The nanoscience community is currently witnessing the blossoming of several different types of molecular nanomotors [1]. Among these, the ones based on DNA seem to be especially promising, since DNA molecules can self-assemble on the nanoscale in a sequence-specific manner and can then assume a large variety of conformations [2]. We report the design and implementation of a nanomotor based on the controlled formation and breakdown of an intramolecular DNA triple-helix that could be used to pull together nano-sized objects or set them apart in space. Our DNA molecular motor is driven by a fast and clean mechanism, based on the formation of a CT-motif DNA triple-helix. This structural motif is constituted of a target duplex and a single stranded ‘triplex-forming’ homopyrimidinic oligonucleotide (TFO). At acidic pH, the imino groups of the TFO cytosines are in protonated form and the TFO binds in a sequence-specific manner to the purine strand of the duplex forming Hoogsteen-type TAT and CGC+ triplets [3]. The transition from the free duplex and single strand to the triplex conformation is critically dependent on pH, therefore enabling the design of a pH-controlled nanomotor based upon it. The nanomotor is generated by the self-assemby of two synthetic DNA single-stranded oligonucleotides of different lenghts. They are designed so that their adduct comprises both a target duplex and a single-stranded overhang that can fold on the duplex and act as a CT-motif TFO. At slightly acidic pH, the adduct is thus folded into a compact structure in which the TFO overhang adheres to the target duplex (closed state). At moderately alkaline pH, the adduct relaxes back into a ‘duplex and overhang’ conformation (open state). The repeated cycling of the pH between 5.0 and 9.0 causes the adduct to intermittently assume the open or the close state, as experimentally confirmed by means of UV, CD and fluorescence spectroscopy, as well as an electrophoretic mobility shift assay. We have demonstrated the possibility of using the DNA duplex-to-triplex transition as a means of producing a robust molecular motor. The cycling of the nanomotor does not produce waste products that could significantly alter its performance, and is not influenced by the local concentration by its constituents. The transmission of the opening and closing signals is directly dependent on the mobility of the very small and fast diffusing species H+ and OH-. These characteristics make the smooth functioning of the nanomotor possible in conditions that could hamper the performance of the DNA nanomotors reported so far, such as in nano-sized pores, or in systems where diffusion is dominant and the mobility of the species involved in the cycling is critical. 1) a) V. Balzani, A. Credi, et al. Angew. Chem, Int. Ed. 2000, 39, 3348; b) V. Balzani, A. Credi, et al. Molecular Devices and Machines, VCH, Weinheim, 2003. 2) a) C. M. Niemeyer, M. Adler, Angew. Chem, Int. Ed. 2002, 41, 3779; b) B. Samorì, G. Zuccheri, Angew. Chem, Int. Ed. (in press). 3) a) J. L. Asensio, A. N. Lane, et al. J. Mol. Biol. 1998, 275, 811; b) M. Mills, P. B. Arimondo, et al. J. Mol. Biol. 1999, 291, 1035.

A pH-Controlled DNA Molecular Motor Based on a Triple Helix

BRUCALE, MARCO;ZUCCHERI, GIAMPAOLO;SAMORI', BRUNO
2004

Abstract

The nanoscience community is currently witnessing the blossoming of several different types of molecular nanomotors [1]. Among these, the ones based on DNA seem to be especially promising, since DNA molecules can self-assemble on the nanoscale in a sequence-specific manner and can then assume a large variety of conformations [2]. We report the design and implementation of a nanomotor based on the controlled formation and breakdown of an intramolecular DNA triple-helix that could be used to pull together nano-sized objects or set them apart in space. Our DNA molecular motor is driven by a fast and clean mechanism, based on the formation of a CT-motif DNA triple-helix. This structural motif is constituted of a target duplex and a single stranded ‘triplex-forming’ homopyrimidinic oligonucleotide (TFO). At acidic pH, the imino groups of the TFO cytosines are in protonated form and the TFO binds in a sequence-specific manner to the purine strand of the duplex forming Hoogsteen-type TAT and CGC+ triplets [3]. The transition from the free duplex and single strand to the triplex conformation is critically dependent on pH, therefore enabling the design of a pH-controlled nanomotor based upon it. The nanomotor is generated by the self-assemby of two synthetic DNA single-stranded oligonucleotides of different lenghts. They are designed so that their adduct comprises both a target duplex and a single-stranded overhang that can fold on the duplex and act as a CT-motif TFO. At slightly acidic pH, the adduct is thus folded into a compact structure in which the TFO overhang adheres to the target duplex (closed state). At moderately alkaline pH, the adduct relaxes back into a ‘duplex and overhang’ conformation (open state). The repeated cycling of the pH between 5.0 and 9.0 causes the adduct to intermittently assume the open or the close state, as experimentally confirmed by means of UV, CD and fluorescence spectroscopy, as well as an electrophoretic mobility shift assay. We have demonstrated the possibility of using the DNA duplex-to-triplex transition as a means of producing a robust molecular motor. The cycling of the nanomotor does not produce waste products that could significantly alter its performance, and is not influenced by the local concentration by its constituents. The transmission of the opening and closing signals is directly dependent on the mobility of the very small and fast diffusing species H+ and OH-. These characteristics make the smooth functioning of the nanomotor possible in conditions that could hamper the performance of the DNA nanomotors reported so far, such as in nano-sized pores, or in systems where diffusion is dominant and the mobility of the species involved in the cycling is critical. 1) a) V. Balzani, A. Credi, et al. Angew. Chem, Int. Ed. 2000, 39, 3348; b) V. Balzani, A. Credi, et al. Molecular Devices and Machines, VCH, Weinheim, 2003. 2) a) C. M. Niemeyer, M. Adler, Angew. Chem, Int. Ed. 2002, 41, 3779; b) B. Samorì, G. Zuccheri, Angew. Chem, Int. Ed. (in press). 3) a) J. L. Asensio, A. N. Lane, et al. J. Mol. Biol. 1998, 275, 811; b) M. Mills, P. B. Arimondo, et al. J. Mol. Biol. 1999, 291, 1035.
Infmeeting: Convegno Nazionale per la Ricerca Interdisciplinare in Fisica della Materia
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Brucale M.; Zuccheri G.; Samorì B.
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/11585/13575
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