Right-Handed (RH) Chiral Gamma PNA
Among the various chemical modifications made to the backbone of peptide nucleic acid (PNA), modifications made at the gamma position have the greatest effect on PNA conformation.
An Enabling Diagnostics Application
Several research groups have made seminal contributions to the development of chiral gamma PNA, including T. Chyau Liang (Tet. Lett. 1994, 35, 5173), Oliver Seitz (Org. Lett. 2005, 7, 4365), and Daniel Appella (Org. Lett. 2005, 7, 3465).
Below are selected publications from the Ly group at Carnegie Mellon University that demonstrated the conformational preorganization of these oligomeric molecules, as individual strands prior to hybridization with their complementary partners.
A simple y-backbone modification preorganizes peptide nucleic acid into a helical structure.
J. Am. Chem. Soc. 2006, 128, 10258.
Strand invasion of extended, mixed-sequence B-DNA by y-PNAs.
J. Am. Chem. Soc. 2009, 131, 12088.
Crystal structure of chiral y-PNA with complementary DNA strand: Insights into the stability and specificity of recognition and conformational preorganization.
J. Am. Chem. Soc. 2010, 132, 10717.
Synthesis and characterization of conformationally preorganized, (R)-diethylene glycol-containing y-peptide nucleic acids with superior hybridization properties and water solubility.
J. Org. Chem. 2011, 76, 5614.
Sequence-unrestricted, Watson-Crick recognition of double helical B-DNA by (R)-miniPEG-yPNAs.
ChemBioChem. 2012, 13, 56.
Electronic barcoding of a viral gene at the single-molecule level
Nano Lett. 2012, 12, 1722.
Left-Handed (LH) Chiral Gamma PNA
Inversion of the stereogenic center at the gamma backbone position results in the oligomer adopting an inverted left-handed (LH) helical motif.
Because of conformational mismatch, LH-PNA is unable to hybridize with RH-PNA, DNA, or RNA, all of which adopt right-handed helical folds. As such, LH-PNA is ideally suited for programmable molecular self-assembly and bioconjugation in biological systems without concern for unintended binding to endogenous genetic material. Moreover, because binding to a complementary partner is exceptionally tight, relatively short oligomers (5–7 units in length) can be employed, compared with other classes of oligonucleotides such as DNA or RNA, which typically require 15–25 units.
Gamma peptide nucleic acids: As orthogonal nucleic acid recognition codes for organizing molecular self-assembly.
J. Am. Chem. Soc. 2015, 137, 8603.
Molecular Translation
Inversion of the stereogenic center at the gamma backbone position results in the oligomer adopting an inverted left-handed (LH) helical motif.
Stereochemical conversion of nucleic acid circuits via strand displacement.
Commun. Chem. 2018, DOI: 10.1038/s42004-018-0089-9.
Bifacial Nucleic Acid Recognition
The conformational preorganization of the RH-yPNA backbone, when coupled with specially designed Janus nucleobases, enables this class of nucleic acid analogues to invade virtually any sequence of double-stranded DNA or RNA under physiologically relevant conditions, and to support the design of relatively short nucleic acid “ligands” that target RNA secondary and tertiary structures with high cooperativity, specificity, and selectivity via a “pot-hold” filling approach.
Molecular Dynamics Simulations of Ligand LG2 Designed to Bind CUG-RNA Repeats
Shape selective bifacial recognition of double helical DNA.
Commun. Chem. 2018, DOI: 10.1038/s42004-018-0080-5.
Design of bivalent nucleic acid ligands for recognition of RNA-repeated expansion associated with Huntington's disease.
Biochemistry 2018, 57, 2094.
A pothole-filling strategy for selective targeting of rCUG-repeats associated with myotonic dystrophy type 1
Proc. Natl. Acad. Sci. U.S.A. 2026, 123, doi.org/10.1073/pnas.2507065123.
Cellular Delivery
PNA can be made cell-permeable by integrating positively charged guanidinium groups directly into its backbone, specifically at the γ-position, creating γGPNAs. This modification induces a preorganized right-handed helical structure that enhances binding to DNA and RNA while simultaneously promoting interaction with cell membranes, enabling efficient cellular uptake without the need for external transfection agents. By embedding the transduction functionality within the molecule itself—rather than attaching separate delivery peptides at the termini—this design minimizes amphiphilic disruption of the cell membrane and is less toxic compared to conventional terminal conjugation strategies, while still maintaining high sequence specificity and biological stability. The placement of γGPNA units is optimal when incorporated at every other or every third position among achiral PNA building blocks, resulting in a total of 5 to 7 γGPNA units.
Synthesis of conformationally preorganized and cell-permeable guanidine-based y-peptide nucleic acids (yGPNAs).
J. Org. Chem. 2009, 74, 1509.
Antitumor effects of EGFR guanidine-based peptide nucleic acids in cancer models
ACS Chem. Biol. 2013, 8, 345.