Direct laser trapping of single DNA molecules in the globular state.

A sharply focused laser is able to trap small particles at the laser focal point due to the difference in refractive index of the particles and that of the surrounding medium. This technique, called laser trapping, can be used to manipulate animal or bacterial cells without any contact and has been widely applied in biological research. However, it has been difficult to trap biological macromolecules such as DNA molecules, because these molecules give a low difference in refractive index and cannot overcome Brownian motion. DNA molecules can be transformed to a condensed globular state. This transformation results in a higher refractive index of DNA due to its increased density. We demonstrate in this paper that a single DNA molecule can be optically trapped using a Nd:YAG laser (1064 nm wavelength) upon transformation from the coiled state to the globular state.     

Optical traps: shedding light on biological processes

Optical traps exploit the radiation forces of laser light to manipulate microscopic particles. The ability to manipulate biological material and quantify the force required has been exploited in the biosciences; from the isolation of single cells to kinetic measurements of single motor molecules. This review describes the theory of optical trapping and using recent publications gives examples of how it has been employed across a broad spectrum of biological research.     

Laser-induced tobacco protoplast fusion

Laser tweezers can manipulate small particles, such as cells and organelles. When coupling them with laser microbeam selective fusion of two tobacco protoplasts containing some chloroplast was achieved. Physical and biological variables that affect laser trapping and laser-induced fusion were also discussed. The results show that the effect of chloroplast content and distribution on the yield of cell fusion is remarkable.     

Laser-induced tobacco protoplast fusion

Laser tweezers can manipulate small particles, such as cells and organdies. When coupling them with laser microbeam selective fusion of two tobacco protoplasts containing some chloroplast was achieved. Physical and biological variables that affect laser trapping and laser-induced fusion were also discussed. The results show that the effect of chloroplast content and distribution on the yield of cell fusion is remarkable.     

Structure-based cross-linking of NF-kappaB p50 homodimer and decoy bearing a novel 2'-disulfide trapping site

Double-stranded oligodeoxyribonucleotides with engineered disulfide units were successfully used for covalent trapping of cysteine containing proteins. In particular, an efficient cross-linking of NF-kappaB p50 homodimer to a sequence-specific decoy was demonstrated. The results suggest that the synthetic oligonucleotides bearing a novel 2'-disulfide trapping site can be used as new tools to study and manipulate biological systems.     

Specific conjugation of DNA binding proteins to DNA templates through thiol-disulfide exchange

The double-stranded oligodeoxyribonucleotides with single internucleotide disulfide linkages were successfully used for covalent trapping of cysteine containing protein. In particular, an efficient conjugation of DNA methyltransferase SsoII to sequence-specific decoys was demonstrated. The obtained results assume that synthetic oligodeoxyribonucleotides bearing a new trapping site can be used as new tools to study and manipulate biological systems.     

Optical tweezers in biology and medicine

Optical trapping techniques provide unique means to manipulate biological particles such as virus, living cells and subcellular organelles. Another area of interest is the measurement of mechanical (elastic) properties of cell membranes, long strands of single DNA molecule, and filamentous proteins. One of the most attractive applications is the study of single motor molecules. With optical tweezers traps, one can measure the forces generated by single motor molecules such as kinesin and myosin, in the piconewton range and, for the first time, resolve their detailed stepping motion.     

Label‐free differentiation of human immunodeficiency virus‐1 infected from uninfected cells using transmission measurement

Transmission measurement has been perceived as a potential candidate for label‐free investigation of biological material. It is a real‐time, label‐free and non‐invasive optical detection technique that has found wide applications in pharmaceutical industry as well as the biological and medical fields. Combining transmission measurement with optical trapping has emerged as a powerful tool allowing stable sample trapping, while also facilitating transmittance data analysis. In this study, a near‐infrared laser beam emitting at a wavelength of 1064 nm was used for both optical trapping and transmission measurement investigation of human immunodeficiency virus 1 (HIV‐1) infected and uninfected TZM‐bl cells. The measurements of the transmittance intensity of individual cells in solution were carried out using a home built optical trapping system combined with laser transmission setup using a single beam gradient trap. Transmittance spectral intensity patterns revealed significant differences between the HIV‐1 infected and uninfected cells. This result suggests that the transmittance data analysis technique used in this study has the potential to differentiate between infected and uninfected TZM‐bl cells without the use of labels. The results obtained in this study could pave a way into developing an HIV‐1 label‐free diagnostic tool with possible applications at the point of care .     

Advances in high-resolution quantitative proteomics: implications for clinical applications

The advances in high-resolution mass spectrometry instrumentation, capable of accurate mass measurement and fast acquisition, have enabled new approaches for targeted quantitative proteomics. More specifically, analyses performed on quadrupole-orbitrap mass spectrometers operated in parallel reaction monitoring (PRM) mode leverage the intrinsic high resolving power and trapping capabilities. The PRM technique offers unmatched degrees of selectivity and analytical sensitivity, typically required to analyze peptides in complex samples, such as those encountered in biomedical research or clinical studies. The features of PRM have provoked a paradigm change in targeted experiments, by decoupling acquisition and data processing. It has resulted in a new analytical workflow comprising distinct methods for each step, thus enabling much larger flexibility. The PRM technique was further enhanced by a new data acquisition scheme, allowing dynamic parameter settings. The potential of the technique may radically impact future quantitative proteomics studies.     

Non-destructive analysis of the nuclei of transgenic living cells using laser tweezers and near-infrared raman spectroscopic technique

Transgenic cell lines of loblolly pine （Pinus taeda L.） were analyzed by a compact laser-tweezers-Raman-spectroscopy （LTRS） system in this investigation. A low power diode laser at 785 nm was used for both laser optical trapping of single transgenic cells and excitation for near-infrared Raman spectroscopy of the nuclei of synchronized cells, which were treated as single organic particles, at the S-phase of the cell cycle. Transgenic living cells with gfp and uidA genes were used as biological samples to test this LTRS technique. As expected, different Raman spectra were observed from the tested biological samples. This technique provides a high sensitivity and enables real-time spectroscopic measurements of transgenic cell lines. It could be a valuable tool for the study of the fundamental cell and molecular biological process by trapping single nucleus and by providing a wealth of molecular information about the nuclei of cells.     

EPR spin trapping of protein radicals

Electron paramagnetic resonance (EPR) spin trapping was originally developed to aid the detection of low-molecular-mass radicals formed in chemical systems. It has subsequently found widespread use in biology and medicine for the direct detection of radical species formed during oxidative stress and via enzymatic reactions. Over the last 15 years this technique has also found increasing use in detecting and identifying radicals formed on biological macromolecules as a result of either radical reactions or enzymatic processes. Though the EPR signals that result from the trapping of large, slowly tumbling radicals are often broad and relatively poor in distinctive features, a number of techniques have been developed that allow a wealth of information to be obtained about the nature, site, and reactions of such radicals. This article summarizes recent developments in this area and reviews selected examples of radical formation on proteins.     

Kinetic analysis-based quantitation of free radical generation in EPR spin trapping

Because short-lived reactive oxygen radicals such as superoxide have been implicated in a variety of disease processes, methods to measure their production quantitatively in biological systems are critical for understanding disease pathophysiology. Electron paramagnetic resonance (EPR) spin trapping is a direct and sensitive technique that has been used to study radical formation in biological systems. Short-lived oxygen free radicals react with the spin trap and produce paramagnetic adducts with much higher stability than that of the free radicals. In many cases, the quantity of the measured adduct is considered to be an adequate measure of the amount of the free radical generated. Although the intensity of the EPR signal reflects the magnitude of free radical generation, the actual quantity of radicals produced may be different due to modulation of the spin adduct kinetics caused by a variety of factors. Because the kinetics of spin trapping in biochemical and cellular systems is a complex process that is altered by the biochemical and cellular environment, it is not always possible to define all of the reactions that occur and the related kinetic parameters of the spin-trapping process. We present a method based on a combination of measured kinetic data for the formation and decay of the spin adduct alone with the parameters that control the kinetics of spin trapping and radical generation. The method is applied to quantitate superoxide trapping with 5-diethoxyphosphoryl-5-methyl-1-pyrroline N-oxide (DEPMPO). In principle, this method is broadly applicable to enable spin trapping-based quantitative determination of free radical generation in complex biological systems.     

Towards biological applications of nanophotonic tweezers

Optical trapping (synonymous with optical tweezers) has become a core biophysical technique widely used for interrogating fundamental biological processes on size scales ranging from the single-molecule to the cellular level. Recent advances in nanotechnology have led to the development of ‘nanophotonic tweezers,’ an exciting new class of ‘on-chip’ optical traps. Here, we describe how nanophotonic tweezers are making optical trap technology more broadly accessible and bringing unique biosensing and manipulation capabilities to biological applications of optical trapping.     

HPLC procedure for the pharmacokinetic study of the spin-trapping agent, alpha-phenyl-N-tert-butyl nitrone (PBN)

Considerable progress has been made in the use of spin-trapping agents for the trapping of free radicals in biological systems. Radicals have been detected in both in vitro and in vivo systems using this methodology. Free radicals have not only been identified by this procedure, but also the intensity of radical generation and the duration of their production has been assessed as well. One of the most widely used spin-trapping agents in biological systems is PBN. This spin trap appears to be relatively nontoxic at the levels required for successful trapping experiments, but there is no information concerning the possible fate of PBN in such biological systems. Metabolism of PBN could alter the concentration of PBN at the site of trapping which may affect the efficiency of radical capture, especially in in vivo systems. In this study, PBN was administered intraperitoneally to rats and the concentration of the spin trap in various organs was determined by high pressure liquid chromatography as a function of time (15 min to 12 h). The concentration of PBN in plasma peaked at 15 min while the maximum in all organs tested occurred at 30 min. The time course of PBN concentrations in all tissues followed similar curves, and declined rather steeply after the 30-min maximum with a biological half-life of 134 min. However, the amount of PBN per gram of tissue was always higher in liver and kidney than in the brain, heart, and lung. PBN was detected in the urine for as long as 24 h after injection of the compound.     

Characterization of Photoactivated Singlet Oxygen Damage in Single-Molecule Optical Trap Experiments

Optical traps or “tweezers” use high-power, near-infrared laser beams to manipulate and apply forces to biological systems, ranging from individual molecules to cells. Although previous studies have established that optical tweezers induce photodamage in live cells, the effects of trap irradiation have yet to be examined in vitro, at the single-molecule level. In this study, we investigate trap-induced damage in a simple system consisting of DNA molecules tethered between optically trapped polystyrene microspheres. We show that exposure to the trapping light affects the lifetime of the tethers, the efficiency with which they can be formed, and their structure. Moreover, we establish that these irreversible effects are caused by oxidative damage from singlet oxygen. This reactive state of molecular oxygen is generated locally by the optical traps in the presence of a sensitizer, which we identify as the trapped polystyrene microspheres. Trap-induced oxidative damage can be reduced greatly by working under anaerobic conditions, using additives that quench singlet oxygen, or trapping microspheres lacking the sensitizers necessary for singlet state photoexcitation. Our findings are relevant to a broad range of trap-based single-molecule experiments—the most common biological application of optical tweezers—and may guide the development of more robust experimental protocols.     

Dielectrophoretic registration of living cells to a microelectrode array

We present a novel microfabricated device to simultaneously and actively trap thousands of single mammalian cells in alignment with a planar microelectrode array. Thousands of 3 Ipm diameter trapping electrodes were fabricated within the bottom of a parallel-plate flow chamber. Cells were trapped on the electrodes and held against destabilizing fluid flows by dielectrophoretic forces generated in the device.In general, each electrode trapped only one cell. Adhesive regions were patterned onto the surface in alignment with the traps such that cells adhered to the array surface and remained in alignment with the electrodes. By driving the device with different voltages, we showed that trapped cells could be killed by stronger electric fields. However, with weaker fields, cells were not damaged during trapping, as indicated by the similar morphologies and proliferation rates of trapped cells versus controls. As a test of the device, we patterned approximately 20,000 cells onto aI cm2 grid of rectangular adhesive regions, with two electrodes and thus two cells per rectangle. Our method obtained 70 +/- 1% fidelity versus 17 +/- 1% when using an existing cell-registration technique. By allowing the placement of desired numbers of cells at specified locations, this approach addresses many needs to manipulate and register cells to the surfaces of biosensors and other devices with high precision and fidelity.     

Dielectrophoretic registration of living cells to a microelectrode array

We present a novel microfabricated device to simultaneously and actively trap thousands of single mammalian cells in alignment with a planar microelectrode array. Thousands of 3 micromdiameter trapping electrodes were fabricated within the bottom of a parallel-plate flow chamber. Cells were trapped on the electrodes and held against destabilizing fluid flows by dielectrophoretic forces generated in the device. In general, each electrode trapped only one cell. Adhesive regions were patterned onto the surface in alignment with the traps such that cells adhered to the array surface and remained in alignment with the electrodes. By driving the device with different voltages, we showed that trapped cells could be killed by stronger electric fields. However, with weaker fields, cells were not damaged during trapping, as indicated by the similar morphologies and proliferation rates of trapped cells versus controls. As a test of the device, we patterned approximately 20000 cells onto a 1cm(2) grid of rectangular adhesive regions, with two electrodes and thus two cells per rectangle. Our method obtained 70+/-1% fidelity versus 17+/-1% when using an existing cell-registration technique. By allowing the placement of desired numbers of cells at specified locations, this approach addresses many needs to manipulate and register cells to the surfaces of biosensors and other devices with high precision and fidelity.     

Optical Trapping of Nanoparticles

Optical trapping is a technique for immobilizing and manipulating small objects in a gentle way using light, and it has been widely applied in trapping and manipulating small biological particles. Ashkin and co-workers first demonstrated optical tweezers using a single focused beam¹. The single beam trap can be described accurately using the perturbative gradient force formulation in the case of small Rayleigh regime particles¹. In the perturbative regime, the optical power required for trapping a particle scales as the inverse fourth power of the particle size. High optical powers can damage dielectric particles and cause heating. For instance, trapped latex spheres of 109 nm in diameter were destroyed by a 15 mW beam in 25 sec¹, which has serious implications for biological matter^2,3.A self-induced back-action (SIBA) optical trapping was proposed to trap 50 nm polystyrene spheres in the non-perturbative regime⁴. In a non-perturbative regime, even a small particle with little permittivity contrast to the background can influence significantly the ambient electromagnetic field and induce a large optical force. As a particle enters an illuminated aperture, light transmission increases dramatically because of dielectric loading. If the particle attempts to leave the aperture, decreased transmission causes a change in momentum outwards from the hole and, by Newton''s Third Law, results in a force on the particle inwards into the hole, trapping the particle. The light transmission can be monitored; hence, the trap can become a sensor. The SIBA trapping technique can be further improved by using a double-nanohole structure.The double-nanohole structure has been shown to give a strong local field enhancement^5,6. Between the two sharp tips of the double-nanohole, a small particle can cause a large change in optical transmission, thereby inducing a large optical force. As a result, smaller nanoparticles can be trapped, such as 12 nm silicate spheres⁷ and 3.4 nm hydrodynamic radius bovine serum albumin proteins⁸. In this work, the experimental configuration used for nanoparticle trapping is outlined. First, we detail the assembly of the trapping setup which is based on a Thorlabs Optical Tweezer Kit. Next, we explain the nanofabrication procedure of the double-nanohole in a metal film, the fabrication of the microfluidic chamber and the sample preparation. Finally, we detail the data acquisition procedure and provide typical results for trapping 20 nm polystyrene nanospheres.     

Translocation induced outgrowth of fungi in nutrient-free environments

The study of alternatives to chemical methods of nematode control in agriculture has received significant recent interest. One such method is biological control using nematode trapping fungi such as Arthrobotrys superba. To understand how these fungi can be implemented as effective nematicides, it is essential to study their outgrowth into soil from localized nutrient resources. In this paper, we use a mathematical model to investigate the outgrowth of fungi into an environment essentially without available nutrients capable of supporting net growth. By comparing model solutions with experimental results, we show that in such circumstances, continual mycelial expansion can only be obtained if internal metabolites are actively translocated through the mycelium. Predictions are made concerning the maximal extension possible from a given quantity of nutrients and a testable functional relationship between the two is derived. Using this modelling technique we are able to map not only biomass extent but also biomass distribution at each stage. The type of environmental heterogeneity investigated here is encountered by many species of fungi in nature and is of relevance for the introduction of specific fungi into soil for biological control or bioremediation purposes.     

Experimentally manipulating fungi with optical tweezers

A short review of the use of optical tweezers in fungal cell biological research is provided. First, we describe how optical tweezers work. Second, we review how they have been used in various experimental live-cell studies to manipulate intracellular organelles, hyphal growth and branching, and whole cells. Third, we indicate how optically trapped microbeads can be used for the localized delivery of chemicals or mechanical stimulation to cells, as well as permitting measurements of the growth forces generated by germ tubes. Finally, the effects of optical trapping on fungal cell viability and growth are assessed. Parts of this review were presented at the Mycological Society of Japan (MSJ) / British Mycological Society (BMS) Joint Symposium, “The new generation mycologists in Japan and the UK” held in Chiba, Japan on June 3, 2006.