Applied Microbiology and Biotechnology

, Volume 71, Issue 5, pp 575–586

Promising nucleic acid analogs and mimics: characteristic features and applications of PNA, LNA, and morpholino



Nucleic acid analogs and mimics are commonly the modifications of native nucleic acids at the nucleobase, the sugar ring, or the phosphodiester backbone. Many forms of promising nucleic acid analogs and mimics are available, such as locked nucleic acids (LNAs), peptide nucleic acids (PNAs), and morpholinos. LNAs, PNAs, and morpholinos can form both duplexes and triplexes and have improved biostability. They have become a general and versatile tool for DNA and RNA recognition. LNA is a general and versatile tool for specific, high-affinity recognition of single-stranded DNA (ssDNA) and single-stranded RNA (ssRNA). LNA can be used for designing LNA oligoes for hybridization studies or as real time polymerase chain reaction probes in the form of Taqman probes. LNA also has therapeutic and diagnostic applications. PNA is another type of DNA analog with neutral charge. The extreme stability of PNA makes it an ideal candidate for the antisense and antigene application. PNA is used as probe for gene cloning, mutation detection, and in homologous recombination studies. It was also used to design transcription factor decoy molecules for target gene induction. Morpholino, another structural type, was devised to circumvent cost problems associated with DNA analogs. It has become the premier knockdown tool in developmental biology due to its cytosolic delivery in the embryos by microinjection. Thus, the nucleic acid analogs provide an advantage to design and implementation, therapies, and research assays, which were not implemented due to limitations associated with standard nucleic acids chemistry.


  1. Armitage B, Ly D, Koch T, Frydenlund H, Orum H, Schuster GB (1998) Hairpin-forming peptide nucleic acid oligomers. Biochemistry 37:9417–9425CrossRefGoogle Scholar
  2. Betts L, Josey JA, Veal JM, Jordan SR (1995) A nucleic acid triple helix formed by a peptide nucleic acid-DNA complex. Science 270:1838–1841CrossRefGoogle Scholar
  3. Brown SC, Thomson SA, Veal JM, Davis DG (1994) NMR solution structure of a peptide nucleic acid complexed with RNA. Science 265:777–780CrossRefGoogle Scholar
  4. Childs JL, Disney MD, Turner DH (2002) Oligonucleotide directed misfolding of RNA inhibits Candida albicans group I intron splicing. Proc Natl Acad Sci U S A 99:11091–11096CrossRefGoogle Scholar
  5. Christensen U, Jacobsen N, Rajwanshi VK, Wengel J, Koch T (2001) Stopped-flow kinetics of locked nucleic acid (LNA)–oligonucleotide duplex formation: studies of LNA–DNA and DNA–DNA interactions. Biochem J 354:481–484CrossRefGoogle Scholar
  6. Crinelli R, Bianchi M, Gentilini L, Magnani M (2002) Design and characterization of decoy oligonucleotides containing locked nucleic acids. Nucleic Acids Res 30:2435–2443CrossRefGoogle Scholar
  7. Cutrona G, Carpaneto EM, Ulivi M, Roncella S, Landt O, Ferrarini M, Boffa LC (2000) Effects in live cells of a c-myc anti-gene PNA linked to a nuclear localization signal. Nat Biotechnol 18:300–303CrossRefGoogle Scholar
  8. Demidov VV, Frank-Kamenetskii MD (1999) PNA directed genome rare cutting. In: Nielsen PE, Egholm M (eds) Peptide nucleic acids: protocols & applications, 2nd edn. Horizon Scientific, Wymondham, UK, pp 187–206Google Scholar
  9. Demidov VV, Frank-Kamenetskii MD (2001) Sequence-specific targeting of duplex DNA by peptide nucleic acids via triplex strand invasion. Methods 23:108–122CrossRefGoogle Scholar
  10. Demidov VV, Frank-Kamenetskii MD (2002) PNA openers and their applications. Methods Mol Biol 208:119–130Google Scholar
  11. Demidov V, Frank-Kamenetskii MD, Egholm M, Buchardt O, Nielsen PE (1993) Sequence selective double strand DNA cleavage by PNA targeting using nuclease S1. Nucleic Acids Res 21:2103–2107CrossRefGoogle Scholar
  12. Demidov VV, Potaman VN, Frank-Kamenetskii MD, Egholm M, Buchard O, Sönnichsen SH, Nielsen PE (1994) Stability of peptide nucleic acids in human serum and cellular extracts. Biochem Pharmacol 48:1310–1313CrossRefGoogle Scholar
  13. Demidov VV, Broude NE, Lavrentieva-Smolina IV, Kuhn H, Frank-Kamenetskii MD (2001a) An artificial primosome: design, function, and applications. Chembiochem 2:133–139CrossRefGoogle Scholar
  14. Demidov VV, Kuhn H, Lavrentieva-Smolina IV, Frank-Kamenetskii MD (2001b) Peptide nucleic acid-assisted topological labeling of duplex DNA. Methods 23:123–131CrossRefGoogle Scholar
  15. Egholm M, Buchardt O, Christensen L, Behrens C, Freier SM, Driver DA, Berg RH, Kim SK, Norden B, Nielsen PE (1993) PNA hybridizes to complementary oligonucleotides obeying the Watson–Crick hydrogen-bonding rules. Nature 365:566–568CrossRefGoogle Scholar
  16. Ekker SC, Larson JD (2001) Morphant technology in model developmental systems. Genesis 30:89–93CrossRefGoogle Scholar
  17. Elayadi AN, Braasch DA, Corey DR (2002) Implications of high-affinity hybridization by locked nucleic acid oligomers for inhibition of human telomerase. Biochemistry 41:9973–9981CrossRefGoogle Scholar
  18. Eriksson M, Nielsen PE (1996) Solution structure of a peptide nucleic acid-DNA duplex. Nat Struct Biol 3:410–413CrossRefGoogle Scholar
  19. Falkiewicz B (1999) Peptide nucleic acids and their structural modification. Acta Biochimica Polonica 46:509–529Google Scholar
  20. Fiandaca MJ, Hyldig-Nielsen JJ, Gildae BD, Coull JM (2001) Self reporting PNA/DNA primers for PCR analysis. Genome Res 11:609–613CrossRefGoogle Scholar
  21. Fraser GL, Holmgren J, Clarke PBS, Wahlestedt C (2000) Antisense inhibition of delta-opioid receptor gene function in vivo by peptide nucleic acids. Mol Pharmacol 57:725–731Google Scholar
  22. Ganesh KN, Nielsen PE (2000) Peptide nucleic acids analogs and derivatives. Curr Org Chem 4:931–943CrossRefGoogle Scholar
  23. Gotfredsen CH, Schultze P, Feigon J (1998) Solution structure of an intramolecular pyrimidine–purine–pyrimidine triplex containing an RNA third strand. J Am Chem Soc 120:4281–4289CrossRefGoogle Scholar
  24. Hamilton SE, Simmons CG, Kathiriya IS, Corey DR (1999) Cellular delivery of peptide nucleic acids and inhibition of human telomerase. Chem Biol 6:343–351CrossRefGoogle Scholar
  25. Hudziak RM, Barofsky E, Barofsky DF, Weller DL, Huang SB, Weller DD (1996) Resistance of morpholino phosphorodiamidate oligomers to enzymatic degradation. Antisense Nucleic Acid Drug Dev 6:267–272Google Scholar
  26. Hyrup B, Nielsen PE (1996) Peptide nucleic acids (PNA): synthesis, properties and potential applications. Bioorg Med Chem 4:5–23CrossRefGoogle Scholar
  27. Izvolsky KI, Demidov VV, Bukanov NO, Frank-Kamenetskii MD (1998) Yeast artificial chromosome segregation from host chromosomes with similar lengths. Nucleic Acids Res 26:5011–5012CrossRefGoogle Scholar
  28. Jepsen JS (2004) Locked nucleic acid (LNA) as cancer-therapeutic agent. Dan Med Bull 51:139Google Scholar
  29. Jensen KK, Orum H, Nielsen PE, Norden B (1997) Hybridization kinetics of peptide nucleic acids (PNA) with DNA and RNA studied with BIAcore technique. Biochemistry 36:5072–5077CrossRefGoogle Scholar
  30. Kang H, Chou PJ, Johnson WC Jr, Weller D, Huang SB, Summerton JE (1992) Stacking interactions of ApA analogues with modified backbones. Biopolymers 32:1351–1363CrossRefGoogle Scholar
  31. Kuhn H, Demidov VV, Coull JM, Fiandaca MJ, Gildea BD, Frank-Kamenetskii MD (2002) Hybridization of DNA and PNA molecular beacons to single-stranded and double-stranded DNA targets. J Am Chem Soc 124:1097–1103CrossRefGoogle Scholar
  32. Kurreck J, Wyszko E, Gillenand C, Erdmann VA (2002) Design of antisense oligonucleotides stabilized by locked nucleic acids. Nucleic Acids Res 30:1911–1918CrossRefGoogle Scholar
  33. Lansdorp PM, Verwoerd NP, van de Rijke FM, Dragowska V, Little MT, Dirks RW, Raap AK, Tanke HJ (1996) Heterogeneity in telomere length of human chromosomes. Hum Mol Genet 5:685–691CrossRefGoogle Scholar
  34. Lohse J, Dahl O, Nielsen PE (1999) Double duplex invasion by peptide nucleic acid: a general principle for sequence specific targeting of double stranded DNA. Proc Natl Acad Sci U S A 96:11804–11808CrossRefGoogle Scholar
  35. Lutz MJ, Benner SA, Hein S, Breipohl G, Uhlmann E (1997) Recognition of uncharged polyamide-linked nucleic acid analogs by DNA polymerases and reverse transcriptases. J Am Chem Soc 119:3177–3178CrossRefGoogle Scholar
  36. Malvy C, Harel-Bellan A, Pritchard LL (1999) Triple helix forming oligonucleotides. Springer, Berlin Heidelberg New YorkGoogle Scholar
  37. McTigue PM, Peterson RJ, Kahn JD (2004) Sequence-dependent thermodynamic parameters for locked nucleic acid (LNA)-DNA duplex formation. Biochemistry 43:5388–5405CrossRefGoogle Scholar
  38. Misra HS, Pandey PK, Modak MJ, Vinayak R, Pandey VN (1998) Polyamide nucleic acid-DNA chimera lacking the phosphate backbone are novel primers for polymerase reaction catalyzed by DNA polymerases. Biochemistry 37:1917–1925CrossRefGoogle Scholar
  39. Mologni L, Nielsen PE, Gambacorti-Passerini C (1999) In vitro transcriptional and translational block of the bcl-2 gene operated by peptide nucleic acid. Biochem Biophys Res Commun 264:537–543CrossRefGoogle Scholar
  40. Nastruzzi C, Cortesi R, Esposito E, Gambari R, Borgatti M, Bianchi N, Feriotto G, Mischiati C (2000) Liposomes as carriers for DNA–PNA hybrids. J Control Release 68:237–249CrossRefGoogle Scholar
  41. Nielsen PE, Egholm M (1999) Peptide nucleic acid (PNA): protocols and applications. Horizon Scientific, NorfolkGoogle Scholar
  42. Nielsen PE, Egholm M, Berg RH, Buchardt O (1991) Sequence-selective recognition of DNA by strand displacement with a thymine-substituted polyamide. Science 254:1497–1500CrossRefGoogle Scholar
  43. Norton JC, Piatyszek MA, Wright WE, Shay JW, Corey DR (1996) Inhibition of human telomerase activity by peptide nucleic acids. Nat Biotechnol 14:615–619CrossRefGoogle Scholar
  44. Obika S, Hemamayi R, Masuda T, Sugimoto T, Nakagawa S, Mayumi T, Imanishi T (2001) Inhibition of ICAM-1 gene expression by antisense 2′, 4′-BNA oligonucleotides. Nucleic Acids Res Suppl 1:145–146Google Scholar
  45. Orum H, Nielsen PE, Egholm M, Berg RH, Buchardt O, Stanley C (1993) Single base pair mutation analysis by PNA directed PCR clamping. Nucleic Acids Res 21:5332–5336CrossRefGoogle Scholar
  46. Orum H, Jakobsev MH, Koch T, Vuust J, Borre MB (1999) Detection of the Factor V Leiden mutation by direct allele-specific hybridization of PCR amplicons to photo immobilized locked nucleic acids. Clin Chem 45:1898–1905Google Scholar
  47. Partridge M, Vincent A, Matthews P, Puma J, Stein D, Summerton J (1996) A simple method for delivering morpholino antisense oligos into the cytoplasm of cells. Antisense Nucleic Acid Drug Dev 6:169–175Google Scholar
  48. Perry-O’Keefe H, Yao XW, Coull JM, Fuchs M, Egholm M (1996) Peptide nucleic acid pre-gel hybridization: an alternative to Southern hybridization. Proc Natl Acad Sci U S A 93:14670–14675CrossRefGoogle Scholar
  49. Petersen M, Wengel J (2003) LNA: a versatile tool for therapeutics and genomics. Trends Biotechnol 21:74–81CrossRefGoogle Scholar
  50. Petersen M, Nielsen CB, Nielsen KE, Jensen GA, Bondensgaard K, Singh SK, Rajwanshi VK, Koshkin AA, Dahl BM, Wengel J, Jacobsen JP (2000) The conformations of locked nucleic acids (LNA). J Mol Recognit 13:44–53CrossRefGoogle Scholar
  51. Pooga M, Soomets U, Hallbrink M, Valkna A, Saar K, Rezaei K, Kahl U, Hao JX, Xu XJ, Wiesenfeld-Hallin Z, Hokfelt T, Bartfai T, Langel U (1998) Cell penetrating PNA constructs regulate galanin receptor levels and modify pain transmission in vivo. Nat Biotechnol 16:857–861CrossRefGoogle Scholar
  52. Rasmussen H, Kastrup JS, Nielsen JN, Nielsen JM, Nielsen PE (1997) Crystal structure of a peptide nucleic acid (PNA) duplex at 1.7 Å resolution. Nat Struct Biol 4:98–101CrossRefGoogle Scholar
  53. Ray A, Norden B (2000) Peptide nucleic acid (PNA): its medical and biotechnical applications and promise for the future. FASEB J 14:1041–1060Google Scholar
  54. Santa Lucia J Jr (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci U S A 95:1460–1465CrossRefGoogle Scholar
  55. Simeonov A, Nikiforov TT (2002) Single nucleotide polymorphism genotyping using short, fluorescently labeled locked nucleic acid (LNA) probes and fluorescence polarization detection. Nucleic Acids Res 30:91CrossRefGoogle Scholar
  56. Singh SK, Nielsen P, Koshkin A, Wengel J (1998) LNA (locked nucleic acids): synthesis and high-affinity nucleic acid recognition. Chem Comm 4:455–456CrossRefGoogle Scholar
  57. Srikanta S, Nilsson L (1998) Molecular dynamics of duplex systems involving PNA: structural and dynamical consequences of the nucleic acid backbone. J Am Chem Soc 120:619–631CrossRefGoogle Scholar
  58. Summerton J (1989) Uncharged nucleic acid analogs for therapeutic and diagnostic applications: oligomers assembled from ribose-derived subunits. In Brakel C (ed) Discoveries in antisense nucleic acids. Portfolio, Woodlands, TX, pp 71–80Google Scholar
  59. Summerton J (1999) Morpholino antisense oligomers: the case for an RNase-H independent structural type. Biochim Biophys Acta 1489:141–158Google Scholar
  60. Taylor MF, Paulauskis JD, Weller DD, Kobzik L (1996) In vitro efficacy of morpholino-modified antisense oligomers directed against tumor necrosis factor alpha mRNA. J Biol Chem 271:17445–17452CrossRefGoogle Scholar
  61. Tomac S, Sarkar M, Ratilainen T, Wittung P, Nielsen PE, Norden B, Graslund A (1996) Ionic effects on the stability and conformation of peptide nucleic acid complexes. J Am Chem Soc 118:5544–5552CrossRefGoogle Scholar
  62. Veselkov AG, Demidov VV, Frank-Kamenetskii MD, Nielsen PE (1996) PNA as a rare genome-cutter. Nature 379:214CrossRefGoogle Scholar
  63. Vester B, Lundberg, LB, Sørensen MD, Babu BR, Douthwaite S, Wengel J (2002) LNAzymes: incorporation of LNA-type monomers into DNAzymes markedly increases RNA cleavage. J Am Chem Soc 124:13682–13683CrossRefGoogle Scholar
  64. Wang G, Xiaoxin SXU (2004) Peptide nucleic acid (PNA) binding-mediated gene regulation. Cell Res 14:111–116CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2006

Authors and Affiliations

  1. 1.Apticraft Systems (P) Ltd. 142, Electronics ComplexIndoreIndia
  2. 2.School of BiochemistryDevi Ahilya UniversityIndoreIndia

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