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Oligonucleotides

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Oligonucleotides are synthetic DNA or RNA molecules that are typically short in length, ranging from a few to a few dozen nucleotides. They are used as essential tools in various molecular biology applications, including gene synthesis, PCR, and genetic analysis.

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Lab products found in correlation

Phosphoramidites, by Glen Research (2 mentions) T4 dna ligase, by Thermo Fisher Scientific (2 mentions) Restriction endonuclease, by Thermo Fisher Scientific (1 mentions) T4 polynucleotide kinase, by Biosan (1 mentions)

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DNA oligonucleotides (2 citations)

2 protocols using oligonucleotides

1

Radiolabeling of oligonucleotides

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Restriction endonucleases and T4 DNA ligase were from Thermo Fisher Scientific (Waltham, MA, USA). Oligonucleotides were synthesized in-house from commercially available phosphoramidites (Glen Research, Sterling, VA, USA). The sequences are listed in Table 2. Oligonucleotides were 5′-labeled using γ[32P]-ATP (ICBFM Laboratory of Biotechnology, Novosibirsk, Russia) and T4 polynucleotide kinase (Biosan, Novosibirsk, Russia). Inhibitors were purchased from Vitas-M Chemical Ltd. (Hong Kong, China).
Diatlova E.A., Mechetin G.V., Yudkina A.V., Zharkov V.D., Torgasheva N.A., Endutkin A.V., Shulenina O.V., Konevega A.L., Gileva I.P., Shchelkunov S.N, & Zharkov D.O. (2023). Correlated Target Search by Vaccinia Virus Uracil–DNA Glycosylase, a DNA Repair Enzyme and a Processivity Factor of Viral Replication Machinery. International Journal of Molecular Sciences, 24(11), 9113.
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2

Purification and Assay of Eco-Fpg DNA Glycosylase

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Eco-Fpg was purified and assayed as described (18 (link),19 (link)) to >98% purity; the fraction of the active enzyme was ∼90%. Site-directed mutants were constructed using the QuikChange kit (Stratagene), purified and analyzed in the same way. Oligonucleotides were synthesized from commercially available phosphoramidites (Glen Research), processed if necessary and purified as described (18 (link)).
Kuznetsov N.A., Bergonzo C., Campbell A.J., Li H., Mechetin G.V., de los Santos C., Grollman A.P., Fedorova O.S., Zharkov D.O, & Simmerling C. (2014). Active destabilization of base pairs by a DNA glycosylase wedge initiates damage recognition. Nucleic Acids Research, 43(1), 272-281.
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