Nucleic Acids Research Advance Access originally published online on October 19, 2006
Nucleic Acids Research 2006 34(20):5790-5799; doi:10.1093/nar/gkl736
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Nucleic Acids Research, 2006, Vol. 34, No. 20 5790-5799
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Structural Biology |
Structural diversity of target-specific homopyrimidine peptide nucleic acid–dsDNA complexes
Department of Medical Biochemistry and Genetics, The Panum Institute, University of Copenhagen, Blegdamsvej 3 2200 Copenhagen N, Denmark
*To whom correspondence should be addressed. Tel: +45 35327762/61; Fax: +45 35396042; Email: pen{at}imbg.ku.dk
Received June 15, 2006. Revised August 25, 2006. Accepted September 22, 2006.
Sequence-selective recognition of double-stranded (ds) DNA by homopyrimidine peptide nucleic acid (PNA) oligomers can occur by major groove triplex binding or by helix invasion via triplex P-loop formation. We have compared the binding of a decamer, a dodecamer and a pentadecamer thymine–cytosine homopyrimidine PNA oligomer to a sequence complementary homopurine target in duplex DNA using gel-shift and chemical probing analyses. We find that all three PNAs form stable triplex invasion complexes, and also conventional triplexes with the dsDNA target. Triplexes form with much faster kinetics than invasion complexes and prevail at lower PNA concentrations and at shorter incubation times. Furthermore, increasing the ionic strength strongly favour triplex formation over invasion as the latter is severely inhibited by cations. Whereas a single triplex invasion complex is formed with the decameric PNA, two structurally different target-specific invasion complexes were characterized for the dodecameric PNA and more than five for the pentadecameric PNA. Finally, it is shown that isolated triplex complexes can be converted to specific invasion complexes without dissociation of the Hoogsteen base-paired triplex PNA. These result demonstrate a clear example of a ‘triplex first’ mechanism for PNA helix invasion.
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.