Nucleic Acids Research Advance Access originally published online on January 20, 2009
Nucleic Acids Research 2009 37(5):1682-1689; doi:10.1093/nar/gkn1042
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Nucleic Acids Research, 2009, Vol. 37, No. 5 1682-1689
© 2009 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.
Chemistry and Synthetic Biology |
DNA models of trinucleotide frameshift deletions: the formation of loops and bulges at the primer–template junction
1Department of Chemistry and Institute of Molecular Biology, University of Oregon, Eugene, OR 97403-1229, USA, 2Université de Toulouse, UPS, IPBS (Institut de Pharmacologie et de Biologie Structurale) and 3CNRS IPBS, F-31077 Toulouse, France
*To whom correspondence should be addressed. Tel: +33 5 61 17 59 60; Fax: +33 5 61 17 59 94; Email: neil.johnson{at}ipbs.fr
Received October 20, 2008. Revised November 26, 2008. Accepted December 12, 2008.
Although mechanisms of single-nucleotide residue deletion have been investigated, processes involved in the loss of longer nucleotide sequences during DNA replication are poorly understood. Previous reports have shown that in vitro replication of a 3'-TGC TGC template sequence can result in the deletion of one 3'-TGC. We have used low-energy circular dichroism (CD) and fluorescence spectroscopy to investigate the conformations and stabilities of DNA models of the replication intermediates that may be implicated in this frameshift. Pyrrolocytosine or 2-aminopurine residues, site-specifically substituted for cytosine or adenine in the vicinity of extruded base sequences, were used as spectroscopic probes to examine local DNA conformations. An equilibrium mixture of four hybridization conformations was observed when template bases looped-out as a bulge, i.e. a structure flanked on both sides by duplex DNA. In contrast, a single-loop structure with an unusual unstacked DNA conformation at its downstream edge was observed when the extruded bases were positioned at the primer–template junction, showing that misalignments can be modified by neighboring DNA secondary structure. These results must be taken into account in considering the genetic and biochemical mechanisms of frameshift mutagenesis in polymerase-driven DNA replication.
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