Heteroduplex analysis using flow cytometric microbead assays to detect deletions, insertions, and single‐strand lesions

We explore the possibilities offered by flow cytometric microbead analysis to develop high throughput methods for the detection of deletions/insertions and single‐strand DNA lesions. The products of PCR reactions derived from reference and test samples are denatured and reannealed, then exposed to e...

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Bibliographic Details
Published in:Cytometry. Part A 2008-03, Vol.73A (3), p.238-245
Main Authors: Hegedüs, Éva, Imre, László, Pataki, Judit, Lizanecz, Erzsébet, Székvölgyi, Lóránt, Fazakas, Ferenc, Bacsó, Zsolt, Tóth, Attila, Szabó, Miklós, Seres, Zoltán, Szabó, Gábor
Format: Article
Language:English
Subjects:
chemical cleavage
deletion
DNA
DNA, Single-Stranded - analysis
DNA, Single-Stranded - genetics
flow cytometry
Flow Cytometry - methods
Gene Deletion
Heteroduplex Analysis - methods
Humans
insertion
Microspheres
mismatch
MLL
Mutagenesis, Insertional - methods
nick‐translation
S1 nuclease
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Summary:We explore the possibilities offered by flow cytometric microbead analysis to develop high throughput methods for the detection of deletions/insertions and single‐strand DNA lesions. The products of PCR reactions derived from reference and test samples are denatured and reannealed, then exposed to enzymatic or chemical treatments distinguishing homoduplices from heteroduplices. The biotin‐ and dye labeled reaction products are immobilized on microbeads and the homo‐ and heteroduplices are assessed in separate fluorescence channels, by flow cytometry. Using a model system based on the mixed lineage leukemia gene breakpoint cluster region, we demonstrate that deletions and insertions in genomic DNA can be detected, using S1 nuclease and chemical cleavage to distinguish hetero‐ from homoduplices, or a restriction enzyme cleaving only the homoduplices. Single‐strand discontinuities can also be detected, by combining nick‐translation, using labeled nucleotide, and flow cytometric microbead analysis. The methodical approaches demonstrated are applicable in a versatile manner in basic cell and molecular biological research and also promise direct application for high throughput screening of genetic diseases and lesions, including insertions or deletions of short sequence elements and single‐strand lesions formed at hypersensitive sites in response to apoptotic stimuli. © 2008 International Society for Analytical Cytology
ISSN:1552-4922
1552-4930
DOI:10.1002/cyto.a.20492