Quantitative microarray profiling of DNA-binding molecules

Journal of the American Chemical Society

Volumn 129, Issue 40, 2007, Pages 12310-12319

  Puckett, James W ^a   Muzikar, Katy A ^a   Tietjen, Josh ^b   Warren, Christopher L ^b   Ansari, Aseem Z ^b   Dervan, Peter B ^a  

^a California Institute of Technology   (United States)

^b UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; DNA; MICROARRAYS; POLYAMIDES; SPECTRUM ANALYSIS;

DNA BINDING PYRROLEIMIDAZOLE POLYAMIDES; INTENSITY SPECTRUM;

MOLECULAR STRUCTURE;

IMIDAZOLE DERIVATIVE; POLYAMIDE; PYRROLE DERIVATIVE;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; DNA BINDING; DNA FOOTPRINTING; DNA MICROARRAY; DNA RESPONSIVE ELEMENT; GENE SEQUENCE; HYPOXIA RESPONSE ELEMENT; QUANTITATIVE ANALYSIS;

BASE PAIR MISMATCH; BASE SEQUENCE; CARBOCYANINES; DEOXYRIBONUCLEASE I; DNA; DNA FOOTPRINTING; KINETICS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; NYLONS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLASMIDS; PROTEIN STRUCTURE, SECONDARY;

EID: 35048850834     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja0744899     Document Type: Article

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25. -5 for polyamide 2.
26. -9 M for polyamide 4.
27. (c) To view plots reflecting the same curve fits of Figure 6 on a log-log scale, please see Supporting Information Figure 3.
28. 3.
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31. Figure 8 utilized 10 variable bases and contained a background GC content of 50%; Figure 9 utilized 10 variable bases and two fixed bases, each flanking the 5′ and 3′ portion of the variable region, and contained a background GC content of 58%. These background GC content corrections were utilized in the motif searching parameters.
32. There are 1258 occurrences of a full 6 bp match sequence, TTACGT. Double this number of highest intensity sequences was also searched yielding only modest changes in the data. The sequence logo is reported for the 2516 highest intensity sequences.
33. There are 24 occurrences of a full 9 bp match sequence, AAGAAGAAG on the microarray. Double this number of highest intensity sequences was searched in addition to searching only the 24 highest intensities, yielding only small changes in the data. The sequence logo reported contains the 48 highest intensity sequences.
34. a = (Intensity - ε)/{[PA] x c}, respectively.
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