In the last two decades, the development of the atomic force microscope has progressed hand-in-hand with its application to the study of DNA. At times, the novel capabilities of probe microscopy have been used to study the many wonders of nucleic acids in their biological context. Other times, DNA was used as a model in physical studies, more than for its biological identity. For many labs, the predictable structure and the relatively easy handling of double-stranded DNA have proved useful to test microscopy performances. Along this line of development, our lab has tried to apply the atomic force microscope to the discovery of the properties of DNA in biological systems. We have tried to exploit the peculiar advantages of the AFM with respect to other ultramicroscopy techniques: 3D imaging allows the visualization and determination of the spatial arrangement and the chirality of molecular systems [1] and it allows to directly compute the volume (albeit with approximation) of macromolecular structures. This was, for example, used by our advantage to visualize the chirality of supercoiled DNA [1] or the 3D structure of nucleosomes or chromatin fibers. The unique abilities of the AFM to perform high-resolution imaging in aqueous liquid environments enable researchers to visualize biological DNA structures in their native environments, albeit outside of the biological tissues. We exploited this potential for imaging fragile DNA superstructures, such as chromatin fibers or to visualize the dynamics of double-stranded DNA molecules [2]. The availability of fully digital images allows for the measurements of molecularly relevant geometrical parameters directly from the AFM images [3-5]. Such quantitative use of microscopy evolved in time and peaked with the determination of structural and dynamic features from single molecules of DNA [6]. Lately, AFM-based molecule manipulation techniques have become a valuable tool for probing the mechanochemical behavior of molecules, rather than simply their structure or dynamics. Even though the forces necessary to drive conformational transitions in DNA are weak relatively to the forces commonly applicable by the AFM, valuable information can still be acquired and the advancement of the AFM technology will further extend such applications. References [1] B. Samorì et al., Angew. Chem. Int. Ed. Eng., 32 (1993) 1461-1463. [2] G. Zuccheri et al., Applied Physics A, 66 (1998) S585-589. [3] G. Zuccheri et al., Journal of Vacuum Science & Technology B, 13 (1995) 158-160. [4] A. Giro et al., Microsc. Res. Tech., 65 (2004) 235-245. [5] G. Zuccheri et al., Proc. Nat. Acad. Sci. U.S.A., 98 (2001) 3074-3079. [6] A. Scipioni et al., Chemistry & Biology, 9 (2002) 1315-1321.
One thing or two you can learn on DNA with the AFM
ZUCCHERI, GIAMPAOLO
2013
Abstract
In the last two decades, the development of the atomic force microscope has progressed hand-in-hand with its application to the study of DNA. At times, the novel capabilities of probe microscopy have been used to study the many wonders of nucleic acids in their biological context. Other times, DNA was used as a model in physical studies, more than for its biological identity. For many labs, the predictable structure and the relatively easy handling of double-stranded DNA have proved useful to test microscopy performances. Along this line of development, our lab has tried to apply the atomic force microscope to the discovery of the properties of DNA in biological systems. We have tried to exploit the peculiar advantages of the AFM with respect to other ultramicroscopy techniques: 3D imaging allows the visualization and determination of the spatial arrangement and the chirality of molecular systems [1] and it allows to directly compute the volume (albeit with approximation) of macromolecular structures. This was, for example, used by our advantage to visualize the chirality of supercoiled DNA [1] or the 3D structure of nucleosomes or chromatin fibers. The unique abilities of the AFM to perform high-resolution imaging in aqueous liquid environments enable researchers to visualize biological DNA structures in their native environments, albeit outside of the biological tissues. We exploited this potential for imaging fragile DNA superstructures, such as chromatin fibers or to visualize the dynamics of double-stranded DNA molecules [2]. The availability of fully digital images allows for the measurements of molecularly relevant geometrical parameters directly from the AFM images [3-5]. Such quantitative use of microscopy evolved in time and peaked with the determination of structural and dynamic features from single molecules of DNA [6]. Lately, AFM-based molecule manipulation techniques have become a valuable tool for probing the mechanochemical behavior of molecules, rather than simply their structure or dynamics. Even though the forces necessary to drive conformational transitions in DNA are weak relatively to the forces commonly applicable by the AFM, valuable information can still be acquired and the advancement of the AFM technology will further extend such applications. References [1] B. Samorì et al., Angew. Chem. Int. Ed. Eng., 32 (1993) 1461-1463. [2] G. Zuccheri et al., Applied Physics A, 66 (1998) S585-589. [3] G. Zuccheri et al., Journal of Vacuum Science & Technology B, 13 (1995) 158-160. [4] A. Giro et al., Microsc. Res. Tech., 65 (2004) 235-245. [5] G. Zuccheri et al., Proc. Nat. Acad. Sci. U.S.A., 98 (2001) 3074-3079. [6] A. Scipioni et al., Chemistry & Biology, 9 (2002) 1315-1321.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
