Computational protocol: Stabilization of G-quadruplex in the BCL2 promoter region in double-stranded DNA by invading short PNAs

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Protocol publication

[…] The DNA oligonucleotides () were synthesized on an ABI394 DNA synthesizer (PE Applied Biosystems, Foster City, CA, USA), and purified by denaturing polyacrylamide gel electrophoresis (PAGE) as described previously (). The absorbance of single-stranded oligonucleotide solutions were measured at 260 nm on an HP 8452A Diode Array Spectrophotometer, and the concentrations were calculated with extinction coefficient calculator software (http://www.basic.northwestern.edu/biotools/oligocalc.html). Several guanosines in BCL2doublePPG (marked as P) were substituted with 8-aza-7-deaza-2′-deoxyguanosine (PPG) (). Partially duplex DNA oligonucleotides were obtained by annealing of complementary strands by slow cooling from 95°C to room temperature. The DNA oligonucleotides were incubated in 20 mM Tris–HCl buffer solution (pH 7.4) at 37°C for 1 h and in the presence or absence of 100 mM NaCl or 100 mM KCl. […]

Pipeline specifications

Software tools Biotools, OligoCalc
Applications Population genetic analysis, qPCR
Organisms Homo sapiens
Chemicals Potassium