Stretch-induced hairpin-coil transitions in designed polynucleotide chains.

The structural property of a poly( dG-dC) or poly( dA-dT) nucleotide is investigated. At low force and room temperatures, the polymer takes on compact hairpin structures. An abrupt transition from hairpin to random coil occurs at certain critical forces, its high cooperativity is related to the unfavorable formation of hairpin and other kinds of looped structures. It is hence necessary to consider the enthalpic effects of single-stranded loops in realistic models of RNA folding. A possible new way to obtain the statistical weights of elementary nucleotide arrangements is by single-macromolecular mechanical measurements on specifically designed polynucleotides.