Plenarvorträge - DPG-Tagungen

Symposium Life Sciences on the Nanometer Scale - Physics Meets Biology Mittwoch
SYLS 3.35 Mi 16:00 B
Translocation of structured RNA molecules through nanopores
— •Ulrich Gerland 1 , Ralf Bundschuh 2 , and Terence Hwa 3 —
1 Sektion Physik, Universität München — 2 Department of Physics, The
Ohio State University — 3 Department of Physics, University of California
at San Diego
We investigate theoretically the translocation of structured RNA/DNA
molecules through narrow pores which allow single but not double
strands to pass. The unzipping of basepaired regions within the molecules
presents significant kinetic barriers for the translocation process. We show
that this circumstance may be exploited to determine the full basepairing
pattern of polynucleotides, including RNA pseudoknots. The crucial
requirement is that the translocation dynamics (i.e., the length of the
translocated molecular segment) needs to be recorded as a function of
time with a spatial resolution of a few nucleotides. This could be achieved,
for instance, by applying a mechanical driving force for translocation and
recording force-extension curves (FEC’s) with a device such as an atomic
force microscope or optical tweezers. Our analysis suggests that with this
added spatial resolution, nanopores could be transformed into a powerful
experimental tool to study the folding of nucleic acids.
SYLS 3.36 Mi 16:00 B
UV-Laser Induced Fluorescence Detection of Proteins in PDMS
Microfluidic Devices — •Wibke Hellmich, Alexandra Ros, and
Dario Anselmetti — Experimental Biophysics, Physics Department,
Bielefeld University, Bielefeld, Germany
Since the complete mapping of the human genome growing interest
in the field of proteomics requires new techniques for protein analysis.
Especially efficient and sensitive methods for separation, detection and
analysis of unlabeled protein solutions are of great importance. This work
focuses on the separation and label free fluorescence detection of proteins
in the UV range in uncoated polydimethylsiloxane (PDMS) microfluidic
devices.
In the visible range we determined a detection limit of 100fM for fluorescein,
a fluorescent dye, and in the UV-range 50µM for tryptophane
(Trp), an aromatic amino acid. In a first test experiment the separation
of a protein mixture, avidin (four Trp) and lysocyme C (six Trp), in a
microfluidic system with UV detection was successfully realized.
Further investigation will include the optimization of the detection system
to enhance the sensitivity of this label free protein analysis method.
SYLS 3.37 Mi 16:00 B
Attraction of similarly-charged macroions — •Ali Naji and
Roland Netz — Sektion Physik, Ludwig-Maximilians-Universitaet
Muenchen, Theresienstr. 37, 80333 Muenchen
We investigate effective electrostatic interaction between similarlycharged
rod-like and spherical macroions in the regime of strong electrostatic
correlations using the asymptotic strong-coupling theory. We examine
the regime of charge parameters, in which dominant electrostatic
attraction is predicted between charged rods and charged spheres. For
highly-charged macroions, such an attraction gives rise to the formation
of closely-packed macroion-macroion bound states with finite surface-tosurface
separation. In this regime, the predictions of the strong-coupling
theory for the equilibrium separation of macroions is found to be in quantitative
agreement with recent numerical simulations both on charged
rods and charged spheres. We study finite size effects (due to confinement)
on the effective interaction: rod-like macroions are found to attract
each other both in confined and unconfined geometries; specifically,
unconfined rods show attraction when the single-rod Manning parameter
becomes larger than 2/3. By contrast, spherical macroions exhibit
attraction only in confinement, and the onset of attraction (the threshold
charge strength) in this case depends on the size of the confining box,
and weakly (logarithmically) increases with the box size. By decreasing
the charge parameter, attracting macroions undergo an unbinding transition
from a closely-packed bound state to a repulsion-dominated state.
This transition occurs continuously for charged rods displaying a scaling
relation, while charged spheres exhibit a discontinuous transition.
SYLS 3.38 Mi 16:00 B
DNA-histone complexes: interaction and conformation —
•Hoda Boroudjerdi and Roland Netz — Sektion Physik,
Ludwig-Maximilians-Universitaet Muenchen, Theresienstr. 37, 80333
Muenchen
We investigate effective interaction between two complexes of semiflex-
ible charged polymers with oppositely-charged spheres with parameters
appropriate for the DNA-histone system. We determine the ground state
of the system numerically by minimizing a free energy expression, which
includes electrostatic effects on a linear level. We obtain the effective
interaction potential between two complexes for various system parameters,
namely, the charge valency of the spheres and the salt concentration.
It is shown that within this model, complexes can attract each other at
short distances depending on the system parameters, which arises from an
interplay between electrostatic interactions, bending rigidity and conformational
behavior of the charged polymers. We examine different phases
of the system based on symmetry arguments, which include bridging and
binding phases. Finally, we present the behavior of the second virial coefficient
of this system in terms of the salt concentration, which exhibits
a non-monotonic behavior with a minimum at moderate salt concentrations.
SYLS 3.39 Mi 16:00 B
Dynamics of Driven Polymers — •Xaver Schlagberger and
Roland Netz — Department of Physics, LMU Munich
A semiflexible charged bead-spring chain in solution under the influence
of an external field is investigated using Brownian Dynamics simulation.
Counterions are explicitly added. Hydrodynamic interactions are
included via an approximate mobility tensor (Rotne-Prager tensor). By
choosing strong stretching and bending moduli we also cover stiff rodlike
objects of the nanometer/micrometer scale. While, in low Reynolds
number flow, highly symmetric rigid objects like cylinders and ellipsoids
are not oriented in an homogeneous flow or by a homogeneous external
force, a slight coupling between flexibility and hydrodynamic interactions
leads to a torque the direction of which depends on the ratio between the
stretching and bending moduli. Polarization effects compete with this
mechanism. We extrapolate the results to experimentally accessible regions.
SYLS 3.40 Mi 16:00 B
Single cell manipulation in microfluidic networks by optical
tweezers — •Kai Leffhalm 1 , Andy Sischka 1 , Wibke Hellmich 1 ,
Thanh Tu Duong 1 , Annika Grabbe 2 , Jürgen Wienands 2 , Katja
Tönsing 1 , Robert Ros 1 , Alexandra Ros 1 , and Dario Anselmetti
1 — 1 Experimental Biophysics, Physics Department, Bielefeld University,
Germany — 2 Biochemistry, Department of Chemistry, Bielefeld
University, Germany
Experiments with single cells gain importance as a tool to better understand
the behaviour of living cells in vivo. Microfluidic networks provide
dimensions small enough to navigate a single cell with optical tweezers
to different areas of the artificial network where the flow properties can
be controlled by electrophoresis and electroosmosis.
The expression of special proteins in a cell can be stimulated or suppressed
by changing the velocity of the flow or the concentration of substances,
e.g. cytokines or (cytostatic) drugs, in the culture medium.
We will present our experimental setup and our first test experiments
for future applications in monitoring the expression level of individuell
cells and microproteomics.
SYLS 3.41 Mi 16:00 B
Untersuchungen der DNS des Bakteriums Streptomyces violaceoruber
mit dem Rasterkraftmikroskop — •A. Kronenberger 1 ,
A. Ehlers 1 , D. Engel 1 , H. Schmoranzer 1 , A. Ehresmann 1 , K.
Kropp 2 , K. Spatz 2 und M. Redenbach 2 — 1 Technische Universität
Kaiserslautern, Fachbereich Physik, Erwin-Schrödinger-Str., 67663 Kaiserslautern
— 2 Technische Universität Kaiserslautern, Fachbereich Biologie,
Erwin-Schrödinger-Str., 67663 Kaiserslautern
Das lineare Plasmid pSV2 des Bakteriums Streptomyces violaceoruber
wurde mit dem Rasterkraftmikroskop untersucht. Ziel war es, das an den
DNS-Strang gebundene Endprotein eindeutig zu bestimmen. Dazu war
es notwendig alle Reagenzien des biologischen Isolationsprozesses zu betrachten,
um mittels Ausschluss die Identifikation des Endproteins zu
ermöglichen. Weiterhin wurden die Messergebnisse für das Endprotein
über Vergleiche mit anderen schon bekannten Proteinen bestätigt. Somit
konnte eine mögliche Lage des Endproteins relativ zum DNS-Strang
ermittelt werden.