A novel family of structurally stable double stranded DNA catenanes

Lohmann, Finn; Valero, Julián; Famulok, Michael

doi:10.1039/c4cc02030h

Cited by 35 publications

(28 citation statements)

References 29 publications

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“…To address this issue, Famulok et al. described a strand displacement method to synthesize free functioning double‐stranded DNA catenanes . An oligonucleotide was first hybridized with the single‐stranded gap of a double‐stranded DNA circle, followed by a ring formation between the oligonucleotide and a pre‐assembled duplex DNA with two protruding ends.…”

Section: Artificial Cnasmentioning

confidence: 99%

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Circular Nucleic Acids: Discovery, Functions and Applications

Mohammed-Elsabagh

Paczkowski

et al. 2020

ChemBioChem

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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.

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Section: Artificial Cnasmentioning

confidence: 99%

“…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

ChemBioChem

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“…Likewise,w ea dded and ligated the rODNs S1/S2 for 126R1/126R2, or XS/YSf or 126X/126Y,r espectively,that are complementary to the ss gaps in the respective axles (Figure 2a,step 2). In the presence of the rODNs,both DCR hyb structures convert into ap roduct with slightly increased electrophoretic mobility,d espite the increase in 16] Interestingly,the lower bands in lanes 4 and 5, which correspond to the dumbbells that form after addition of the rODNs,differ significantly in their intensities (Figure 2b,u pper panel), thus indicating that ring and axle gaps hybridize to some extent externally,t hat is,w ithout interlocking.I nt he 126X/126Y pair, this external hybridization occurs less frequently than in the 126R1/126R2system, which likely arises from the additional base pair in the former system.…”

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confidence: 98%

Daisy Chain Rotaxanes Made from Interlocked DNA Nanostructures

et al. 2016

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We report the stepwise assembly of supramolecular daisy chain rotaxanes (DCR) made of double‐stranded DNA: Small dsDNA macrocycles bearing an axle assemble into a pseudo‐DCR precursor that was connected to rigid DNA stoppers to form DCR with the macrocycles hybridized to the axles. In presence of release oligodeoxynucleotides (rODNs), the macrocycles are released from their respective hybridization sites on the axles, leading to stable mechanically interlocked DCRs. Besides the expected threaded DCRs, certain amounts of externally hybridized structures were observed, which dissociate into dumbbell structures in presence of rODNs. We show that the genuine DCRs have significantly higher degrees of freedom in their movement along the thread axle than the hybridized DCR precursors. Interlocking of DNA in DCRs might serve as a versatile principle for constructing functional DNA nanostructures where the movement of the subunits is restricted within precisely confined tolerance ranges.

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“…In DNA architectures like rotaxanes 26 27 28 29 30 or catenanes 31 32 33 34 35 36 , the interlocked parts can be switched between stalled and mobile states 28 29 33 34 , without falling apart into individual components. Moreover, in contrast to flexible interlocked single-stranded (ss) DNA architectures 33 34 35 , double-stranded (ds) DNA counterparts are more rigid and easily visualized by atomic force microscopy (AFM) 26 27 29 .…”

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confidence: 99%

Interlocked DNA nanostructures controlled by a reversible logic circuit

Lohmann

Famulok

2014

Nat Commun

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DNA nanostructures constitute attractive devices for logic computing and nanomechanics. An emerging interest is to integrate these two fields and devise intelligent DNA nanorobots. Here we report a reversible logic circuit built on the programmable assembly of a double-stranded (ds) DNA [3]pseudocatenane that serves as a rigid scaffold to position two separate branched-out head-motifs, a bimolecular i-motif and a G-quadruplex. The G-quadruplex only forms when preceded by the assembly of the i-motif. The formation of the latter, in turn, requires acidic pH and unhindered mobility of the head-motif containing dsDNA nanorings with respect to the central ring to which they are interlocked, triggered by release oligodeoxynucleotides. We employ these features to convert the structural changes into Boolean operations with fluorescence labelling. The nanostructure behaves as a reversible logic circuit consisting of tandem YES and AND gates. Such reversible logic circuits integrated into functional nanodevices may guide future intelligent DNA nanorobots to manipulate cascade reactions in biological systems.

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A novel family of structurally stable double stranded DNA catenanes

Cited by 35 publications

References 29 publications

Circular Nucleic Acids: Discovery, Functions and Applications

Circular Nucleic Acids: Discovery, Functions and Applications

Daisy Chain Rotaxanes Made from Interlocked DNA Nanostructures

Interlocked DNA nanostructures controlled by a reversible logic circuit

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