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Interlocked DNA nanostructures controlled by a reversible logic circuit.

Li T, Lohmann F, Famulok M - Nat Commun (2014)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Chemical Biology and Medicinal Chemistry Unit, Life and Medical Science (LIMES) Institute, University of Bonn, 53121 Bonn, Germany.

ABSTRACT
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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Related in: MedlinePlus

Schematic for the synthesis and programmable assembly of dsDNA [3]pseudocatenane.(a) The synthesized [3]pseudocatenane contains C-rich (cyan, C6TC6) and G-rich (purple, G3ACG3) branches. The rings L-M and M-R are held together by hybridization in short sections, to form the interlocked structure. (b) Addition of RO-L and RO-R (that is, ROs) triggers a structural conversion from [3]pseudocatenane to [3]catenane, where RO-L and RO-R (underlined: the active sequences) are hybridized with two gaps of ring M to displace L and R thereby allowing them to move freely. A bimolecular i-motif (cyan) can then form in the presence of H+, resulting in head-motif cyclization in the interlocked system.
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f1: Schematic for the synthesis and programmable assembly of dsDNA [3]pseudocatenane.(a) The synthesized [3]pseudocatenane contains C-rich (cyan, C6TC6) and G-rich (purple, G3ACG3) branches. The rings L-M and M-R are held together by hybridization in short sections, to form the interlocked structure. (b) Addition of RO-L and RO-R (that is, ROs) triggers a structural conversion from [3]pseudocatenane to [3]catenane, where RO-L and RO-R (underlined: the active sequences) are hybridized with two gaps of ring M to displace L and R thereby allowing them to move freely. A bimolecular i-motif (cyan) can then form in the presence of H+, resulting in head-motif cyclization in the interlocked system.

Mentions: The synthesized [3]pseudocatenane (Fig. 1a), which is verified by a new and very slowly moving band (Fig. 2a, lane 3) in native polyacrylamide gel electrophoresis, consists of a dsDNA nanocircle with two 13-mer ss-gap regions in the middle (M) to which two dsDNA nanocircles with a 10-mer ss-gap region are interlocked (L and R). Rings L and R also contain a branched-out head-motif bearing one half of a bimolecular i-motif sequence and half of a potential bimolecular G-quadruplex structure. The ss-gaps of the nanocircles L and R are complementary to the gaps in M to which they hybridize so that the branched-out motifs arrange in opposite directions (Fig. 1a). This design ensures that the nanocircles L and R are stably positioned with their two heads held separate, thereby preventing the formation of the bimolecular i-motif and G-quadruplex, respectively. Moreover, L and R contain a rhodamine green fluorophore (RG) at the border of the gap sequence, while M contains two black hole quencher (BHQ1) dyes at the gap borders. In the hybridized, pseudocatenated state RG and BHQ1 arrange opposite to each other, resulting in FQ (Fig. 1, Supplementary Fig. 1). On addition of ROs that are complementary to the entire gap regions in M, all nanocircles dehybridize from the stalled pseudocatenated into the mobile catenated state. This change in mobility can be visualized by native polyacrylamide gel electrophoresis and is indicated by the appearance of a slower band accompanied by the disappearance of the [3]pseudocatenane band (Fig. 2c, lane 2 versus lane 1). We observed complete conversion of the band corresponding to the [3]pseudocatenane into the [3]catenane. The shift in the electrophoretic mobility of the pseudocatenane/catenane structures most likely originates from the marked difference in their structures. In the pseudocatenane, three circles are locked immobile in an almost linear arrangement, as verified by high-resolution AFM (Fig. 3a, Supplementary Fig. 2). Figure 3a also shows that the head-groups point into opposite directions in almost all observed structures, as was intended by our design.


Interlocked DNA nanostructures controlled by a reversible logic circuit.

Li T, Lohmann F, Famulok M - Nat Commun (2014)

Schematic for the synthesis and programmable assembly of dsDNA [3]pseudocatenane.(a) The synthesized [3]pseudocatenane contains C-rich (cyan, C6TC6) and G-rich (purple, G3ACG3) branches. The rings L-M and M-R are held together by hybridization in short sections, to form the interlocked structure. (b) Addition of RO-L and RO-R (that is, ROs) triggers a structural conversion from [3]pseudocatenane to [3]catenane, where RO-L and RO-R (underlined: the active sequences) are hybridized with two gaps of ring M to displace L and R thereby allowing them to move freely. A bimolecular i-motif (cyan) can then form in the presence of H+, resulting in head-motif cyclization in the interlocked system.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4199106&req=5

f1: Schematic for the synthesis and programmable assembly of dsDNA [3]pseudocatenane.(a) The synthesized [3]pseudocatenane contains C-rich (cyan, C6TC6) and G-rich (purple, G3ACG3) branches. The rings L-M and M-R are held together by hybridization in short sections, to form the interlocked structure. (b) Addition of RO-L and RO-R (that is, ROs) triggers a structural conversion from [3]pseudocatenane to [3]catenane, where RO-L and RO-R (underlined: the active sequences) are hybridized with two gaps of ring M to displace L and R thereby allowing them to move freely. A bimolecular i-motif (cyan) can then form in the presence of H+, resulting in head-motif cyclization in the interlocked system.
Mentions: The synthesized [3]pseudocatenane (Fig. 1a), which is verified by a new and very slowly moving band (Fig. 2a, lane 3) in native polyacrylamide gel electrophoresis, consists of a dsDNA nanocircle with two 13-mer ss-gap regions in the middle (M) to which two dsDNA nanocircles with a 10-mer ss-gap region are interlocked (L and R). Rings L and R also contain a branched-out head-motif bearing one half of a bimolecular i-motif sequence and half of a potential bimolecular G-quadruplex structure. The ss-gaps of the nanocircles L and R are complementary to the gaps in M to which they hybridize so that the branched-out motifs arrange in opposite directions (Fig. 1a). This design ensures that the nanocircles L and R are stably positioned with their two heads held separate, thereby preventing the formation of the bimolecular i-motif and G-quadruplex, respectively. Moreover, L and R contain a rhodamine green fluorophore (RG) at the border of the gap sequence, while M contains two black hole quencher (BHQ1) dyes at the gap borders. In the hybridized, pseudocatenated state RG and BHQ1 arrange opposite to each other, resulting in FQ (Fig. 1, Supplementary Fig. 1). On addition of ROs that are complementary to the entire gap regions in M, all nanocircles dehybridize from the stalled pseudocatenated into the mobile catenated state. This change in mobility can be visualized by native polyacrylamide gel electrophoresis and is indicated by the appearance of a slower band accompanied by the disappearance of the [3]pseudocatenane band (Fig. 2c, lane 2 versus lane 1). We observed complete conversion of the band corresponding to the [3]pseudocatenane into the [3]catenane. The shift in the electrophoretic mobility of the pseudocatenane/catenane structures most likely originates from the marked difference in their structures. In the pseudocatenane, three circles are locked immobile in an almost linear arrangement, as verified by high-resolution AFM (Fig. 3a, Supplementary Fig. 2). Figure 3a also shows that the head-groups point into opposite directions in almost all observed structures, as was intended by our design.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Chemical Biology and Medicinal Chemistry Unit, Life and Medical Science (LIMES) Institute, University of Bonn, 53121 Bonn, Germany.

ABSTRACT
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.

Show MeSH
Related in: MedlinePlus