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Detection Of Cross‐Hybridized DNA Strands within Pools Using SYBR Green I Fluorescence
Author(s) -
Ray Arunima,
Wood Lauren,
Macula Anthony,
Pogozelski Wendy
Publication year - 2007
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.21.5.a266-d
Subject(s) - dna , computational biology , sybr green i , oligonucleotide , fluorescence , biology , double stranded , dna microarray , biological system , genetics , gene , physics , polymerase chain reaction , gene expression , quantum mechanics
The ability to quickly identify cross‐hybridized DNA duplexes is important the design of DNA libraries for use of microarrays, mutation analysis, DNA computing, and combinatorial group testing. These applications rely on hybridization of perfect Watson‐Crick complements to ensure predictable results. We designed a method suitable for detecting cross‐hybridizations in pools of up to 36 different non‐hybridizing strands using the fluorescent dye SYBR Green I. Test strands of length 16 bp were designed to test a variety of bulges and dangling ends. Some of these test strands formed duplexes that were detected in a pool with 35 other non‐hybridizing strands. Testing in pools allows the verification of multiple strands at once, leading to faster confirmation of DNA libraries. We are applying these methods to the classical group testing theory which allows us to test randomly constructed pools and identify the specific mispaired strands.