Abstract
Catenation is the process by which cyclic strands are combined like the links of a chain, whereas knotting changes the linking properties of a single strand. In the cell, topoisomerases catalyzing strand passage operations enable the knotting and catenation of DNA so that single- or double-stranded segments can be passed through each other. Here, we use a system of closed DNA structures involving a paranemic motif, called PX-DNA, to bind double strands of DNA together. These PX-cohesive closed molecules contain complementary loops whose linking by Escherichia coli topoisomerase 1 (Topo 1) leads to various types of catenated and knotted structures. We were able to obtain specific DNA topological constructs by varying the lengths of the complementary tracts between the complementary loops. The formation of the structures was analyzed by denaturing gel electrophoresis, and the various topologies of the constructs were characterized using the program Knotilus.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 10296-10303 |
| Number of pages | 8 |
| Journal | ACS Nano |
| Volume | 9 |
| Issue number | 10 |
| DOIs | |
| State | Published - Sep 13 2015 |
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Keywords
- 3′,3′ and 5′,5′ linkages
- DNA catenane
- DNA knot
- linking number
- paranemic cohesion
- topoisomers
- topological linkage
ASJC Scopus subject areas
- Engineering(all)
- Materials Science(all)
- Physics and Astronomy(all)
Cite this
Topological Linkage of DNA Tiles Bonded by Paranemic Cohesion. / Ohayon, Yoel P.; Sha, Ruojie; Flint, Ortho; Chandrasekaran, Arun Richard; Abdallah, Hatem O.; Wang, Tong; Wang, Xing; Zhang, Xiaoping; Seeman, Nadrian.
In: ACS Nano, Vol. 9, No. 10, 13.09.2015, p. 10296-10303.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Topological Linkage of DNA Tiles Bonded by Paranemic Cohesion
AU - Ohayon, Yoel P.
AU - Sha, Ruojie
AU - Flint, Ortho
AU - Chandrasekaran, Arun Richard
AU - Abdallah, Hatem O.
AU - Wang, Tong
AU - Wang, Xing
AU - Zhang, Xiaoping
AU - Seeman, Nadrian
PY - 2015/9/13
Y1 - 2015/9/13
N2 - Catenation is the process by which cyclic strands are combined like the links of a chain, whereas knotting changes the linking properties of a single strand. In the cell, topoisomerases catalyzing strand passage operations enable the knotting and catenation of DNA so that single- or double-stranded segments can be passed through each other. Here, we use a system of closed DNA structures involving a paranemic motif, called PX-DNA, to bind double strands of DNA together. These PX-cohesive closed molecules contain complementary loops whose linking by Escherichia coli topoisomerase 1 (Topo 1) leads to various types of catenated and knotted structures. We were able to obtain specific DNA topological constructs by varying the lengths of the complementary tracts between the complementary loops. The formation of the structures was analyzed by denaturing gel electrophoresis, and the various topologies of the constructs were characterized using the program Knotilus.
AB - Catenation is the process by which cyclic strands are combined like the links of a chain, whereas knotting changes the linking properties of a single strand. In the cell, topoisomerases catalyzing strand passage operations enable the knotting and catenation of DNA so that single- or double-stranded segments can be passed through each other. Here, we use a system of closed DNA structures involving a paranemic motif, called PX-DNA, to bind double strands of DNA together. These PX-cohesive closed molecules contain complementary loops whose linking by Escherichia coli topoisomerase 1 (Topo 1) leads to various types of catenated and knotted structures. We were able to obtain specific DNA topological constructs by varying the lengths of the complementary tracts between the complementary loops. The formation of the structures was analyzed by denaturing gel electrophoresis, and the various topologies of the constructs were characterized using the program Knotilus.
KW - 3′,3′ and 5′,5′ linkages
KW - DNA catenane
KW - DNA knot
KW - linking number
KW - paranemic cohesion
KW - topoisomers
KW - topological linkage
UR - http://www.scopus.com/inward/record.url?scp=84945899449&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84945899449&partnerID=8YFLogxK
U2 - 10.1021/acsnano.5b04333
DO - 10.1021/acsnano.5b04333
M3 - Article
C2 - 26364680
AN - SCOPUS:84945899449
VL - 9
SP - 10296
EP - 10303
JO - ACS Nano
JF - ACS Nano
SN - 1936-0851
IS - 10
ER -