Peptide Nucleic Acid (PNA) is a synthetic polymer developed in the early 1990s. PNA has become a valuable tool in molecular biology research and medical diagnostics. Its unique chemical stability and binding characteristics allow it to interact with genetic material in ways that traditional nucleic acids cannot, offering significant advantages over its natural counterparts.
Defining the Peptide Backbone
The defining feature of Peptide Nucleic Acid is the replacement of the sugar-phosphate backbone found in DNA and RNA. Natural nucleic acids rely on alternating sugar units connected by negatively charged phosphodiester bonds. In contrast, PNA employs a neutral, pseudo-peptide chain built from repeating N-(2-aminoethyl)glycine units.
These repeating units are linked together by amide bonds, forming a backbone that resembles a protein rather than a sugar-phosphate chain. The four canonical nucleobases—adenine, guanine, cytosine, and thymine—are attached to this synthetic skeleton via methylene-carbonyl linkers. This structural substitution gives PNA its name, combining characteristics of both peptides and nucleic acids.
A significant consequence of this peptide-like architecture is the absence of any electrical charge on the backbone. The phosphodiester groups in DNA and RNA carry a negative charge at physiological pH, which causes electrostatic repulsion between the two strands of a double helix. Since PNA’s backbone is electrically neutral, it eliminates this repulsion. This charge neutrality allows PNA to interact with complementary strands in a highly stable manner.
How PNA Interacts with DNA and RNA
PNA binds to complementary DNA or RNA sequences following Watson-Crick base pairing rules, forming stable duplexes or triplexes. The lack of charge repulsion results in a superior binding affinity compared to natural DNA-DNA pairing. This stronger interaction translates into a significantly higher melting temperature, meaning the hybrid complex requires more energy to separate.
One of the most remarkable properties of PNA is its ability to perform “strand invasion” on double-stranded DNA. A PNA oligomer displaces one of the two strands in a DNA double helix. The PNA then binds to the exposed complementary sequence, forming a stable PNA/DNA duplex or a PNA-DNA-PNA triplex. This action effectively opens up the double helix in a sequence-specific manner.
The synthetic backbone provides resistance to degradation by biological enzymes. Unlike DNA and RNA, which are broken down by nucleases, PNA is not cleaved by these enzymes. Its peptide-like structure is also resistant to degradation by proteases, offering metabolic stability. This inherent stability makes PNA an excellent tool for use in complex biological environments.
Current Applications in Science and Medicine
The stability and high binding affinity of PNA have made it an indispensable tool across molecular biology and clinical medicine. In diagnostics, PNA-based probes identify specific genetic sequences. PNA is used in Fluorescence In Situ Hybridization (PNA-FISH) assays to rapidly identify bacterial or fungal pathogens directly from patient samples.
PNA is useful for distinguishing between closely related species or detecting genetic markers for drug resistance. PNA probes are also incorporated into specialized Polymerase Chain Reaction (PNA-PCR) protocols, where they selectively block the amplification of unwanted DNA sequences.
In therapeutics, PNA is investigated for gene expression control through antisense and antigene strategies. As an antisense agent, PNA binds to a specific messenger RNA (mRNA) sequence, blocking translation into a harmful protein. As an antigene agent, PNA uses strand invasion to bind directly to a target DNA sequence, preventing transcription into mRNA.
This ability to inhibit gene expression holds promise for treating diseases like cancer, where PNA could silence oncogenes, or for developing new antibacterial and antiviral drugs. PNA also serves as a general research tool for purifying nucleic acids and stabilizing target sequences.