Rna and dna oligonucleotides

Manufactured by Merck Group

Sourced in Spain

RNA and DNA oligonucleotides are synthetic, short, single-stranded nucleic acid molecules used in various laboratory applications. They serve as essential tools for genetic research, molecular biology, and diagnostic assays.

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Lab products found in correlation

Electrophoretic mobility shift assay kit, by Thermo Fisher Scientific (1 mentions)

Close spelling variants of this product

Oligonucleotides (237 citations) DNA oligonucleotides (53 citations) RNA oligonucleotides (16 citations)

3 protocols using rna and dna oligonucleotides

Validating microRNA-mRNA Interactions Using EMSA

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The validation of microRNA-mRNA interactions was performed using the Molecular Probes' fluorescence-based Electrophoretic Mobility Shift Assay (EMSA) Kit (Invitrogen, Gaithersburg, MD) according to the manufacturer's protocol. For the binding assays, the following RNA and DNA oligonucleotides (Sigma-Aldrich, Madrid, Spain) were designed and used: miR-142, an RNA sequence corresponding to the mature form of miR-142-5p; Ulk1-UTR, a 23-mer RNA sequence for the 3′UTR corresponding to Ulk1 with the target site for miR-142-5p; anti-miR-142, a modified antisense oligodeoxynucleotide complementary to the sequence of the mature form of miR-142-5p; and anti-miR-142MIS, an antisense oligodeoxynucleotide containing 11 mismatches compared to anti-miR-142. All RNA and DNA oligonucleotides were purchased from Sigma-Aldrich (Madrid, Spain), and their specific sequences are listed in the Table S1. The corresponding RNA or DNA molecules were incubated in binding buffer (750 mM KCl, 0.5 mM dithiothreitol, 0.5 mM EDTA, 50 mM Tris, pH 7.4) for 30 min at 37°C, and the reaction products were then separated on a 10% non-denaturing polyacrylamide gel. After staining the gel with SYBR® Green solution for 20 min in the dark, it was photographed using 300 nm UV transillumination.

Li Z., Lan Y., Zhao K., Lv X., Ding N., Lu H., Zhang J., Yue H., Shi J., Song D., Gao F, & He W. (2017). miR-142-5p Disrupts Neuronal Morphogenesis Underlying Porcine Hemagglutinating Encephalomyelitis Virus Infection by Targeting Ulk1. Frontiers in Cellular and Infection Microbiology, 7, 155.

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Purification and Characterization of Organic Compounds

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Reagents and solvents used were obtained from commercial sources and used without further purification. All organic reactions were monitored with the use of thin layer chromatography (TLC) using aluminum sheets silica gel 60 F254 (Merck). Compounds were purified by flash column chromatography using silica gel with ethyl acetate/petroleum ether mixture as the eluting solvent. All ¹H and ¹³C NMR spectra were obtained at room temperature on 300, 400 (100 MHz, ¹³C) or 500 MHz Bruker spectrometer. The chemical shifts (δ) are shown in parts per million (ppm). The residual solvent peaks were used as references for the ¹H (chloroform-d: 7.26; dimethyl sulfoxide-d₆: 2.50) and ¹³C (chloroform-d: 77.0; dimethyl sulfoxide-d₆: 39.5) NMR spectra. The mass spectra of the compounds were obtained via liquid chromatography-mass spectrometry with electrospray ionization source (LCMS-ESI) and high-resolution mass spectrometry (electron ionization) (HRMS-EI). Reverse-phase high performance liquid chromatography (RP-HPLC) purified RNA and DNA oligonucleotides were purchased from Sigma-Aldrich Singapore.

Patil K.M., Toh D.F., Yuan Z., Meng Z., Shu Z., Zhang H., Ong A.A., Krishna M.S., Lu L., Lu Y, & Chen G. (2018). Incorporating uracil and 5-halouracils into short peptide nucleic acids for enhanced recognition of A–U pairs in dsRNAs. Nucleic Acids Research, 46(15), 7506-7521.

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Synthesis and Purification of Nucleic Acid Substrates

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RNA and DNA oligonucleotides used in this study were purchased from Sigma and Dharmacon. Sequences of oligonucleotides used in this study are as follows (G-tetrads and duplex region underlined). GQ⁴: 5’ UUAGGGGGAAAAAAAAAAAAAAA 3’. GQ^I: 5’ UUAGGGGGAGGGGGAUGGGGGAGGGGGAAAAAAAAAAAAAAA 3’. R16 (top strand): 5’ AGCACCGUAAAGACGC 3’ and R31 (bottom strand with 3’ end overhang): 5’ GCGUCUUUACGGUGCUAAAAAAAAAAAAAAA 3’. The sequence of DNA TRAP used for GQ^I remodeling assays: 5’ TCCCCCATCCCCCTCCCCC 3’. The 5’-end of the RNA (GQ⁴, GQ^I and R16) was radiolabeled using T4 polynucleotide kinase (NEB) followed by purification on denaturing PAGE. The duplex substrate was generated by annealing the radiolabeled top strand (R16) to its corresponding bottom strand (R31) in 10mM MOPS, pH 6.5, 50mM KCl and 1mM EDTA, followed by purification on non-denaturing PAGE. The intermolecular and intramolecular G4 substrates were formed by adding the respective radiolabeled oligos to a buffer containing 10mM MOPS, pH 6.5, 50mM KCl and 1mM EDTA. The solution was heated to 98 °C for 10 min, slow cooled to 0 °C overnight. Following this, the structured substrates were purified on non-denaturing PAGE. The annealed radiolabeled G4 and duplex substrates were gel eluted and stored in a buffer containing 10mM MOPS, pH 7, 50mM KCl and 0.1 mM MgCl_2.

Srinivasan S., Liu Z., Chuenchor W., Xiao T.S, & Jankowsky E. (2020). Function of Auxiliary Domains of the DEAH/RHA Helicase DHX36 in RNA Remodeling. Journal of molecular biology, 432(7), 2217-2231.

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