Quantitative microarray profiling of DNA-binding molecules.
A high-throughput Cognate Site Identity (CSI) microarray platform interrogating all 524 800 10-base pair variable sites is correlated to quantitative DNase I footprinting data of DNA binding pyrrole-imidazole polyamides. An eight-ring hairpin polyamide programmed to target the 5 bp sequence 5'-TACGT-3' within the hypoxia response element (HRE) yielded a CSI microarray-derived sequence motif of 5'-WWACGT-3' (W = A,T). A linear beta-linked polyamide programmed to target a (GAA)3 repeat yielded a CSI microarray-derived sequence motif of 5'-AARAARWWG-3' (R = G,A). Quantitative DNase I footprinting of selected sequences from each microarray experiment enabled quantitative prediction of Ka values across the microarray intensity spectrum.
Puckett
James W
JW
Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA.
Muzikar
Katy A
KA
Tietjen
Josh
J
Warren
Christopher L
CL
Ansari
Aseem Z
AZ
Dervan
Peter B
PB
D020137:Base Pair Mismatch; D001483:Base Sequence; D002232:Carbocyanines / Q000737:chemistry; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D018983:DNA Footprinting / Q000379:methods*; D003850:Deoxyribonuclease I / Q000737:chemistry* / Q000378:metabolism; D007700:Kinetics; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009757:Nylons / Q000737:chemistry*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010957:Plasmids / Q000737:chemistry / Q000235:genetics; D017433:Protein Structure, Secondary
D002232:Carbocyanines; D009757:Nylons; C089187:cyanine dye 3; D004247:DNA; D003850:Deoxyribonuclease I