A B
Supplementary Figure S1. 1R-Bodipy staining of HEK293 cells. Cells were incubated overnight i n culture medium supplemented with 500 µM 1R-bodipy polyamide and visualized either by phase contrast microscopy (A) or by fluorescence (B). Nuclear localization of the bodipy-labeled polyamide is evident.
Synthesis and the characterization of pyrrole-imidiazole polyamides
The pyrrole-imidizole (Py-Im) polyamide 1R was synthesized utilizing the solid phase methods described by Baird and Dervan 1 and incorporated

-( R) -diaminobutyric
acid as the hairpin turn amino acid 2, 3 . The carboxylic acid of chlorambucil (Sigma-
Aldrich, WI) was activated and selectively coupled to amino group of the turn amino acid

as described 4 to yield 1R-Chl (Fig. 1 a ). Alternatively, the fluorescent dye bodipy-FL was similarly coupled at this position to yield 1R-bodipy 5 . Compounds were analyzed by mass spectrometry (MALDI-TOF-MS and ES-MS) and analytical HPLC. DNA binding and alkylation was confirmed as previously described 5 .
Cell lines and cell proliferation assays
The human embryonic kidney cell line HEK293 (CRL-1573) and the human pancreatic cancer cell line MIA PaCa-2 (CRL-1420) were obtained form the ATCC. Cells were grown and maintained in Dulbecco's Modified Eagle's medium containing 10%
FBS, under standard mammalian cell culture conditions, as recommended by the ATCC.
Direct phase contrast microscopic visualization was used to monitor the effects of polyamide-Chl conjugates on cell growth rates and cell morphology. To examine cell proliferation, the Promega CellTiter 96 Aqueous One Solution Cell Proliferation assay
(Promega, WI; utilizing [3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4sulfophenyl)-2H tetrazolium (MTS)]) was used.
Quantitative RT-PCR assays
RNA was extracted using Absolutely RNA Miniprep kit from Stratagene according to the manufacturer’s protocol. Sequences for primers were adopted from PrimerBank
( http://pga.mgh.harvard.edu/primerbank/ ) and primer specificity was confirmed by amplicon sequencing. Quantitative reverse transcription PCR analysis was performed using B-R One-Step SYBR Green qRT-PCR kit (Quanta Biosciences). Primers for H4c and GAPDH were previously described 6 . Other primers used in qRT-PCR experiments are listed below, where the sequences are s hown in the 5’ to 3’ direction.
HIST1H4A
Forward Primer AAGGGTTTGGGTAAGGGGG

Reverse Primer TAGATCAGACCAGAGATCCGC
HIST1H4D
Forward Primer CCGTAAGGTATTGCGTGACAA
Reverse Primer CTCCGCGAGTTTCCTCATAAAT
HIST1H4JK
Forward Primer CGCGACAATATCCAGGGCAT
Reverse Primer CACCGAAACCGTAGAGGGT
HIST1H4H
Forward Primer GCTAAGCGTCATCGCAAGGT
Reverse Primer TTCAGAACACCACGAGTCTCC
HIST1H4B
Forward Primer AAGGCGGTAAAGGTTTGGGTA
Reverse Primer GGAAATTCGCTTAACCCCACC
HIST1H4E
Forward Primer GCGGAAAGGGACTGGGTAAAG
Reverse Primer AGTCACAGCATCACGAATCAC
HIST1H4L
Forward Primer AAAGTTCTGCGCGACAACATT
Reverse Primer CTCCGCGTGTCTCCTCGTA
HIST2H4AB
Forward Primer GAAAAGGCTTAGGCAAAGGGG
Reverse Primer CCAGAGATCCGCTTAACGC
HIST4H4
Forward Primer ATGTCTGGGCGAGGTAAAGGT
Reverse Primer CCGGCTTTGTAATGCCTTGG
Chromatin immunoprecipitation assays
ChIP assays were performed as described previously 7 . Anti-histone H3 and antiacetylated histone H3 antibodies were purchased from Abcam (ab1791) and Millipore
(06-599), respectively. The sequences of the primers used are described above. Histone
H3 occupancy on the

-actin gene was used as recovery standard. Primer sequences for the

-actin gene are:
Forward Primer ACAAGGCCATGAGGCTGGTGTAAAGC
Reverse Primer AAAGAACACGGCTAAGTGTGCTGG

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