The preparation of DNA-based nanostructures is usually accomplished in solution, by the controlled-temperature assembly of a number of oligonucleotides into complex, often multi-modular structures. Several techniques are then used to lay the nanostructures on solid surfaces, either to make them amenable to further studies with surface techniques (such as the atomic force microscope) or to integrate them on microfabricated devices. The adsorption of nucleic acids on inorganic surfaces can take place with orientational preference as a function of the DNA base sequence. Evidence was obtained of the capability of the mica surface of recognising the two faces of a strongly curved DNA fragment.[1] The differential free energy involved in that recognition mechanism was estimated, and the modulation, by the same recognition process, of the conformational space accessible to a DNA molecule upon its deposition on mica was evidenced. On the basis of these data a tentative model based on sequence-dependent unbalances of the charge distribution along the chain is proposed. This model suggests that the crystal surface can recognise such unbalances of charge, and that the recognition process does not necessarily require curved tracts: it could act also in straights DNAs.[2] A fine control of surface adsorption properties could also prove beneficial for the control and tailoring of DNA-based nanostructure growth, as this can be accomplished directly on surfaces. We have evidence that growing DNA nanostructures based on the stable Holliday junction could take place through only some of the possible pathways when performed on the surface, if compared to solution growth. We collected experimental data on a system based on the DNA parallelogram motif introduced by Prof. Seeman [3] where the assembly could be made more efficient to the point that kinetically-trapped unwanted structures could be avoided by forcing the growth to take place while all the components are adsorbed on a surface. As a fringe benefit, the reduction of dimensionality inherent in the surface adsorption enables the assembly to take place at strongly reduced oligonucleotide concentrations if compared to solution assembly. [1] Sampaolese, B., Bergia, A., Scipioni, A., Zuccheri, G., Savino, M., Samorì, B., and De Santis, P. Recognition of the DNA sequence by an inorganic crystal surface. Proc Natl Acad Sci U S A, 2002. 99(21): p. 13566-70. [2] Scipioni, A., Pisano, S., Bergia, A., Savino M., Samorì, B., and De Santis, P. Sequence-dependent DNA recognition by an inorganic crystal surface in the nanoscale (in pubbl.) [3] Mao, C., W. Sun, and N.C. Seeman, Designed Two-Dimensional DNA Holliday Junction Arrays Visualized by Atomic Force Microscopy. J. Am. Chem. Soc., 1999. 121: p. 5437-544'.

"DNA adsorption on inorganic surfaces and nanostructure growth".

SAMORI', BRUNO;ZUCCHERI, GIAMPAOLO;BRUCALE, MARCO;
2006

Abstract

The preparation of DNA-based nanostructures is usually accomplished in solution, by the controlled-temperature assembly of a number of oligonucleotides into complex, often multi-modular structures. Several techniques are then used to lay the nanostructures on solid surfaces, either to make them amenable to further studies with surface techniques (such as the atomic force microscope) or to integrate them on microfabricated devices. The adsorption of nucleic acids on inorganic surfaces can take place with orientational preference as a function of the DNA base sequence. Evidence was obtained of the capability of the mica surface of recognising the two faces of a strongly curved DNA fragment.[1] The differential free energy involved in that recognition mechanism was estimated, and the modulation, by the same recognition process, of the conformational space accessible to a DNA molecule upon its deposition on mica was evidenced. On the basis of these data a tentative model based on sequence-dependent unbalances of the charge distribution along the chain is proposed. This model suggests that the crystal surface can recognise such unbalances of charge, and that the recognition process does not necessarily require curved tracts: it could act also in straights DNAs.[2] A fine control of surface adsorption properties could also prove beneficial for the control and tailoring of DNA-based nanostructure growth, as this can be accomplished directly on surfaces. We have evidence that growing DNA nanostructures based on the stable Holliday junction could take place through only some of the possible pathways when performed on the surface, if compared to solution growth. We collected experimental data on a system based on the DNA parallelogram motif introduced by Prof. Seeman [3] where the assembly could be made more efficient to the point that kinetically-trapped unwanted structures could be avoided by forcing the growth to take place while all the components are adsorbed on a surface. As a fringe benefit, the reduction of dimensionality inherent in the surface adsorption enables the assembly to take place at strongly reduced oligonucleotide concentrations if compared to solution assembly. [1] Sampaolese, B., Bergia, A., Scipioni, A., Zuccheri, G., Savino, M., Samorì, B., and De Santis, P. Recognition of the DNA sequence by an inorganic crystal surface. Proc Natl Acad Sci U S A, 2002. 99(21): p. 13566-70. [2] Scipioni, A., Pisano, S., Bergia, A., Savino M., Samorì, B., and De Santis, P. Sequence-dependent DNA recognition by an inorganic crystal surface in the nanoscale (in pubbl.) [3] Mao, C., W. Sun, and N.C. Seeman, Designed Two-Dimensional DNA Holliday Junction Arrays Visualized by Atomic Force Microscopy. J. Am. Chem. Soc., 1999. 121: p. 5437-544'.
DNA-based Nanoscale Integration International Symposium
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B. Samorì; G. Zuccheri; M. Brucale; P. De Santis
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/11585/30571
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