Computational protocol: Site specific replacements of a single loop nucleoside with a dibenzyl linker may switch the activity of TBA from anticoagulant to antiproliferative

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Protocol publication

[…] TBA and TBA-bs were synthesized using standard solid phase DNA chemistry on a controlled pore glass (CPG) support following the β-cyanoethyl phosphoramidite method (,). The coupling time for the modified monomer was prolonged from 2 min to 10 min. The oligomers were detached from the solid support and deprotected by treatment with an aqueous ammonia solution (33%) at 55°C overnight. The combined filtrates and washings were concentrated in vacuo, dissolved in H2O, and purified by HPLC using an anionic exchange column eluted with a linear gradient (from 0% to 100% B in 30 min) of phosphate buffer at pH 7.0 (A: 20 mM NaH2PO4 aqueous solution containing 20% CH3CN; B: 1.0 M NaCl, 20 mM NaH2PO4 aqueous solution containing 20% CH3CN, elution time 18.9 min). The oligomers were successively desalted by molecular exclusion chromatography on Biogel P-2 Fine. The purity (95%) was checked on HPLC using an analytical reverse phase column (Phenomenex, Clarity Oligo-RP, 3 μm, 2 × 10 mm) eluted with a gradient of CH3CN in triethylamine acetate (pH = 7.4, CH3CN from 0% to 100% in 40 min). The concentrations of the samples used in CD and UV experiments were determined by measuring the absorbance at 260 nm at 80°C and using the open access program available at http://basic.northwestern.edu/biotools/OligoCalc.html (). […]

Pipeline specifications

Software tools Biotools, OligoCalc
Applications Population genetic analysis, qPCR
Diseases Hamartoma Syndrome, Multiple
Chemicals Benzene, Nucleosides