Identification and suppression of secondary structures formed from deoxy-oligonucleotides during electrophoresis in denaturing polyacrylamide-gels.
Nature and stability of secondary structures formed from DNA-fragments during electrophoresis in urea containing polyacrylamide-gels were investigated. Duplices and especially hairpin loops were found to be surprisingly stable. Polyacrylamide-gels containing high concentrations of formamide effectively melt these structures. Such gels will improve nucleotide sequence analysis in regions of dyad symmetry that often cause 'band compressions' under standard electrophoresis conditions.
D004591:Electrophoresis, Polyacrylamide Gel / Q000379:methods; D005559:Formamides; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009838:Oligodeoxyribonucleotides / Q000032:analysis*; D009841:Oligonucleotides / Q000032:analysis*; D014508:Urea
D005559:Formamides; D009838:Oligodeoxyribonucleotides; D009841:Oligonucleotides; D014508:Urea