Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
2
pubmed:dateCreated
2007-1-30
pubmed:abstractText
The DNA binding of novel threading bis-intercalators V1, trans-D1, and cis-C1, which contain two naphthalene diimide (NDI) intercalation units connected by a scaffold, was evaluated using electrospray ionization mass spectrometry (ESI-MS) and DNAse footprinting techniques. ESI-MS experiments confirmed that V1, the ligand containing the -Gly3-Lys- peptide scaffold, binds to a DNA duplex containing the 5'-GGTACC-3' specific binding site identified in previous NMR-based studies. The ligand formed complexes with a ligand/DNA binding stoichiometry of 1:1, even when there was excess ligand in solution. Trans-D1 and cis-C1 are new ligands containing a rigid spiro-tricyclic scaffold in the trans- and cis- orientations, respectively. Preliminary DNAse footprinting experiments identified possible specific binding sites of 5'-CAGTGA-5' for trans-D1 and 5'-GGTACC-3' for cis-C1. ESI-MS experiments revealed that both ligands bound to DNA duplexes containing the respective specific binding sequences, with cis-C1 exhibiting the most extensive binding based on a higher fraction of bound DNA value. Cis-C1 formed complexes with a dominant 1:1 binding stoichiometry, whereas trans-D1 was able to form 2:1 complexes at ligand/DNA molar ratios >or=1 which is suggestive of nonspecific binding. Collisional activated dissociation (CAD) experiments indicate that DNA complexes containing V1, trans-D1, and cis-C1 have a unique fragmentation pathway, which was also observed for complexes containing the commercially available bis-intercalator echinomycin, as a result of similar binding interactions, marked by intercalation in addition to hydrogen bonding by the scaffold with the DNA major or minor groove.
pubmed:grant
pubmed:commentsCorrections
http://linkedlifedata.com/resource/pubmed/commentcorrection/17098442-10587629, http://linkedlifedata.com/resource/pubmed/commentcorrection/17098442-10589098, http://linkedlifedata.com/resource/pubmed/commentcorrection/17098442-10790849, http://linkedlifedata.com/resource/pubmed/commentcorrection/17098442-11358689, http://linkedlifedata.com/resource/pubmed/commentcorrection/17098442-11455562, http://linkedlifedata.com/resource/pubmed/commentcorrection/17098442-11480976, http://linkedlifedata.com/resource/pubmed/commentcorrection/17098442-11562309, http://linkedlifedata.com/resource/pubmed/commentcorrection/17098442-11598462, http://linkedlifedata.com/resource/pubmed/commentcorrection/17098442-11691940, http://linkedlifedata.com/resource/pubmed/commentcorrection/17098442-11712252, http://linkedlifedata.com/resource/pubmed/commentcorrection/17098442-11746919, http://linkedlifedata.com/resource/pubmed/commentcorrection/17098442-11902864, http://linkedlifedata.com/resource/pubmed/commentcorrection/17098442-12465032, http://linkedlifedata.com/resource/pubmed/commentcorrection/17098442-12950163, http://linkedlifedata.com/resource/pubmed/commentcorrection/17098442-15465350, http://linkedlifedata.com/resource/pubmed/commentcorrection/17098442-15506767, http://linkedlifedata.com/resource/pubmed/commentcorrection/17098442-15514752, http://linkedlifedata.com/resource/pubmed/commentcorrection/17098442-15548010, http://linkedlifedata.com/resource/pubmed/commentcorrection/17098442-15638325, http://linkedlifedata.com/resource/pubmed/commentcorrection/17098442-16104746, http://linkedlifedata.com/resource/pubmed/commentcorrection/17098442-16220501, http://linkedlifedata.com/resource/pubmed/commentcorrection/17098442-16503153, http://linkedlifedata.com/resource/pubmed/commentcorrection/17098442-6089341, http://linkedlifedata.com/resource/pubmed/commentcorrection/17098442-6204275, http://linkedlifedata.com/resource/pubmed/commentcorrection/17098442-7093231, http://linkedlifedata.com/resource/pubmed/commentcorrection/17098442-9373959
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Feb
pubmed:issn
1044-0305
pubmed:author
pubmed:issnType
Print
pubmed:volume
18
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
311-21
pubmed:dateRevised
2011-3-16
pubmed:meshHeading
pubmed:year
2007
pubmed:articleTitle
Screening of threading bis-intercalators binding to duplex DNA by electrospray ionization tandem mass spectrometry.
pubmed:affiliation
Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712-0165, USA.
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't, Research Support, N.I.H., Extramural