Journal article
Distance and affinity dependence of triplex-induced recombination
Biochemistry (Easton), Vol.44(10), pp.3856-3864
03/15/2005
DOI: 10.1021/bi0481040
PMID: 15751961
Abstract
Triplex-forming oligonucleotides (TFOs) have the potential to serve as gene therapeutic agents on the basis of their ability to mediate site-specific genome modification via induced recombination. However, high-affinity triplex formation is limited to polypurine/polypyrimidine sites in duplex DNA. Because of this sequence restriction, careful analysis is needed to identify suitable TFO target sites within or near genes of interest. We report here an examination of two key parameters which influence the efficiency of TFO-induced recombination: (1) binding affinity of the TFO for the target site and (2) the distance between the target site and the mutation to be corrected. To test the influence of binding affinity, we compared induced recombination in human cell-free extracts by a series of G-rich oligonucleotides with an identical base composition and an increasing number of mismatches in the third strand binding code. As the number of mismatches increased and, therefore, binding affinity decreased, induced recombination frequency also dropped. There was an apparent threshold at an equilibrium dissociation constant (K(d)) of 1 x 10(-)(7) M. In addition, TFO chemical modification with N,N-diethylethylenediamine (DEED) internucleoside linkages to confer improved binding was found to yield increased levels of induced recombination. To test the ability of triplex formation to induce recombination at a distance, episomal targets with informative reporter genes were constructed to contain polypurine TFO target sites at varying distances from the mutations to be corrected. TFO-induced recombination in mammalian cells between a plasmid vector and a donor oligonucleotide was detected at distances ranging from 24 to 750 bp. Together, these results indicate that TFO-induced recombination requires high-affinity binding but can affect sites hundreds of base pairs away from the position of triplex formation.
Details
- Title: Subtitle
- Distance and affinity dependence of triplex-induced recombination
- Creators
- Melissa P Knauert - Department of Therapeutic Radiology, Yale University School of Medicine, P.O. Box 208040, New Haven, Connecticut 06520, USAJanice A LloydFaye A RogersHirock J DattaMichael L BennettDaniel L WeeksPeter M Glazer
- Resource Type
- Journal article
- Publication Details
- Biochemistry (Easton), Vol.44(10), pp.3856-3864
- Publisher
- United States
- DOI
- 10.1021/bi0481040
- PMID
- 15751961
- ISSN
- 0006-2960
- eISSN
- 1520-4995
- Grant note
- P50HL062178 / NHLBI NIH HHS R55 GM056277-01 / NIGMS NIH HHS GM07205 / NIGMS NIH HHS CA103543 / NCI NIH HHS R01CA64186 / NCI NIH HHS R55 GM056277 / NIGMS NIH HHS R01GM54731 / NIGMS NIH HHS
- Language
- English
- Date published
- 03/15/2005
- Academic Unit
- Stead Family Department of Pediatrics; Biochemistry and Molecular Biology
- Record Identifier
- 9984024413902771
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