Deciphering the genomic targets of alkylating polyamide conjugates using high-throughput sequencing.
Chemically engineered small molecules targeting specific genomic sequences play an important role in drug development research. Pyrrole-imidazole polyamides (PIPs) are a group of molecules that can bind to the DNA minor-groove and can be engineered to target specific sequences. Their biological effects rely primarily on their selective DNA binding. However, the binding mechanism of PIPs at the chromatinized genome level is poorly understood. Herein, we report a method using high-throughput sequencing to identify the DNA-alkylating sites of PIP-indole-seco-CBI conjugates. High-throughput sequencing analysis of conjugate 2: showed highly similar DNA-alkylating sites on synthetic oligos (histone-free DNA) and on human genomes (chromatinized DNA context). To our knowledge, this is the first report identifying alkylation sites across genomic DNA by alkylating PIP conjugates using high-throughput sequencing.
Department of Chemistry, Graduate School of Science Kyoto University, Sakyo, Kyoto 606-8502, Japan.
Anandhakumar
A
Chandran
Department of Chemistry, Graduate School of Science Kyoto University, Sakyo, Kyoto 606-8502, Japan.
Junetha
J
Syed
Department of Chemistry, Graduate School of Science Kyoto University, Sakyo, Kyoto 606-8502, Japan.
Rhys D
RD
Taylor
Department of Chemistry, Graduate School of Science Kyoto University, Sakyo, Kyoto 606-8502, Japan.
Gengo
G
Kashiwazaki
Institute for Integrated Cell-Materials Science (iCeMS) Kyoto University, Sakyo, Kyoto 606-8502, Japan.
Shinsuke
S
Sato
Department of Chemistry, Graduate School of Science Kyoto University, Sakyo, Kyoto 606-8502, Japan.
Kaori
K
Hashiya
Department of Chemistry, Graduate School of Science Kyoto University, Sakyo, Kyoto 606-8502, Japan.
Toshikazu
T
Bando
Department of Chemistry, Graduate School of Science Kyoto University, Sakyo, Kyoto 606-8502, Japan Institute for Integrated Cell-Materials Science (iCeMS) Kyoto University, Sakyo, Kyoto 606-8502, Japan CREST, Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan hs@kuchem.kyoto-u.ac.jp.
Hiroshi
H
Sugiyama
D000477:Alkylating Agents / Q000737:chemistry*; D000478:Alkylation; D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D015894:Genome, Human / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007093:Imidazoles / Q000737:chemistry*; D009757:Nylons / Q000737:chemistry*; D011401:Promoter Regions, Genetic / Q000235:genetics; D011758:Pyrroles / Q000737:chemistry*; D018719:Erb-b2 Receptor Tyrosine Kinases / Q000235:genetics*
D000477:Alkylating Agents; D004247:DNA; D007093:Imidazoles; D009757:Nylons; D011758:Pyrroles; D018719:Erb-b2 Receptor Tyrosine Kinases; C029899:imidazole; C508053:ERBB2 protein, human