Synthetic oligonucleotides

Manufactured by Biomers

Sourced in Spain

Synthetic oligonucleotides are short, chemically synthesized DNA or RNA molecules. They are used as building blocks for various applications in molecular biology, genetics, and biotechnology.

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Lab products found in correlation

Soda lime glass slides, by Merck Group (2 mentions) Kod xl polymerase, by Merck Group (2 mentions) Natural dntps, by Thermo Fisher Scientific (2 mentions) Powerup sybr green master mix, by Thermo Fisher Scientific (1 mentions) Gelred nucleic acid gel stain, by Biotium (1 mentions)

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Oligonucleotides (13 citations)

4 protocols using synthetic oligonucleotides

Optimized PCR and Microfluidics Setup

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For PCR experiments,
we used KOD XL polymerase purchased from Merck Millipore (Madrid,
Spain), synthetic oligonucleotides obtained from Biomers (Ulm, Germany),
natural dNTPs from ThermoFischer Scientific (Barcelona, Spain), and dA^EFcTP synthesized following
the Sonogashira reaction.^{16 (link)} For qPCR experiments,
we used the PowerUp SYBRGreen master mix from Applied Biosystems.
For agarose gel electrophoresis, we employed certified molecular
biology agarose gel powder from ThemoFischer Scientific (Barcelona,
Spain), GelRed Nucleic Acid Gel Stain from Biotium (Barcelona, Spain),
Tris-borate-EDTA (TBE) buffer prepared in house (10.8 g of TRIS-base,
5.5 g of boric acid, and 4 mL of ETDA 0.5 M per liter of solution),
and the DNA gene ruler low range DNA Ladder from Thermo Scientific.
To fabricate the electrode array and microfluidics, we used soda-lime
glass slides from Sigma-Aldrich (Spain), three-millimeter thick polymethylmethacrylate
(PMMA) from La Indústria de la Goma (Tarragona, Spain), and
double-sided adhesive gasket ARSeal 90880 from Adhesive Research (Ireland).
All other chemicals were obtained from Sigma-Aldrich S.A. (Barcelona,
Spain) and used as received.
We used DNA free water provided
by Fisher Bioreagents to prepare
PCR solutions and high purity deionized water (18 MΩ) produced
with a Milli-Q RG system (Millipore Ibérica, Spain) for all
other solutions.

Magriñá I., Jauset-Rubio M., Ortiz M., Tomaso H., Simonova A., Hocek M, & O’Sullivan C.K. (2019). Duplex Electrochemical DNA Sensor to Detect Bacillus anthracis CAP and PAG DNA Targets Based on the Incorporation of Tailed Primers and Ferrocene-Labeled dATP. ACS Omega, 4(26), 21900-21908.

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Synthesis and Characterization of Oligonucleotides

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All synthetic oligonucleotides have been purchased by Biomers (Germany), purified employing standard HPLC protocols and checked for their integrity by MALDI mass spectrometry. In particular, the following DNA sequences have been used for the experiments: two different truncations of human telomeric DNA sequence, namely 5′-TAGGGTTAGGGTTAGGGTTAGGG-3′ (tel23) and 5′-TTAGGGTTAGGGTTAGGGTTAGGGTT-3′ (tel26); two sequences from the promoter region of the c-kit oncogene, namely 5′-AGGGAGGGCGCTGGGAGGAGGG-3′ (ckit1) and 5′-CGGGCGGGCGCGAGGGAGGGG-3′ (ckit2); the self-complementary duplex-forming Dickerson dodecamer 5′-CGCGAATTCGCG-3′ (ds12).

Amato J., Iaccarino N., Pagano B., Morigi R., Locatelli A., Leoni A., Rambaldi M., Zizza P., Biroccio A., Novellino E, & Randazzo A. (2014). Bis-indole derivatives with antitumor activity turn out to be specific ligands of human telomeric G-quadruplex. Frontiers in Chemistry, 2, 54.

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Routine DNA Manipulation Techniques

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DNA manipulations (enzyme digestions, PCR, and electrophoresis) were done following standard methods according to (Sambrook et al., 1989 ). Most of the enzymes were from Promega or Sigma. Synthetic oligonucleotides were from Biomers.

Ramírez M., Velázquez R., Maqueda M., López-Piñeiro A, & Ribas J.C. (2015). A new wine Torulaspora delbrueckii killer strain with broad antifungal activity and its toxin-encoding double-stranded RNA virus. Frontiers in Microbiology, 6, 983.

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Electrochemical Detection of Toxic Dinoflagellate

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KOD XL polymerase was purchased
from Merck Millipore (Madrid, Spain), synthetic oligonucleotides were
obtained from Biomers (Ulm, Germany) (Table 1), natural dNTPs were purchased from Thermo
Fisher Scientific (Barcelona, Spain), and DNA free water was provided
by Fisher Bioreagents. dA^EFcTP was synthesized and characterized
following the Sonogashira reaction, as previously described.^{13 (link)}Electrode
arrays were fabricated using soda-lime glass slides from
Sigma-Aldrich (Spain), 3 mm thick poly(methylmethacrylate) (PMMA)
from La Indústria de la Goma (Tarragona, Spain), and a double-adhesive
gasket ARSeal 90880 from Adhesive Research (Ireland).
All other
reagents were obtained from Sigma-Aldrich S.A. (Barcelona,
Spain) and used as received. High-purity deionized water (18 MΩ
cm^–1) produced with a Milli-Q RG system (Millipore
Ibérica, Spain) was used throughout. As a model system, amplification
and detection of the toxic dinoflagellate K. armiger was used.

Magriñá I., Ortiz M., Simonova A., Hocek M., O’ Sullivan C.K, & Forster R.J. (2021). Ferrocene-Containing DNA Monolayers: Influence of Electrostatics on the Electron Transfer Dynamics. Langmuir, 37(11), 3359-3369.

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