DNA is the molecule that can bear the highest possible informational content. The different codes embedded in DNA can rule its molecular behaviour, from the assembly of different single chains into double-, triple- quadruple-stranded molecules or complex nanostructures, to the interaction of a DNA molecule with other molecules and with surfaces [1]. The knowledge and the control of the interaction of DNA molecules with other molecules and surfaces is key to the mastering of the creation and control of a number of DNA-bases nanostructures and of their formation or adsorption at surfaces [2], and also to the creation of functional elements based on DNA [3]. Many methods are nowadays available to drive the adsorption of DNA on surfaces. Molecules ranging from short oligodeoxynucleotides to large genomic DNA’s can be controllably adsorbed on a variety of surfaces, either covalently or non-covalently. The atomic force microscope (AFM) has proved a valuable tool to study the interaction of DNA with surfaces and its modes of adsorption [4]. When the surface adsorption is under control, the AFM can also be used to gather a large quantity of interesting data on the adsorbed nucleic acids. Information such as the persistence length of single- and double-stranded DNA [5], or the sequence-dependent microscopic curvature and flexibility of double-stranded DNA [6] have been measured directly on the AFM micrographs, with distinct advantages with respect to other available techniques. The refinement of the AFM techniques, for what concerns the data processing, the experimental procedures and the instruments, have lead to novel measurements in the last years. It has been possible to more intimately study the mode of adsorption of DNA on surfaces such as mica. For example, thanks to experiments conducted with the novel single-molecule force spectroscopy technique, it has been possible for us to study the forces necessary to unbind DNA molecules from surfaces [7]. Furthermore, it has been possible to study the dynamic behaviour of single molecules in quasi-physiologic environment, one at a time, and still gather quantitative thermodynamic data out of this incredibly small specimen [8]. Thanks to the quantitative evaluation of the conformation of adsorbed DNA molecules it has been possible for us to determine that there are orientational preferences for the adsorption of double-stranded molecules on flat surfaces so that, when equilibrated, molecules seem to expose to the surface their T-rich faces (thus exposing A-rich faces to the solvent) [9]. Such preference is especially measured for intrinsically curved DNA molecules and it has lead us to the conclusion that the same DNA sequence elements that lead to DNA curvature can be used to compile a code to direct the orientation of DNA adsorption at surfaces. Such code, which could have had practical importance in pre-biotic stages of life development, is an additional informational code embedded in the already rich DNA molecule. [1] Samorì, B. and G. Zuccheri, DNA Codes for Nanoscience. Angew Chem Int Ed Engl, 2005. 44(8): p. 1166-1181; Zuccheri, G., M. Brucale, and B. Samorì, The Tube or the Helix? This is the Question: Towards the Fully Controlled DNA-Directed Assembly of Carbon Nanotubes. Small, 2005. 1(6): p. 590-592; Seeman, N.C., DNA in a material world. Nature, 2003. 421(6921): p. 427-31. [2] Brucale, M., G. Zuccheri, and B. Samori, Mastering the Complexity of DNA Nanostructures. 2006. in press. [3] Brucale, M., G. Zuccheri, and B. Samorì, The dynamic properties of an intramolecular transition from DNA duplex to cytosine-thymine motif triplex. Org Biomol Chem, 2005. 3(4): p. 575-7; Niemeyer, C.M. and M. Adler, Nanomechanical devices based on DNA. Angew. Chem. Int. Ed. Engl., 2002. 41(20): p. 3779-3783; Seeman, N.C., From genes to machines: DNA nanomechanical devices. Trends Biochem Sci, 2005. 30(3): p. 119-25. [4] Rivetti, C., M. Guthold, and C. Bustamante, Scanning force micros...

"The interaction of DNA with surfaces and such other trifles".

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

Abstract

DNA is the molecule that can bear the highest possible informational content. The different codes embedded in DNA can rule its molecular behaviour, from the assembly of different single chains into double-, triple- quadruple-stranded molecules or complex nanostructures, to the interaction of a DNA molecule with other molecules and with surfaces [1]. The knowledge and the control of the interaction of DNA molecules with other molecules and surfaces is key to the mastering of the creation and control of a number of DNA-bases nanostructures and of their formation or adsorption at surfaces [2], and also to the creation of functional elements based on DNA [3]. Many methods are nowadays available to drive the adsorption of DNA on surfaces. Molecules ranging from short oligodeoxynucleotides to large genomic DNA’s can be controllably adsorbed on a variety of surfaces, either covalently or non-covalently. The atomic force microscope (AFM) has proved a valuable tool to study the interaction of DNA with surfaces and its modes of adsorption [4]. When the surface adsorption is under control, the AFM can also be used to gather a large quantity of interesting data on the adsorbed nucleic acids. Information such as the persistence length of single- and double-stranded DNA [5], or the sequence-dependent microscopic curvature and flexibility of double-stranded DNA [6] have been measured directly on the AFM micrographs, with distinct advantages with respect to other available techniques. The refinement of the AFM techniques, for what concerns the data processing, the experimental procedures and the instruments, have lead to novel measurements in the last years. It has been possible to more intimately study the mode of adsorption of DNA on surfaces such as mica. For example, thanks to experiments conducted with the novel single-molecule force spectroscopy technique, it has been possible for us to study the forces necessary to unbind DNA molecules from surfaces [7]. Furthermore, it has been possible to study the dynamic behaviour of single molecules in quasi-physiologic environment, one at a time, and still gather quantitative thermodynamic data out of this incredibly small specimen [8]. Thanks to the quantitative evaluation of the conformation of adsorbed DNA molecules it has been possible for us to determine that there are orientational preferences for the adsorption of double-stranded molecules on flat surfaces so that, when equilibrated, molecules seem to expose to the surface their T-rich faces (thus exposing A-rich faces to the solvent) [9]. Such preference is especially measured for intrinsically curved DNA molecules and it has lead us to the conclusion that the same DNA sequence elements that lead to DNA curvature can be used to compile a code to direct the orientation of DNA adsorption at surfaces. Such code, which could have had practical importance in pre-biotic stages of life development, is an additional informational code embedded in the already rich DNA molecule. [1] Samorì, B. and G. Zuccheri, DNA Codes for Nanoscience. Angew Chem Int Ed Engl, 2005. 44(8): p. 1166-1181; Zuccheri, G., M. Brucale, and B. Samorì, The Tube or the Helix? This is the Question: Towards the Fully Controlled DNA-Directed Assembly of Carbon Nanotubes. Small, 2005. 1(6): p. 590-592; Seeman, N.C., DNA in a material world. Nature, 2003. 421(6921): p. 427-31. [2] Brucale, M., G. Zuccheri, and B. Samori, Mastering the Complexity of DNA Nanostructures. 2006. in press. [3] Brucale, M., G. Zuccheri, and B. Samorì, The dynamic properties of an intramolecular transition from DNA duplex to cytosine-thymine motif triplex. Org Biomol Chem, 2005. 3(4): p. 575-7; Niemeyer, C.M. and M. Adler, Nanomechanical devices based on DNA. Angew. Chem. Int. Ed. Engl., 2002. 41(20): p. 3779-3783; Seeman, N.C., From genes to machines: DNA nanomechanical devices. Trends Biochem Sci, 2005. 30(3): p. 119-25. [4] Rivetti, C., M. Guthold, and C. Bustamante, Scanning force micros...
CHEXTAN Meeting and The Netherland's Supramolecular Spring School
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G. Zuccheri; M. Brucale; A. Bergia; B. Samorì
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/11585/30569
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