Double duplex invasion by peptide nucleic acid: A general principle for sequence-specific targeting of double-stranded DNA

Abstract

Pseudocomplementary PNAs containing diaminopurine⅐thiouracil base pairs have been prepared and are shown to bind with high specificity and efficiency to complementary targets in doublestranded DNA by a mechanism termed ''double duplex invasion'' in which the duplex is unwound and both DNA strands are targeted simultaneously, each by one of the two pseudocomplementary peptide nucleic acids (PNAs). On the basis of our results we predict that (for decameric targets) more than 80% of all sequences can be targeted by straightforward Watson-Crick base pairing by using this approach in its present form. Targeting of pseudocomplementary PNAs to the promoter of the T7 phage RNA polymerase effectively inhibits transcription initiation. These results have important implications in the development of gene therapeutic agents as well as for genetic diagnostic and molecular biology applications.

Metal-containing peptide nucleic acid conjugates

“…It must be noted that modified nucleobases termed A* and T* were used instead of A and T. A* and T* recognize T and A respectively, but A* and T* do not recognize each other (See Figure 11a for a schematic of the base pairing and Figure 11b for the structure of the combinatorial library of cyclen derivatives containing PNA oligomers). 89 Base pairing among PNA mixtures present in the library can thus be suppressed by using A* and T*. These findings are very promising and show that a library of PNAs can be used not only to recognise specific DNA or RNA strands but also to selectively bind a target protein.…”

Combination of a new generation of PNAs with a peptide-based carrier enables efficient targeting of cell cycle progression

“…Strand invasion by PNAs has been demonstrated on supercoiled DNA using mixed sequences 37 and on relaxed dsDNA with polypyrimidine PNAs targeting polypurine motifs. [38][39][40] Moreover, although in vivo, there is little evidence for antigene activity of PNAs, several groups have reported that PNAs can induce downregulation of target mRNA and have suggested either an antigene mechanism by interaction with target DNA, which inhibits the transcription machinery, or that PNA interaction with mRNA targets triggers its degradation through a hypothetical mechanism. [11][12][13][14] However, the PNAs used in these studies do not target homo-purine motifs, and would not be able to form a stable complex with DNA in order to block RNA polymerase.…”

Artificial site-selective DNA cutters to manipulate single-stranded DNA

“…16,56,57 This cutter is composed of two pcPNAs [58][59][60][61] and Ce(IV)/EDTA ( Figure 11). The pcPNAs used are designed to be laterally shifted to one another by five nucleobases.…”

“…The site specificity and target site of this artificial DNA cutter can be almost freely modulated; therefore, this cutter should be useful in developing new biotechnology. For instance, viruses with single-stranded genomes can be manipulated to produce 59 Lohse et al 60 and Komiyama et al 61 ).…”