Stabilities of intrastrand pyrimidine motif DNA and RNA triple helices

Nucleic acid triple helices have provoked interest since their discovery mo re than 40 years ago, but it remains unknown whether such structures occur naturally in cells, To pursue this question, it is important to determine t he stabilities of representative triple helices at physiological temperatur e and pH, Previous investigations have concluded that while both DNA and RN A can participate in the pyrimidine tripler motif under mildly acidic condi tions, these structures are often relatively unstable at neutral pH, We are now exploring the stability of intrastrand DNA and RNA pyrimidine motif tr iplexes at physiological temperature and pH, Duplex and tripler formation w ere monitored by thermal denaturation analysis, circular dichroism spectros copy and gel shift experiments. Short intrastrand triplexes were observed t o form in the pyrimidine motif in both DNA and RNA, In the presence of phys iological concentrations of Mg2+ and at physiological pH, all detected trip lexes were sufficiently stable to persist at physiological temperature. If sequences specifying such intrastrand triplexes are encoded in genomes, the potential exists for the formation of stable structures in RNA or DNA in v ivo.