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Background

1.DNA catenanes

DNA catenanes, a new promising subfield in DNA nanotechnology, are mechanically interlocked rings systems composed of two or more interlocked DNA rings that are unable to be separated without breaking the covalent bonds between the macrocycles.

In the biological context, catenanes are widely acknowledged to be essential intermediates in gene activities. One discovery worthy to be mentioned is the mitocondrial DNA of trypanosomatid protozoa termed kinetoplast DNA (kDNA).It is composed of a giant network of many interlocked dsDNA maxicircles and minicircles, which is similar to the medieval hauberk[1].

Enlightened by these striking natural structures, supstantial efforts towards artificial fabrication of DNA catenanes have been made for further understanding and utility of their distinct features. Synthesis of both double-stranded (ds) and single-stranded (ss) DNA catenanes have been reported. Generally, most of the catenanes contained in topologically interlocked structures are based on ssDNA. Examples include Seeman’s cube[2], ssDNA rotary motors[3] and catenated scaffolds for assembly of hierarchical nanostructures[4].

There are several ways of synthesizing two-ring interlocked ssDNA catenanes, which pave the way for more complex interlocked ssDNA catenane nanostructures. For instance, linking two rings together by enzymatic ligation of two inter-threaded strands using splints or by circularizing a DNA oligonucleotide over a premade DNA ring[5]. Fabrication of three-, five-, and seven-ring catenanes has been achieved following several paths[3]. Controlling topology (linking number, Lk: the number of turns intertwining between two circles) between catenated rings strictly and effectively is another problem that worth attention[6]. Only if Lk is finely controlled can the nanostructure accord with expectation.

Recently, our laboratory has developed an efficient approach for preparing linear ssDNA three-ring catenanes, using an oligonucleotide scaffold, which hasn’t been used before, to draw close pre-rings[7]. We took advantage of the scaffold to create the topologically linked DNA network, DNA hauberk as well.

2.Artificial DNA networks

The conceptual foundation for DNA nanotechnology was first laid out by Nadrian Seeman, who realized that it was possible to generate covalently joined three-dimensional networks of nucleic acids in the 1980s[8]. A network is any system with sup-units that are linked into a whole, and in the case of DNA nanotechnology, a great many nucleotides are deeply connected with one another, resulting in complex periodic arrangements. Most typical examples are DNA tiles and DNA origami.

DNA tile structures provide the foundation for developing artificial DNA network. The core concept of tile-based assembly is combining numerous branched DNA junction with sticky-end associations to form two-dimensional (2D) lattices[9]. A variety of DNA tile arrays with increased complexity have been produced, bringing about functional nanoarchitectures, as they are excellent templates for positioning functional nanoparticles, for instance, proteins. Using DNA tiles makes it possible to build artificial enzymatic networks and molecular pegboards for functional nanoelectronics.

Figure 1.Key concept of DNA tile based self-assembly: combining branched DNA junction with sticky-end associations (e.g. a-a’ and b-b’ pairings) to self-assemble 2D lattices.

Fig.1 Key concept of DNA tile based self-assembly: combining branched DNA junction with sticky-end associations (e.g. a-a’ and b-b’ pairings) to self-assemble 2D lattices[9].

DNA origami is a method for folding a long, single-stranded M13mp18 DNA with sets of ‘staple’ strands into arbitrary 2D shapes, which is also widely used to construct artificial DNA network. The arrangement of 2D DNA origami networks with uniform densities has attracted much attention and many accomplishments have been made, as this type of network structure composed of junctions and junctures is another fascinating approach to forthcoming nanoscale network devices[10].

Fig.2  Schematic structure of origami tiles (two different tiles, A and B) with orthogonal directions of propagation.

Figure 2.Schematic structure of origami tiles (two different tiles, A and B) with orthogonal directions of propagation.[11].

3.Application of ssDNA catenanes

Scaffold

ssDNA catenane scaffolds can be used to orient nanoparticles, proteins, or fluorophores onto a single scaffold with precise relative spatial orientation. When nanoparticles, proteins or fluorophores are attached to complementary ssDNA sequences, they can bind ssDNA domains of the catenated system. If the code of sequences are modified to aptamers they are able to bind specific target molecules.The potential of hierarchical nanoassemblies in biosensing, catalyzing enzymatic cascades are just part of the promise of topologically interlocked ssDNA catenanes[4].

Figure 3. Functionalization of the polycatenated DNA with the fluorescent labeled ssDNA

Figure 3. Functionalization of the polycatenated DNA with the fluorescent labeled ssDNA[4].

Nanomachines

Nanomachines have attracted great attention in recent years, as the most typical example is that the Nobel Prize in Chemistry 2016 was awarded jointly to three outstanding scientists for the design and synthesis of molecular machines. Building molecular machine may be one of the most promising applications of DNA catenanes. The number of dynamic transitions in systems increases with the number of interlocked catenanes. Meanwhile, various methods can be used to trigger the machine to operate in an anticipant approach, especially the fuel/anti-fuel strands[3,12].

Figure 4. Reversible reconfiguration of the five-ring interlocked DNA catenane across the states I, II, III and IV using appropriate fuel/anti-fuel strands

Figure 4. Reversible reconfiguration of the five-ring interlocked DNA catenane across the states I, II, III and IV using appropriate fuel/anti-fuel strands[12].

Besides operating as positional switches and nanomotors, strand-dictated reconfigurable multi-ring catenanes also provide a rich arena of different states or functional groups that can act as functional elements for computing automata or as a scaffold for multi-valued logics. Furthermore, the fact that DNA circles lack 3′ and 5′ termini indicates that such structures, and particularly catenanes that include non-natural nucleotide bases, should reveal enhanced stabilities toward enzymatic degradation, as compared to linear analogues[3].

Our goals

Up till now, generally single-stranded (ss) DNA have been used to produce topological macrocycle units, or catenated systems composed of 7 rings[12] at most. Artificial DNA networks always appear in the form of DNA tiles or origami, and no DNA catenane has been used to produce topologically interlocked network structure. This summer, enlightened by the natural kDNA network and previous studies towards DNA catenanes, we intend to build new ssDNA catenanes which can offer inspiration to others in the future. Specified purposes are listed as follow:

1.Build multi-ring ssDNA systems and control its topology which mainly focuses on the linking number (Lk) between two adjacent rings.

2.Explore the relationships between our yield and the application of hinges along with linking domains of different length. Improve the yield based on the results.

3.Fabricate a brand new type of DNA network: DNA hauberk based on ssDNA catenanes.

The structure we decided to build

The structure we decided to build

References

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[2]Chen J H, Seeman N C. Synthesis from DNA of a molecule with the connectivity of a cube[J]. Nature, 1991, 350(6319):631-633.

[3]Lu C H, Cecconello A, Willner I. Recent Advances in the Synthesis and Functions of Reconfigurable Interlocked DNA Nanostructures[J]. Journal of the American Chemical Society, 2016, 138(16):5172.

[4]Weizmann Y, Braunschweig A B, Wilner O I, et al. A polycatenated DNA scaffold for the one-step assembly of hierarchical nanostructures.[J]. Proceedings of the National Academy of Sciences of the United States of America, 2008, 105(14):5289.

[5]Billen L P, Li Y. Synthesis and characterization of topologically linked single-stranded DNA rings[J]. Bioorganic Chemistry, 2004, 32(6):582-598.

[6]Liang X, Kuhn H, Frankkamenetskii M D. Monitoring Single-Stranded DNA Secondary Structure Formation by Determining the Topological State of DNA Catenanes[J]. Biophysical Journal, 2006, 90(8):2877-89.

[7]Qi L, Wu G, Wu W, et al. Efficient Synthesis of Topologically Linked Three‐Ring DNA Catenanes[J]. Chembiochem A European Journal of Chemical Biology, 2016, 17(12):1127.

[8]Seeman N C. Nucleic acid junctions and lattices[J]. Journal of Theoretical Biology, 1982, 99(2):237-247.

[9]Lin C, Liu Y, Rinker S, et al. DNA Tile Based Self-Assembly: Building Complex Nanoarchitectures[J].Chemphyschem A European Journal of Chemical Physics & Physical Chemistry, 2006, 7(8):1641.

[10]Hirano Y, Ojima K, Miyake Y, et al. Emergence of High-density DNA Origami Network by Dewetting with a Binary Solvent[J]. Chemistry Letters, 2012, 41(11):1459-1461.

[11]Liu W, Zhong H, Wang R, et al. Crystalline Two‐Dimensional DNA‐Origami Arrays[J]. Angewandte Chemie, 2011, 50(1):264.

[12]Lu C H, Qi X J, Cecconello A, et al. Switchable reconfiguration of an interlocked DNA olympiadanenanostructure[J]. AngewandteChemie, 2014, 53(29):7499-503.