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NMR solution structure of a peptide nucleic acid complexed with RNA.

Brown SC, Thomson SA, Veal JM, Davis DG
Science 265 777-80 (1994)
Cited: 86 times
EuropePMC logo PMID: 7519361

Abstract

Peptide nucleic acids (PNA) incorporating nucleic acid bases into an achiral polyamide backbone bind to DNA in a sequence-dependent manner. The structure of a PNA-ribonucleic acid (RNA) complex was determined with nuclear magnetic resonance methods. A hexameric PNA formed a 1:1 complex with a complementary RNA that is an antiparallel, right-handed double helix with Watson-Crick base pairing similar to the "A" form structure of RNA duplexes. The achiral PNA backbone assumed a distinct conformation upon binding that differed from previously proposed models and provides a basis for further structure-based design of antisense agents.

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  1. The structural diversity of artificial genetic polymers. Anosova I, Kowal EA, Dunn MR, Chaput JC, Van Horn WD, Egli M. Nucleic Acids Res 44 1007-1021 (2016)
  2. Antibacterial Peptide Nucleic Acids-Facts and Perspectives. Wojciechowska M, Równicki M, Mieczkowski A, Miszkiewicz J, Trylska J. Molecules 25 E559 (2020)
  3. Multifunctional Delivery Systems for Peptide Nucleic Acids. Volpi S, Cancelli U, Neri M, Corradini R. Pharmaceuticals (Basel) 14 14 (2020)

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  1. Designing a polycationic probe for simultaneous enrichment and detection of microRNAs in a nanopore. Tian K, He Z, Wang Y, Chen SJ, Gu LQ. ACS Nano 7 3962-3969 (2013)
  2. Exploitation of a very small peptide nucleic acid as a new inhibitor of miR-509-3p involved in the regulation of cystic fibrosis disease-gene expression. Amato F, Tomaiuolo R, Nici F, Borbone N, Elce A, Catalanotti B, D'Errico S, Morgillo CM, De Rosa G, Mayol L, Piccialli G, Oliviero G, Castaldo G. Biomed Res Int 2014 610718 (2014)
  3. Focus on PNA Flexibility and RNA Binding using Molecular Dynamics and Metadynamics. Verona MD, Verdolino V, Palazzesi F, Corradini R. Sci Rep 7 42799 (2017)
  4. Peptide Nucleic Acids as miRNA Target Protectors for the Treatment of Cystic Fibrosis. Zarrilli F, Amato F, Morgillo CM, Pinto B, Santarpia G, Borbone N, D'Errico S, Catalanotti B, Piccialli G, Castaldo G, Oliviero G. Molecules 22 E1144 (2017)
  5. Effects of hypoxanthine substitution in peptide nucleic acids targeting KRAS2 oncogenic mRNA molecules: theory and experiment. Sanders JM, Wampole ME, Chen CP, Sethi D, Singh A, Dupradeau FY, Wang F, Gray BD, Thakur ML, Wickstrom E. J Phys Chem B 117 11584-11595 (2013)
  6. Molecular Dynamics Study of the Hybridization between RNA and Modified Oligonucleotides. Jing Z, Qi R, Thibonnier M, Ren P. J Chem Theory Comput 15 6422-6432 (2019)
  7. Orientation preferences of backbone secondary amide functional groups in peptide nucleic acid complexes: quantum chemical calculations reveal an intrinsic preference of cationic D-amino acid-based chiral PNA analogues for the P-form. Topham CM, Smith JC. Biophys J 92 769-786 (2007)


Reviews citing this publication (22)

  1. Peptide nucleic acid (PNA): its medical and biotechnical applications and promise for the future. Ray A, Nordén B. FASEB J 14 1041-1060 (2000)
  2. Peptide nucleic acids (PNA): synthesis, properties and potential applications. Hyrup B, Nielsen PE. Bioorg Med Chem 4 5-23 (1996)
  3. Promising nucleic acid analogs and mimics: characteristic features and applications of PNA, LNA, and morpholino. Karkare S, Bhatnagar D. Appl Microbiol Biotechnol 71 575-586 (2006)
  4. Antisense properties of peptide nucleic acid. Larsen HJ, Bentin T, Nielsen PE. Biochim Biophys Acta 1489 159-166 (1999)
  5. Peptide nucleic acids as therapeutic agents. Nielsen PE. Curr Opin Struct Biol 9 353-357 (1999)
  6. Backbone modifications in oligonucleotides and peptide nucleic acid systems. De Mesmaeker A, Altmann KH, Waldner A, Wendeborn S. Curr Opin Struct Biol 5 343-355 (1995)
  7. Peptide nucleic acids: expanding the scope of nucleic acid recognition. Corey DR. Trends Biotechnol 15 224-229 (1997)
  8. PNA-nucleic acid complexes. Structure, stability and dynamics. Eriksson M, Nielsen PE. Q Rev Biophys 29 369-394 (1996)
  9. Applications of peptide nucleic acids (PNAs) and locked nucleic acids (LNAs) in biosensor development. Briones C, Moreno M. Anal Bioanal Chem 402 3071-3089 (2012)
  10. Primitive genetic polymers. Engelhart AE, Hud NV. Cold Spring Harb Perspect Biol 2 a002196 (2010)
  11. Progress in developing PNA as a gene-targeted drug. Good L, Nielsen PE. Antisense Nucleic Acid Drug Dev 7 431-437 (1997)
  12. Peptide nucleic acids: versatile tools for gene therapy strategies. Dean DA. Adv Drug Deliv Rev 44 81-95 (2000)
  13. Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications. Brodyagin N, Katkevics M, Kotikam V, Ryan CA, Rozners E. Beilstein J Org Chem 17 1641-1688 (2021)
  14. Update on computer-aided drug design. Jackson RC. Curr Opin Biotechnol 6 646-651 (1995)
  15. Unusual DNA conformations. Lebrun A, Lavery R. Curr Opin Struct Biol 7 348-354 (1997)
  16. Antisense peptide nucleic acids as a potential anti-infective agent. Lee HT, Kim SK, Yoon JW. J Microbiol 57 423-430 (2019)
  17. Perspectives on conformationally constrained peptide nucleic acid (PNA): insights into the structural design, properties and applications. Suparpprom C, Vilaivan T. RSC Chem Biol 3 648-697 (2022)
  18. Three's a crowd - stabilisation, structure, and applications of DNA triplexes. Dalla Pozza M, Abdullrahman A, Cardin CJ, Gasser G, Hall JP. Chem Sci 13 10193-10215 (2022)
  19. De Novo Nucleic Acids: A Review of Synthetic Alternatives to DNA and RNA That Could Act as Bio-Information Storage Molecules. Devine KG, Jheeta S. Life (Basel) 10 E346 (2020)
  20. Integration of chemically modified nucleotides with DNA strand displacement reactions for applications in living systems. Kabza AM, Kundu N, Zhong W, Sczepanski JT. Wiley Interdiscip Rev Nanomed Nanobiotechnol 14 e1743 (2022)
  21. Artificial genetic polymers against human pathologies. Ivanov GS, Tribulovich VG, Pestov NB, David TI, Amoah AS, Korneenko TV, Barlev NA. Biol Direct 17 39 (2022)
  22. Promising strategies employing nucleic acids as antimicrobial drugs. Moreira L, Guimarães NM, Santos RS, Loureiro JA, Pereira MC, Azevedo NF. Mol Ther Nucleic Acids 35 102122 (2024)

Articles citing this publication (54)

  1. Antisense properties of duplex- and triplex-forming PNAs. Knudsen H, Nielsen PE. Nucleic Acids Res 24 494-500 (1996)
  2. Letter Crystal structure of a peptide nucleic acid (PNA) duplex at 1.7 A resolution. Rasmussen H, Kastrup JS, Nielsen JN, Nielsen JM, Nielsen PE. Nat Struct Biol 4 98-101 (1997)
  3. Letter Solution structure of a peptide nucleic acid-DNA duplex. Eriksson M, Nielsen PE. Nat Struct Biol 3 410-413 (1996)
  4. Insights into peptide nucleic acid (PNA) structural features: the crystal structure of a D-lysine-based chiral PNA-DNA duplex. Menchise V, De Simone G, Tedeschi T, Corradini R, Sforza S, Marchelli R, Capasso D, Saviano M, Pedone C. Proc Natl Acad Sci U S A 100 12021-12026 (2003)
  5. An assessment of the antisense properties of RNase H-competent and steric-blocking oligomers. Bonham MA, Brown S, Boyd AL, Brown PH, Bruckenstein DA, Hanvey JC, Thomson SA, Pipe A, Hassman F, Bisi JE. Nucleic Acids Res 23 1197-1203 (1995)
  6. Crystal structure of chiral gammaPNA with complementary DNA strand: insights into the stability and specificity of recognition and conformational preorganization. Yeh JI, Shivachev B, Rapireddy S, Crawford MJ, Gil RR, Du S, Madrid M, Ly DH. J Am Chem Soc 132 10717-10727 (2010)
  7. Unwinding of nucleic acids by HCV NS3 helicase is sensitive to the structure of the duplex. Tackett AJ, Wei L, Cameron CE, Raney KD. Nucleic Acids Res 29 565-572 (2001)
  8. Application of peptide nucleic acid to the direct detection of deoxyribonucleic acid amplified by polymerase chain reaction. Sawata S, Kai E, Ikebukuro K, Iida T, Honda T, Karube I. Biosens Bioelectron 14 397-404 (1999)
  9. PNA beacons for duplex DNA. Kuhn H, Demidov VV, Gildea BD, Fiandaca MJ, Coull JC, Frank-Kamenetskii MD. Antisense Nucleic Acid Drug Dev 11 265-270 (2001)
  10. Structural analysis of the catalytic core of human telomerase RNA by FRET and molecular modeling. Gavory G, Symmons MF, Krishnan Ghosh Y, Klenerman D, Balasubramanian S. Biochemistry 45 13304-13311 (2006)
  11. On the stability of peptide nucleic acid duplexes in the presence of organic solvents. Sen A, Nielsen PE. Nucleic Acids Res 35 3367-3374 (2007)
  12. The PNA-DNA hybrid I-motif: implications for sugar-sugar contacts in i-motif tetramerization. Modi S, Wani AH, Krishnan Y. Nucleic Acids Res 34 4354-4363 (2006)
  13. Detection of PCR products of Escherichia coli O157:H7 in human stool samples using surface plasmon resonance (SPR). Kai E, Ikebukuro K, Hoshina S, Watanabe H, Karube I. FEMS Immunol Med Microbiol 29 283-288 (2000)
  14. Evaluating the effect of ionic strength on duplex stability for PNA having negatively or positively charged side chains. De Costa NT, Heemstra JM. PLoS One 8 e58670 (2013)
  15. Design, biological activity and NMR-solution structure of a DNA analogue of yeast tRNA(Phe) anticodon domain. Basti MM, Stuart JW, Lam AT, Guenther R, Agris PF. Nat Struct Biol 3 38-44 (1996)
  16. PNA-based artificial nucleases as antisense and anti-miRNA oligonucleotide agents. Gaglione M, Milano G, Chambery A, Moggio L, Romanelli A, Messere A. Mol Biosyst 7 2490-2499 (2011)
  17. News Peptide nucleic acids and prebiotic chemistry. Miller SL. Nat Struct Biol 4 167-169 (1997)
  18. Inhibition of bacterial translation and growth by peptide nucleic acids targeted to domain II of 23S rRNA. Xue-Wen H, Jie P, Xian-Yuan A, Hong-Xiang Z. J Pept Sci 13 220-226 (2007)
  19. Molecular dynamics simulations of PNA-PNA and PNA-DNA duplexes by the use of new parameters implemented in the GROMACS package: a conformational and dynamics study. Autiero I, Saviano M, Langella E. Phys Chem Chem Phys 16 1868-1874 (2014)
  20. A short phosphodiester window is sufficient to direct RNase H-dependent RNA cleavage by antisense peptide nucleic acid. Malchère C, Verheijen J, van der Laan S, Bastide L, van Boom J, Lebleu B, Robbins I. Antisense Nucleic Acid Drug Dev 10 463-468 (2000)
  21. Methods for assessing DNA hybridization of peptide nucleic acid-titanium dioxide nanoconjugates. Brown EM, Paunesku T, Wu A, Thurn KT, Haley B, Clark J, Priester T, Woloschak GE. Anal Biochem 383 226-235 (2008)
  22. Synthetic, Structural, and RNA Binding Studies on 2-Aminopyridine-Modified Triplex-Forming Peptide Nucleic Acids. Kotikam V, Kennedy SD, MacKay JA, Rozners E. Chemistry 25 4367-4372 (2019)
  23. The structure of a gamma-modified peptide nucleic acid duplex. He W, Crawford MJ, Rapireddy S, Madrid M, Gil RR, Ly DH, Achim C. Mol Biosyst 6 1619-1629 (2010)
  24. Molecular dynamics structures of peptide nucleic acid x DNA hybrid in the wild-type and mutated alleles of Ki-ras proto-oncogene--stereochemical rationale for the low affinity of PNA in the presence of an AC mismatch. Rathinavelan T, Yathindra N. FEBS J 272 4055-4070 (2005)
  25. New studies on the Murchison meteorite shed light on the pre-RNA world. Strasdeit H. Chembiochem 6 801-803 (2005)
  26. Thermal Stability of Peptide Nucleic Acid Complexes. Jasiński M, Miszkiewicz J, Feig M, Trylska J. J Phys Chem B 123 8168-8177 (2019)
  27. BioShuttle-mediated plasmid transfer. Braun K, von Brasch L, Pipkorn R, Ehemann V, Jenne J, Spring H, Debus J, Didinger B, Rittgen W, Waldeck W. Int J Med Sci 4 267-277 (2007)
  28. Enhanced splicing correction effect by an oligo-aspartic acid-PNA conjugate and cationic carrier complexes. Bae YM, Kim MH, Yu GS, Um BH, Park HK, Lee HI, Lee KT, Suh YD, Choi JS. J Control Release 175 54-62 (2014)
  29. Conformational studies of chiral D-Lys-PNA and achiral PNA system in binding with DNA or RNA through a molecular dynamics approach. Autiero I, Saviano M, Langella E. Eur J Med Chem 91 109-117 (2015)
  30. Expanding the repertoire of pyrrolidyl PNA analogues for DNA/RNA hybridization selectivity: aminoethylpyrrolidinone PNA (aepone-PNA). Sharma NK, Ganesh KN. Chem Commun (Camb) 2484-2485 (2003)
  31. Extending the chemistry that supports genetic information transfer in vivo: phosphorothioate DNA, phosphorothioate RNA, 2'-O-methyl RNA, and methylphosphonate DNA. Thaler DS, Liu S, Tombline G. Proc Natl Acad Sci U S A 93 1352-1356 (1996)
  32. Peptide nucleic acid (PNA) from DNA recognition to antisense and DNA structure. Nielsen PE. Biophys Chem 68 103-108 (1997)
  33. Spermine conjugated peptide nucleic acids (spPNA): UV and fluorescence studies of PNA-DNA hybrids with improved stability. Gangamani BP, Kumar VA, Ganesh KN. Biochem Biophys Res Commun 240 778-782 (1997)
  34. Unique base-pair breathing dynamics in PNA-DNA hybrids. Leijon M, Sehlstedt U, Nielsen PE, Gräslund A. J Mol Biol 271 438-455 (1997)
  35. A pyrenyl-PNA probe for DNA and RNA recognition: Fluorescence and UV absorption studies. Tedeschi T, Tonelli A, Sforza S, Corradini R, Marchelli R. Artif DNA PNA XNA 1 83-89 (2010)
  36. Interresidue hydrogen bonding in a peptide nucleic acid.RNA heteroduplex. Torres RA, Bruce TC. Proc Natl Acad Sci U S A 93 649-653 (1996)
  37. Structure of the alpha-homo-DNA:RNA duplex and the function of twist and slide to catalogue nucleic acid duplexes. Nauwelaerts K, Lescrinier E, Herdewijn P. Chemistry 13 90-98 (2007)
  38. Synthesis and properties of chiral peptide nucleic acids with a N-aminoethyl-D-proline backbone. Vilaivan T, Khongdeesameor C, Harnyuttanakorn P, Westwell MS, Lowe G. Bioorg Med Chem Lett 10 2541-2545 (2000)
  39. The first synthesis of chiral PNA monomer-cyclen conjugates. Ma LJ, Zhang GL, Chen SY, Wu B, You JS, Xia CQ, Yu XQ. J Pept Sci 11 812-817 (2005)
  40. Triplex-Forming Peptide Nucleic Acids with Extended Backbones. Kumar V, Brodyagin N, Rozners E. Chembiochem 21 3410-3416 (2020)
  41. Gemdimethyl Peptide Nucleic Acids (α/β/γ-gdm-PNA): E/Z-Rotamers Influence the Selectivity in the Formation of Parallel/Antiparallel gdm-PNA:DNA/RNA Duplexes. Kulkarni P, Datta D, Ganesh KN. ACS Omega 7 40558-40568 (2022)
  42. Structural Insights on Tiny Peptide Nucleic Acid (PNA) Analogues of miRNA-34a: An in silico and Experimental Integrated Approach. Moccia M, Mercurio FA, Langella E, Piacenti V, Leone M, Adamo MFA, Saviano M. Front Chem 8 568575 (2020)
  43. The influence of helix morphology on co-operative polyamide backbone conformational flexibility in peptide nucleic acid complexes. Topham CM, Smith JC. J Mol Biol 292 1017-1038 (1999)
  44. Base pair opening kinetics study of the aegPNA:DNA hydrid duplex containing a site-specific GNA-like chiral PNA monomer. Seo YJ, Lim J, Lee EH, Ok T, Yoon J, Lee JH, Lee HS. Nucleic Acids Res 39 7329-7335 (2011)
  45. C3'-endo-puckered pyrrolidine containing PNA has favorable geometry for RNA binding: novel ethano locked PNA (ethano-PNA). Banerjee A, Kumar VA. Bioorg Med Chem 21 4092-4101 (2013)
  46. Chimeric (aeg-pyrrolidine)PNAs: synthesis and stereo-discriminative duplex binding with DNA/RNA. Lonkar PS, Ganesh KN, Kumar VA. Org Biomol Chem 2 2604-2611 (2004)
  47. Detection of toxic chemicals with high sensitivity by measuring the quantity of induced P450 mRNAs based on surface plasmon resonance. Oyama M, Ikeda T, Lim T, Ikebukuro K, Masuda Y, Karube I. Biotechnol Bioeng 71 217-222 (2000)
  48. Synthesis and structural characterization of monomeric and dimeric peptide nucleic acids prepared by using microwave-promoted multicomponent reactions. Ovadia R, Lebrun A, Barvik I, Vasseur JJ, Baraguey C, Alvarez K. Org Biomol Chem 13 11052-11071 (2015)
  49. Crystallization and preliminary X-ray analysis of a PNA-DNA complex. Kastrup JS, Pilgaard M, Jørgensen FS, Nielsen PE, Rasmussen H. FEBS Lett 363 115-117 (1995)
  50. Synthesis and properties of PNA oligomers containing orotic acid derivatives. Hudson RH, Wojciechowski F. Nucleosides Nucleotides Nucleic Acids 24 1123-1126 (2005)
  51. Detection of PCR products using PNA strand invasion. Drewe LJ, Brightwell G, Hall EA. Mol Cell Probes 14 269-283 (2000)
  52. Fluorinated peptide nucleic acid. Hollenstein M, Gautschi D, Leumann CJ. Nucleosides Nucleotides Nucleic Acids 22 1191-1194 (2003)
  53. Peptide nucleic acid Hoogsteen strand linker design for major groove recognition of DNA thymine bases. Topham CM, Smith JC. J Comput Aided Mol Des 35 355-369 (2021)
  54. Synthesis and characterization of a tetranucleotide analogue containing alternating phosphonate-amide backbone linkages. Yu P, Wang W, Zhang H, Yang X, Liang TC, Gao X. Bioorg Med Chem 9 107-119 (2001)


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