Covalent Linkage of One-Dimensional DNA Arrays Bonded by Paranemic Cohesion.
The construction of DNA nanostructures from branched DNA motifs, or tiles, typically relies on the use of sticky-ended cohesion, owing to the specificity and programmability of DNA sequences. The stability of such constructs when unligated is restricted to a specific range of temperatures, owing to the disruption of base pairing at elevated temperatures. Paranemic (PX) cohesion was developed as an alternative to sticky ends for the cohesion of large topologically closed species that could be purified reliably on denaturing gels. However, PX cohesion is also of limited stability. In this work, we added sticky-ended interactions to PX-cohesive complexes to create interlocked complexes by functionalizing the sticky ends with psoralen, which can form cross-links between the two strands of a double helix. We were able to reinforce the stability of the constructs by creating covalent linkages between the 3'-ends and 5'-ends of the sticky ends; the sticky ends were added to double crossover domains via 3'-3' and 5'-5' linkages. Catenated arrays were obtained either by enzymatic ligation or by UV cross-linking. We have constructed finite-length one-dimensional arrays linked by interlocking loops and have positioned streptavidin-gold particles on these constructs.
Department of Chemistry, New York University , New York, New York 10003, United States.
Yoel P
YP
Ohayon
Department of Chemistry, New York University , New York, New York 10003, United States.
Ruojie
R
Sha
Department of Mathematics, University of Western Ontario , London, ON N6A 5B7, Canada.
Ortho
O
Flint
Department of Chemistry, New York University , New York, New York 10003, United States.
Wenyan
W
Liu
Department of Chemistry, New York University , New York, New York 10003, United States.
Banani
B
Chakraborty
Department of Chemistry, New York University , New York, New York 10003, United States.
Hari K K
HK
Subramanian
Department of Chemistry, New York University , New York, New York 10003, United States.
Jianping
J
Zheng
Department of Chemistry, New York University , New York, New York 10003, United States.
Arun Richard
AR
Chandrasekaran
Department of Chemistry, New York University , New York, New York 10003, United States.
Hatem O
HO
Abdallah
Department of Chemistry, New York University , New York, New York 10003, United States.
Xing
X
Wang
Department of Chemistry, New York University , New York, New York 10003, United States.
Xiaoping
X
Zhang
Department of Chemistry, New York University , New York, New York 10003, United States.
Nadrian C
NC
Seeman
D020029:Base Pairing; D004264:DNA Topoisomerases, Type I / Q000378:metabolism; D043864:DNA, Catenated / Q000737:chemistry* / Q000378:metabolism; D004926:Escherichia coli / Q000201:enzymology; D006046:Gold / Q000737:chemistry; D008958:Models, Molecular; D049329:Nanostructures / Q000737:chemistry* / Q000648:ultrastructure; D036103:Nanotechnology / Q000379:methods; D009690:Nucleic Acid Conformation; D059372:Nucleotide Motifs; D020411:Oligonucleotide Array Sequence Analysis
D043864:DNA, Catenated; D006046:Gold; D004264:DNA Topoisomerases, Type I
3′,3′ and 5′,5′ linkages; UV cross-linking; catenanes; ligated DNA constructs; one-dimensional DNA arrays; paranemic cohesion; topological linkage