Peptide nucleic acids on microarrays and other biosensors

doi:10.1016/j.tibtech.2004.10.003

Trends in Biotechnology

Volume 22, Issue 12, December 2004, Pages 617-622

https://doi.org/10.1016/j.tibtech.2004.10.003 Get rights and content

The analysis of biomolecules using microarrays and other biosensors has a significant role in molecular biotechnology, and will become even more important in the future as a versatile tool for research and diagnostics. For many applications, the synthetic DNA mimic peptide nucleic acid (PNA) could be advantageous as a probe molecule, owing to its unique physicochemical and biochemical properties. PNA exhibits superior hybridization characteristics and improved chemical and enzymatic stability relative to nucleic acids. Furthermore, its different molecular structure enables new modes of detection, especially procedures that avoid the introduction of a label. In our opinion, all of these factors contribute significantly toward the establishment of faster and more reliable analytical processes and opens new fields of application.

Section snippets

Investigation of labeled analytes

Most analyses in this area are extensions of assays using DNA-probes. The substitution of PNA for DNA is considered to improve the quality of the assay, rather than introducing entirely new processes. However, for DNA microarrays, currently the most prominent assay format, the main advantage lies in the fact that a new means of detection becomes possible – and, in particular, one that avoids the labeling of the probe and the target altogether – and is therefore discussed below.

Detection by means of labeled probe molecules

Alternative to the introduction of a label into the analyzed sample, the probe molecule itself can also carry the reporter element. This has the advantage that the processing of the analyte is simplified, decreasing the degree of variability and reducing the effort required in sample preparation.

Detection with unlabeled probe and target molecules

It would be advantageous to avoid labeling altogether, especially for routine applications. Besides speeding up the analytical process, all labeling steps introduce a bias because of differences in label incorporation. Moreover, direct electronic detection, for example, could assist in the integration of the assay into automated analysis systems, which are needed for high-throughput sample analysis.

Conclusion

Although PNA has still not had quite the impact that was initially predicted, it is a DNA mimic that offers enormous potential for improved assay performance. Its main advantage is the combination of many features that are very similar to those of natural DNA with additional characteristics that are rather different. In view of the chemical and biological consequences of this hybrid status, PNA has a unique position compared with the many other nucleic acid derivatives, and could make an

Acknowledgements

We thank Anette Jacob for valuable discussions and her comments on the manuscript. The work of the authors was funded by the German Federal Ministry of Education and Research (BMBF) as part of the ‘Leitprojekt Medizin’, Nanotechnology and DHGP programs.

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Citation Excerpt :
Unlabeled molecular hybridization was evaluated by phosphate (PO2− and PO3−) detection, which was an integral part of the DNA. Hence, it could be recognized the unlabeled DNA by combining PNA microarrays and TOF-SIMS (time-of-flight-secondary ion mass spectrometry) (Fig. 6) [57]. Jang and co-workers designed an array for determination of point mutations related to resistant antiviral agents (adefovir, lamivudine and entecavir) in the HBV (hepatitis B virus) in 68 clinical DNA specimens by using the PNA probe.
The analogs of DNA are unique biomedical tools that are broadly utilized to develop different types of biosensors. Peptide nucleic acids (PNA) are an individual and notable class of nucleic acid analogs due to their unique, novel physicochemical and biochemical characteristics, stability and resistance to nuclease and protease enzymes, significant interactions with complementary strands and remarkable hybridization attributes. Therefore, they are employed in the preparation and fabrication of various types of functional biosensors. In other words, immobilization of PNA as an appropriate diagnostic probe on the surface of electrochemical and optical converters lead to the fabrication of PNA-based biosensors which could be applied for sensitive and selective determination of diverse analytes. In this article, we are purposed to demonstrate an overview of physicochemical and biochemical features, modifications of peptide nucleic acid backbone and its usages as a bio-receptor in the PNA-based biosensors in recognition of viruses, RNA, bacteria, DNA, SNP (single-nucleotide polymorphism) and etc.
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Trends in Biotechnology

Peptide nucleic acids on microarrays and other biosensors

Section snippets

Investigation of labeled analytes

Detection by means of labeled probe molecules

Detection with unlabeled probe and target molecules

Conclusion

Acknowledgements

Anal. Biochem.

Biochem. Pharmacol.

Trends Biochem. Sci.

Anal. Biochem.

Mol. Cell. Probes

Anal. Biochem.

Mol. Cell. Probes

Lab. Invest.

Bioelectrochemistry

Anal. Chim. Acta

Sequence-selective recognition of DNA by strand displacement with a thymine-substituted polyamide

Science

PNA hybridizes to complementary oligonucleotides obeying the Watson-Crick hydrogen-bonding rules

Nature

Variability in the stability of DNA-peptide nucleic acid (PNA) single-base mismatched duplexes: real-time hybridization during affinity electrophoresis in PNA containing gels

Proc. Natl. Acad. Sci. U. S. A.

PNA: synthetic polyamide nucleic acids with unusual binding properties

Angew. Chem. Int. Ed. Engl.

Antisense PNA effects in Escherichia coli are limited by the outer-membrane LPS layer

Microbiology

PD-loop technology: PNA openers at work

Expert Rev. Mol. Diagn.

PCR clamping

Curr. Issues Mol. Biol.

PNA-mediated PCR clamping. Applications and methods

Methods Mol. Biol.

Peptide nucleic acid probe detection of mutations in Mycobacterium tuberculosis genes associated with drug resistance

Biotechniques

PNA for one-base differentiating protection of DNA from nuclease and its use for SNPs detection

J. Am. Chem. Soc.

Straightforward detection of SNPs in double-stranded DNA by using exonuclease III/nuclease S1/PNA system

Nucleic Acids Res.