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PNA Technology

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Peptide Nucleic Acids

Part of the book series: Methods in Molecular Biology ((MIMB,volume 208))

Abstract

Peptide nucleic acids (PNA) were originally conceived and designed as sequence-specific DNA binding reagents targeting the DNA major groove in analogy to triplex-forming oligonucleotides. However, instead of the sugar-phosphate backbone of oligonucleotides PNA was designed with a pseudopeptide backbone (1). Once synthesized, it was apparent that PNA oligomers based on the aminoethylglycin backbone with acetyl linkers to the nucleobases (see Fig. 1) are extremely good structural mimics of DNA (or RNA), being able to form very stable duplex structures with Watson-Crick complementary DNA, RNA (or PNA) oligomers (2–4). It also quickly became clear that triplexes formed between one homopurine DNA (or RNA) strand and two sequence complementary PNA strands are extraordinarily stable. Furthermore, this stability is the reason why homopyrimidine PNA oligomers when binding complementary targets in double-stranded DNA do not do so by conventional (PNA-DNA2) triplex formation, but rather prefer to form a triplex-invasion complex in which the DNA duplex is invaded by an internal PNA2-DNA triplex (see Fig. 2) (5,6). This type of binding is restricted to homopurine/homopyrimidine DNA targets in full analogy to dsDNA targeting by triplex forming oligo nucleotides (see Fig. 3). However, other binding modes for targeting dsDNA is available for PNA (7) of which the double duplex invasion (8) is believed to become very important, because it allows the formation of very stable complexes at mixed purine-pyrimidine targets as long as they have a reasonable (∼ 50%) A/T content (see Fig. 4). The DNA/RNA recognition properties of PNA combined with excellent chemical and biological stability and tremendous chemical-synthetic flexibility has made PNA of interest to a range of scientific disciplines ranging from (organic) chemistry to biology to medicine (9–16).

Chemical structures of PNA as compared to DNA. In terms of binding properties, the amino-end of the PNA corresponds to the 5’-end of the DNA.

Structural modes for binding of PNA oligomers to sequence complementary targets in double-stranded DNA.

Triplex invasion by homopyrimidine PNA oligomers. One PNA strand binds via Watson-Crick base pairing (preferably in the antiparallel orientation), whereas the other binds via Hoogsteen base pairing (preferably in the parallel orientation). It is usually advantageous to connect the two PNA strands covalently via a flexible linker into a bis-PNA, and to substitute all cytosines in the Hoogsteen strand with pseudoisocytosines (ψiC), which do not require low pH for N3 “protonation.”

Double-duplex invasion of pseudo complementary PNAs. In order to obtain efficient binding the target (and thus the PNAs) should contain at least 50% AT (no other sequence constraints), and in the PNA oligomers all A/T base pairs are substituted with 2,6-diaminopurine/ 2-thiouracil “base pairs.” This base pair is very unstable due to steric hindrance. Therefore the two sequence-complementary PNAs will not be able to bind each other, but they bind their DNA complement very well.

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Authors and Affiliations

  1. Center for Biomolecular Recognition, IMBG, Biochemistry B, The Panum Institute, University of Copenhagen, Copenhagen N, Denmark

    Peter E. Nielsen

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  1. Peter E. Nielsen
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  1. Center for Biomolecular Recognition The Panum Institute, University of Copengagen, Copenhagen, Denmark

    Peter E. Nielsen

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© 2002 Humana Press Inc.

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Nielsen, P.E. (2002). PNA Technology. In: Nielsen, P.E. (eds) Peptide Nucleic Acids. Methods in Molecular Biology, vol 208. Springer, Totowa, NJ. https://doi.org/10.1385/1-59259-290-2:03

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  • DOI: https://doi.org/10.1385/1-59259-290-2:03

  • Publisher Name: Springer, Totowa, NJ

  • Print ISBN: 978-0-89603-976-6

  • Online ISBN: 978-1-59259-290-6

  • eBook Packages: Springer Protocols

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