title: Supramolecular self-assembling cyanine as an alternative to ethidium bromide displacement in DNA-drug model interactions during high throughput screening.
abstract: Supramolecular self-assembling cyanine and spermine binding to genomic DNA was a model for DNA-drug interactions during high throughput screening. Spermine competitively inhibited the self-assembly of cyanine upon DNA scaffolds as signaled by decreased fluorescence from the DNA-cyanine J-aggregate. The sequence of DNA exposure to cyanine or spermine was critical in determining the magnitude of inhibition. Methanol potentiated spermine inhibition by >10-fold. The IC(50) and association constant (K(a)) in 16% methanol were 0.35 +/- 0.03 microM and 2.86 x 10(6) M(-1) respectively, relative to 3.97 +/- 0.47 microM and 0.25 x 10(6) M(-1) respectively, in buffer. Increasing concentrations of cyanine overcame spermine inhibition, demonstrating the reversibility of DNA-drug interactions. LambdaDNA interacted similarly with spermine and cyanine, confirming system flexibility. The model drug, dye and methanol effects are discussed in detail. Cyanine might be a safer alternative to the mutagenic ethidium bromide for investigating DNA-drug interactions.
authors.affiliation: Biosensors and Nanomaterials Department, Sandia National Laboratories, Albuquerque, NM, USA. kachyut@sandia.gov
authors.forename: Komandoor E
authors.initials: KE
authors.lastname: Achyuthan
authors.forename: David G
authors.initials: DG
authors.lastname: Whitten
authors.forename: Darren W
authors.initials: DW
authors.lastname: Branch
mesh_terms: D002021:Buffers; D002232:Carbocyanines / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D004269:DNA, Bacterial / Q000737:chemistry; D004353:Drug Evaluation, Preclinical; D004926:Escherichia coli / Q000737:chemistry; D004996:Ethidium / Q000737:chemistry*; D007202:Indicators and Reagents; D007700:Kinetics; D000432:Methanol / Q000737:chemistry; D004364:Pharmaceutical Preparations / Q000737:chemistry*; D011073:Polyamines / Q000737:chemistry; D012997:Solvents; D017550:Spectroscopy, Fourier Transform Infrared; D013096:Spermine / Q000737:chemistry
chemical_list: D002021:Buffers; D002232:Carbocyanines; D004269:DNA, Bacterial; D007202:Indicators and Reagents; D004364:Pharmaceutical Preparations; D011073:Polyamines; D012997:Solvents; D013096:Spermine; D004247:DNA; D004996:Ethidium; D000432:Methanol