The forgotten variables of DNA array hybridization.
The reproducibility and reliability of DNA array measurements have been repeatedly questioned during the years. A reassessment of fundamental variables of nucleic acid hybridization might help to solve some of these problems. The hybridization equilibrium, t(1/2), is 41 days for a target human genome. Similar hybridization t(1/2) are expected for whole-transcriptome chips hybridized with tissue cDNA. This implies that most studies on mammalian cells have not been performed under equilibrium conditions. Non-equilibrium binding introduces a stochastic factor into hybridization dynamics; in other words, hybridization will prevail at different spots in different experiments, everything else being equal. A careful re-evaluation of results obtained under non-equilibrium conditions might prove fruitful and help to explain instances where findings conflict.
Carletti
Erminia
E
Unit of Cancer Pathology, Department of Oncology and Neurosciences and CeSI, Fondazione G. D'Annunzio, University of Chieti, 66013 Chieti Scalo (Chieti), Italy.
Guerra
Emanuela
E
Alberti
Saverio
S
D015342:DNA Probes / Q000737:chemistry*; D020869:Gene Expression Profiling / Q000379:methods*; D007700:Kinetics; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015203:Reproducibility of Results; D013269:Stochastic Processes
D015342:DNA Probes