pH induced reversible assembly of DNA wrapped carbon nanotubes
© Wan et al.; licensee Chemistry Central Ltd. 2013
Received: 30 October 2012
Accepted: 14 January 2013
Published: 24 January 2013
Reversible assembly and disassembly of nanostructures has important function in controllable construction of nanodevices. There are several methods to achieve reversible assembly/disassembly, such as pH, temperature, DNA hybridization and so on. Among these methods, pH driven reversible assembly presents superiority due to its ease-of-use and no waste produced. Herein we report a novel design that use two single-stranded (ss) DNAs wrapped single walled carbon nanotubes (SWCNTs) for the pH controlled assembly of SWCNTs without generation of waste.
Both of the two DNAs with a same wrapping sequence of d(GT)20 and different free terminals showed a very high tendency to wrap around carbon nanotubes. The assembly was driven by the hybridization between the two free terminals of wrapped DNAs on the neighboring SWCNTs: i-motif (four-stranded C-quadruplex) and its complemental stranded G-quadruplex which would form tight tetraplexes and break the hybridization under slightly acidic conditions. Thus the assembly and disassembly are reversibly controlled by pH. And this assembly/disassembly process can be easily distinguished by naked eyes. Gel electrophoresis and Atomic Force Microscope are used to demonstrate the assembly and disassembly of SWCNTs at different pH.
A novel pH induced reversible assembly and disassembly of SWCNTs was realized which may have potential applications in the area of controlled assembly of nanostructures.
KeywordspH controlled reversible assembly Single walled carbon nanotubes (SWCNTs) i-motif G-quadruplex
Nanostructure has potential applications in future fabricating and nanodevices [1–8]. “Bottom up” construction of exquisite nanostructure based on different kinds of nanomaterials has attracted numerous attentions [9–13]. Several studies are particularly devoted to nanostructure based on DNA and other nanomaterials such as gold nanoparticles [14, 15], carbon nanotubes [16, 17], graphene  and so on [19, 20]. Nanostructures formed by single-walled carbon nanotubes (SWCNTs) and DNA combine both the size-dependent properties of the SWCNT and the molecular recognition and biological function of DNA, which have potential applications in molecular electronics [21, 22] and biomedical engineering [23–25]. Both covalent  and noncovalent  associations are used to construct SWCNT–DNA complexes. However, self-assembly strategies based on the biorecognition capability of single-stranded DNA (ssDNA) have been proposed to be a promising one [16, 25].
Reversible assembly and disassembly of nanostructures has important function in controllable construction of nanodevices [28–30]. There are several methods to achieve reversible assembly/disassembly, such as pH, temperature, DNA hybridization and so on. Deng and co-workers demonstrated reversible assembly/disassembly of DNA–SWCNT conjugates switched by DNA hybridization . However, changes in pH offered a simple but versatile way to control the assembly of materials. Qu et al. reported a duplex-based DNA-SWCNT self-assembled nanostructure based on a four-stranded DNA structure, G-quadruplex, and i-motif DNA . This driven mechanism is reversibly controlled by pH, but still need complex covalent modification of SWCNT.
Herein we report a pH driven reversible assembly of DNA wrapped SWCNTs. SWCNTs were wrapped by two single strand DNAs which differed at their terminal: one had an i-motif sequence and the other had its complemental sequence G-quadruplex. Both of the DNAs with a wrapping sequence of d(GT)20 had a very high tendency to wrap around carbon nanotubes and made the SWCNTs stably water dispersed. However, The SWCNTs formed conjugates as the two DNA terminals hybridized to each other under slightly basic conditions, and they were disassembled under slightly acid conditions as the tight G-quadruplex and i-motif DNA structure formed. Thus the design of a reversible SWCNTs nanostructure driven by pH changes realized.
Results and discussion
SWCNTs at slightly basic solution and slightly acid solution
Reversible assembly of SWCNT by adjusting pH
Gel electrophoresis and atomic force microscopy (AFM) illustration
Agarose gel electrophoresis and AFM were employed to interrogate the assembly and disassembly extent of SWCNT–C4/SWCNT–G4 at both acidic and basic conditions.
The kinatic of aggregation
Synthesis of DNA wrapped SWCNT
DNA oligonucleotides were purchased from Sangon Inc. (Shanghai, China) with their sequences listed in Figure 1. A mutation of the G-quadruplex domain with a single base (from GGG to GTG) will disrupt the formation of the interparticle G-quadruplex and prevent the SWCNTs assembly. DNA wrapped SWCNT was prepared following a reported process. In briefly, 100 μL of aqueous solution containing about 0.1 mg of SWCNTs (Sigma Chemicals), 0.025 mg G4 or C4, and 0.1 M NaCl was sonicated at a power of about 4 W using a VC130PB probe-type sonicator (Sonics materials inc.). The whole sonication process was incubated in an ice-water bath. Then free DNA was removed using centrifugation. Before centrifugation, MgCl2 was added to the DNA and SWCNT mixture with the concentration of 30 mM to help precipitation of the SWCNT/DNA conjugates from the solution. A centrifugation at 2000 g was taken for 2 min. The supernatant solution was carefully removed using a pipette tip. The resulted DNA/SWCNT conjugate was redispersed in 0.5xTBE buffer (Tris, 44.5 mM; EDTA, 1 mM; and boric acid, 44.5 mM, pH 8.0) containing 30 mM NaCl plus 10 mM extra EDTA to complex with residual Mg2+ in the precipitate. This step was cycled several times.
pH driven reversible SWCNT-DNA assembly
SWCNT-G4 and SWCNT-C4 were mixed in stoichiometric equivalents in a vial. Then the pH was adjusted to 5.0 by adding 1 M HCl, and then the solution was incubated for 30 min at 25°C. The resulted mixture was centrifuged at 2000 g for 30 s and observed. Then the pH was adjusted to 8.0 by adding NaOH and the solution was treated same as pH 5.0. The process was repeated several times. Assembled and disassembly products were both checked by gel electrophoresis or AFM.
Kinetic of the assembly of two SWCNTs
SWCNT-G4 and SWCNT-C4 were mixed in stoichiometric equivalents in a vial and the pH was adjusted to 8.0. Then the solution was incubated at 25°C and observed at different time.
Agarose gel electrophoresis
SWCNT-DNA conjugates were loaded into 0.5% agarose gel and run in 0.5 × TBE at 10 V/cm. The DNA-hybridization leaded to the SWCNT aggregates which could not run into the 0.5% agarose gel and was held as black deposit in the gel-loading wells.
AFM images were recorded using a Nanoscope IIIa apparatus (Digital Instruments, USA) equipped with a J Scanner. A droplet of SWCNTs mixture sample was cast onto a freshly cleaved mica surface, followed by drying at room temperature.
In summary, we provided a pH controlled reversible assembly of SWCNTs. SWCNTs were wrapped by two ssDNAs which contained wrapped sequence and different free terminals. This assembly was driven by the hybridization between their free terminals: i-motif and G-quadruplex. A mutation of the G-quadruplex domain with a single base (from GGG to GTG) was used to disrupt the formation of the interparticle G-quadruplex and prevent the nonspecific SWCNTs assembly. As i-motif and G-quadruplex were both formed at slightly acidic conditions, the assembly was controlled by pH and reversible. This assembly/disassembly process was easy to control without generation of waste and accompanied by precipitation that was clearly visible to the naked eye. This system may develop into a fast, highly reversible pH-sensitive device that may have potential applications in the area of nanobiotechnology. For example, this pH induced controllable assembly of SWCNTs can offer a potential method to desired novel pH-sensitive multifunctional architectures and/or biosensing devices.
Single walled carbon nanotube
This work was supported by National Science Foundation (No. 21105048, 21205079), NUST Research Funding (No. 2011XQTR08), Shanghai Natural Science Foundation for young scholar (12ZR1448300).
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