PNA-nucleic acid complexes. Structure, stability and dynamics

Quarterly Reviews of Biophysics

Volumn 29, Issue 4, 1996, Pages 369-394

  Eriksson, Magdalena ^a   Nielsen, Peter E ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA; PEPTIDE NUCLEIC ACID;

BASE PAIRING; CHEMICAL STRUCTURE; CONFORMATIONAL TRANSITION; DNA PROTEIN COMPLEX; ELECTRICITY; PRIORITY JOURNAL; REVIEW; SOLUBILITY;

EID: 0030440962     PISSN: 00335835     EISSN: None     Source Type: Journal    
DOI: 10.1017/s0033583500005886     Document Type: Review

References (42)

1. ALMARSON, Ø. & BRUICE, T. C. (1993). Peptide nucleic acid (PNA) conformation and polymorphism in PNA-DNA and PNA-RNA hybrids, Proc. Natl. Acad. Sci. USA 90, 9542-9546.
2. BENTIN, T. & NIELSEN, P. E. (1996). Enhanced peptide nucleic acid (PNA) binding to supercoiled DNA: possible implications for DNA 'breathing' dynamics. Biochemistry, in press.
3. BETTS, L., JOSEY, J. A., VEAL, J. M. & JORDAN, S. R. (1995). A nucleic acid triple helix formed by a peptide nucleic acid-DNA complex. Science 270, 1838-1841.
4. BROWN, S. C., THOMSON, S. A., VEAL, J. M. & DAVIS, D. G. (1994). NMR solution structure of a peptide nucleic acid complexed with RNA. Science 265, 777-780.
5. CHEN, S.-M., MOHAN, V., KIELY, J. S., GRIFFITH, M. C. & GRIFFEY, R. H. (1994). Molecular dynamics and NMR studies of single-stranded PNAs. Tetrahedron Letters 35, 5105-5108.
6. CHERNY, D. Y., BELOTSERKOVSKII, B. P., FRANK-KAMENETSKII, M. D., EGHOLM, M., BUCHARDT, O., BERG, R. H. & NIELSEN, P. E. (1993). Proc. Natl. Acad. Sci. USA 90, 1667-1670.
7. CHRISTENSEN, L., FITZPATRICK, R., GILDEA, B., PETERSEN, K. H., HANSEN, H. F., KOCH, T., EGHOLM, M., BUCHARDT, O., NIELSEN, P. E., COULL, J. & BERG, R. H. (1995). Solid-phase synthesis of peptide nucleic acids (PNA) J. Peptide Sci. 3, 175-183.
8. DEMIDOV, V. V., POTAMAN, V. N., FRANK-KAMENETSKII, M., EGHOLM, M., BUCHARDT, O., SÖNNICHSEN, S. H. & NIELSEN, P. E. (1994). Stability of of peptide nucleic acids in human serum and cellular extracts. Biochemical Pharmacology 48, 1310-1313.
9. DEMIDOV, V. V., YAVNILOVICH, M. V., BELOTSERKOVSKII, B. P., FRANK-KAMENETSKII, M. & NIELSEN, P. E. (1995). Kinetics and mechanism of polyamide ('peptide') nucleic acid binding to duplex DNA. Proc. Natl. Acad. Sci. USA 92, 2637-2641.
10. EGHOLM, M., BUCHARDT, O., NIELSEN P. E, & BERG, R. H. (1992). Peptide nucleic acids (PNA). Oligonucleotide analogues with an achiral peptide backbone. Amer. Chem. Soc. 114, 1895-1897.
11. EGHOLM, M., BUCHARDT, O., CHRISTENSEN, L., BEHRENS, K., FREIER, S. M., DRIVER, D. A., BERG, R. H., KIM, S. K., NORDÉN, B. & NIELSEN, P. E. (1993). PNA hybridizes to complementary oligonucleotides obeying the Watson-Crick hydrogen-bonding rules. Nature 365, 566-568.
12. EGHOLM, M., CHRISTENSEN, L., DUEHOLM, K. L., BUCHARDT, O., COULL, J. & NIELSEN, P. E. (1995). Efficient pH-independent sequence-specific DNA binding by pseudoisocytosine-containing bis-PNA. Nucleic Acids Res. 23, 217-222.
13. ERIKSSON, M. & NIELSEN, P. E. (1996). Solution structure of a peptide nucleic acid-DNA duplex, Nature Struct. Biol. 3, 410-413.
14. GRIFFITH , M. C., RISEN, L. M., GREIG, M. J., LESNIK, E. A., SPRANKLE, K. G., GRIFFEY, R. H,. KIELY, J. S & FREIER, S. M. (1995). Single and bis peptide nucleic acid as triplexing agents: binding and stoichiometry. J. Amer. Chem. Soc. 117, 831-832.
15. HAAIMA, G., LOHSE, A., BUCHARDT, O. & NIELSEN, P. E. (1996). Peptide nucleic acids (PNA) containing thymine monomers derived from chiral amino acids. PNAs with increased binding and sequence discrimination. Angewandte Chemie. In press.
16. HANVEY , J. C., PEFFER, N. J., BISI, J. E., THOMSON, S. A., CADILLA, R., JOSEY, J, A., RICCA, D. J., HASSMAN, C. F., BONHAM, M. A., AU, K. G., CARTER, S. G., BRUCKENSTEIN, D. A., BOYD, A. L., NOBLE, S. A. & BABISS, L. E. (1992). Antisense and antigene properties of peptide nucleic acids. Science 258, 1481-1485.
17. HYRUP, B. & NIELSEN, P. E. (1996). Peptide nucleic acids (PNA): synthesis, properties and potential applications. Bioorganic & Medicinal Chemistry 4, 5-23.
18. JENSEN, K. K., ØRUM, H., NIELSEN, P. E. & NORDÉN, B. (1996). Hybridization kinetics of peptide nucleic acids (PNA) with DNA and RNA studied with BIAcore technique. Submitted manuscript.
19. JUPE, E. R., SINDEN, R. R. & CARTWRIGHT, I.L. (1993). Stably maintained microdomain of localized unrestrained supercoiled at a Drosophila heat shock protein locus. EMBO J. 12, 1067-1075.
20. 8 and Poly(dA) shown by linear and circular dichroism spectroscopy. J. Am. Chem. Soc. 115, 6477-6481.
21. LEIJON, M., GRÄSLUND, A., NIELSEN, P. E., BUCHARDT, O., NORDÉN, B., KRISTENSEN, S. M. & ERIKSSON, M. (1994). Structural characterization of PNA-DNA duplexes by NMR. Evidence or DNA in a B-like Conformation. Biochemistry 33, 9820-9825.
22. LJUNGMAN, M. & HANAWALT, P. C. (1995). Presence of negative torsional tension in the promoter region of the transcriptionally poised dihydrofolate reductase gene in vivo. Nucleic Acids Res. 23, 1782-1789.
23. MESMAEKER, A. D., ALTMAXN, K.-H., WALDNER, A. & WENDEBORN, S. (1995). Backbone modifications in oligonucleotides and peptide nucleic acid systems. Current Opinion in Structural Biology 5, 343-355.
24. MOSER, H. E. & DERVAN, P. B. (1987). Sequence specific cleavage of double helical DNA by triple helix formation. Science 238, 645-650.
25. NICHOLLS, A., SHARP, K. A. & HONIG, B. H. (1991). Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins II, 281-296.
26. NIELSEN, P. E. (1995). DNA analogues with nonphophodiester backbones. Annu. Rev. Biophys. Biomol. Struct. 24, 167-183.
27. NIELSEN, P. E. (1996). Peptide nucleic acids (PNA). A new dimension to peptide libraries and aptamers. Methods Enzymol. 267, 426-433.
28. NIELSEN, P. E. & CHRISTENSEN, L. (1996). Strand displacement binding of a duplexforming homopurine PNA to a homopyrimidine duplex DNA target. J. Am. Chem. Soc. 118, 2287-2288.
29. NIELSEN, P. E. & ØRUM, H. (1995). Peptide nucleic acid (PNA) as new biomolecular tools. In Molecular biology: Current innovations and future trends (H. Griffin, ed.) Horizon Scientific Press, UK, p. 73-86.
30. NIELSEN, P. E., EGHOLM, M., BERG, R. H. & BUCHARDT, O. (1991). Sequence-selective recognition by strand displacement with a thymine-substituted polyamide. Science 254, 1497-1500.
31. NIELSEN, P. E., EGHOLM, M. & BUCHARDT, O. (1994a). Peptide nucleic acid (PNA). A DNA mimic with a peptide backbone. Bioconjugate Chemistry 5, 3-7.
32. 2/DNA triplex structure upon binding of PNA to dsDNA by strand displacement. J. Mol. Recogn. 7, 165-170.
33. NOBLE, S. A., BONHAM, M. A., BISI, J. E., BRUCKENSTEIN, D. A., BROAVN, P. H., BROWN, S. C., CADILLA, R., GAUL, M. D., HANVEY, J. C. et al. (1995). Impact of biophysical parameters on the biological assessment of peptide nucleic acids, antisense inhibitors of gene expression. Drug Development Research 34, 184-195.
34. ØRUM, H., NIELSEN, P. E., EGHOLM, M., BERG, R. H., BUCHARDT, O., STANLEY, C. (1993). Single base pair mutation analysis by PNA directed PCR clamping. Nucleic Acids Res. 21, 5332-5336.
35. PEFFER, X. J., HANVEY, J. C., BISI, J. E., THOMSON, S. A., HASSMAN, C. F., NOBLE, S. A. & BABISS, L. E. (1993). Strand-invasion of duplex DNA by peptide nucleic acid oligomers. Proc. Natl. Acad. Sci. USA 90, 10648-10652.
36. RADHAKRISHNAN, I. & PATEL, D. J. (1995). DNA triplex: solution structures, hydration sites, energetics, interactions, and function. Biochemistry 33, 11405-11416.
37. TOMAC, S., SARKAR, M., RATILAINEN, T., WITTUNG, P., XIELSEN, P. E., NORDÉN, B. & GRÄSLUND, A. (1996). Iionic effects on the stability and conformation of peptide nucleic acid (PNA) complexes. J. Amer. Chem. Soc. In press.
38. WITTUNG, P., NIELSEN, P. E., BUCHARDT, O., EGHOLM, M. & NORDÉN, B. (1994a). DNA-like double helix formed by peptide nucleic acid. Nature 368, 561-563.
39. WITTUNG, P., KIM, S. K., BUCHARDT, O., NIELSEN, P. E. & NORDÉN, B. (1994b). Interactions of DNA binding ligands with PNA-DNA hybrids. Nucleic Acids Res. 22, 5371-5377.
40. WITTUNG, P., ERIKSSON, M., LYNG, R., XIELSEN, P. E. & NORDÉN, B. (1995a). Induced chirality in PNA-PNA duplexes. J. Amer. Chem. Soc. 117, 10167-10173.
41. WITTUNG, P., KAJANUS, J., EDWARDS, K., NIELSEN, P. E., NORDÉN, B. & MALMSTRÖM, B. G. (1995b). Phospholopid membrane permeability of peptide nucleic acid. FEBS Letters 365, 27-29.
42. WITTUNG, P., NIELSEN, P. E. & NORDÉN, B. (1996). Direct observation od strand invasion by peptide nucleic acid (PNA) into double-stranded DNA. J. Amer. Chem. Soc. 118, 7049-7054.