Interactions of DNA with fluorescent dyes: by scanning tunneling microscopy. 1998

M H Zareie, and F I Sahin, and M A Ergün, and C Koçum, and S Menevşe, and A Menevşe, and E Pişkin
Chemical Engineering Department, Hacettepe University, Beytepe, Ankara, Turkey.

Genomic DNA was obtained from peripheral blood samples of healthy volunteers and interacted with two fluorescent dyes (i.e. Hoechst 33,258 and ethidium bromide) in aqueous media. These media containing DNA-dye complexes deposited on the gold coated mica surfaces. Then, STM images were obtained in which the STM was operated in air at atmospheric pressure with a tip-to-substrate bias voltage of 250-1000 mV (sample positive) and the tunneling currents in the range of 10-20 pA by using etched tips of Pt/Ir, in constant current mode. Both dyes from molecular clusters on DNA. While, the Hoechst molecules were observed on the DNA chains at regular distances, the ethidium bromide molecular clusters did not.

UI MeSH Term Description Entries
D007364 Intercalating Agents Agents that are capable of inserting themselves between the successive bases in DNA, thus kinking, uncoiling or otherwise deforming it and therefore preventing its proper functioning. They are used in the study of DNA. Intercalating Agent,Intercalating Ligand,Intercalative Compound,Intercalator,Intercalators,Intercalating Ligands,Intercalative Compounds,Agent, Intercalating,Agents, Intercalating,Compound, Intercalative,Compounds, Intercalative,Ligand, Intercalating,Ligands, Intercalating
D009690 Nucleic Acid Conformation The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape. DNA Conformation,RNA Conformation,Conformation, DNA,Conformation, Nucleic Acid,Conformation, RNA,Conformations, DNA,Conformations, Nucleic Acid,Conformations, RNA,DNA Conformations,Nucleic Acid Conformations,RNA Conformations
D010316 Particle Size Relating to the size of solids. Particle Sizes,Size, Particle,Sizes, Particle
D004247 DNA A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine). DNA, Double-Stranded,Deoxyribonucleic Acid,ds-DNA,DNA, Double Stranded,Double-Stranded DNA,ds DNA
D004996 Ethidium A trypanocidal agent and possible antiviral agent that is widely used in experimental cell biology and biochemistry. Ethidium has several experimentally useful properties including binding to nucleic acids, noncompetitive inhibition of nicotinic acetylcholine receptors, and fluorescence among others. It is most commonly used as the bromide. Ethidium Bromide,Homidium Bromide,Novidium,Bromide, Ethidium,Bromide, Homidium
D005456 Fluorescent Dyes Chemicals that emit light after excitation by light. The wave length of the emitted light is usually longer than that of the incident light. Fluorochromes are substances that cause fluorescence in other substances, i.e., dyes used to mark or label other compounds with fluorescent tags. Flourescent Agent,Fluorescent Dye,Fluorescent Probe,Fluorescent Probes,Fluorochrome,Fluorochromes,Fluorogenic Substrates,Fluorescence Agents,Fluorescent Agents,Fluorogenic Substrate,Agents, Fluorescence,Agents, Fluorescent,Dyes, Fluorescent,Probes, Fluorescent,Substrates, Fluorogenic
D006690 Bisbenzimidazole A benzimidazole antifilarial agent; it is fluorescent when it binds to certain nucleotides in DNA, thus providing a tool for the study of DNA replication; it also interferes with mitosis. Bisbenzimide,4-(5-(4-Methyl-1-piperazinyl)(2,5'-bi-1H-benzimidazol)-2'-yl)phenol, trihydrochloride,Bisbenzimidazole Trihydrochloride,Hoe-33258,Hoechst 33258,NSC-322921,Pibenzimol,Hoe 33258,Hoe33258,NSC 322921,NSC322921
D006801 Humans Members of the species Homo sapiens. Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man
D016252 Microscopy, Scanning Tunneling A type of scanning probe microscopy in which a very sharp conducting needle is swept just a few angstroms above the surface of a sample. The tiny tunneling current that flows between the sample and the needle tip is measured, and from this are produced three-dimensional topographs. Due to the poor electron conductivity of most biological samples, thin metal coatings are deposited on the sample. Scanning Tunneling Microscopy,Scanning Tunnelling Microscopy,Microscopies, Scanning Tunneling,Microscopies, Scanning Tunnelling,Microscopy, Scanning Tunnelling,Scanning Tunneling Microscopies,Scanning Tunnelling Microscopies,Tunneling Microscopies, Scanning,Tunneling Microscopy, Scanning,Tunnelling Microscopies, Scanning,Tunnelling Microscopy, Scanning
D046911 Macromolecular Substances Compounds and molecular complexes that consist of very large numbers of atoms and are generally over 500 kDa in size. In biological systems macromolecular substances usually can be visualized using ELECTRON MICROSCOPY and are distinguished from ORGANELLES by the lack of a membrane structure. Macromolecular Complexes,Macromolecular Compounds,Macromolecular Compounds and Complexes,Complexes, Macromolecular,Compounds, Macromolecular,Substances, Macromolecular

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