Kinetic Sequence Discrimination of Cationic Bis-PNAs Upon Targeting of Double-stranded DNA

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 1998 Feb 28

PMID 9421519

Citations 27

Authors

H Kuhn

V V Demidov

M D Frank-Kamenetskii

P E Nielsen

Affiliations

Soon will be listed here.

Abstract

Strand displacement binding kinetics of cationic pseudoisocytosine-containing linked homopyrimidine peptide nucleic acids (bis-PNAs) to fully matched and singly mismatched decapurine targets in double-stranded DNA (dsDNA) are reported. PNA-dsDNA complex formation was monitored by gel mobility shift assay and pseudo-first order kinetics of binding was obeyed in all cases studied. The kinetic specificity of PNA binding to dsDNA, defined as the ratio of the initial rates of binding to matched and mismatched targets, increases with increasing ionic strength, whereas the apparent rate constant for bis-PNA-dsDNA complex formation decreases exponentially. Surprisingly, at very low ionic strength two equally charged bis-PNAs which have the same sequence of nucleobases but different linkers and consequently different locations of three positive charges differ in their specificity of binding by one order of magnitude. Under appropriate experimental conditions the kinetic specificity for bis-PNA targeting of dsDNA is as high as 300. Thus multiply charged cationic bis-PNAs containing pseudoisocytosines (J bases) in the Hoogsteen strand combined with enhanced binding affinity also exhibit very high sequence specificity, thereby making such reagents extremely efficient for sequence-specific targeting of duplex DNA.

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References

Smulevitch S, Simmons C, Norton J, Wise T, Corey D . Enhancement of strand invasion by oligonucleotides through manipulation of backbone charge. Nat Biotechnol. 1996; 14(13):1700-4. DOI: 10.1038/nbt1296-1700. View

Nielsen P, Egholm M, Berg R, Buchardt O . Sequence specific inhibition of DNA restriction enzyme cleavage by PNA. Nucleic Acids Res. 1993; 21(2):197-200. PMC: 309092. DOI: 10.1093/nar/21.2.197. View

Good L, Nielsen P . Progress in developing PNA as a gene-targeted drug. Antisense Nucleic Acid Drug Dev. 1997; 7(4):431-7. DOI: 10.1089/oli.1.1997.7.431. View

Egholm M, Christensen L, Dueholm K, Buchardt O, Coull J, Nielsen P . Efficient pH-independent sequence-specific DNA binding by pseudoisocytosine-containing bis-PNA. Nucleic Acids Res. 1995; 23(2):217-22. PMC: 306657. DOI: 10.1093/nar/23.2.217. View

Wetmur J . DNA probes: applications of the principles of nucleic acid hybridization. Crit Rev Biochem Mol Biol. 1991; 26(3-4):227-59. DOI: 10.3109/10409239109114069. View

Gottesfeld J, NEELY L, Trauger J, BAIRD E, Dervan P . Regulation of gene expression by small molecules. Nature. 1997; 387(6629):202-5. DOI: 10.1038/387202a0. View

Veselkov A, Demidov V, Frank-Kamenetskii M, Nielsen P . PNA as a rare genome-cutter. Nature. 1996; 379(6562):214. DOI: 10.1038/379214a0. View

Demidov V, Yavnilovich M, Belotserkovskii B, Frank-Kamenetskii M, Nielsen P . Kinetics and mechanism of polyamide ("peptide") nucleic acid binding to duplex DNA. Proc Natl Acad Sci U S A. 1995; 92(7):2637-41. PMC: 42273. DOI: 10.1073/pnas.92.7.2637. View

Kutyavin I, Rhinehart R, Lukhtanov E, Gorn V, Meyer Jr R, Gamper Jr H . Oligonucleotides containing 2-aminoadenine and 2-thiothymine act as selectively binding complementary agents. Biochemistry. 1996; 35(34):11170-6. DOI: 10.1021/bi960626v. View

10.

Veselkov A, Demidov V, NIELSON P, Frank-Kamenetskii M . A new class of genome rare cutters. Nucleic Acids Res. 1996; 24(13):2483-7. PMC: 145980. DOI: 10.1093/nar/24.13.2483. View

11.

Corey D . Peptide nucleic acids: expanding the scope of nucleic acid recognition. Trends Biotechnol. 1997; 15(6):224-9. DOI: 10.1016/S0167-7799(97)01037-8. View

12.

Nielsen P, Egholm M, Buchardt O . Sequence-specific transcription arrest by peptide nucleic acid bound to the DNA template strand. Gene. 1994; 149(1):139-45. DOI: 10.1016/0378-1119(94)90422-7. View

13.

Bentin T, Nielsen P . Enhanced peptide nucleic acid binding to supercoiled DNA: possible implications for DNA "breathing" dynamics. Biochemistry. 1996; 35(27):8863-9. DOI: 10.1021/bi960436k. View

14.

Demidov V, Frank-Kamenetskii M, Egholm M, Buchardt O, Nielsen P . Sequence selective double strand DNA cleavage by peptide nucleic acid (PNA) targeting using nuclease S1. Nucleic Acids Res. 1993; 21(9):2103-7. PMC: 309471. DOI: 10.1093/nar/21.9.2103. View

15.

Nilsson M, Malmgren H, Samiotaki M, Kwiatkowski M, Chowdhary B, Landegren U . Padlock probes: circularizing oligonucleotides for localized DNA detection. Science. 1994; 265(5181):2085-8. DOI: 10.1126/science.7522346. View

16.

Nielsen P, Egholm M, Berg R, Buchardt O . Sequence-selective recognition of DNA by strand displacement with a thymine-substituted polyamide. Science. 1991; 254(5037):1497-500. DOI: 10.1126/science.1962210. View

17.

Mollegaard N, Buchardt O, Egholm M, Nielsen P . Peptide nucleic acid.DNA strand displacement loops as artificial transcription promoters. Proc Natl Acad Sci U S A. 1994; 91(9):3892-5. PMC: 43688. DOI: 10.1073/pnas.91.9.3892. View

18.

Kool E . Preorganization of DNA: Design Principles for Improving Nucleic Acid Recognition by Synthetic Oligonucleotides. Chem Rev. 1997; 97(5):1473-1488. PMC: 2790533. DOI: 10.1021/cr9603791. View

19.

Peffer N, Hanvey J, Bisi J, Thomson S, Hassman C, Noble S . Strand-invasion of duplex DNA by peptide nucleic acid oligomers. Proc Natl Acad Sci U S A. 1993; 90(22):10648-52. PMC: 47834. DOI: 10.1073/pnas.90.22.10648. View

20.

Demidov V, Cherny D, Kurakin A, Yavnilovich M, Malkov V, Frank-Kamenetskii M . Electron microscopy mapping of oligopurine tracts in duplex DNA by peptide nucleic acid targeting. Nucleic Acids Res. 1994; 22(24):5218-22. PMC: 332063. DOI: 10.1093/nar/22.24.5218. View