced after coliphage N4 infection. It has a monomeric molecular weight of 31,000 and contains 10 tyrosine and 1-2 tryptophan amino acid residues. Its fluorescence spectrum is dominated by the tyrosine residues, and their fluorescence is quenched when the protein binds single-stranded DNA. Fluorescence quenching...

Permeabilized nuclei from mammalian cells encapsulated within agarose microbeads in an isotonic buffer are active in transcription and replication (Jackson, D. A., and P. R. Cook. 1985. EMBO (Eur. Mol. Biol. Organ.) J. 4:913-918). Their DNA is intact and the nuclei are accessible to macromolecules. Myeloma nuclei prepared in this way were used to probe the extent of DNA negative supercoiling an...

The AraC DNA binding domain is inactive in a monomeric form but can activate transcription from the arabinose operon promoters upon its dimerization. We used this property to identify plasmids encoding peptide additions to the AraC DNA binding domain that could dimerize the domain. We generated a high diversity library of plasmids by inserting 90-base oligonucleotides of random sequence ahead o...

We construct a mathematical model for in vitro molecular selection with amplification. Using DNA-protein binding as the illustrative example, we obtain an expression for the probability that a randomly selected molecule from the final in vitro selection products is a molecule with the highest binding affinity. Experiments of this type have been reported for several examples of DNA binding prote...

A long-lived and sequence-specific ligand-DNA complex would make possible the modulation of biological processes for extended periods. For this purpose, we are investigating a polyintercalation approach to DNA recognition in which flexible chains of aromatic units thread back and forth repeatedly through the double helix. Here we describe the DNA-binding behaviour of a threading tetra-intercala...

YOYO-1 is a fluorescent dye widely used for probing the statistical-mechanical properties of DNA. However, currently contradicting data exist how YOYO-1 binding alters the DNA structure and rigidity. Here, we systematically address this problem using magnetic tweezers. Remarkably, we find that the persistence length of DNA remains constant independent of the amount of bound YOYO-1, which contra...

In the present work, the interaction ofFe3O4@CaAl LDH@ Lamivudine with human serum albumin (HSA) was investigated by applying UV–vis and fluorescence spectra. The nanocomposite was quenching the natural fluorescence of HSA, which was indicated the static quenching mechanism. The consequences demonstrated that this nanocomposite can strongly bind to HSA molecules. According to fluorescence quenc...