Better than the real thing: peptide nucleic acids

Reagents capable of sequence-specificrecognition of nucleic acids are becom-ing more and more important forresearch, diagnosis and therapy. Rapidprogress is being made in the eluci-dation of the human genome sequence,as well as that of other organisms,including human pathogens. As thisinformation emerges, there is an increas-ing need for new tools to probe genestructure and function and for novelreagents to allow development of gene-based diagnostics and therapeutics.Over the past few years, peptidenucleic acids (PNAs) have emerged asone of the most promising new types ofmolecules for recognition of nucleicacids. PNAs are actually neither peptidenor nucleic acid, but have a hybridstructure consisting of repeating N-(2-aminoethyl)-glycine units linked byamide bonds. The purine (A, G) andpyrimidine (T, C) nucleobases areattached to this backbone via methylenecarbonyl linkages. There are no sugar orphosphate groups. Hence, the unmodi-fied PNAs are not charged at neutralpH.Originally, PNAs were designed torecognize and bind to duplex DNA inthe major groove via Hoogsteen bond-ing to form triple helices. Although cer-tain PNA sequences can do this, it wassoon discovered that PNA oligomerscan bind to single-stranded nucleic acidsto form duplexes, either PNA–DNA orPNA–RNA, with affinity and specificitysubstantially exceeding that of compa-rable DNA or RNA oligonucleotides. In addition, triplex formation involv-ing PNAs can occur either withPNA–DNA–DNA triplexes or the morefavored PNA–DNA–PNA triplexes. Thestability of the PNA interaction withDNA is such that strand invasion ofDNA by PNAs is thermodynamicallyfavored, and can take place via eitherduplex, triplex or double duplex formation.The foregoing constitutes just a shortlist of the capabilities of PNAs. In fact,the known properties of PNAs and theirpotential applications in biomedicineare rapidly expanding as researcherscontinue to examine these fascinatingmolecules. It is therefore quite timelythat Peter Nielsen and Michael Egholm,two of the inventors of PNAs, have puttogether a book reviewing the state ofthe art in PNA research.The emphasis here is on timely. Theeditors have clearly made an effort toinclude up-to-the-minute material andto publish it quickly. As a result, thetopics include most, if not all, of therecent PNA advances, all by keyresearchers in the field. The book beginswith a useful overview by the editorsputting the development and use ofPNAs in perspective, and serving as anintroduction for those new to this area. This is followed by a series of chap-ters focusing on the fundamental chem-istry of PNA synthesis. Several of thesecover newer chemical strategies such asthe synthesis of PNA–DNA andPNA–peptide chimeras and PNA conju-gation to labeling compounds such asbiotin, fluorescein and rhodamine. Theemphasis here is on the protocols. Trueto the book’s subtitle, these chaptersread like a good manual, with substan-tial detail as well as useful discussionproviding experimental and technicalinsight. Although these sections will bemost useful to synthetic chemists, theywill also serve biologists by highlightingthe versatility of PNAs and identifyingthe possible syntheses and novel mol-ecules that can be made.Another section focuses onhybridization-based techniques, andthese chapters provide a sophisticateddiscussion of the nucleic acid-bindingproperties of the PNAs, both in a sec-tion devoted to the thermodynamics ofPNA–nucleic acid interactions as well ina series of application chapters. In thisportion of the book, a wide variety ofemerging properties and applications ofPNAs are examined. The use of PNAsfor