Ligand-Assisted Complex Formation of Two DNA Hairpin Loops

摘要

Hairpin loops of RNA can hybridize with other single-stranded and hairpin-loop regions of RNA to provide structural features such as pseudoknots and loop-loop interactions for building up higher-order structures. In fact, tertiary structures of tRNA, rRNA, and riboswitches consist of a number of these interactions. A loop-loop kissing interaction at the palindromic 5'-GUGCAC-3' sequence in the purine-rich stem loop of the HIV-1 genome initiates dimerization of the RNA genome, eventually leading to the formation of an extended dimer.Besides the biological significance, loop-loop interactions have been used for the construction of nanoscaled structures of RNA. Despite the many examples of loop-loop interactions in RNA structures, interactions of DNA hairpin loops have attracted only limited attention.Hybridization of DNA fragments with hairpin DNA that leads to hairpin opening has been used as basis for molecular beacons that detect genetic mutations and as fuel to drive DNA-based nanomachines.