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 effe...
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| Published in | Nucleic acids research Vol. 44; no. 9; pp. 4014 - 4024 |
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| Main Authors | , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
England
Oxford University Press
19.05.2016
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| Abstract | 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. |
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| AbstractList | 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. 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. |
| Author | Chandran, Anandhakumar Taylor, Rhys D Syed, Junetha Kashiwazaki, Gengo Hashiya, Kaori Sato, Shinsuke Sugiyama, Hiroshi Bando, Toshikazu |
| Author_xml | – sequence: 1 givenname: Anandhakumar surname: Chandran fullname: Chandran, Anandhakumar organization: Department of Chemistry, Graduate School of Science Kyoto University, Sakyo, Kyoto 606-8502, Japan – sequence: 2 givenname: Junetha surname: Syed fullname: Syed, Junetha organization: Department of Chemistry, Graduate School of Science Kyoto University, Sakyo, Kyoto 606-8502, Japan – sequence: 3 givenname: Rhys D surname: Taylor fullname: Taylor, Rhys D organization: Department of Chemistry, Graduate School of Science Kyoto University, Sakyo, Kyoto 606-8502, Japan – sequence: 4 givenname: Gengo surname: Kashiwazaki fullname: Kashiwazaki, Gengo organization: Department of Chemistry, Graduate School of Science Kyoto University, Sakyo, Kyoto 606-8502, Japan – sequence: 5 givenname: Shinsuke surname: Sato fullname: Sato, Shinsuke organization: Institute for Integrated Cell-Materials Science (iCeMS) Kyoto University, Sakyo, Kyoto 606-8502, Japan – sequence: 6 givenname: Kaori surname: Hashiya fullname: Hashiya, Kaori organization: Department of Chemistry, Graduate School of Science Kyoto University, Sakyo, Kyoto 606-8502, Japan – sequence: 7 givenname: Toshikazu surname: Bando fullname: Bando, Toshikazu organization: Department of Chemistry, Graduate School of Science Kyoto University, Sakyo, Kyoto 606-8502, Japan – sequence: 8 givenname: Hiroshi surname: Sugiyama fullname: Sugiyama, Hiroshi email: hs@kuchem.kyoto-u.ac.jp organization: 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 |
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| SubjectTerms | Alkylating Agents - chemistry Alkylation Base Sequence Chemical Biology and Nucleic Acid Chemistry DNA - chemistry Genome, Human - genetics High-Throughput Nucleotide Sequencing Humans Imidazoles - chemistry Nylons - chemistry Promoter Regions, Genetic - genetics Pyrroles - chemistry Receptor, ErbB-2 - genetics |
| Title | Deciphering the genomic targets of alkylating polyamide conjugates using high-throughput sequencing |
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