Formation and Characterization of PNA-Containing Heteroquadruplexes

The guanine quadruplex is a secondary structure formed by DNA and RNA that has been implicated in regulation of gene expression and maintenance of genome stability. Guanine-rich PNA oligomers can invade DNA or RNA quadruplex targets to form heteroquadruplex structures. Affinities in the low nanomolar range are routinely observed, making PNAs among the tightest binding of all quadruplex-targeted agents. Although inherently more promiscuous than heteroduplex formation based on Watson–Crick pairing, selectivity of heteroquadruplex formation can be improved through rational design of the sequence and backbone structure of the PNA. This chapter presents design rules and methods for characterizing PNA–DNA/RNA heteroquadruplexes.