The Molecular Basis for Pyrimidine-Selective DNA Binding:  Analysis of Calicheamicin Oligosaccharide Derivatives by Capillary Electrophoresis

Abstract

Synthetic derivatives of the calicheamicin oligosaccharide were designed to probe the molecular basis for pyrimidine recognition. Binding affinities of the oligosaccharide derivatives for a range of DNA sequences were determined using capillary electrophoresis. The results show that having an iodo-substituted C-ring is neither necessary nor sufficient for pyrimidine-selective binding. Pyrimidine-selective binding depends on maintaining the overall shape and rigidity of the calicheamicin oligosaccharide. These experiments support the proposal that the novel pyrimidine selectivity of calicheamicin is the result of a shape-dependent inducedfit interaction with DNA sequences.

Interaction between netropsin and double-stranded DNA in capillary zone electrophoresis and affinity capillary electrophoresis

“…K was 4 21 calculated to be (4.7560.30)?10 M . The results of K in CZE and ACE were a little smaller than the value obtained by Biswas et al using CZE [19]. The buffer used in our work and theirs.…”

“…concerning the research of DNA-drug interactions Capillary electrophoresis (CE) has become a and even quantitative determination of the binding robust separation technique in the past few years constants using CE [17][18][19][20]. Small duplex oligoowing to its several advantages such as short analysis nucleotides can be used as appropriate molecules for time, low sample size requirement, high efficiency the investigation of binding properties.…”

“…The UV dissolved in Tris-acetate buffer (20 mM Tris, 10 electroosmotic flow (EOF) and the adsorption of mM NaCl, the pH was adjusted to 7.2 by acetic acid) DNA to the capillary wall, the capillary was coated at various concentrations. The concentration of netwith polyacrylamide by the following process: ropsin was calculated from the absorbance at 296 nm (a) An untreated capillary was rinsed with the 21 21 with a coefficient of 20 200 M cm [19]. These cycle: 1 mol / l NaOH, water, 1 mol / l HCl, water and netropsin buffers were used as running buffers.…”

Structural and conformational features relevant to the anti‐tumor activity of calicheamicin γ

“…In their initial modeling study, Hawley et al had first suggested a prominent role for the aromatic iodine for DNA binding. 42 These studies revealed that in the iodo-containing aryl rhamnoside part of the oligosaccharide, the ring C iodo-guanine amino interaction is worth $ 0.6 kcal/mol. Li et al using gel cleavage kinetics with calicheamicin observed decreased binding affinity in sequences containing an exocylic guanine amino group on the targeted nucleotide on the AGGA side of the TCCT/AGGA tracts when the iodine was replaced in the order of bromine, chlorine, fluorine, methyl, and hydrogen.…”

Recent advances in the study of biomolecular interactions by capillary electrophoresis

“…CZE was used to evaluate the interactions between calicheamicin and oligonucleotides containing different sequences. It is the first CE study reporting a binder that utilizes a carbohydrate moiety to recognize DNA and a minor groove binder that is selective for pyrimidine sequences such as TCCT, though most of DNA minor groove binders prefer AT-rich regions of DNA [113]. When actinomycin D (Act D) served as ligand in the running buffer, a self-complementary oligomer d(CGTGCACG) showed a migration acceleration due to Act D binding.…”