Related Experiment Video
Updated: Jul 18, 2026

Genome-wide Mapping of Drug-DNA Interactions in Cells with COSMIC (Crosslinking of Small Molecules to Isolate Chromatin)
Published on: January 20, 2016
Sequence-specific gene silencing by alkylating Py-Im polyamide
Ken-ichi Shinohara1, Shunta Sasaki, Toshikazu Bando
1Graduate School of Science, Kyoto University, Kitashirakawa Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan.
Abstract:
We have demonstrated that hairpin pyrrole (Py)-imidazole (Im) polyamide-CPI conjugates selectively induced luciferase gene silencing by sequence-specific alkylation of the coding region. Recently, we developed a new type of Py-Im polyamide CBI conjugate with an indole linker as a stable sequence-specific alkylating agent. In this study, we investigated the gene silencing ability of polyamides A, B and C, which potentially target specific sequences in the promoter region, non-coding strand, and coding strand of the green fluorescent protein (GFP) gene, respectively. The GFP vectors were transfected into human colon carcinoma cells (HCT116), and the cells treated with 100 nM of the polyamides for 24 h. Using direct observation of cell by fluorescence microscopy, a significant GFP-gene silencing effect was only seen with treatment with polyamide C. Polyamides A and B did not show such activity.
Related Concept Videos
Experimental RNAi
siRNA - Small Interfering RNAs
In the cytoplasm, siRNA is processed from a double-stranded RNA, which comes from either endogenous DNA transcription or exogenous sources like a virus. This double-stranded RNA is then cleaved by the ATP-dependent...
RNA Interference
This process occurs naturally in cells, often through the activity of genomically-encoded microRNAs. Researchers can take advantage of this mechanism by introducing synthetic RNAs to deactivate specific genes for research or therapeutic purposes. For example, RNAi could be used...
Maxam-Gilbert Sequencing
Challenges of the Maxam-Gilbert Method
The...
piRNA - Piwi-interacting RNAs
Allosteric Proteins-ATCase
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis pathway,...

