38 research outputs found
Direct Measurement of Hydrodynamic Cross Correlations between Two Particles in an External Potential
We report a direct measurement of the hydrodynamic interaction between two colloidal particles. Two micron-sized latex beads were held at varying distances in optical tweezers while their Brownian displacements were measured. In spite of the fact that fluid systems at low Reynolds number are generally considered to have no âmemory,â the cross-correlation function of the bead positions shows a pronounced, time-delayed anticorrelation. We show that the anticorrelations can be understood in terms of the standard Oseen tensor hydrodynamic coupling
A Generalized Theory of DNA Looping and Cyclization
We have developed a generalized semi-analytic approach for efficiently
computing cyclization and looping factors of DNA under arbitrary binding
constraints. Many biological systems involving DNA-protein interactions impose
precise boundary conditions on DNA, which necessitates a treatment beyond the
Shimada-Yamakawa model for ring cyclization. Our model allows for DNA to be
treated as a heteropolymer with sequence-dependent intrinsic curvature and
stiffness. In this framework, we independently compute enthlapic and entropic
contributions to the factor and show that even at small length scales
entropic effects are significant. We propose a simple
analytic formula to describe our numerical results for a homogenous DNA in
planar loops, which can be used to predict experimental cyclization and loop
formation rates as a function of loop size and binding geometry. We also
introduce an effective torsional persistence length that describes the coupling
between twist and bending of DNA when looped.Comment: 6 pages, 4 figures, submitted to EP
Topologic mixing on a microfluidic chip
Mixing two liquids on a microfluidic chip is notoriously hard because the small dimensions and velocities on the chip effectively prevent turbulence. We present a topological mixing scheme that exploits the laminarity of the flow to repeatedly fold the flow and exponentially increase the concentration gradients to obtain fast and efficient mixing by diffusion. It is based on helical flow channels with opposite chiralities that split, rotate, and recombine the fluid stream in a topology reminiscent of a series of Möbius bands. This geometry is realized in a simple six-stage, two-layer elastomer structure with a footprint of 400âÎŒmĂ300âÎŒm400ÎŒmĂ300ÎŒm per stage that mixes two solutions efficiently at Reynolds numbers between 0.1 and 2. This represents more than an order of magnitude reduction in the size of microfluidic mixers that can be manufactured in standard multilayer soft lithography techniques. © 2004 American Institute of Physics.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/69745/2/APPLAB-84-12-2193-1.pd
Determining the Elasticity of Short DNA Fragments using Optical Tweezers and Protein-Mediated DNA Loop Formation Assays
All-Optical Constant-Force Laser Tweezers
AbstractOptical tweezers are a powerful tool for the study of single biomolecules. Many applications require that a molecule be held under constant tension while its extension is measured. We present two schemes based on scanning-line optical tweezers to accomplish this, providing all-optical alternatives to force-clamp traps that rely on electronic feedback to maintain constant-force conditions for the molecule. In these schemes, a laser beam is rapidly scanned along a line in the focal plane of the microscope objective, effectively creating an extended one-dimensional optical potential over distances of up to 8Όm. A position-independent lateral force acting on a trapped particle is created by either modulating the laser beam intensity during the scan or by using an asymmetric beam profile in the back focal plane of the microscope objective. With these techniques, forces of up to 2.69 pN have been applied over distances of up to 3.4Όm with residual spring constants of <26.6fN/Όm. We used these techniques in conjunction with a fast position measurement scheme to study the relaxation of λ-DNA molecules against a constant external force with submillisecond time resolution. We compare the results to predictions from the wormlike chain model
Protein-mediated DNA Loop Formation and Breakdown in a Fluctuating Environment
Living cells provide a fluctuating, out-of-equilibrium environment in which
genes must coordinate cellular function. DNA looping, which is a common means
of regulating transcription, is very much a stochastic process; the loops arise
from the thermal motion of the DNA and other fluctuations of the cellular
environment. We present single-molecule measurements of DNA loop formation and
breakdown when an artificial fluctuating force, applied to mimic a fluctuating
cellular environment, is imposed on the DNA. We show that loop formation is
greatly enhanced in the presence of noise of only a fraction of , yet
find that hypothetical regulatory schemes that employ mechanical tension in the
DNA--as a sensitive switch to control transcription--can be surprisingly robust
due to a fortuitous cancellation of noise effects
Femtonewton Force Spectroscopy of Single Extended DNA Molecules
We studied the thermal fluctuations of single DNA molecules with a novel optical tweezer based force spectroscopy technique. This technique combines femtonewton sensitivity with millisecond time resolution, surpassing the sensitivity of previous force measurements in aqueous solution with comparable bandwidth by a hundredfold. Our data resolve long-standing questions concerning internal hydrodynamics of the polymer and anisotropy in the molecular relaxation times and friction coefficients. The dynamics at high extension show interesting nonlinear behavior
Tethered Particle Motion Reveals that LacI·DNA Loops Coexist with a Competitor-Resistant but Apparently Unlooped Conformation
AbstractThe lac repressor protein (LacI) efficiently represses transcription of the lac operon in Escherichia coli by binding to two distant operator sites on the bacterial DNA and causing the intervening DNA to form a loop. We employed single-molecule tethered particle motion to observe LacI-mediated loop formation and breakdown in DNA constructs that incorporate optimized operator binding sites and intrinsic curvature favorable to loop formation. Previous bulk competition assays indirectly measured the loop lifetimes in these optimized DNA constructs as being on the order of days; however, we measured these same lifetimes to be on the order of minutes for both looped and unlooped states. In a range of single-molecule DNA competition experiments, we found that the resistance of the LacI-DNA complex to competitive binding is a function of both the operator strength and the interoperator sequence. To explain these findings, we present what we believe to be a new kinetic model of loop formation and DNA competition. In this proposed new model, we hypothesize a new unlooped state in which the unbound DNA-binding domain of the LacI protein interacts nonspecifically with nonoperator DNA adjacent to the operator site at which the second LacI DNA-binding domain is bound
Under the microscope: Single molecule symposium at the University of Michigan, 2006
In recent years, a revolution has occurred in the basic sciences, which exploits novel single molecule detection and manipulation tools to track and analyze biopolymers in unprecedented detail. A recent Gordon Research Conference style meeting, hosted by the University of Michigan, highlighted current status and future perspectives of this rising field as researchers begin to integrate it with mainstream biology and nanotechnology. © 2006 Wiley Periodicals, Inc. Biopolymers 85:106â114, 2007Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/55865/1/20621_ftp.pd