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rdf:type |
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lifeskim:mentions |
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pubmed:issue |
16
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pubmed:dateCreated |
1998-9-22
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pubmed:abstractText |
Metal-ion and sequence dependent changes in the stacking interactions of bases surrounding abasic (AB) sites in 10 different DNA duplexes were examined by incorporating the fluorescent nucleotide probe 2-aminopurine (2-AP), opposite to the site (AB-APopp) or adjacent to the site (AB-APadj) on either strand. A detailed study of the fluorescence emission and excitation spectra of these AB duplexes and their corresponding parent duplexes indicates that AB-APoppis significantly less stacked than 2-AP in the corresponding normal duplex. In general, AB-APadjon the AB strand is stacked, but AB-APadjon the opposite strand shows destabilized stacking interactions. The results also indicate that divalent cation binding to the AB duplexes contributes to destabilizaton of the base stacking interactions of AB-APopp, but has little or no effect on the stacking interactions of AB-APadj. Consistent with these results, the fluorescence of AB-APoppis 18-30-fold more sensitive to an externally added quenching agent than the parent normal duplex. When uracil DNA glycosylase binds to AB-APoppin the presence of 2.5 mM MgCl2, a 3-fold decrease in fluorescence is observed ( K d = 400 +/- 90 nM) indicating that the unstacked 2-APoppbecomes more stacked upon binding. On the basis of these fluorescence studies a model for the local base stacking interactions at these AB sites is proposed.
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pubmed:grant |
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pubmed:commentsCorrections |
http://linkedlifedata.com/resource/pubmed/commentcorrection/9685503-1327102,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9685503-1846560,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9685503-1911785,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9685503-2009265,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9685503-2207092,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9685503-2295611,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9685503-2342108,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9685503-2440861,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9685503-2471157,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9685503-2545258,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9685503-2605243,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9685503-2706253,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9685503-324994,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9685503-3259144,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9685503-3368313,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9685503-353875,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9685503-3671070,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9685503-3676273,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9685503-4626532,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9685503-6548562,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9685503-7326360,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9685503-7559436,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9685503-7979257,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9685503-8011623,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9685503-8068635,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9685503-8068666,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9685503-8218287,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9685503-8672436,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9685503-8823167,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9685503-8900285,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9685503-8942631,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9685503-8942637,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9685503-9125502,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9685503-9341165
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pubmed:language |
eng
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pubmed:journal |
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pubmed:citationSubset |
IM
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pubmed:chemical |
http://linkedlifedata.com/resource/pubmed/chemical/2-Aminopurine,
http://linkedlifedata.com/resource/pubmed/chemical/Acrylamide,
http://linkedlifedata.com/resource/pubmed/chemical/Acrylamides,
http://linkedlifedata.com/resource/pubmed/chemical/Cations, Divalent,
http://linkedlifedata.com/resource/pubmed/chemical/DNA,
http://linkedlifedata.com/resource/pubmed/chemical/DNA Glycosylases,
http://linkedlifedata.com/resource/pubmed/chemical/Fluorescent Dyes,
http://linkedlifedata.com/resource/pubmed/chemical/Magnesium Chloride,
http://linkedlifedata.com/resource/pubmed/chemical/N-Glycosyl Hydrolases,
http://linkedlifedata.com/resource/pubmed/chemical/Uracil-DNA Glycosidase
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pubmed:status |
MEDLINE
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pubmed:month |
Aug
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pubmed:issn |
0305-1048
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pubmed:author |
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pubmed:issnType |
Print
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pubmed:day |
15
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pubmed:volume |
26
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pubmed:owner |
NLM
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pubmed:authorsComplete |
Y
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pubmed:pagination |
3837-44
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pubmed:dateRevised |
2009-11-18
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pubmed:meshHeading |
pubmed-meshheading:9685503-2-Aminopurine,
pubmed-meshheading:9685503-Acrylamide,
pubmed-meshheading:9685503-Acrylamides,
pubmed-meshheading:9685503-Base Sequence,
pubmed-meshheading:9685503-Binding Sites,
pubmed-meshheading:9685503-Cations, Divalent,
pubmed-meshheading:9685503-DNA,
pubmed-meshheading:9685503-DNA Glycosylases,
pubmed-meshheading:9685503-Fluorescent Dyes,
pubmed-meshheading:9685503-Kinetics,
pubmed-meshheading:9685503-Magnesium Chloride,
pubmed-meshheading:9685503-N-Glycosyl Hydrolases,
pubmed-meshheading:9685503-Nucleic Acid Conformation,
pubmed-meshheading:9685503-Spectrometry, Fluorescence,
pubmed-meshheading:9685503-Temperature,
pubmed-meshheading:9685503-Uracil-DNA Glycosidase
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pubmed:year |
1998
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pubmed:articleTitle |
2-Aminopurine fluorescence studies of base stacking interactions at abasic sites in DNA: metal-ion and base sequence effects.
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pubmed:affiliation |
Center for Advanced Research in Biotechnology, University of Maryland, Biotechnology Institute and theNational Institute for Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850, USA. stivers@carb.nist.gov
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pubmed:publicationType |
Journal Article,
Research Support, U.S. Gov't, P.H.S.
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