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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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Fluorescence monitoring of the structural changes of DNA nanoarchitectures.(a) Fluorescence signal of RG/BHQ1 FQ system in response to the structural changes. The toehold strand displacement is reflected by an increase in the RG fluorescence, while a decrease indicates the reverse process. (b) Kinetic data for the toehold-mediated release experiment in the working solution at different temperatures. The addition of ROs induces a sharp increase in the fluorescence in about 1 h at 37 °C, while in about 3 h at 25 °C (inset).
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f4: Fluorescence monitoring of the structural changes of DNA nanoarchitectures.(a) Fluorescence signal of RG/BHQ1 FQ system in response to the structural changes. The toehold strand displacement is reflected by an increase in the RG fluorescence, while a decrease indicates the reverse process. (b) Kinetic data for the toehold-mediated release experiment in the working solution at different temperatures. The addition of ROs induces a sharp increase in the fluorescence in about 1 h at 37 °C, while in about 3 h at 25 °C (inset).

Mentions: In contrast, circles R and L of the [3]catenane can move unhindered along the central circle M, and can also rotate. By AFM, a shift from the regularly linear into a more compact arrangement can be visualized (Fig. 3b, Supplementary Fig. 3). Interestingly, in agarose gel electrophoresis (Fig. 2b) the electrophoretic mobility is exactly the opposite: now the pseudocatenane migrates slower than the catenane (lane 2 versus lane 1), similar to our previous observations using dsDNA rotaxanes262829. The pseudocatenane→catenane conversion can be reset almost quantitatively by adding oligodeoxynucleotides (ODNs) that are complementary to the ROs (cROs) to remove the ROs (Fig. 2c, lane 3). Further proof for the pseudocatenane→catenane conversion was obtained from FQ data (Fig. 4a). The addition of ROs results in a sharp increase of the fluorescence signal, indicating the separation of RG from the quencher. The fluorescence decreases on addition of the cROs to remove the ROs, and thus the interlocked structure is reset to the original state. The addition of ROs in the presence of H+ does not result in an obvious change in the fluorescence signal as compared with the addition of ROs alone. Consequently, the addition of alkali to the sample containing ROs+H+ has almost no influence on the fluorescence.


Interlocked DNA nanostructures controlled by a reversible logic circuit.

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

Fluorescence monitoring of the structural changes of DNA nanoarchitectures.(a) Fluorescence signal of RG/BHQ1 FQ system in response to the structural changes. The toehold strand displacement is reflected by an increase in the RG fluorescence, while a decrease indicates the reverse process. (b) Kinetic data for the toehold-mediated release experiment in the working solution at different temperatures. The addition of ROs induces a sharp increase in the fluorescence in about 1 h at 37 °C, while in about 3 h at 25 °C (inset).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f4: Fluorescence monitoring of the structural changes of DNA nanoarchitectures.(a) Fluorescence signal of RG/BHQ1 FQ system in response to the structural changes. The toehold strand displacement is reflected by an increase in the RG fluorescence, while a decrease indicates the reverse process. (b) Kinetic data for the toehold-mediated release experiment in the working solution at different temperatures. The addition of ROs induces a sharp increase in the fluorescence in about 1 h at 37 °C, while in about 3 h at 25 °C (inset).
Mentions: In contrast, circles R and L of the [3]catenane can move unhindered along the central circle M, and can also rotate. By AFM, a shift from the regularly linear into a more compact arrangement can be visualized (Fig. 3b, Supplementary Fig. 3). Interestingly, in agarose gel electrophoresis (Fig. 2b) the electrophoretic mobility is exactly the opposite: now the pseudocatenane migrates slower than the catenane (lane 2 versus lane 1), similar to our previous observations using dsDNA rotaxanes262829. The pseudocatenane→catenane conversion can be reset almost quantitatively by adding oligodeoxynucleotides (ODNs) that are complementary to the ROs (cROs) to remove the ROs (Fig. 2c, lane 3). Further proof for the pseudocatenane→catenane conversion was obtained from FQ data (Fig. 4a). The addition of ROs results in a sharp increase of the fluorescence signal, indicating the separation of RG from the quencher. The fluorescence decreases on addition of the cROs to remove the ROs, and thus the interlocked structure is reset to the original state. The addition of ROs in the presence of H+ does not result in an obvious change in the fluorescence signal as compared with the addition of ROs alone. Consequently, the addition of alkali to the sample containing ROs+H+ has almost no influence on the fluorescence.

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