title: Hybridization properties and enzymatic replication of oligonucleotides containing the photocleavable 7-nitroindole base analog.
abstract: Universal DNA base analogs having photocleavable properties would be of great interest for development of new nucleic acid fragmentation tools. The photocleavable 7-nitroindole 2'-deoxyribonucleoside d(7-Ni) was previously shown to furnish a highly efficient approach to photochemically trigger DNA backbone cleavage at preselected position when inserted in a DNA fragment. In the present report, we examine its potential use as universal DNA nucleoside, by analogy with the 5-nitroindole analog that is generally considered as universal base. The d(7-Ni) phosphoramidite was incorporated into oligonucleotides. Hybridization properties of resulting 11mer duplexes indicated a behavior close to that of the 5-nitroindole analog. Enzymatic recognition by Klenow fragment exonuclease-free using 40mers containing the unnatural bases as templates indicated notably a decrease of the polymerase activity with preferential incorporation of dAMP opposite both the 7-Ni and 5-Ni bases. Incorporation of the d(7-Ni) triphosphate was also studied indicating absence of significant differences between the incorporation kinetics opposite each natural base in the template. All the hybridization and enzymatic data indicate that 7-nitroindole can be considered as a cleavable base analog, although not strictly fulfilling, like the 5-nitro isomer, all properties required for a universal base.
authors.affiliation: LEDSS UMR 5616 CNRS, ICMG FR2607, Université Joseph Fourier BP53, 38041 Grenoble Cédex 9, France.
authors.forename: Caroline
authors.initials: C
authors.lastname: Crey-Desbiolles
authors.forename: Nathalie
authors.initials: N
authors.lastname: Berthet
authors.forename: Mitsuharu
authors.initials: M
authors.lastname: Kotera
authors.forename: Pascal
authors.initials: P
authors.lastname: Dumy
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D004256:DNA Polymerase I / Q000378:metabolism*; D017931:DNA Primers; D004261:DNA Replication; D003853:Deoxyribonucleosides / Q000737:chemistry* / Q000633:toxicity; D003854:Deoxyribonucleotides / Q000138:chemical synthesis / Q000737:chemistry / Q000378:metabolism; D007211:Indoles / Q000138:chemical synthesis / Q000737:chemistry* / Q000378:metabolism / Q000633:toxicity; D008027:Light; D008969:Molecular Sequence Data; D009693:Nucleic Acid Hybridization; D009838:Oligodeoxyribonucleotides / Q000096:biosynthesis* / Q000737:chemistry*; D013698:Templates, Genetic
chemical_list: C114223:5-nitroindole-2'-deoxyribose-5'-triphosphate; C498168:7-nitroindole 2'-deoxyribonucleoside; D017931:DNA Primers; D003853:Deoxyribonucleosides; D003854:Deoxyribonucleotides; D007211:Indoles; D009838:Oligodeoxyribonucleotides; D004256:DNA Polymerase I; C090067:5-nitroindole