Peptide nucleic acids as therapeutic agents

Current Opinion in Structural Biology

Volumn 9, Issue 3, 1999, Pages 353-357

  Nielsen, Peter E ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; PEPTIDE NUCLEIC ACID;

GENE EXPRESSION REGULATION; GENE TARGETING; NERVE CELL CULTURE; NONHUMAN; PRIORITY JOURNAL; REVIEW;

EID: 0033150790     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(99)80047-5     Document Type: Article

References (46)

1. Nielsen PE, Egholm M, Berg RH, Buchardt O: Sequence selective recognition of DNA by strand displacement with a thymine-substituted polyamide. Science 1991, 254:1497-1500.
2. Cherny DY, Belotserkovskii BP, Frank-Kamenetskii MD, Egholm M, Buchardt O, Berg RH, Nielsen PE: DNA unwinding upon strand displacement of binding of PNA to double stranded DNA. Proc Natl Acad Sci USA 1993, 90:1667-1670.
3. 2/DNA triplex structure upon binding of PNA to dsDNA by strand displacement. J Mol Recognit 1994, 7:165-170.
4. Egholm M, Buchardt O, Christensen L, Behrens C, Freier SM, Driver DA, Berg RH, Kim SK, Norden B, Nielsen PE: PNA hybridizes to complementary oligonucleotides obeying the watson-crick hydrogen bonding rules. Nature 1993, 365:556-568.
5. Jensen KK, Orum H, Nielsen PE, Norden B: Kinetics for hybridization of peptide nucleic acids (PNA) with DNA and RNA studied with the BIAcore technique. Biochemistry 1997, 36:5072-5077.
6. Giesen U, Kleider W, Berding C, Geiger A, ørum H, Nielsen PE: A formula for thermal stability (Tm) prediction of PNA/DNA duplexes. Nucleic Acids Res 1998, 26:5004-5006. An empirical method for calculating the thermal stability (Tm) of PNA-DNA duplexes (6-20 base pairs) has been derived using the Tm calculated from the nearest neighbor model for the corresponding DNA-DNA duplex and applying linear correction factors. The model is based on over 300 measured Tms and was validated using an independent data set. More than 95% of the determinations fell within 5°C of the measured Tm.
7. Brown SC, Thomson SA, Veal JM, Davis DG: NMR solution structure of a peptide nucleic acid complexed with RNA. Science 1994, 265:777-780.
8. Eriksson M, Nielsen PE: Solution structure of a peptide nucleic acid-DNA duplex. Nat Struct Biol 1996, 3:410-413.
9. Betts L, Josey JA, Veal JM, Jordan SR: A nucleic acid triple helix formed by a peptide nucleic acid-DNA complex. Science 1995, 270:1838-1841.
10. Rasmussen H, Kastrup JS, Nielser JN, Nielsen JM, Nielsen PE: Crystal structure of a peptide nucleic acid (PNA) duplex at 1.7 å resolution. Nat Struct Biol 1997, 4:98-101.
11. Demidov VV, Yavnilovich MV, Belotserkovskii BP, Frank-Kamenetskii MD, Nielsen PE: Kinetics and mechanism of PNA binding to duplex DNA. Proc Natl Acad Sci USA 1995, 92:2637-2641.
12. Demidov V, Potaman VN, Frank-Kamenetskii MD, Buchardt O, Egholm M, Nielsen PE: Stability of peptide nucleic acids in human serum and cellular extracts. Biochem Pharmacol 1994, 48:1309-1313.
13. Hanvey JC, Peffer NC, Bisi JE, Thomson SA, Cadilla R, Josey JA, Ricca DJ, Hassman CF, Bonham MA, Au KG et al.: Antisense and antigene properties of peptide nucleic acids. Science 1992, 258:1481-1485.
14. Knudsen H, Nielsen PE: Antisense properties of duplex and triplex forming PNA. Nucleic Acids Res 1996, 24:494-500.
15. Gambacorti-Passerini C, Mologni L, Bertazzoli C, Marchesi E, Grignani F, Nielsen PE: In vitro transcription and translation inhibition by anti-PML/RARα and -PML peptide nucleic acid (PNA). Blood 1996, 88:1411-1417.
16. Mologni L, Le Coutre P, Nielsen PE, Gambacorti-Passerini C: Additive antisense effects of different PNAs on the in vitro translation of the PML/RARα gene. Nucleic Acids Res 1998, 26:1934-1938.
17. Nielsen PE, Egholm M, Buchardt O: Sequence specific transcription arrest by PNA bound to the template strand. Gene 1994, 149:139-145.
18. Vickers TA, Griffith MC, Ramasamy K, Risen LM, Freier SM: Inhibition of NF-kappa B specific transcriptional activation by PNA strand invasion. Nucleic Acids Res 1995, 23:3003-3008.
19. Praseuth D, Grigoriev M, Guieysse AL, Pritchard LL, Harel-Bellan A, Nielsen PE, Helene C: Peptide nucleic acids directed to the promoter of the α-chain of the interleukin-2 receptor. Biochim Biophys Acta 1996, 1309:226-238.
20. Taylor RW, Chinnery PF, Turnbull DM, Lightowlers RN: Selective inhibition of mutant human mitochondrial DNA replication in vitro by peptide nucleic acids. Nat Genet 1997, 15:212-215.
21. Norton JC, Piatyszek MA, Wright WE, Shay JW, Corey DR: Inhibition of human telomerase activity by peptide nucleic acids. Nat Biotechnol 1996, 14:615-618.
22. Hamilton SE, Pitts AE, Katipally RR, Jia X, Rutter JP, Davies BA, Shay JW, Wright WE, Corey DR: Identification of determinants for inhibitor binding within the RNA active site of human telomerase using PNA scanning. Biochemistry 1997, 36:11873-11880.
23. Bonham MA, Brown S, Boyd AL, Brown PH, Bruckenstein DA, Hanvey JC, Thomson SA, Pipe A, Hassman F, Bisi JE et al.: An assessment of the antisense properties of RNAse H-competent and steric-blocking oligomers. Nucleic Acids Res 1995, 23:1197-1203.
24. Derossi D, Chassaing G, Prochiantz A: Trojan peptides: The penetratin system for intracellular delivery. Trends Cell Biol 1998, 8:84-87.
25. Simmons CG, Pitts AE, Mayfield LD, Shay JW, Corey DR: Synthesis and membrane permeability of PNA-peptide conjugates. Bioorg Med Chem Lett 1997, 7:3001-3006.
26. Pooga H, Soomets U, Hällbrink M, Valkna A, Saar K, Rezaei K, Kahl U, Hao J-X, Xu X-J, Wiesenfeld-Hallin Z et al.: Cell penetrating PNA constructs regulate galanin receptor levels and modify pain transmission in vivo. Nat Biotechnol 1998, 16:857. This paper reports the use of a PNA-peptide conjugate in the down regulation of the galanin receptor in neuronal cells in culture. 21 (or 20)-mer PNAs targeted to position 1-21 (or 18-38) of the human galanin receptor gene were conjugated via disulfides to the cationic peptide transportan or p-Antp(43-58). Only peptide-coupled PNAs caused a decrease in the number of galanin receptors in Bowes cells, as measured by receptor-ligand binding and the 18-38-positioned PNA was approximately 10 times more potent than the 1-21-positioned PNA. Intrathecal administration of the corresponding rat PNA also caused decreased galanin binding in the dorsal horn, as well as an attenuated electrophysiological response in rats in vivo. These results are fully consistent with a specific antisense effect of such PNA-peptide constructs in neural cells in vivo. This paper, together with [27••], is the first to report the (antisense) effects of PNA in animal systems; however, it is pertinent to establish whether such effects are peculiar to the nervous system.
27. Tyler BM, McCormick DJ, Hoshall CV, Douglas CL, Jansen K, Lacy BW, Cusack B, Richelson E: Specific gene blockade shows that peptide nucleic acids readily enter neuronal cells in vivo. FEBS Lett 1998, 421:280-284. This study used short (12-14-mer) naked PNAs to target mu and NTR-1 neuronal receptors in the brain of rats. The PNAs were injected directly into the brain; the effect was scored as a 'pain response' and was supported by subsequent measurement of the receptor-binding capacity of neuronal homogenates from sacrificed animals. The results are fully compatible with specific antisense down regulation of receptor synthesis, but no measurements of receptor protein levels were reported. Thus, an antisense mechanism is not demonstrated. It is noteworthy that naked PNAs showed good efficacy in this study, whereas such PNAs were without effect in the system of Pooga et al. [26••].
28. Aldrian-Herrada G, Desarménien MG, Orcel H, Boissin-Agasse L, Méry J, Brugidou J, Rabie A: A peptide nucleic acid (PNA) is more rapidly internalized in cultured neurons when coupled to a retro-inverso delivery peptide. The antisense activity depresses the target mrna and protein in magnocellular oxytocin neurons. Nucleic Acids Res 1998, 26:4910-4916. This study reports the uptake of a 'naked' 15-mer PNA in primary nerve cells in culture. Twofold more efficient uptake was achieved using the PNA conjugated to a 'retro-inverso' analog of the 16-mer p-Antp peptide. An antisense effect was implied by a decreased level of prepro-oxytocin mRNA, as measured by quantitative reverse transcriptase PCR. In contrast to natural peptides, the 'retro-inverso' peptide should exhibit good biostability and therefore could be employed in in vivo applications.
29. Monia BP, Johnston JF, Geiger T, Muller M, Fabbro D: Antitumor activity of a phosphorothioate antisense oligodeoxynucleotide targeted against C-raf kinase. Nat Med 1996, 2:668-675.
30. Good L, Nielsen PE: Antisense inhibition of gene expression in bacteria by PNA targeted to mRNA. Nat Biotechnol 1998, 16:355-358. 15-mer PNAs were targeted to the AUG initiation codon of the β-galactosidase and β-lactamase genes in E. coli. Gene-specific, dose-dependent antisense down regulation of these genes is demonstrated in the more permeable AS19 strain (effects were also seen in wild-type K12). Furthermore, down regulation of the β-lactamase gene resensitized the bacteria to amphicillin by six orders of magnitude. These results open possibilities for developing 'genetic antibiotics' and provide a means for performing target validation and functional genomics studies using the antisense technique in bacteria.
31. Good L, Nielsen PE: Inhibition of translation and bacterial growth by peptide nucleic acid targeted to ribosomal RNA. Proc Natl Acad Sci USA 1998, 95:2073-2076. PNAs were designed to bind to ribosomal RNA in E. coli. Of the 10 PNAs tested, two inhibited in vitro translation and bacterial growth of AS19 at low micromolar concentrations. These were triplex-forming bis-PNAs that target homopurine sequences in the α-sarcin loop or in the peptidyl transferase center. These results introduce ribosomal RNA as a target for (microbial) antisense drugs.
32. Koppelhus U, Zachar V, Nielsen PE, Liu X, Eugen-Olsen J, Ebbesen P: Efficient in vitro inhibition of HIV-1 gag reverse transcription by peptide nucleic acid (PNA) at minimal ratios of PNA/RNA. Nucleic Acids Res 1997, 25:2167-2173.
33. Lee R, Kaushik N, Modak MJ, Vinayak R, Pandey VN: Polyamide nucleic acid targeted to the primer binding site of the HIV-1 RNA genome blocks in vitro HIV-1 reverse transcription. Biochemistry 1998, 37:900-910.
34. Boffa LC, Carpaneto EM, Mariani MR, Louissaint M, Allfrey VG: Contrasting effects of PNA invasion of the chimeric DMMYC gene on transcription of its myc and PVT domains. Oncol Res 1997, 9:41-51.
35. Faruqi AF, Egholm M, Glazer PM: Peptide nucleic acid-targeted mutagenesis of a chromosomal gene in mouse cells. Proc Natl Acad Sci USA 1998, 95:1398-1403. Apart from indicating that PNA triplex invasion complexes are somewhat mutagenic in eukaryotic cells, the most important result of this study is implicitly that PNA double-stranded DNA gene targeting is feasible in living cells.
36. Larsen HJ, Nielsen PE: Transcription-mediated binding of peptide nucleic acid (PNA) to double stranded DNA: Sequence specific suicide transcription. Nucleic Acids Res 1996, 24:458-463.
37. Bentin T, Nielsen PE: Enhanced peptide nucleic acid (PNA) binding to supercoiled DNA: Possible implications for DNA 'breathing' dynamics. Biochemistry 1996, 35:8863-8869.
38. Kurakin A, Larsen HJ, Nielsen PE: Cooperative duplex invasion of peptide nucleic acids (PNA). Chem Biol 1998, 5:81-89.
39. Bastide L, Boehmer PE, Villani G, Lebleu B: Inhibition of a DNA-helicase by peptide nucleic acids. Nucleic Acids Res 1999, 27:551-554.
40. Møllegaard NE, Buchardt O, Egholm M, Nielsen PE: PNA-DNA strand displacement loops as artificial transcription promoters. Proc Natl Acad Sci USA 1994, 91:3892-3895.
41. Uhlmann E, Peyman A, Breipohl G, Will DW: PNA: Synthetic polyamide nucleic acids with unusual binding properties. Angew Chem Int Ed Engl 1998, 37:2796-2823.
42. Püschl A, Sforza S, Haaima G, Dahl O, Nielsen PE: Peptide nucleic acids (PNAs) with a functional backbone. Tetrahedron Lett 1998, 39:4707-4710.
43. Efimov VA, Choob MV, Buryakova AA, Kalinkina AL, Chakhmakhcheva OG: Synthesis and evaluation of some properties of chimeric oligomers containing PNA and phosphono-PNA residues. Nucleic Acids Res 1998, 26:566-575.
44. van der Laan AC, Havenaar P, Oosting RS, Kuyl-Yeheskiely E, Uhlmann E, Van Boom JH: Optimization of the binding properties of PNA-(5=)-DNA chimerae. Bioorg Med Chem Lett 1998, 8:663-668.
45. Rusckowski M, Qu T, Chang F, Hnatowich DJ: Pretargeting using peptide nucleic acid. Cancer 1997, 80:2699-2705. The authors utilized PNAs as general recognition reagents with an overwhelming number of code combinations. Further applications along these lines should be interesting to pursue.
46. Eriksson M, Nielsen PE: PNA-nucleic acid complexes: Structure, stability and dynamics. Q Rev Biophys 1996, 29:369-394.