16780376

Source:http://linkedlifedata.com/resource/pubmed/id/16780376

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Predicate	Object
rdf:type	pubmed:Citation
lifeskim:mentions	umls-concept:C0020202, umls-concept:C0022702, umls-concept:C0028953, umls-concept:C0205148, umls-concept:C0681814, umls-concept:C0871935, umls-concept:C0920585, umls-concept:C1707455
pubmed:issue	1
pubmed:dateCreated	2006-6-19
pubmed:abstractText	The optimal design of oligonucleotide microchips and efficient discrimination between perfect and mismatch duplexes strongly depend on the external transport of target DNA to the cells with immobilized probes as well as on respective association and dissociation rates at the duplex formation. In this paper we present the relevant theory for hybridization of DNA fragments with oligonucleotide probes immobilized in the cells on flat substrate. With minor modifications, our theory also is applicable to reaction-diffusion hybridization kinetics for the probes immobilized on the surface of microbeads immersed in hybridization solution. The main theoretical predictions are verified with control experiments. Besides that, we compared the characteristics of the surface and gel-based oligonucleotide microchips. The comparison was performed for the chips printed with the same pin robot, for the signals measured with the same devices and processed by the same technique, and for the same hybridization conditions. The sets of probe oligonucleotides and the concentrations of probes in respective solutions used for immobilization on each platform were identical as well. We found that, despite the slower hybridization kinetics, the fluorescence signals and mutation discrimination efficiency appeared to be higher for the gel-based microchips with respect to their surface counterparts even for the relatively short hybridization time about 0.5-1 hour. Both the divergence between signals for perfects and the difference in mutation discrimination efficiency for the counterpart platforms rapidly grow with incubation time. In particular, for hybridization during 3 h the signals for gel-based microchips surpassed their surface counterparts in 5-20 times, while the ratios of signals for perfect-mismatch pairs for gel microchips exceeded the corresponding ratios for surface microchips in 2-4 times. These effects may be attributed to the better immobilization efficiency and to the higher thermodynamic association constants for duplex formation within gel pads.
pubmed:language	eng
pubmed:journal	http://linkedlifedata.com/resource/pubmed/journal/8404176
pubmed:citationSubset	IM
pubmed:status	MEDLINE
pubmed:month	Aug
pubmed:issn	0739-1102
pubmed:author	pubmed-author:BarskyV EVE, pubmed-author:ChechetkinV RVR, pubmed-author:DonnikovM YMY, pubmed-author:LivshitsM AMA, pubmed-author:Pan'kovS VSV, pubmed-author:SomovaO GOG, pubmed-author:SorokinN VNV, pubmed-author:TuryginA YAY, pubmed-author:ZasedatelevA SAS
pubmed:issnType	Print
pubmed:volume	24
pubmed:owner	NLM
pubmed:authorsComplete	Y
pubmed:pagination	57-66
pubmed:meshHeading	pubmed-meshheading:16780376-Electrophoresis, pubmed-meshheading:16780376-Kinetics, pubmed-meshheading:16780376-Nucleic Acid Hybridization, pubmed-meshheading:16780376-Oligonucleotide Array Sequence Analysis
pubmed:year	2006
pubmed:articleTitle	Kinetics of hybridization on surface oligonucleotide microchips: theory, experiment, and comparison with hybridization on gel-based microchips.
pubmed:affiliation	Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Vavilov str., 32, Moscow, Russia 119991.
pubmed:publicationType	Journal Article, Comparative Study, Research Support, Non-U.S. Gov't