Laser manipulation and UV induced single molecule reactions of individual DNA molecules

Manipulation of cells with laser microbeam scissors and optical tweezers: a review

The use of laser microbeams and optical tweezers in a wide field of biological applications from genomic to immunology is discussed. Microperforation is used to introduce a well-defined amount of molecules into cells for genetic engineering and optical imaging. The microwelding of two cells induced by a laser microbeam combines their genetic outfit. Microdissection allows specific regions of genomes to be isolated from a whole set of chromosomes. Handling the cells with optical tweezers supports investigation on the attack of immune systems against diseased or cancerous cells. With the help of laser microbeams, heart infarction can be simulated, and optical tweezers support studies on the heartbeat. Finally, laser microbeams are used to induce DNA damage in living cells for studies on cancer and ageing.

An integrated system for enzymatic cleavage and electrostretching of freely-suspended single DNA molecules

A novel polyacrylamide gel-based femtolitre microchamber system for performing single-molecule restriction enzyme assay on freely-suspended DNA molecules and subsequent DNA electrostretching by applying an alternating electric field has been developed. We attempted the integration by firstly initiating restriction enzyme reaction on a fluorescent-stained lambdaDNA molecule, encapsulated in a microchamber, using magnesium as an external trigger. Upon complete digestion, the cleaved DNA fragments were electrostretched to analyze the DNA lengths optically. The critical parameters for electrostretching of encapsulated DNA were investigated and optimum stretching was achieved by using 1.5 kHz pulses with electric field strength in the order of 10(3) V cm(-1) in 7% linear polyacrylamide (LPA) solution. LPA was adopted to minimize the adverse effects of ionic thermal agitation on molecular dielectrophoretic elongation in the microchamber. In our experiments, as the fragments were not immobilized throughout the entire protocol, it was found from repeated tests that digestion always occurred, producing the expected number of cleaved fragments. This versatile microchamber approach realized direct observation of these biological reactions on real-time basis at a single-molecule level. Furthermore, with the employment of porous polyacrylamide gel, the effective manipulation of DNA assays and the ability to combine conventionally independent bioanalytical processes have been demonstrated.

Extension of a DNA molecule by local heating with a laser

Thermal convection and thermophoresis induced by mum-scale local heating are shown to elongate a single DNA molecule. An infrared laser used as a point heat source is converged into a dispersion solution of DNA molecules, which is observed under a fluorescent microscope. The thermal convection around the laser focus manifests as extensional flow for the long DNA chain. A simulation of thermal convection that reproduces the experimental condition provides numerical support for the stretching caused by thermal convection. This DNA elongation technique is a novel method for manipulating the intact single DNA molecules, and it can be applied to a "lab on a chip".

Single-Molecule Studies on DNA and RNA

DNA and RNA are the most individual molecules known. Therefore, single-molecule experiments with these nucleic acids are particularly useful. This review reports on recent experiments with single DNA and RNA molecules. First, techniques for their preparation and handling are summarised including the use of AFM nanotips and optical or magnetic tweezers. As important detection techniques, conventional and near-field microscopy as well as fluorescence resonance energy transfer (FRET) and fluorescence correlation spectroscopy (FCS) are touched on briefly. The use of single-molecule techniques currently includes force measurements in stretched nucleic acids and in their complexes with binding partners, particularly proteins, and the analysis of DNA by restriction mapping, fragment sizing and single-molecule hybridisation. Also, the reactions of RNA polymerases and enzymes involved in DNA replication and repair are dealt with in some detail, followed by a discussion of the transport of individual nucleic acid molecules during the readout and use of genetic information and during the infection of cells by viruses. The final sections show how the enormous addressability in nucleic acid molecules can be exploited to construct a single-molecule field-effect transistor and a walking single-molecule robot, and how individual DNA molecules can be used to assemble a single-molecule DNA computer.

Activation of restriction enzyme by electrochemically released magnesium ion

Observation and cutting of DNA molecules at intended positions permit several new experimental methods that are completely different from conventional molecular biology methods; therefore several cutting methods have been proposed and studied. In this paper, a new cutting method for a DNA molecule by localizing the activity of a restriction enzyme is presented. Since most restriction enzymes require magnesium ions for their activation, local restriction enzyme activity can be controlled by the local concentration of magnesium ions. Applying a direct current (dc) voltage to a needle electrode of metallic magnesium made it possible to control the local magnesium ion concentration at the tip of the needle. The restriction enzyme was activated only when magnesium ions were electrochemically supplied.

Direct Observation of Anomalous Single-Molecule Enzyme Kinetics

We report the direct measurement of the single-molecule enzymatic cleavage rates of ApaI-DNA complex in the presence of various concentrations of MgCl2 solution with total internal reflection fluorescence microscopy. We made use of the native adsorption properties of the two 12-base sticky ends of the DNA molecules to partially immobilize and stretch out the ApaI-DNA complex onto a glass surface. Synchronous initiation of reaction was achieved by the influx of Mg2+ solution. Once the DNA was cut, the two fragments (38 and 10 kb) would either collapse or further stretch out depending on the solution flow. The time required for cleaving each ApaI-lambda-DNA complex was recorded and analyzed. At low concentrations, the higher the concentration of Mg2+, the faster the DNA was cut. However, Mg2+ ion is no longer the limiting factor when its concentration is greater than 5 mM. A surprising result is that at all concentrations the decrease in intact DNA population as a function of time is linear rather than exponential. This suggests that there exists a distribution of ApaI conformations around the restriction site.

Towards a general procedure for sequencing single DNA molecules

In this paper we report on the latest technical advances towards single molecule sequencing, a useful method currently developed especially for fast and easy de novo sequencing. Different approaches for complete labeling of DNA with fluorescent dyes are described. In addition, the experimental set-up for the sequencing process is shown. We demonstrate the ability to purify the buffer and enzyme solutions. Inorganic buffers were purified down to at least 20 fM of remaining fluorescent impurities. The exonuclease buffer solution could be cleaned down to 0.8 pM whereby its full activity was kept. Finally, we show a selection procedure for beads and present the data of a model experiment, in which immobilized DNA is degraded by an exonuclease within a polymethylmethacrylate (PMMA) microstructure. Furthermore, the mathematical processing of the obtained raw data is described. A first complete experimental cycle is shown, combining all preparatory steps which are necessary for single molecule sequencing in microstructures.

Study of single-molecule dynamics and reactions with classic light microscopy

Single-molecule studies in the life sciences often deal with observation or spectroscopy. Studies of reactions are rare, and the light microscope has been used for such experiments only occasionally. In an experimental environment, for example, as is required for most nearfield scanning or electron microscopies, it is difficult to study single-molecule reactions of biological relevance. Therefore, we have developed techniques to study single-molecule reactions with classic (nonscanning) farfield light microscopy. The conversion of nicotinamide adenine dinucleotide (NAD+) and lactate to NADH (a reduced form of NAD+), pyruvate, and H+ catalyzed by a few LDH-1 enzyme molecules has been studied in substrate solutions with different viscosity using the NADH autofluorescence. It is even possible to monitor the progress of the reaction by phase-contrast microscopy via scattering or absorption by product molecules. As an example for a single-molecule reaction with a macromolecule as substrate, the handling and enzymatic cutting of fluorescently stained lambda-DNA is studied. In solutions containing 10 mM magnesium and 66 mM potassium ions at pH 7.9, an individual DNA molecule tends to collapse into a globular structure. When moved through an aqueous solution, it becomes stretched by viscosity drag. After stopping the motion, the molecule collapses and the dynamics of this process can be quantified. When a restriction enzyme is present, sequence-specific cutting can be directly observed in the light microscope. The theoretical restriction pattern, as predicted from the sequence of the molecule, can be generated directly under visual inspection.

Single-molecule manipulation of double-stranded DNA using optical tweezers: interaction studies of DNA with RecA and YOYO-1

By using optical tweezers and a specially designed flow cell with an integrated glass micropipette, we constructed a setup similar to that of Smith et al. (Science 271:795-799, 1996) in which an individual double-stranded DNA (dsDNA) molecule can be captured between two polystyrene beads. The first bead is immobilized by the optical tweezers and the second by the micropipette. Movement of the micropipette allows manipulation and stretching of the DNA molecule, and the force exerted on it can be monitored simultaneously with the optical tweezers. We used this setup to study elongation of dsDNA by RecA protein and YOYO-1 dye molecules. We found that the stability of the different DNA-ligand complexes and their binding kinetics were quite different. The length of the DNA molecule was extended by 45% when RecA protein was added. Interestingly, the speed of elongation was dependent on the external force applied to the DNA molecule. In experiments in which YOYO-1 was added, a 10-20% extension of the DNA molecule length was observed. Moreover, these experiments showed that a change in the applied external force results in a time-dependent structural change of the DNA-YOYO-1 complex, with a time constant of approximately 35 s (1/e2). Because the setup provides an oriented DNA molecule, we determined the orientation of the transition dipole moment of YOYO-1 within DNA by using fluorescence polarization. The angle of the transition dipole moment with respect to the helical axis of the DNA molecule was 69 degrees +/- 3.

Fluorescence microscopic observation of catalysis by single or few LDH-1 enzyme molecules

Lactate dehydrogenase (LDH-1) catalyzes the reaction of lactate and nonfluorescent NAD+ to pyruvate, NADH (fluorescence at lambda em = 455 nm, lambda em = 365 nm) and H+. The injection of highly diluted LDH-1 solution into a drop of substrate solution results in the formation of a bubble of enzyme inside the drop of substrate. At the contact surface between the enzyme solution and the substrate, discrete and statistically distributed zones of increasing fluorescence intensity and different size can be observed after enzyme injection. These zones can be interpreted as clouds of NADH around a single or a few enzyme molecules. The kinetics of the NADH formation in every fluorescent zone, and the size of the zone, can be described by a zero order production combined with a diffusion controlled loss of the reaction's product NADH from the reaction zone. From the dilution of the enzyme solution and from statistical analysis one can conclude that only few enzyme molecules in the center of the fluorescent reaction zones catalyze the NADH formation.