Protected 5-(hydroxymethyl)uracil nucleotides bearing visible-light photocleavable groups as building blocks for polymerase synthesis of photocaged DNA

Nucleosides, nucleotides and 2′-deoxyribonucleoside triphosphates (dNTPs) containing 5-(hydroxymethyl)uracil protected with photocleavable groups (2-nitrobenzyl-, 6-nitropiperonyl or 9-anthrylmethyl) were prepared and tested as building blocks for the polymerase synthesis of photocaged oligonucleoti...

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Bibliographic Details
Published in:Organic & biomolecular chemistry 2018-02, Vol.16 (9), p.1527-1535
Main Authors: Bohá ová, So a, Ludvíková, Lucie, Poštová Slav tínská, Lenka, Vaníková, Zuzana, Klán, Petr, Hocek, Michal
Format: Article
Language:English
Subjects:
Buildings
Chemical synthesis
Deoxyribonucleic acid
DNA
DNA - biosynthesis
DNA - chemistry
DNA polymerase
DNA probes
DNA-directed DNA polymerase
DNA-Directed DNA Polymerase - metabolism
Irradiation
Light
Models, Molecular
Nucleic Acid Conformation
Nucleosides
Nucleotide sequence
Nucleotides
Nucleotides - chemistry
Oligonucleotides
Pentoxyl - analogs & derivatives
Pentoxyl - chemistry
Photochemical Processes
Substrates
Ultraviolet radiation
Uracil
Wavelengths
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Summary:Nucleosides, nucleotides and 2′-deoxyribonucleoside triphosphates (dNTPs) containing 5-(hydroxymethyl)uracil protected with photocleavable groups (2-nitrobenzyl-, 6-nitropiperonyl or 9-anthrylmethyl) were prepared and tested as building blocks for the polymerase synthesis of photocaged oligonucleotides and DNA. Photodeprotection (photorelease) reactions were studied in detail on model nucleoside monophosphates and their photoreaction quantum yields were determined. Photocaged dNTPs were then tested and used as substrates for DNA polymerases in primer extension or PCR. DNA probes containing photocaged or free 5-hydroxymethylU in the recognition sequence of restriction endonucleases were prepared and used for the study of photorelease of caged DNA by UV or visible light at different wavelengths. The nitropiperonyl-protected nucleotide was found to be a superior building block because the corresponding dNTP is a good substrate for DNA polymerases, and the protecting group is efficiently cleavable by irradiation by UV or visible light (up to 425 nm). Protected 5-(hydroxymethyl)uracil nucleotides bearing photocleavable groups as building blocks for polymerase synthesis of photocaged DNA.
ISSN:1477-0520
1477-0539
DOI:10.1039/c8ob00160j