Engineering interlocking DNA rings with weak physical interactions

Topologically controlled DNA catenanes are promising elements for the construction of molecular machines but present a significant effort in DNA nanotechnology. We report an efficient approach for preparing linear three-ring catenanes (L3C) composed of single-stranded DNA. The linking number was strictly controlled by using short complementary regions (6 nt) between each two DNA rings. High efficiency of forming three-ring catenanes (yield as high as 63 %) was obtained by using an 80 nt oligonucleotide as the scaffold to draw close the three pre-rings for hybridization between short complementary DNA. After assembly, three pre-rings were closed by DNA ligation using three 12 nt oligonucleotides as splints to form interlocked three-ring catenanes. L3C nanostructures were imaged in air by AFM: the catenane exhibited a smooth circular shape and was arranged in a line with well-defined structure, as expected.

Section: Methodsmentioning

confidence: 99%

Efficient Synthesis of Topologically Linked Three‐Ring DNA Catenanes

et al. 2016

“…To create DNA catenanes having weak physical interactions between each other, Li et al. adopted a random library approach to generate two‐ring DNA catenanes without a linking duplex (Figure D) . The weak physical interactions and capability of operating as independent units of the representative catenanes were signified by double‐stranded catenane synthesis, DNA hybridization, and rolling circle amplification experiments.…”

Section: Artificial Cnasmentioning

confidence: 99%

“…Template‐mediated enzymatic ligation could also be used to produce topologically linked ring structures known as catenanes. For example, DNA ligation reactions can be used to synthesize single‐stranded DNA catenanes with 2 or more component rings, including the ones with weak physical interactions between resident rings . They can also be used to prepare double‐stranded circular DNAs with excellent rigidity as components of nanodevices …”

Section: Introductionmentioning

confidence: 99%

Circular Nucleic Acids: Discovery, Functions and Applications

Mohammed-Elsabagh

Paczkowski

et al. 2020

Self Cite

acids (CNAs) are nucleic acid molecules with a closed-loop structure. This feature comes with a number of advantages including complete resistance to exonuclease degradation, much better thermodynamic stability, and the capability of being replicated by a DNA polymerase in a rolling circle manner. Circular functional nucleic acids, CNAs containing at least a ribozyme/DNAzyme or a DNA/RNA aptamer, not only inherit the advantages of CNAs but also offer some unique application opportunities, such as the design of topologycontrolled or enabled molecular devices. This article will begin by summarizing the discovery, biogenesis, and applications of naturally occurring CNAs, followed by discussing the methods for constructing artificial CNAs. The exploitation of circular functional nucleic acids for applications in nanodevice engineering, biosensing, and drug delivery will be reviewed next. Finally, the efforts to couple functional nucleic acids with rolling circle amplification for ultra-sensitive biosensing and for synthesizing multivalent molecular scaffolds for unique applications in biosensing and drug delivery will be recapitulated.[a] Dr.

Section: Figurementioning

confidence: 99%

“…By taking an in vitro selection approach, we have recently derived a number of DNA sequences from a random pool of DNAs that are able to form DNA [2]catenanes (D2Cs; two interlocked DNA rings) with a premade ssDNA circle without requiring the formation of a strong linking duplex . We have further shown that the constituent rings within these catenanes have minimal physical interactions . As we show in this work, the weak physical interactions between component rings of these D2Cs also make it possible to fabricate even more complex nanostructures such as DNA [3]catenanes (D3Cs; three interlocked DNA rings) consisting of a central mother ring and two identical or fraternal twin daughter rings: unusual nanostructures that have never been reported before.…”

Section: Figurementioning

confidence: 99%

Topological DNA Assemblies Containing Identical or Fraternal Twins

Tram

Salena

et al. 2016

Self Cite

DNA catenanes are assemblies made up of two or more DNA rings linked together through mechanical bonds, and they are desirable for engineering unique nanoscale devices. However, current methods of synthesizing DNA catenanes rely on the formation of strong linking duplexes between component units to enable interlocking and thus do not permit the synthesis of complex single-stranded DNA structures with freely functioning units. We have recently reported DNA sequences that can thread through a DNA circle without the formation of a linking duplex. Here we show that these unique DNA molecules can be further used to make intricate symmetric or asymmetric DNA [3]catenanes, single-stranded DNA assemblies made up of a central mother ring interlocked to two identical or fraternal twin daughter rings, which have never been reported before. These addressable freely functioning interlocked DNA rings should facilitate the design of elaborate nanoscale machines based on DNA.