Linked Life Data

11410675

Source:http://linkedlifedata.com/resource/pubmed/id/11410675

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
12
pubmed:dateCreated
2001-6-18
pubmed:abstractText
A generic hexadeoxyribonucleotide microchip has been applied to test the DNA-binding properties of HU histone-like bacterial protein, which is known to have a low sequence specificity. All 4096 hexamers flanked within 8mers by degenerate bases at both the 3'- and 5'-ends were immobilized within the 100 x 100 x 20 mm polyacrylamide gel pads of the microchip. Single-stranded immobilized oligonucleotides were converted in some experiments to the double-stranded form by hybridization with a specified mixture of 8mers. The DNA interaction with HU was characterized by three type of measurements: (i) binding of FITC-labeled HU to microchip oligonucleotides; (ii) melting curves of complexes of labeled HU with single-stranded microchip oligonucleotides; (iii) the effect of HU binding on melting curves of microchip double-stranded DNA labeled with another fluorescent dye, Texas Red. Large numbers of measurements of these parameters were carried out in parallel for all or many generic microchip elements in real time with a multi-wavelength fluorescence microscope. Statistical analysis of these data suggests some preference for HU binding to G/C-rich single-stranded oligonucleotides. HU complexes with double-stranded microchip 8mers can be divided into two groups in which HU binding either increased the melting temperature (T(m)) of duplexes or decreased it. The stabilized duplexes showed some preference for presence of the sequence motifs AAG, AGA and AAGA. In the second type of complex, enriched with A/T base pairs, the destabilization effect was higher for longer stretches of A/T duplexes. Binding of HU to labeled duplexes in the second type of complex caused some decrease in fluorescence. This decrease also correlates with the higher A/T content and lower T(m). The results demonstrate that generic microchips could be an efficient approach in analysis of sequence specificity of proteins.
pubmed:commentsCorrections
http://linkedlifedata.com/resource/pubmed/commentcorrection/11410675-10092454, http://linkedlifedata.com/resource/pubmed/commentcorrection/11410675-10497276, http://linkedlifedata.com/resource/pubmed/commentcorrection/11410675-10508175, http://linkedlifedata.com/resource/pubmed/commentcorrection/11410675-1103148, http://linkedlifedata.com/resource/pubmed/commentcorrection/11410675-2001682, http://linkedlifedata.com/resource/pubmed/commentcorrection/11410675-209942, http://linkedlifedata.com/resource/pubmed/commentcorrection/11410675-222478, http://linkedlifedata.com/resource/pubmed/commentcorrection/11410675-227733, http://linkedlifedata.com/resource/pubmed/commentcorrection/11410675-2581810, http://linkedlifedata.com/resource/pubmed/commentcorrection/11410675-6160958, http://linkedlifedata.com/resource/pubmed/commentcorrection/11410675-8089835, http://linkedlifedata.com/resource/pubmed/commentcorrection/11410675-8643503, http://linkedlifedata.com/resource/pubmed/commentcorrection/11410675-8774893, http://linkedlifedata.com/resource/pubmed/commentcorrection/11410675-8849452, http://linkedlifedata.com/resource/pubmed/commentcorrection/11410675-8855227, http://linkedlifedata.com/resource/pubmed/commentcorrection/11410675-9013649, http://linkedlifedata.com/resource/pubmed/commentcorrection/11410675-9245440, http://linkedlifedata.com/resource/pubmed/commentcorrection/11410675-9407524, http://linkedlifedata.com/resource/pubmed/commentcorrection/11410675-9415887, http://linkedlifedata.com/resource/pubmed/commentcorrection/11410675-9490800, http://linkedlifedata.com/resource/pubmed/commentcorrection/11410675-9520383, http://linkedlifedata.com/resource/pubmed/commentcorrection/11410675-9611254, http://linkedlifedata.com/resource/pubmed/commentcorrection/11410675-9843981
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Jun
pubmed:issn
1362-4962
pubmed:author
pubmed:issnType
Electronic
pubmed:day
15
pubmed:volume
29
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
2654-60
pubmed:dateRevised
2009-11-18
pubmed:meshHeading
pubmed:year
2001
pubmed:articleTitle
Massive parallel analysis of the binding specificity of histone-like protein HU to single- and double-stranded DNA with generic oligodeoxyribonucleotide microchips.
pubmed:affiliation
Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Street, 119991 Moscow, Russia.
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't