Developed in the early 1990's, PNA has emerged as a promising class of nucleic acid mimic because of its strong binding affinity and sequence selectivity towards DNA and RNA, and resistance to enzymatic degradation by proteases and nucleases; however, the main drawbacks, as compared to other classes of oligonucleotides, are water solubility and biocompatibility. Herein we show that installation of a relatively small, hydrophilic (R)-diethylene glycol (`miniPEG') unit at the γ-backbone transforms a randomly-folded PNA into a right-handed helix. Synthesis of optically pure R-MPγPNA monomers is described, which can be accomplished in a few simple steps from a commercially available and relatively cheap Boc-L-serine. Once synthesized, R-MPγPNA oligomers are preorganized into a right-handed helix and hybridize to DNA and RNA with greater affinity and sequence selectivity, and are more water soluble and less aggregating than the parental PNA oligomers. The results presented herein have important implications for the future design and application of PNA in biology, biotechnology and medicine, as well as in other disciplines including drug discovery and molecular engineering.

A general method for preparing optically-pure guanidine-based γ-peptide nucleic acid (γGPNA) monomers for all four natural nucleobases (A, C, G and T) is described. These second-generation γGPNAs differ from the first in that the guanidinium group is installed at the γ-instead of the α-position of the N-(2-aminoethyl)glycine backbone unit. This positional switch enables GPNAs to be synthesized from relatively cheap L- as opposed to D-amino acids. Unlike their α-predecessors, which are randomly-folded, γGPNAs prepared from L-amino acids are preorganized into a right-handed helix and bind to DNA and RNA with exceptionally high affinity and sequence selectivity, and are readily taken up by mammalian cells.

In this Communication we show that peptide nucleic acids (PNAs), 15 to 20nt in length, when preorganized into a right-handed helix, can invade mixed-sequence double helical B-form DNA (B-DNA). Strand-invasion occurs in a highly sequence-specific manner through direct Watson-Crick base-pairing. Unlike the previously developed double-duplex invasion strategy that requires simultaneous binding of two strands of pseudocomplementary PNAs to DNA, only a single strand of γPNA is required for invasion in this case, and no nucleobase substitution is needed.Peptide nucleic acids (PNAs) are a promising class of nucleic acid mimics, developed in the last two decades, in which the naturally occurring sugar phosphodiester backbone has been replaced by achiral N-(2-aminoethyl) glycine units (Scheme 1A). 1 In addition to their ability to hybridize to complementary DNA or RNA strands, PNAs can invade double-stranded DNA. 2 Strand-invasion occurs predominantly in two modes, through Watson-Crick base-pairing to form a 1:1 3 or in combination with Hoogsteen base-pairing to form a 2:1 (PNA:DNA) complex, 4 depending on the target sequence. The simplicity and generality of their recognition, along with the ease and flexibility of their synthesis make PNAs an attractive class of antigene reagents. However, with the current design, not every sequence can be accessed by PNAsin particular, those that are comprised of all four nucleobases. Mixed-sequence PNAs have been shown to be capable of invading supercoiled plasmid DNA 5-7 and certain regions of genomic DNA; 8 but they are not capable of invading intact, linear double helical B-form DNA (B-DNA). Recently, two approaches, "tail-clamp" 9,10 and "double duplex invasion," 11 have been developed, enabling mixed-sequence PNAs to invade B-DNA. But, they are not without limitations. The first approach still requires a stretch of homopurine target for anchoring triplex binding while the second, although more relaxed in sequence selection, requires an elaborate nucleobase substitution and the need to use two strands of PNAs to invade B-DNA-which complicates their design and greatly limits their utility. 12 In this Communication we show that mixed-sequence PNAs, 15 to 20 nucleotides in length, when preorganized into a right-handed helix, can invade double helical B-DNA. Strand-invasion occurs in a sequence-specific manner through direct Watson-Crick base-pairing. In this case only a single strand of γPNA is required for invasion, and no nucleobase substitution is needed.Recently, we showed that PNAs, which, as individual strands do not have well-defined conformations, can be preorganized into a right-handed helix by installing an (S)-Me stereogenic center at the γ-backbone position (Scheme 1A). 13 These helical γPNAs exhibit strong binding affinity for complementary DNA and RNA strands. As decamers, mixedsequence γPNAs are unable to invade B-DNA, but strand-invasion can be rescued by appending an acridine moiety (DNA-intercalator) to one of the termini 13 or by replacing a cytosine nucle...

Invasion of the strand snatchers: We have synthesized chiral γ‐peptide nucleic acids containing miniPEG side chains. Using gel shift assays we show that this particular type of nucleic acid mimic can invade any sequence of double helical B‐form DNA (see figure), and this recognition occurs through direct Watson–Crick base pairing.