Chiral introduction of positive charges to PNA for double-duplex invasion to versatile sequences

Abstract

Invasion of two PNA strands to double-stranded DNA is one of the most promising methods to recognize a predetermined site in double-stranded DNA (PNA = peptide nucleic acid). In order to facilitate this ‘double-duplex invasion’, a new type of PNA was prepared by using chiral PNA monomers in which a nucleobase was bound to the α-nitrogen of N-(2-aminoethyl)-d-lysine. These positively charged monomer units, introduced to defined positions in Nielsen's PNAs (poly[N-(2-aminoethyl)glycine] derivatives), promoted the invasion without impairing mismatch-recognizing activity. When pseudo-complementary nucleobases 2,6-diaminopurine and 2-thiouracil were bound to N-(2-aminoethyl)-d-lysine, the invasion successfully occurred even at highly G–C-rich regions [e.g. (G/C)7(A/T)3 and (G/C)8(A/T)2] which were otherwise hardly targeted. Thus, the scope of sequences available as the target site has been greatly expanded. In contrast with the promotion by the chiral PNA monomers derived from N-(2-aminoethyl)-d-lysine, their l-isomers hardly invaded, showing crucial importance of the d-chirality. The promotion of double-duplex invasion by the chiral (d) PNA monomer units was ascribed to both destabilization of PNA/PNA duplex and stabilization of PNA/DNA duplexes.

Gene Modulation by Peptide Nucleic Acids (PNAs) Targeting microRNAs (miRs)

“…PNAs bearing modified nucleobases able to induce additional interactions providing high improvement in RNA and DNA binding affinities have also been described (Wojciechowski et al, 2009). Combination of modified nucleobases and backbone modification with C2 or C5 modified residues was found to be the best approach in order to achieve strand invasion into mixed DNA sequences (Ishizuka et al, 2008, Chenna et al, 2008, a strategy which could also be very fruitful in challenging double-stranded miRs.…”

PNA zipper as a dimerization tool: Development of a bZip mimic

“…19 The PNA duplex, unless destabilized, hardly opens up to give strand invasion phenomena on DNA, therefore it is expected it will not interfere in the protein/DNA complex formation. 20 We describe the design and the synthesis by chemical ligation of a miniaturized version of the GCN4 protein (PNA zipper-GCN4), where the leucine-zipper was replaced by the PNA zipper, whereas the basic DNA-binding domain was covalently attached to the PNA. We show the ability of the PNA zipper-GCN4 to bind selected DNA duplexes and to fold upon complexation with DNA.…”

Peptide Nucleic Acids (PNA) in Chemical Biology and Drug Discovery

“…This requires that the two (PNA) oligomers are pseudocomplementary, i.e., that they both recognize sequence-complementary DNA, but they do not, or only poorly, recognize each other. One solution to the problem was suggested both in a DNA [75] as well as in a PNA [76] context using the pseudocomplementary diaminopurine -thiouracil (or -thymine) base pair (Fig. 4).…”

“…This system may be used for restriction of large DNA molecules (chromosomes?) [76] using recognition sites of 12 -17 bases that may be unique within a chromosome or even within a genome.…”