Biomedical subjects

U Bockelmann

Publications and source records attributed to U Bockelmann.

16 recordsLinked to original sources

PubMed2006

Single molecule study of DNA conductivity in aqueous environment.

The dc electrical conductivity of double stranded DNA is investigated experimentally. Single DNA molecules are manipulated with subpiconewton force and deposited on gold nanoelectrodes by optical traps. The DNA is modified at its ends for specific bead attachments and along the chain to favor charge transfer between the DNA base pair stack and the electrodes. For an electrode separation of 70 nm we find, in aqueous environment, electrical resistances above 100 G Omega indicating that even for weak stretching the double helix is almost insulating at this length scale.

Computer Simulation↗

PubMed2006

Probing DNA and RNA single molecules with a double optical tweezer.

A double-tweezer setup is used to induce mechanical stress in systems of molecular biology. A double strand of DNA is first stretched and the data is compared to precedent experiments to check the experimental setup. Then a short foldable fragment of RNA is probed; the typical unfolding/refolding hysteresis behaviour of this kind of construction is shown and followed by a study of its elasticity and a comparison to a worm-like chain model. Eventually, we describe the unfolding of a larger RNA structure, which unfolds by multiple steps. We show that this unfolding is not reversible and that it presents numerous unfolding pathways.

DNA↗

PubMed2004

Spatially resolved electronic detection of biopolymers.

An integrated array of field-effect transistor structures is used to detect two oppositely charged biopolymers: poly(L-lysine) and DNA. Local deposition of polymer solutions on part of the array induces sizeable variations in the dc current-voltage characteristics of the transistors exposed to the molecular charge. The whole transistor array is measured in the presence of a common electrolyte. Differential signals are studied as a function of electrolyte salt and polymer concentrations. The measurements provide information on the interface electrostatic potentials of the (semiconductor/biopolymer/electrolyte) system and the experimental data are compared to an analytical model which accounts for screening of the adsorbed charge by mobile ions.

Biopolymers↗

PubMed2004

Dynamics of the DNA duplex formation studied by single molecule force measurements.

DNA is partly denatured in vitro by applying a force that mechanically separates the two strands of the double helix. Sudden reduction of the imposed displacement triggers spontaneous reannealing of the molecule. The corresponding force signals are measured by optical trapping interferometry for backward steps of various amplitudes and base sequence intervals. The measured signals frequently show plateaus of varying duration at discrete values that are dependent on the base sequence. Additional measurements are performed with proteins bound to the double helix. When the opening fork encounters such a protein during mechanical unzipping, force increases until the protein is ejected. This ejection induces fast release of tension and fast unzipping. Comparing our different measurements, we find that both DNA unzipping and the relaxation of tension in DNA are faster than the formation of the double helix.

Computer Simulation↗

PubMed2002

Unzipping DNA with optical tweezers: high sequence sensitivity and force flips.

Force measurements are performed on single DNA molecules with an optical trapping interferometer that combines subpiconewton force resolution and millisecond time resolution. A molecular construction is prepared for mechanically unzipping several thousand-basepair DNA sequences in an in vitro configuration. The force signals corresponding to opening and closing the double helix at low velocity are studied experimentally and are compared to calculations assuming thermal equilibrium. We address the effect of the stiffness on the basepair sensitivity and consider fluctuations in the force signal. With respect to earlier work performed with soft microneedles, we obtain a very significant increase in basepair sensitivity: presently, sequence features appearing at a scale of 10 basepairs are observed. When measured with the optical trap the unzipping force exhibits characteristic flips between different values at specific positions that are determined by the base sequence. This behavior is attributed to bistabilities in the position of the opening fork; the force flips directly reflect transitions between different states involved in the time-averaging of the molecular system.

Calibration↗

PubMed1997

Mechanical separation of the complementary strands of DNA.

We describe the mechanical separation of the two complementary strands of a single molecule of bacteriophage lambda DNA. The 3' and 5' extremities on one end of the molecule are pulled progressively apart, and this leads to the opening of the double helix. The typical forces along the opening are in the range of 10-15 pN. The separation force signal is shown to be related to the local GC vs. AT content along the molecule. Variations of this content on a typical scale of 100-500 bases are presently detected.

Bacteriophage lambda↗

PubMed1996