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Nucleic Acids Research, 2003, Vol. 31, No. 14 3929-3935
© 2003 Oxford University Press

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

Ekaterina Protozanova, Vadim V. Demidov, Peter E. Nielsen1 and Maxim D. Frank-Kamenetskii*

Center for Advanced Biotechnology, Boston University, Boston, MA 02215, USA and 1 Center for Biomolecular Recognition, The Panum Institute, Copenhagen N, DK-2200, Denmark

*To whom correspondence should be addressed. Tel: +1 617 353 8498; Fax: +1 617 353 8501; Email: mfk{at}bu.edu
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors

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.


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