The application of Peptide nucleic acids (PNAs)

The definition of Peptide nucleic acids (PNAs)

Peptide nucleic acids are synthetic DNA analogs in which the phosphodiester
backbone is replaced by repetitive units of N-(2-aminoethyl) glycine to which the purine
and pyrimidine bases are attached via a methyl carbonyl linker (Figure. 1). The PNA
molecules can routinely be labelled with biotin or various fluorophores. The unique
chemical makeup provides PNA with unique hybridization characteristics. Unlike DNA
and RNA, the PNA backbone is not charged. Consequently, there is no electrostatic
repulsion when PNA hybridizes to its target nucleic acid sequence, giving a higher
stability to the PNA-DNA or PNA-RNA duplexes than the natural homo- or
heteroduplexes. This greater stability results in higher thermal melting temperature (Tm)
values than is observed for DNA-DNA or DNA-RNA duplexes. An additional
consequence of the polyamide backbone is that PNAs hybridize virtually independently of
the salt concentration. Thus, the Tm of PNA-DNA duplex is barely affected by low ionic
strength. This significantly facilitates the hybridization with the PNAs. The unnatural
backbone of PNAs also means that PNAs are particularly resistant to protease and
nuclease degradation. Because of this resistance to the enzyme degradation, the lifetime
of PNAs is extended both in vivo and in vitro. Also, PNAs are not recognized by
polymerases and therefore cannot be directly used as primers or be copied.
Figure 1

Applications of PNAs

The artificially synthesized biopolymer PNA is a powerful biomolecular tool in the

molecular genetic diagnostics with a wide range of vital applications. Due to the ability to
interact with the selected target with large sequence specificity in a gene sequence,
PNAs are of great interest in wide range of applications in medicinal and biotechnological
areas. They are highly promising in the expansion of gene therapeutic agents, diagnostic
and molecular tools for genetic analysis. It was also indicated by in vitro studies that
PNAs could inhibit both transcription and translation of genes to which they have been
targeted which guarantee their use as antigene and antisense agents.

Antigene Agents

PNA molecules were first used in antigene and antisense assays. Several in vitro studies
demonstrated the ability of PNAs to inhibit both eukaryotic translation and transcription.
PNA-mediated inhibition of gene transcription is mainly due to the formation of strand-
invaded complexes or strand displacement in DNA targets. PNA targeted against the
promoter region of a gene can form stable PNA–DNA complexes that restrict the DNA
access of the polymerase, whereas PNA complexes located far from the promoter can
block the polymerase progression and lead to the production of truncated RNA
transcripts.

Antisense Agents

1. Antibacterial agents and Antibiotics

One of the serious problem which is emerging at an alarming rate is the increasing
multidrug resistant bacteria. These bacterial pathogens exhibit resistance towards
conventional antibiotics due to excessive use of these antibiotics and resistance genes
transfer within the bacteria. Researchers desperately require new antibacterial drugs for
the treatment of patients infected with drug resistant bacteria. Antisense PNAs as
antibacterial agents were found to treat infections caused by multidrug resistant bacteria.

2. Antiviral agents

PRF-1 signal is responsible for synthesizing RNA replicase polyproteins in virus for
genome replication, especially for severe acute respiratory syndrome coronavirus
replication. Lee et al. evaluated the potential antiviral effect of APNAs with RNA
sequence on the PRF-1 signal as target.

PNA Probes in Polymerase Chain Reaction (PCR)

In medical and biological research laboratories, polymerase chain reaction (PCR) is a

frequent technique to amplify a DNA target sequence, generating thousands of copies for
a variety of biomedical applications. PNA-mediated PCR clamping was also used for the
amplification and consequently identification of minor allele in blood chimerism whereas
direct sequencing of ordinary PCR product could not identify it.

Use of PNA probes in Fluorescence In Situ Hybridization (PNA-FISH)

Techniques like PNA-FISH are used for the specific and selective identification of S.
aureus. PNA-FISH methodology was also used for the diagnosis of bacterial vaginosis
which is a common vaginal infection. The method was found to be time saving, highly
specific and provided a valuable and trustful diagnostic tool. PNA-FISH was found to be
useful for the detection of pathogenic oomycete Aphanomyces invadans which is
responsible for ulcerative mycosis, a skin disease caused by a fungus-like agent of wild
and cultured fish. In another study, PNA probe-FISH assay was used for detecting
mycobacteria with great specificity and sensitivity which helps in the fast and effective
treatment of tuberculosis.

PNA based Biosensors

During past few decades, biosensor technology has gained considerable attention in
playing a significant analytical role in different industrial and academic applications
especially in certain areas like medical, environmental, food, quarantine control, safety,
security, as well as defense. Singh et al. reviewed the use of PNA based biosensors that
provide rapid, selective, sensitive, cost effective, simple, and precise detection of DNA
hybridization. These biosensors are quite functional in perceiving targeted genes which
are responsible for particular disease.

PNA/DNA hybridization with Nanoparticles

Colorimetric assay is another important method of DNA detection which is based on the
aggregation of unmodified metallic nanoparticles. In this hybridization based method,
charged neutral PNA were used as a “coagulant” of citrate anion-coated particles and the
assay was validated using gold (Au) and silver (Ag) nanoparticles (NPs). It was found
that for discriminating single-base-mismatch, the Ag NPs possess greater sensitivity than
Au NPs, further improving the accuracy of result with the use of the multiple aggregation
signatures from the two types of nanoparticles. SPR imaging enhanced by ultrasensitive
nanoparticles also uses PNA probes for detecting single-nucleotide mismatches in DNA
sequences with greater selectivity.

About Creative Peptides

Creative Peptides is increasingly involved with the fight against Alzheimer’s disease by offering a
wide range of peptide fragments for research purpose such as β-Amyloid Fragments and Tau
Fragments, etc. Apart from that, other peptides like chelate peptides, isotope labeled peptides ,
ghrelin peptides can also be easily reached at Creative Peptides. With concerted efforts from all
parties, the cause and better cure for Alzheimer’s disease can be found earlier.

References:

Paulasova, P., & Pellestor, F. (2004, October). The peptide nucleic acids (PNAs): a new
generation of probes for genetic and cytogenetic analyses. In Annales de genetique (Vol.
47, No. 4, pp. 349-358). Elsevier Masson.

Gupta, A., Mishra, A., & Puri, N. (2017). Peptide nucleic acids: advanced tools for
biomedical applications. Journal of biotechnology, 259, 148-159.

Source: https://www.creative-peptides.com/blog/index.php/the-application-of-peptide-
nucleic-acids-pnas/