Quantitative Microarray Profiling of DNA-Binding Molecules

Im A·T, 2003, Curr. Opin. Struct. Biol., 13, 299

Trauger J. W., 2001, Methods Enzymol., 340, 466, 10.1016/S0076-6879(01)40437-X

Doss R. M., 2006, J. Am. Chem. Soc., 128, 9079

Marques M. A., 2004, J. Am. Chem. Soc., 126, 10349, 10.1021/ja0486465

Foister S., 2003, Bioorg. Med. Chem., 11, 4340, 10.1016/S0968-0896(03)00502-9

For, 2006, Methods Enzymol., 410, 299

For, 2004, Acc. Chem. Res., 37, 69

For, 2006, Proc. Natl. Acad. Sci. U.S.A., 103, 872

Schneider T. D., 1990, Nucleic Acids Res., 18, 6100

(a) Bailey, T. L.; Elkan, C. InProceedings of the Second InternationalConference on Intelligent Systems for Molecular Biology; Altman, R., Brutlag, D., Karp, P., Lathrop, R., Searls, D., Eds.; AAAI Press:  Menlo Park, 1994, pp 28−36.

Liu X. S., 2002, Nat. Biotechnol., 20, 839, 10.1038/nbt715

Hughes J. D., 2000, J. Mol. Biol., 296, 1214, 10.1006/jmbi.2000.3519

Olenyuk B. Z., 2004, Proc. Natl. Acad. Sci. U.S.A., 101, 16773, 10.1073/pnas.0407617101

Nickols N. G., 2007, Nucleic Acids Res., 35, 370, 10.1093/nar/gkl1042

Burnett R., 2006, Proc. Natl. Acad. Sci. U.S.A., 103, 11502

(a) Dervan, P. B.; Urbach, A. R. InEssays in ContemporaryChemistry; Quinkert, G., Kisakürek, M. V., Eds.; Verlag Helvetica Chimica Acta:  Zurich, 2000; pp 327−339.

Urbach A. R., 2001, Proc. Natl. Acad. Sci. U.S.A., 98, 4348, 10.1073/pnas.081070798

Urbach A. R., 2002, J. Mol. Biol., 320, 71, 10.1016/S0022-2836(02)00430-8

Marques M. A., 2002, Helv. Chim. Acta, 85, 4517, 10.1002/hlca.200290024

Singh-Gasson S., 1999, Nat. Biotechnol., 17, 978, 10.1038/13664

Trauger J. W., 1996, Nature, 382, 561, 10.1038/382559a0

Trauger J. W. Ph.D., 1999, California Institute of Technology

Supporting Information, 2001, Proc. Natl. Acad. Sci. U.S.A., 98, 7163

(a)c× [PA] was 1.7 × 10-5for polyamide2.

(b)cwas 80.2 × 103and [PA] was 5.5 × 10-9M for polyamide4.

Although the data for polyamide2(Figure 6a) maps intensity andKavalues using the linearized equation 2, this fit is distinct from that obtained by fitting the data to a line of the formy=mx+b, which includes an intensity-axis intercept term. While very small in this case, the differences in the slopes and intercepts of the lines may indicate error both in the background correction of the microarray and in the DNase I footprinting data. To correct for this possibility, we propose the use of an error term, ε, that would modify eqs 1 and 2 to the following:  Intensity =c× ϑ + ε =c× {Ka[PA]}/{1 +Ka[PA]} + ε =c× {[PA]}/{Kd+ [PA]} + ε (eq 1e) and Intensity =c× [PA]/Kd+ ε =c× [PA] ×Ka+ε(eq 2e). When fitting the intensity andKadata for polyamide2to the modified equation 2e, one finds a marginally improved fit (R2= 0.97), although the curve fit for polyamide4using equation 1e is unimproved (R2= 0.99). For polyamide2,c× [PA] = 1.5 × 10-5and ε = 5.5 × 103. For polyamide4,c= 81.2 × 103, [PA] = 5.7 × 10-9M, and ε = −1.1 × 103.

Workman C. T., 2005, Nucleic Acids Res., 33, W392, 10.1093/nar/gki439

Van Dyke M. M., 1984, Science, 225, 1127, 10.1126/science.6089341

Kong D., 2005, Cancer Res., 65, 9055

Colantuoni C., 2002, Bioinformatics, 18, 1541, 10.1093/bioinformatics/18.11.1540

Bolstad B. M., 2003, Bioinformatics, 19, 193, 10.1093/bioinformatics/19.2.185