title: Single-molecule fluorescence studies on DNA looping.
abstract: Structure and dynamics of DNA impact how the genetic code is processed and maintained. In addition to its biological importance, DNA has been utilized as building blocks of various nanomachines and nanostructures. Thus, understanding the physical properties of DNA is of fundamental importance to basic sciences and engineering applications. DNA can undergo various physical changes. Among them, DNA looping is unique in that it can bring two distal sites together, and thus can be used to mediate interactions over long distances. In this paper, we introduce a FRET-based experimental tool to study DNA looping at the single molecule level. We explain the connection between experimental measurables and a theoretical concept known as the J factor with the intent of raising awareness of subtle theoretical details that should be considered when drawing conclusions. We also explore DNA looping-assisted protein diffusion mechanism called intersegmental transfer using protein induced fluorescence enhancement (PIFE). We present some preliminary results and future outlooks.
authors.affiliation: School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta 30332, USA. Electronic address: jjeong41@gatech.edu.
authors.forename: Jiyoun
authors.initials: J
authors.lastname: Jeong
authors.affiliation: School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta 30332, USA. Electronic address: ttl43@cornell.edu.
authors.forename: Tung T
authors.initials: TT
authors.lastname: Le
authors.affiliation: School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta 30332, USA. Electronic address: harold.kim@physics.gatech.edu.
authors.forename: Harold D
authors.initials: HD
authors.lastname: Kim
mesh_terms: D004247:DNA / Q000737:chemistry*; D031541:Fluorescence Resonance Energy Transfer / Q000379:methods*; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry; D000072760:Single Molecule Imaging / Q000379:methods*
chemical_list: D011506:Proteins; D004247:DNA
keywords: DNA looping; FRET; J factor; PIFE; Single-molecule fluorescence