Chemical synthesis, DNA incorporation and biological study of a new photocleavable 2'-deoxyadenosine mimic.
The phototriggered cleavage of chemical bonds has found numerous applications in biology, particularly in the field of gene sequencing through photoinduced DNA strand scission. However, only a small number of modified nucleosides that are able to cleave DNA at selected positions have been reported in the literature. Herein, we show that a new photoactivable deoxyadenosine analogue, 3-nitro-3-deaza-2'-deoxyadenosine (d(3-NiA)), was able to induce DNA backbone breakage upon irradiation (lambda > 320 nm). The d(3-NiA) nucleoside was chemically incorporated at desired positions into 40-mer oligonucleotides as a phosphoramidite monomer and subsequent hybridization studies confirmed that the resulting modified duplexes display a behaviour that is close to that of the related natural sequence. Enzymatic action of the Klenow fragment exonuclease free revealed the preferential incorporation of dAMP opposite the 3-NiA base. On the other hand, incorporation of the analogous 3-NiA triphosphate to a primer revealed high enzyme efficiency and selectivity for insertion opposite thymine. Furthermore, only the enzymatically synthesized base pair 3-NiA:T was a substrate for further extension by the enzyme. All the hybridization and enzymatic data indicate that this new photoactivable 3-NiA triphosphate can be considered as a photochemically cleavable dATP analogue.
Berthet
Nathalie
N
Département de Chimie Moléculaire-Equipe Ingénierie et Interactions BioMoléculaires, UMR-5250, ICMG FR-2607, CNRS, Université Joseph Fourier, BP53, 38041 Grenoble Cedex 9, France. Nathalie.Berthet@ujf-grenoble.fr
Crey-Desbiolles
Caroline
C
Kotera
Mitsuharu
M
Dumy
Pascal
P
D020029:Base Pairing; D004247:DNA / Q000096:biosynthesis / Q000737:chemistry* / Q000528:radiation effects; D053837:DNA Cleavage; D004261:DNA Replication; D004259:DNA-Directed DNA Polymerase / Q000378:metabolism; D003838:Deoxyadenine Nucleotides / Q000138:chemical synthesis / Q000737:chemistry / Q000378:metabolism; D003839:Deoxyadenosines / Q000737:chemistry* / Q000528:radiation effects; D055668:Photochemical Processes; D013698:Templates, Genetic; D013816:Thermodynamics
C492391:3-nitro-3-deaza-2'-deoxyadenosine; D003838:Deoxyadenine Nucleotides; D003839:Deoxyadenosines; D004247:DNA; D004259:DNA-Directed DNA Polymerase