Related Experiment Video
Updated: Aug 15, 2026

Single-Molecule Dwell-Time Analysis of Restriction Endonuclease-Mediated DNA Cleavage
Published on: February 7, 2021
Photo-cross-linked oligonucleotide duplex as a decoy-DNA for inhibition of restriction endonuclease activity
A Murakami1, Y Yamamoto, M Namba
1Department of Polymer Science and Engineering, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan. akiram@ipc.kit.ac.jp
Abstract:
As a novel type of regulator molecule for DNA-recognizing proteins, a photo-cross-linked oligonucleotide duplex was designed and synthesized. The molecule regulated the activity of a restriction endonuclease by being recognized as a substrate. This type of regulating molecule is regarded as a decoy-DNA. 4,5',8-[4-Aminoethylaminomethyl]-trioxalen (aeAMT) was conjugated with an oligodeoxyribonucleotide (ODN) at the 5'-end and the aeAMT was cross-linked with the thymine residue of the complementary oligonucleotide upon UVA irradiation. The terminally cross-linked oligonucleotides, singly clipped (SC) decoy-DNA, acquired thermal stability. An oligonucleoside phosphorothioate (OPT) was also introduced as one or both components, yielding three types of decoy-DNAs, SC-ODN-ODN (SC.DD), SC-OPT-ODN (SC.SD), and SC-OPT-OPT (SC.SS). The SC decoy-DNAs inhibited the function of the restriction endonuclease, AatII, in a sequence-specific and concentration-dependent manner with an appreciable IC50 value (1.3 microM for SC.DD, 0.016 microM for SC.SD, 0.002 microM for SC.SS). The SC decoy-DNAs were found to be effective for regulating the DNA recognizing proteins.
More Related Videos
Related Concept Videos
Restriction Enzymes
The host bacteria protect their own genomic DNA from these enzymes by methylating these sites. Some...
Inhibitors of Bacterial DNA Synthesis
Single-Strand DNA Binding Proteins
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...
Homologous Recombination

