Pseudocomplementary PNAs as selective modifiers of protein activity on duplex DNA: the case of type IIs restriction enzymes.

This study evaluates the potential of pseudocomplementary peptide nucleic acids (pcPNAs) for sequence-specific modification of enzyme activity towards double-stranded DNA (dsDNA). To this end, we analyze the ability of pcPNA-dsDNA complexes to site-selectively interfere with the action of four type IIs restriction enzymes. We have found that pcPNA-dsDNA complexes exhibit a different degree of DNA protection against cleaving/nicking activity of various isoschizomeric endonucleases under investigation (PleI, MlyI and N.BstNBI) depending on their type and mutual arrangement of PNA-binding and enzyme recognition/cleavage sites. We have also found that the pcPNA targeting to closely located PleI or BbsI recognition sites on dsDNA generates in some cases the nicking activity of these DNA cutters. At the same time, MlyI endonuclease, a PleI isoschizomer, does not exhibit any DNA nicking/cleavage activity, being completely blocked by the nearby pcPNA binding. Our results have general implications for effective pcPNA interference with the performance of DNA-processing proteins, thus being important for prospective applications of pcPNAs.

[1]  E. Lukhtanov,et al.  Oligonucleotides containing 2-aminoadenine and 2-thiothymine act as selectively binding complementary agents. , 1996, Biochemistry.

[2]  C. Giovannangeli,et al.  Triplex-forming molecules for modulation of DNA information processing. , 2000, Current opinion in molecular therapeutics.

[3]  M. Egholm,et al.  Efficient pH-independent sequence-specific DNA binding by pseudoisocytosine-containing bis-PNA. , 1995, Nucleic acids research.

[4]  D. Crothers,et al.  Nucleic Acids: Structures, Properties, and Functions , 2000 .

[5]  M. Waring,et al.  Drug-nucleic acid interactions , 2001 .

[6]  V V Demidov,et al.  Sequence-specific protection of duplex DNA against restriction and methylation enzymes by pseudocomplementary PNAs. , 2000, Biochemistry.

[7]  K R Fox,et al.  Targeting DNA with triplexes. , 2000, Current medicinal chemistry.

[8]  P. Nielsen.  Peptide nucleic acid targeting of double-stranded DNA. , 2001, Methods in enzymology.

[9]  J. Barton,et al.  Detection of DNA base mismatches using DNA intercalators. , 2002, Methods in enzymology.

[10]  M. Egholm,et al.  Sequence selective double strand DNA cleavage by peptide nucleic acid (PNA) targeting using nuclease S1. , 1993, Nucleic acids research.

[11]  D. Gowers,et al.  Towards mixed sequence recognition by triple helix formation. , 1999, Nucleic acids research.

[12]  Winter Ta.  Gene targeted agents: new opportunities for rational drug development. , 2000 .

[13]  David R Corey,et al.  Novel antisense and peptide nucleic acid strategies for controlling gene expression. , 2002, Biochemistry.

[14]  P. Nielsen,et al.  Double duplex invasion by peptide nucleic acid: a general principle for sequence-specific targeting of double-stranded DNA. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[15]  C. Bailly,et al.  DNA recognition by intercalator-minor-groove binder hybrid molecules. , 1991, Bioconjugate chemistry.

[16]  J. Heitman,et al.  A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. , 2003, Nucleic acids research.

[17]  M. Egholm,et al.  Sequence specific inhibition of DNA restriction enzyme cleavage by PNA. , 1993, Nucleic acids research.

[18]  M. Waring,et al.  DNA recognition by intercalators and hybrid molecules , 1994, Journal of molecular recognition : JMR.

[19]  P. Nielsen,et al.  PNA as a rare genome-cutter , 1996, Nature.

[20]  R. Sinden.  DNA Structure and Function , 1994 .

[21]  Peter E. Nielsen,et al.  Kinetics and mechanism of the DNA double helix invasion by pseudocomplementary peptide nucleic acids , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[22]  H. Kong,et al.  The nicking endonuclease N.BstNBI is closely related to type IIs restriction endonucleases MlyI and PleI. , 2001, Nucleic acids research.

[23]  M. Frank-Kamenetskii,et al.  Kinetic analysis of specificity of duplex DNA targeting by homopyrimidine peptide nucleic acids. , 1997, Biophysical journal.

[24]  M. Egholm,et al.  Sequence-specific transcription arrest by peptide nucleic acid bound to the DNA template strand. , 1994, Gene.

[25]  B. Armitage.  The impact of nucleic acid secondary structure on PNA hybridization. , 2003, Drug discovery today.

[26]  P. Nielsen.  Peptide nucleic acids : protocols and applications , 2004 .

[27]  Richard J. Roberts,et al.  REBASE-restriction enzymes and methylases , 1993, Nucleic Acids Res..

[28]  Peter E. Nielsen,et al.  A new class of genome rare cutters , 1996, Nucleic Acids Res..

[29]  V V Demidov,et al.  Stability of peptide nucleic acids in human serum and cellular extracts. , 1994, Biochemical pharmacology.

[30]  I. Haq.  Thermodynamics of drug-DNA interactions. , 2002, Archives of biochemistry and biophysics.

[31]  E. Protozanova,et al.  Monitoring of single nicks in duplex DNA by gel electrophoretic mobility‐shift assay , 2002, Electrophoresis.

[32]  J. Lown,,et al.  Recent developments in sequence selective minor groove DNA effectors. , 2000, Current medicinal chemistry.

[33]  M. Frank-Kamenetskii,et al.  Tailoring the activity of restriction endonuclease PleI by PNA‐induced DNA looping , 2002, EMBO reports.

[34]  R. Bürli,et al.  Sequence-specific DNA recognition by polyamides. , 1999, Current opinion in chemical biology.

[35]  P. Dervan,et al.  Molecular recognition of DNA by small molecules. , 2001, Bioorganic & medicinal chemistry.

[36]  S Neidle,et al.  DNA minor-groove recognition by small molecules. , 2001, Natural product reports.

[37]  D. Dean.  Peptide nucleic acids: versatile tools for gene therapy strategies. , 2000, Advanced drug delivery reviews.

[38]  Yongbo Hu,et al.  Artificial site-specific DNA-nicking system based on common restriction enzyme assisted by PNA openers. , 2003, Biochemistry.

[39]  V V Demidov,et al.  Kinetic sequence discrimination of cationic bis-PNAs upon targeting of double-stranded DNA. , 1998, Nucleic acids research.

[40]  N. Gormley,et al.  Many Type IIs Restriction Endonucleases Interact with Two Recognition Sites before Cleaving DNA* , 2002, The Journal of Biological Chemistry.

[41]  V V Demidov,et al.  Kinetics and mechanism of polyamide ("peptide") nucleic acid binding to duplex DNA. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[42]  T. Creighton.  Methods in Enzymology , 1968, The Yale Journal of Biology and Medicine.

[43]  S. Mirkin,et al.  Triplex DNA structures. , 1995, Annual review of biochemistry.

[44]  R J Roberts,et al.  REBASE ? restriction enzymes and methylases , 2000, Nucleic Acids Res..

[45]  M. Egholm,et al.  Sequence-selective recognition of DNA by strand displacement with a thymine-substituted polyamide. , 1991, Science.

[46]  P. Glazer,et al.  Triplex forming oligonucleotides: sequence-specific tools for gene targeting. , 2001, Human molecular genetics.

[47]  P. Nielsen,et al.  Applications of peptide nucleic acids. , 1999, Current opinion in biotechnology.

[48]  V V Demidov,et al.  Sequence-specific targeting of duplex DNA by peptide nucleic acids via triplex strand invasion. , 2001, Methods.

[49]  V. Demidov.  PD-loop technology: PNA openers at work , 2001, Expert review of molecular diagnostics.

[50]  A. Jeltsch,et al.  Structure and function of type II restriction endonucleases. , 2001, Nucleic acids research.

[51]  B. Potter,et al.  Cleavage of phosphorothioate-substituted DNA by restriction endonucleases. , 1984, The Journal of biological chemistry.

[52]  B. Nordén,et al.  Peptide nucleic acid (PNA): its medical and biotechnical applications and promise for the future , 2000, The FASEB Journal.

[53]  G. Snounou,et al.  Supercoiling and the mechanism of restriction endonucleases. , 1984, European journal of biochemistry.

[54]  V. A. Efimov,et al.  Synthesis and evaluation of some properties of chimeric oligomers containing PNA and phosphono-PNA residues. , 1998, Nucleic acids research.