PCR incorporation of dUMPs modified with aromatic hydrocarbon substituents of different hydrophilicities: Synthesis of C5-modified dUTPs and PCR studies using Taq, Tth, Vent (exo-) and Deep Vent (exo-) polymerases

• Published in: Bioorganic chemistry Vol. 99; p. 103829
• Main Authors: Zasedateleva, Olga A., Surzhikov, Sergey A., Shershov, Valeriy E., Miftakhov, Rinat A., Yurasov, Dmitry A., Kuznetsova, Viktoriya E., Chudinov, Alexander V.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.06.2020
• Subjects: Aromatic hydrocarbon groups; C5-modified dUTPs; Deoxyuracil Nucleotides - biosynthesis; Deoxyuracil Nucleotides - chemistry; Deoxyuracil Nucleotides - genetics; DNA-Directed DNA Polymerase - chemistry; DNA-Directed DNA Polymerase - metabolism; Hydrocarbons, Aromatic - chemistry; Hydrocarbons, Aromatic - metabolism; Hydrophilicity; Hydrophobic and Hydrophilic Interactions; Modified DNA; Molecular Structure; PCR incorporation; Polymerase Chain Reaction; C5-modified dUTPs; Modified DNA; Hydrophilicity; PCR incorporation; Aromatic hydrocarbon groups
• ISSN: 0045-2068; 1090-2120
• DOI: 10.1016/j.bioorg.2020.103829

[Display omitted] •Seven dUTPs modified with aromatic hydrocarbon substituents were synthesized.•Modified dUMPs were PCR incorporated using Taq, Tth, Vent (exo-) and Deep Vent (exo-)•The yield of PCR depended on the hydrophilicity of the substituent at C5 of the dUMPs.•PCR-amplified DNA strands contained up to three adjacent modified dUMPs. Deoxyuridine triphosphate derivatives (dUTPs) modified at the C5 position of the pyrimidine ring with various aromatic hydrocarbon substituents of different hydrophilicities have been synthesized. The aromatic hydrocarbon substituents were attached to dUTPs via a CHCHCH2NHCOCH2 linker. The efficiency of the PCR incorporation of modified dUMPs using Taq, Tth, Vent (exo-) and Deep Vent (exo-) polymerases and a model DNA template containing one, two and three adjacent adenine nucleotides at three different sites within the sequence was investigated. For all the polymerases used, the yield of the modified PCR product was significantly increased with increasing hydrophilicity of the aromatic hydrocarbon substituent. In particular, for the above polymerases, the efficiency of the incorporation of dUMPs modified with the most hydrophilic of the studied aromatic hydrocarbon substituents, a 4-hydroxyphenyl residue, was 60–85% of the efficiency of dTMP incorporation. At the same time, the relative efficiencies of the incorporation of dUMPs modified with 2-, 4-methoxyphenyl, phenyl and 4-nitrophenyl substituents ranged from 20 to 50% and were 2–18% for the 1-naphthalene and 4-biphenyl groups, which were the most hydrophobic of the studied aromatic hydrocarbon substituents.