PNA2/DNA triplexes: Stability and specificity

Russian Journal of Genetics

Volumn 41, Issue 7, 2005, Pages 707-719

  Krupnik, O V ^a   Lazurkin, Yu S ^a  

^a INSTITUTE OF MOLECULAR GENETICS   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 23944517966     PISSN: 10227954     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11177-005-0150-5     Document Type: Article

References (85)

1. Nielsen, P.E., Egholm, M., Berg, R.H., and Buchardt, O., Sequence-Selective Recognition of DNA by Strand Displacement with a Thymine-Substituted Polyamide, Science, 1991, vol. 254, pp. 1497-1500.
2. Uhlmann, E., Peyman, A., Breipohl, G., and Will, D.W., PNA: Synthetic Polyamide Nucleic Acids with Unusual Binding Properties, Angew. Chem., Int. Ed. Engl., 1998, vol. 37, pp. 2796-2823.
3. Nelson, K.E., Levy, M., and Miller, S.L., Peptide Nucleic Acids Rather Than RNA May Have Been the First Genetic Molecule, Proc. Natl. Acad. Sci. USA, 2000, vol. 97, pp. 3868-3871.
4. Knight, R.D. and Landweber, L.F., The Early Evolution of the Genetic Code, Cell (Cambridge, Mass.), 2000, vol. 101, pp. 569-572.
5. Egholm, M., Buchardt, O., Christensen, L., et al., PNA Hybridizes to Complementary Oligonucleotides Obeying the Watson-Crick Hydrogen Bonding Rules, Nature, 1993, vol. 365, pp. 566-568.
6. Eriksson, M. and Nielsen, P.E., PNA Nucleic Acid Complexes - Structure, Stability and Dynamics, Quart. Rev. Biophys., 1996, vol. 29, pp. 369-394.
7. Hyrup, B. and Nielsen, P.E., Peptide Nucleic Acids (PNA): Synthesis, Properties and Potential Applications, Bioorg. Med. Chem., 1996, vol. 4, pp. 5-23.
8. Nielsen, P.E and Egholm, M., An Introduction to PNA, Peptide Nucleic Acids: Protocols and Applications, Nielsen, P.E. and Egholm, M., Eds., Wymondham: Horizon Sci., 1999, pp. 1-20.
9. Haaima, G., Lohse, A., Buchardt, O., and Nielsen, P.E., Peptide Nucleic Acids (PNA) Containing Thymine Monomers Derived from Chiral Amino Acids: Hybridization and Solubility Properties of D-Lysine PNA, Angewandte Chemie, 1996, vol. 35, pp. 1939-1941.
10. Peffer, N.J., Hanvey, J.C., Bisi, J.E., et al., Strand-Invasion of Duplex DNA by Peptide Nucleic Acid Oligomers, Proc. Natl. Acad. Sci. USA, 1993, vol. 90, pp. 10648-10652.
11. Schwarz, F.P., Robinson, S., and Butler, J.M., Thermodynamic Comparison of PNA/DNA and DNA/DNA Hybridization Reactions at Ambient Temperature, Nucleic Acids Res., 1999, vol. 27, pp. 4792-4800.
12. Chakrabarti, M.C. and Schwarz, F.P., Thermal Stability of PNA/DNA and DNA/DNA Duplexes by Differential Scanning Calorimetry, Nucleic Acids Res., 1999, vol. 27, pp. 4801-4806.
13. Tomac, S., Sarkar, M., Ratilainen, T., et al., Ionic Effects on the Stability and Conformation of Peptide Nucleic Acid Complexes, J. Am. Chem. Soc., 1996, vol. 118, pp. 5544-5552.
14. Dueholm, K.L. and Nielsen, P.E., Chemistry, Properties and Applications of PNA, New J. Chem., 1997, vol. 21, pp. 19-31.
15. Wittung, P., Nielsen, P.E., and Norden, B., Direct Observation of Strand Invasion by Peptide Nucleic Acid (PNA) into Double-Stranded DNA, J. Am. Chem. Soc., 1996, vol. 118, pp. 7049-7054.
16. Cherny, D.I., Belotserkovskii, B.P., Frank-Kamenetskii, M.D., et al., DNA Unwinding upon Strand-Displacement of Binding of Thymine-Substituted Polyamide to Double-Stranded DNA, Proc. Natl. Acad. Sci. USA, 1993, vol. 90, pp. 1667-1670.
17. 2/DNA Triplex Structure upon Binding of PNA to dsDNA by Strand Displacement, J. Mol. Recognition, 1994, vol. 7, pp. 165-170.
18. Demidov, V.V., Cherny, D.I., Kurakin, A.V., et al., Electron Microscopy Mapping of Oligo Purine Tracts in Duplex DNA by Peptide Nucleic Acid Targeting, Nucleic Acids Res., 1994, vol. 22, pp. 5218-5222.
19. Kosaganov, Yu.N., Stetsenko, D.A., Lubyako, E.N., et al., Effect of Temperature and Ionic Strength on the Dissociation Kinetics and Lifetime of PNA-DNA Triplexes, Biochemistry, 2000, vol. 39, 11 742-11 747.
20. Lazurkin, Yu.S., Stability and Specificity of Triplexes Formed by Peptide Nucleic Acid with DNA, Mol. Biol. (Moscow), 1999, vol. 33, pp. 94-99.
21. Egholm, M., Christensen, L., Dueholm, K.L., et al., Efficient pH-Independent Sequence-Specific DNA Binding by Pseudo-Isocytosine Containing Bis-PNA, Nucleic Acids Res., 1995, vol. 23, pp. 217-222.
22. Betts, L., Josey, J.A., Veal, J.M., and Jordan, S.R., Crystal Structure of a Nucleic Acid Triplex at 2.5 Å: A Peptide Nucleic Acid-DNA Complex, Science, 1995, vol. 270, pp. 1838-1841.
23. Griffith, M.C., Risen, L.M., Greig, M.J., et al., Single and Bis Peptide Nucleic Acids As Triplexing Agents: Binding and Stoichiometry, J. Am. Chem. Soc., 1995, vol. 117, pp. 831-832.
24. Lohse, J., Dahl, O., and Nielsen, P.E., Double Duplex Invasion by Peptide Nucleic Acid: A General Principle for Sequence-Specific Targeting of Double-Stranded DNA, Proc. Natl. Acad. Sci. USA, 1999, vol. 96, pp. 11804-11808.
25. Larsen, H.J. and Nielsen, P.E., Transcription-Mediated Binding of Peptide Nucleic Acid (PNA) to Double-Stranded DNA: Sequence-Specific Suicide Transcription, Nucleic Acids Res., 1996, vol. 24, pp. 458-463.
26. Mollegaard, N.E., Buchardt, O., Egholm, M., and Nielsen, P.E., Peptide Nucleic Acid-DNA Strand Displacement Loops As Artificial Transcription Promoters, Proc. Natl. Acad. Sci. USA, 1994, vol. 91, pp. 3892-3895.
27. Good, L. and Nielsen, P.E., Antisense Inhibition of Gene Expression in Bacteria by PNA Targeted to mRNA, Nat. Biotechnol., 1998, vol. 16, pp. 355-358.
28. Nulf, C.J. and Corey, D., Intracellular Inhibition of Hepatitis C Virus (HCV) Internal Ribosomal Entry Site (IRES)-Dependent Translation by Peptide Nucleic Acids (PNAs) and Locked Nucleic Acids (LNAs), Nucleic Acids Res., 2004, vol. 19, pp. 3792-3798.
29. Siwkowski, A.M., Malik, L., Esau, C.C., et al., Identification and Functional Validation of PNAs that Inhibit Murine CD40 Expression by Redirection of Slicing, Nucleic Acids Res., 2004, vol. 32, pp. 2695-2706.
30. Nielsen, P.E., Egholm, M., Berg, R.H., and Buchardt, O., Sequence-Specific Inhibition of DNA Restriction Enzyme Cleavage by PNA, Nucleic Acids Res., 1993, vol. 21, pp. 197-200.
31. Krasil'nikova, M.M., Izvol'skii, K.I., Krupnik, O.V., and Lazurkin, Yu.S., The Use of the Specific Binding of Peptide Nucleic Acid to DNA in the Achilles Heel Method, Dokl. Akad. Nauk SSSR, 1995, no. 344, pp. 156-159.
32. Krasil'nikova, M.M., Izvol'skii, K.I., Krupnik, O.V., and Lazurkin, Yu.S., Use of Peptide Nucleic Acid in the Achilles Heel Approach, Mol. Biol., (Moscow), 1996, vol. 30, pp. 282-284.
33. Tyler, B.M., McCormich, D.J., Hoshall, C.V., et al., Specific Gene Blockade Shows That Peptide Nucleic Acids Readily Enter Neuronal Cells in Vivo, FEBS Lett., 1998, vol. 421, pp. 280-284.
34. Demidov, V.V., Potaman, V.N., Frank-Kamenetskii, M.D., et al., Stability of Peptide Nucleic Acids in Human Serum and Cellular Extracts, Biochem. Pharmacol., 1994, vol. 48, pp. 1310-1313.
35. Oehlke, J., Wallukat, G., Wolf, Y., et al., Enhancement of Intracellular Concentration and Biological Activity of PNA after Conjugation with a Cell-Penetrating Synthetic Model Peptide, Eur. J. Biochem., 2004, vol. 271, pp. 3043-3049.
36. Morris, M.C., Chaloin, L., Choob, M., et al., Combination of a New Generation of PNAs with a Peptide-Based Carrier Enables Efficient Targeting of Cell Cycle Progression, Gene Ther., 2004, vol. 11, pp. 757-764.
37. Fisher, L., Soomets, U., Cortes Toro, V., et al., Cellular Delivery of a Double-Stranded Oligonucleotide: NF-κB Decoy by Hybridization to Complementary PNA Linked to a Cell-Penetrating Peptide, Gene Ther., 2004, vol. 11, pp. 1264-1272.
38. Bentin, T. and Nielsen, P.E., Enhanced Peptide Nucleic Acid Binding to Supercoiled DNA: Possible Implications for DNA "Breathing" Dynamics, Biochemistry, 1996, vol. 35, pp. 8863-8869.
39. Liu, L.F. and Wang, J.C., Supercoiling of the DNA Template during Transcription, Proc. Natl. Acad. Sci. USA, 1987, vol. 84, pp. 7024-7027.
40. Veselkov, A.G., Demidov, V.V., Frank-Kamenetskii, M.D., and Nielsen, P.E., PNA As a Rare Genome Cutter, Nature, 1996, vol. 379, p. 214.
41. Veselkov, A.G., Demidov, V.V., Nielsen, P.E., and Frank-Kamenetskii, M.D., A New Class of Genome Rare Cutters, Nucleic Acids Res., 1996, vol. 24, pp. 2483-2487.
42. Ørum, H., PCR Clamping, Peptide Nucleic Acids: Protocols and Applications, Nielsen, P.E. and Egholm, M., Eds., Wymondham: Horizon Sci., 1999, pp. 193-200.
43. Thisted, M., Just, T., Pluzek, K.-J., et al., Application of Peptide Nucleic Acid Probes for in Situ Hybridization, Peptide Nucleic Acids: Protocols and Applications, Nielsen, P.E.. and Egholm, M., Eds., Wymondham: Horizon Sci., 1999, pp. 99-118.
44. Thisted, M., Just, T., Pluzek, K.-J., et al., Detection of Immunoglobulin κ Light Chain mRNA in Paraffin Sections by in Situ Hybridization Using Peptide Nucleic Acid Probes, Cell Vision, 1996, vol. 3, pp. 358-363.
45. Just, T., Andersen, T., Mathiassen, M.A., and Nielsen, K.V., Detection of Human Telomere Sequences with Fluorescein- and Cy3-Labelled Peptide Nucleic Acid (PNA) Probes, Am. Ass. Cancer Res., 1998, vol. 39, p. 2389.
46. Stender, H., Mollerup, T.A., Lund, K., et al., Direct Detection and Identification of Mycobacterium tuberculosis in Smear-Positive Sputum Samples by Fluorescence in Situ Hybridization (FISH) Using Peptide Nucleic Acid (PNA) Probes, Int. J. Tub. Lung Dis., 1999, vol. 3, no. 9, pp. 830-837.
47. Stender, H., Lund, K., Petersen, K.H., et al., A Fluorescence in Situ Hybridization (FISH) Assay for the Differentiation between Tuberculosis and Non-Tuberculosis Mycobacterium Species in Smears of Mycobacterium Cultures Using Peptide Nucleic Acid (PNA) Probes, J. Clin. Microbiol., 1999, vol. 37, pp. 2760-2765.
48. Gonzalez, V., Padilla, E., Gimenez, M., et al., Rapid Diagnosis of Staphylococcus aureus Bacteremia Using S. aureus PNA FISH, Eur. J. Clin. Microbiol. Infect. Dis., 2004, vol. 23, pp. 396-398.
49. Stender, H., Broomer, A., Oliveira, K., et al., Rapid Detection, Identification, and Enumeration of Pseudomonas aeruginosa in Bottled Water Using Peptide Nucleic Acid Probes, J. Microbiol. Methods, 2000, vol. 42, pp. 245-253.
50. Stender, H., Kurtzmann, C., Hyldig-Nielsen, J.J., et al., Identification of Dekkera bruxellensis (Brettanomyces) from Wine by Fluorescence in Situ Hybridization Using Peptide Nucleic Acid Probes, Appl. Environ. Microbiol., 2001, vol. 67, pp. 938-941.
51. Stender, H., Broomer, A., Oliveira, K., et al., Rapid Detection, Identification, and Enumeration of Escherichia coli Cells in Municipal Water by Chemiluminescent in Situ Hybridization, Appl. Environ. Microbiol., 2001, vol. 67, pp. 142-147.
52. Perry-O'Keefe, H., Stender, H., Broomer, A., et al., Filler-Based PNA in Situ Hybridization for Rapid Detection, Identification, and Enumeration of Specific Microorganisms, J. Appl. Microbiol., 2001, vol. 90, pp. 180-189.
53. Stender, H., Fiandaca, M., Hyldig-Nielsen, J.J., and Coull, J., PNA for Rapid Microbiology, J. Microbiol. Methods, 2002, vol. 48, pp. 1-17.
54. Hashimoto, K. and Ishimori, Y., Preliminary Evaluation of Electrochemical PNA Array for Detection of Single Base Mismatch Mutations, Lab. Chip, 2001, vol. 1, pp. 61-63.
55. Germini, A., Mezzelani, A., Lesignoli, F., et al., Detection of Genetically Modified Soybean Using Peptide Nucleic Acids (PNAs) and Microarray Technology, J. Agric. Food Chem., 2004, vol. 52, pp. 4535-4540.
56. Demidov, V.V., Frank-Kamenelskii, M.D., Egholm, M., et al., Sequence Selective Double Strand DNA Cleavage by PNA Targeting Using Nuclease S1, Nucleic Acids Res., 1993, vol. 21, pp. 2103-2107.
57. Nielsen, P.E., Egholm, M., Berg, R.H., and Buchardt, O., Peptide Nucleic Acids (PNAs): Potential Anti-Sense and Anti-Gene Agents, Anti-Cancer Drug Design, 1993, vol. 8, pp. 53-63.
58. Bukanov, N.O., Demidov, V.V., Nielsen, P.E., and Frank-Kamenetskii, M.D., PD-Loop: A Complex of Duplex DNA with an Oligonucleotide, Proc. Natl. Acad. Sci. USA, 1998, vol. 95, pp. 5516-5520.
59. Demidov, V.V., Bukanov, N.O., and Frank-Kamenetskii, M.D., Duplex DNA Capture, Peptide Nucleic Acids: Protocols and Applications, Nielsen, P.E. and Egholm, M., Eds., Wymondham: Horizon Sci., 1999, pp. 175-184.
60. Demidov, V.V., Bukanov, N.O., and Frank-Kamenetskii, M.D., Duplex DNA Capture, Curr. Issues Mol. Biol., 2000, vol. 2, pp. 31-35.
61. Broude, N.E., Demidov, V.V., Kuhn, H., et al., PNA Openers As a Tool for Direct Quantification of Specific Targets in Duplex DNA, J. Biomol. Struct. Dyn., 1999, vol. 17, pp. 237-244.
62. Kuhn, H., Demidov, V.V., and Frank-Kamenetskii, M.D., Topological Links between Duplex DNA and a Circular DNA Single Strand, Angew. Chem., Int. Ed. Engl., 1999, vol. 38, pp. 1446-1449.
63. Demidov, V.V., Broude, N.E., Lavrentyeva-Smolina, I.V., et al., An Artificial Primosome: Design, Function and Applications, ChemBioChem, 2001, vol. 2, pp. 133-139.
64. Demidov, V.V. and Frank-Kamenetskii, M.D., PNA-Directed Genome Rare Cutting, Peptide Nucleic Acids: Protocols and Applications, Nielsen, P.E.. and Egholm, M., Eds., Wymondham: Horizon Sci., 1999, pp. 163-174.
65. Knudsen, H. and Nielsen, P.E., Application of Peptide Nucleic Acid in Cancer Therapy, Anti-Cancer Drugs, 1997, vol. 8, pp. 113-118.
66. Wang, K., Zhang, Q.F., Wang, X.S., et al., Peptide Nucleic Acids Arrest the Growth of Gastric Cancer Cells SGC7901, Chin. Med. J., 2004, vol. 117, pp. 566-570.
67. Shammas, M.A., Liu, X., Gavory, G., et al., Targeting the Single-Strand G-Rich Overhang of Telomeres with PNA Inhibits Cell Growth and Induces Apoptosis of Human Immortal Cells, Exp. Cell Res., 2004, vol. 295, pp. 204-214.
68. Karadag, A., Riminucci, M., Bianco, P., et al., A Novel Technique Based on PNA Hybridization Probe and FRET Principle for Quantification of Mutant Genotype in Fibrous Dysplasia/McCune-Albright Syndrome, Nucleic Acids Res., 2004, vol. 32, no. 7, p. 63.
69. Boules, M., Williams, K., Gollatz, E., et al., Down-Regulation of Amyloid Precursor Protein by Peptide Nucleic Acid in Vivo, J. Mol. Neurosci., 2004, vol. 24, pp. 123-128.
70. Cherny, D.I., Kurakin, A.V., Lyamichev, V.I., et al., Electron Microscopic Studies of Sequence-Specific Recognition of Duplex DNA by Different Ligands, J. Mol. Recognition, 1994, vol. 7, pp. 171-176.
71. Demidov, V.V., Yavnilovich, M.V., Belotserkovskii, B.P., et al., Kinetics and Mechanism of Polyamide ("Peptide") Nucleic Acid Binding to Duplex DNA, Proc. Natl. Acad. Sci. USA, 1995, vol. 92, pp. 2637-2641.
72. Kuhn, H., Demidov, V.V., Nielsen, P.E., and Frank-Kamenetskii, M.D., An Experimental Study of Mechanism and Specificity of Peptide Nucleic Acid (PNA) Binding to Duplex DNA, J. Mol. Biol., 1999, vol. 286, pp. 1337-1345.
73. Demidov, V.V., Yavnilovich, M.V., and Frank-Kamenetskii, M.D., Kinetic Analysis of Specificity of Duplex DNA Targeting by Homopyrimidine Peptide Nucleic Acids, Biophys. J., 1997, vol. 72, pp. 2763-2769.
74. Lomakin, A. and Frank-Kamenetskii, M.D., A Theoretical Analysis of Specificity of Nucleic Acid Interactions with Oligonucleotides and Peptide Nucleic Acids (PNAs), J. Mol. Biol., 1998, vol. 276, pp. 57-70.
75. Demidov, V.V. and Frank-Kamenetskii, M.D., Two Sides of the Coin: Affinity and Specificity of Nucleic Acid Interactions, Trends Biochem. Sci., 2004, vol. 29, pp. 62-71.
76. Krasil'nikova, M.M. and Veselkov, A.G., Improvement of the Specificity of the Binding of Peptide Nucleic Acid with DNA, Mol. Biol. (Moscow), 1996, vol. 30, pp. 379-386.
77. Kuhn, H., Demidov, V.V., Frank-Kamenetskii, M.D., and Nielsen, P.E., Kinetic Sequence Discrimination of Cationic Bis-PNAs upon Targeting of Double-Stranded DNA, Nucleic Acids Res., 1998, vol. 26, pp. 582-587.
78. 2/DNA Triple Helices, J. Biomol. Struct. Dyn., 2001, vol. 19, pp. 535-542.
79. Marky, L.A. and Breslauer, K.J., Calculating Thermodynamic Data for Transitions of Any Molecularity from Equilibrium Melting Curves, Biopolymers, 1987, vol. 26, pp. 1601-1620.
80. Krupnik, O.V., Bis-PNA/DNA Triplexes: Stability and Polymorphism, Cand. Sci. (Physmath.) Dissertation, Moscow: Moscow Phys.-Techn. Inst., 2004.
81. Kurakin, A., Larsen, H.J., and Nielsen, P.E., Cooperative Strand Displacement by Peptide Nucleic Acid (PNA), Chem. Biol., 1998, vol. 5, pp. 81-89.
82. Hansen, G.I., Bentin, T., Larsen, H.J., and Nielsen, P.E., Structural Isomers of Bis-PNA Bound to a Target in Duplex DNA, J. Mol. Biol., 2001, vol. 307, pp. 67-74.
83. Krupnik, O.V., Fadeeva, N.V., and Lazurkin, Yu.S., Polymorphism of PNA-DNA Complexes, Mol. Biol. (Moscow), 2002, vol. 36, pp. 236-238.
84. Krupnik, O.V., Fadeeva, N.V., Kvitko, N.P., et al., Stability and Transformations of Bis-PNA/DNA Triplex Structural Isomers, J. Biomol. Struct. Dyn., vol. 21, pp. 503-512.
85. Ratilainen, T., Holmen, A., Tuite, E., et al., Hybridization of Peptide Nucleic Acid, Biochemistry, 1998, vol. 37, pp. 12331-12342.