We report a direct technique for determining the binding sites of small molecules on naturally occurring heterogeneous DNA. Methidiumpropyl-EDTA.Fe(II) [MPE.Fe(II) cleaves double helical DNA with low sequence specificity. Using a combination of MPE.Fe(II) cleavage of drug-protected DNA fragments and Maxam-Gilbert gel methods of sequence analysis, we have determined the preferred binding sites o...

A redox active and electrochemiluminescent (ECL) threading bis-intercalator, consisting of two N,N'-bis(3-propyl-imidazole)-1,4,5,8-naphthalene diimides (PIND) linked by a Ru(dmbpy)2(2+) (dmbpy = 4,4'-dimethyl-2,2'-bipyridine) complex (PIND-Ru-PIND), was synthesized for the first time. Its optical, electrochemical, and ECL properties were studied. UV-vis spectrophotometric measurements indicate...

Nanoelectrode ensembles (NEEs) have been fabricated by the electrodeposition of Au nanoparticles (AuNPs) on single-layer graphene oxide (GO) sheets coated on a glassy carbon electrode (GCE). The fabricated NEEs show a typical sigmoidal shaped voltammetric profile, arising from the low coverage density of AuNPs on GCE and large distance among them, which can be easily controlled by varying the e...

We compare two techniques which enable selective, nucleotide-specific covalent modification of human genomic DNA, as assayed by quantitative ligation- mediated PCR. In the first, a purine motif triplex-forming oligonucleotide with a terminally appended chlorambucil was shown to label a target guanine residue adjacent to its binding site in 80% efficiency at 0.5 microM. Efficiency was higher in ...

We studied fluorescence resonance energy transfer between donors and acceptors bound to double-helical DNA. The donor Hoechst 33258 binds to the minor groove of DNA and the acceptor propidium iodide (PI) is an intercalator. The time-resolved donor decays were measured in the frequency domain. The donor decays were consistent with a random 1-dimensional distribution of acceptors. The decays were...

Structural and functional properties of double stranded deoxyribonucleic acid (dsDNA) are investigated by atomic force microscopy (AFM) on a single molecule level. Here, we characterize different linear and circular DNA systems in terms of their geometry and topology, and visualize enzyme binding of restriction endonuclease Hae III to DNA. Manipulation of single DNA molecules is demonstrated by...

We have investigated a rapidly reversible hydrophobization of therapeutic agents for improving first-pass uptake in locoregional drug therapy. This approach involves the attachment of a hydrophobic moiety to the drug by highly labile chemical linkages that rapidly hydrolyze upon injection. Hydrophobization drastically enhances cell-membrane association of the prodrug and, consequently, drug upt...

A complete characterization of DNA binding agents requires that their mode of binding to DNA be established. In the absence of high resolution structural data, the mode of binding is, of necessity, usually inferred indirectly from various solution studies. The purpose of this study is to show that only certain methods can be used reliably to infer the DNA binding mode. Comparative fluorescence ...