TY - JOUR
T1 - Topologically-Interlocked Minicircles as Probes of DNA Topology and DNA-Protein Interactions
AU - Rajendran, Arivazhagan
AU - Krishnamurthy, Kirankumar
AU - Park, Seojeong
AU - Nakata, Eiji
AU - Kwon, Youngjoo
AU - Morii, Takashi
N1 - Funding Information:
We acknowledge the kind help of Prof. Takayuki Uchihashi with AFM. We thank the Ministry of Education, Culture, Sports, Science and Technology (MEXT, Japan) for the Grants-in-Aid for Scientific Research to A.R. (16K17934 and 21K05274), E.N. (19H04653 and 20H02860), and T.M. (17H01213), and JST CREST to T.M. (JPMJCR18H5). This work was inspired by the international and interdisciplinary environments of the JSPS Core-to-Core Program, ?Asian Chemical Biology Initiative? (JPJSCCB20190004). A.R. thanks The Kyoto University Foundation for the research grant. A.R. and E.N. thank the Institute of Advanced Energy, Kyoto University for the Research Grant for Collaboration Program of the Laboratory for Complex Energy Processes. K.K. thanks the MEXT-SGU for the scholarship.
Funding Information:
We acknowledge the kind help of Prof. Takayuki Uchihashi with AFM. We thank the Ministry of Education, Culture, Sports, Science and Technology (MEXT, Japan) for the Grants‐in‐Aid for Scientific Research to A.R. (16K17934 and 21K05274), E.N. (19H04653 and 20H02860), and T.M. (17H01213), and JST CREST to T.M. (JPMJCR18H5). This work was inspired by the international and interdisciplinary environments of the JSPS Core‐to‐Core Program, “Asian Chemical Biology Initiative” (JPJSCCB20190004). A.R. thanks The Kyoto University Foundation for the research grant. A.R. and E.N. thank the Institute of Advanced Energy, Kyoto University for the Research Grant for Collaboration Program of the Laboratory for Complex Energy Processes. K.K. thanks the MEXT‐SGU for the scholarship.
Publisher Copyright:
© 2022 Wiley-VCH GmbH
PY - 2022
Y1 - 2022
N2 - DNA minicircles exist in biological contexts, such as kinetoplast DNA, and are promising components for creating functional nanodevices. They have been used to mimic the topological features of nucleosomal DNA and to probe DNA-protein interactions such as HIV-1 and PFV integrases, and DNA gyrase. Here, we synthesized the topologically-interlocked minicircle rotaxane and catenane inside a frame-shaped DNA origami. These minicircles are 183 bp in length, constitute six individual single-stranded DNAs that are ligated to realize duplex interlocking, and adopt temporary base pairing of single strands for interlocking. To probe the DNA-protein interactions, restriction reactions were carried out on DNAs with different topologies such as free linear duplex or duplex constrained inside origami and free or topologically-interlocked minicircles. Except the free linear duplex, all tested structures were resistant to restriction digestion, indicating that the topological features of DNA, such as flexibility, curvature, and groove orientation, play a major role in DNA-protein interactions.
AB - DNA minicircles exist in biological contexts, such as kinetoplast DNA, and are promising components for creating functional nanodevices. They have been used to mimic the topological features of nucleosomal DNA and to probe DNA-protein interactions such as HIV-1 and PFV integrases, and DNA gyrase. Here, we synthesized the topologically-interlocked minicircle rotaxane and catenane inside a frame-shaped DNA origami. These minicircles are 183 bp in length, constitute six individual single-stranded DNAs that are ligated to realize duplex interlocking, and adopt temporary base pairing of single strands for interlocking. To probe the DNA-protein interactions, restriction reactions were carried out on DNAs with different topologies such as free linear duplex or duplex constrained inside origami and free or topologically-interlocked minicircles. Except the free linear duplex, all tested structures were resistant to restriction digestion, indicating that the topological features of DNA, such as flexibility, curvature, and groove orientation, play a major role in DNA-protein interactions.
KW - DNA catenane
KW - DNA origami
KW - DNA rotaxane
KW - DNA-protein interactions
KW - restriction reactions
UR - http://www.scopus.com/inward/record.url?scp=85126286051&partnerID=8YFLogxK
U2 - 10.1002/chem.202200108
DO - 10.1002/chem.202200108
M3 - Article
C2 - 35218108
AN - SCOPUS:85126286051
JO - Chemistry - A European Journal
JF - Chemistry - A European Journal
SN - 0947-6539
ER -