Article

Nanofabricated quartz cylinders for angular trapping: DNA supercoiling torque detection.

Department of Physics, Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, New York 14853, USA.
Nature Methods (Impact Factor: 25.95). 04/2007; 4(3):223-5. DOI: 10.1038/nmeth1013
Source: PubMed

ABSTRACT We designed and created nanofabricated quartz cylinders well suited for torque application and detection in an angular optical trap. We made the cylinder axis perpendicular to the extraordinary axis of the quartz crystal and chemically functionalized only one end of each cylinder for attachment to a DNA molecule. We directly measured the torque on a single DNA molecule as it underwent a phase transition from B-form to supercoiled P-form.

0 Followers
 · 
93 Views
  • Chemical Reviews 12/2014; 115(3). DOI:10.1021/cr500119k · 45.66 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: We consider a simple lattice model of a topological phase transition in open polymers. To be precise, we study a model of self-avoiding walks on the simple cubic lattice tethered to a surface and weighted by an appropriately defined writhe. We also consider the effect of pulling the untethered end of the polymer from the surface. Regardless of the force we find a first-order phase transition which we argue is a consequence of increased knotting in the lattice polymer, rather than due to other effects such as the formation of plectonemes.
    Journal of Physics A Mathematical and Theoretical 10/2014; 48(6). DOI:10.1088/1751-8113/48/6/065002 · 1.69 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: The composition and geometry of the genetic information carriers was described as double-stranded right helices sixty years ago. The flexibility of their sugar-phosphate backbones and the chemistry of their nucleotide subunits, which give rise to the RNA and DNA polymers, were soon reported to generate two main structural duplex states with biological relevance: the so-called A and B forms. Double-stranded (ds) RNA adopts the former whereas dsDNA is stable in the latter. The presence of flexural and torsional stresses in combination with environmental conditions in the cell or in the event of specific sequences in the genome can, however, stabilize other conformations. Single-molecule manipulation, besides affording the investigation of the elastic response of these polymers, can test the stability of their structural states and transition models. This approach is uniquely suited to understanding the basic features of protein binding molecules, the dynamics of molecular motors and to shedding more light on the biological relevance of the information blocks of life. Here, we provide a comprehensive single-molecule analysis of DNA and RNA double helices in the context of their structural polymorphism to set a rigorous interpretation of their material response both inside and outside the cell. From early knowledge on static structures to current dynamic investigations, we review their phase transitions and mechanochemical behaviour and harness this fundamental knowledge not only through biological sciences, but also for Nanotechnology and Nanomedicine.
    Integrative Biology 08/2014; 6(10). DOI:10.1039/C4IB00163J · 4.00 Impact Factor

Full-text (2 Sources)

Download
8 Downloads
Available from
Aug 18, 2014