title: Fluorescence quenching in oligonucleotides containing 7-substituted 7-deazaguanine bases prepared by the nicking enzyme amplification reaction.
abstract: Recently, we reported the use of the Nicking Enzyme Amplification Reaction (NEAR) for the enzymatic synthesis of short oligonucleotides (ONs) containing 5-substituted pyrimidine or 7-substituted 7-deazaadenine nucleotides. Since no oligonucleotide products were visible on agarose gels stained by an intercalating dye (GelRed), we assumed that the method did not work for 7-substituted 7-deazaguanine deoxyribonucleoside triphosphates. We revisited the work and found that the NEAR method works for 7-deazaguanine nucleotides as well but that the resulting modified ONs quench the fluorescence of DNA intercalators, rendering them invisible on gel electrophoresis stained by them. Here, we report on the modified methodology for the NEAR synthesis and analysis of G-modified ONs and on quantification of the fluorescence quenching.
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center , Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic.
authors.forename: Petra
authors.initials: P
authors.lastname: Ménová
authors.forename: Dmytro
authors.initials: D
authors.lastname: Dziuba
authors.forename: Pedro
authors.initials: P
authors.lastname: Güixens-Gallardo
authors.forename: Piotr
authors.initials: P
authors.lastname: Jurkiewicz
authors.forename: Martin
authors.initials: M
authors.lastname: Hof
authors.forename: Michal
authors.initials: M
authors.lastname: Hocek
mesh_terms: D001483:Base Sequence; D005453:Fluorescence; D005456:Fluorescent Dyes / Q000737:chemistry*; D006147:Guanine / Q000031:analogs & derivatives* / Q000138:chemical synthesis / Q000737:chemistry; D009841:Oligonucleotides / Q000138:chemical synthesis / Q000737:chemistry*; D013050:Spectrometry, Fluorescence
chemical_list: D005456:Fluorescent Dyes; D009841:Oligonucleotides; D006147:Guanine; C066856:7-deazaguanine