PNA-Based DNA Nanostructures
Homopyrimidine peptide nucleic acid (hpyPNA) has a unique property to bind to one of two strands of double-stranded DNA (dsDNA) displacing the second DNA strand. The structure formed is known as the P-loop. The displaced dsDNA strand in the P-loop may become accessible for Watson-Crick pairing with a DNA (or PNA) oligomer. This idea has become a starting point for assembly of a series of PNA-based DNA nanostructures. The bis-PNA, which consists of two hpyPNAs connected via a flexible linker, proved to be a very convenient tool for the nanostructure assembly. First, we assembled the PD-loop on dsDNA consisting of two bis-PNAs bound to the same DNA strand and a DNA (or PNA) oligomer bound to the opposite strand (1). Next, we assembled the earring label consisting of a circular oligonucleotide topologically linked to one of two strands of dsDNA (2). Most recently, we have assembled the earring on specially prepared dumbbell DNA. The PNA-based DNA nanostructures are very promising for applications. The PD-loop with a biotinylated oligonucleotide can be used for extremely sequence-specific dsDNA capturing (1). We have demonstrated that the PD-loop serves as an artificial primosome capable of initiating the primer extension reaction on dsDNA. As a result, new techniques can be developed for incorporation of numerous radiolabels into dsDNA and for isothermally sequencing dsDNA. In case of the earring label, the circular oligonucleotide formation has proved to be an extremely sequence-specific process. In addition, the rolling circle amplification of the circular label is possible, which provides with a very sensitive detection method. As a result, the development of new highly specific and sensitive DNA diagnostics have become possible.
1. N.O. Bukanov, V.V. Demidov, P.E. Nielsen and M.D. Frank-Kamenetskii, Proc. Natl. Acad. Sci. 95, 5516 (1998).
Maxim D. Frank-Kamenetskii, Heiko Kuhn and Vadim V. Demidov
Center for Advanced Biotechnology and Department of Biomedical Engineering