Recent Advances in Optical Tweezers

Combining optical trapping, fluorescence microscopy and micro-fluidics for single molecule studies of DNA-protein interactions

Complexity and heterogeneity are common denominators of the many molecular events taking place inside the cell. Single-molecule techniques are important tools to quantify the actions of biomolecules. Heterogeneous interactions between multiple proteins, however, are difficult to study with these technologies. One solution is to integrate optical trapping with micro-fluidics and single-molecule fluorescence microscopy. This combination opens the possibility to study heterogeneous/complex protein interactions with unprecedented levels of precision and control. It is particularly powerful for the study of DNA-protein interactions as it allows manipulating the DNA while at the same time, individual proteins binding to it can be visualized. In this work, we aim to illustrate several published and unpublished key results employing the combination of fluorescence microscopy and optical tweezers. Examples are recent studies of the structural properties of DNA and DNA-protein complexes, the molecular mechanisms of nucleo-protein filament assembly on DNA and the motion of DNA-bound proteins. In addition, we present new results demonstrating that single, fluorescently labeled proteins bound to individual, optically trapped DNA molecules can already be tracked with localization accuracy in the sub-10 nm range at tensions above 1 pN. These experiments by us and others demonstrate the enormous potential of this combination of single-molecule techniques for the investigation of complex DNA-protein interactions.

Processive behaviour of kinesin observed using micro-fabricated cantilevers

The mechanical characterization of biomolecular motors requires force sensors with sub-piconewton resolution. The coupling of a nanoscale motor to this type of microscale sensors introduces structural deformations in the motor according to the thermally activated degrees of freedom of the sensor. At present, no simple solution is available to reduce these effects. Here, we exploit the advantages of micro-fabricated cantilevers to produce a force sensor with essentially one degree of freedom and a spring constant of 0.03 pN nm(-1) for the study of the molecular motor protein kinesin-1. During processive runs, the cantilever constrains the movement of the cargo binding domain of kinesin in a straight line, parallel to the microtubule track, and excludes specific reaction coordinates such as cargo rotation. In these conditions, we measured a step size of 8.0 ± 0.4 nm and a maximal unloaded velocity of 820 ± 80 nm s(-1) at saturated adenosine triphosphate (ATP) concentration. We concluded that the motor does not need to rotate its tail as it moves through consecutive stepping cycles.

Transverse interaction in DNA molecule

Interaction between nucleotides at a same site belonging to different strands is studied. This interaction is modelled by a Morse potential which depends on two parameters. We study a relationship between the parameters characterizing AT and CG pairs. We show that certain circumstances, i.e. certain values of these parameters, bring about a negligible influence of inhomogeneity on the solitonic dynamics.

Functional modes and residue flexibility control the anisotropic response of guanylate kinase to mechanical stress

The coupling between the mechanical properties of enzymes and their biological activity is a well-established feature that has been the object of numerous experimental and theoretical works. In particular, recent experiments show that enzymatic function can be modulated anisotropically by mechanical stress. We study such phenomena using a method for investigating local flexibility on the residue scale that combines a reduced protein representation with Brownian dynamics simulations. We performed calculations on the enzyme guanylate kinase to study its mechanical response when submitted to anisotropic deformations. The resulting modifications of the protein's rigidity profile can be related to the changes in substrate binding affinity observed experimentally. Further analysis of the principal components of motion of the trajectories shows how the application of a mechanical constraint on the protein can disrupt its dynamics, thus leading to a decrease of the enzyme's catalytic rate. Eventually, a systematic probe of the protein surface led to the prediction of potential hotspots where the application of an external constraint would produce a large functional response both from the mechanical and dynamical points of view. Such enzyme-engineering approaches open the possibility to tune catalytic function by varying selected external forces.

Soft magnetic tweezers: a proof of principle

We present here the principle of soft magnetic tweezers which improve the traditional magnetic tweezers allowing the simultaneous application and measurement of an arbitrary torque to a deoxyribonucleic acid (DNA) molecule. They take advantage of a nonlinear coupling regime that appears when a fast rotating magnetic field is applied to a superparamagnetic bead immersed in a viscous fluid. In this work, we present the development of the technique and we compare it with other techniques capable of measuring the torque applied to the DNA molecule. In this proof of principle, we use standard electromagnets to achieve our experiments. Despite technical difficulties related to the present implementation of these electromagnets, the agreement of measurements with previous experiments is remarkable. Finally, we propose a simple way to modify the experimental design of electromagnets that should bring the performances of the device to a competitive level.

Electrons, photons, and force: quantitative single-molecule measurements from physics to biology

Single-molecule measurement techniques have illuminated unprecedented details of chemical behavior, including observations of the motion of a single molecule on a surface, and even the vibration of a single bond within a molecule. Such measurements are critical to our understanding of entities ranging from single atoms to the most complex protein assemblies. We provide an overview of the strikingly diverse classes of measurements that can be used to quantify single-molecule properties, including those of single macromolecules and single molecular assemblies, and discuss the quantitative insights they provide. Examples are drawn from across the single-molecule literature, ranging from ultrahigh vacuum scanning tunneling microscopy studies of adsorbate diffusion on surfaces to fluorescence studies of protein conformational changes in solution.

Moving into the cell: single-molecule studies of molecular motors in complex environments

Much has been learned in the past decades about molecular force generation. Single-molecule techniques, such as atomic force microscopy, single-molecule fluorescence microscopy and optical tweezers, have been key in resolving the mechanisms behind the power strokes, 'processive' steps and forces of cytoskeletal motors. However, it remains unclear how single force generators are integrated into composite mechanical machines in cells to generate complex functions such as mitosis, locomotion, intracellular transport or mechanical sensory transduction. Using dynamic single-molecule techniques to track, manipulate and probe cytoskeletal motor proteins will be crucial in providing new insights.

Introduction to optical tweezers: background, system designs, and commercial solutions

Optical tweezers are a means to manipulate objects with light. With the technique, microscopically small objects can be held and steered while forces on the trapped objects can be accurately measured and exerted. Optical tweezers can typically obtain a nanometer spatial resolution, a piconewton force resolution, and a millisecond time resolution, which make them excellently suited to study biological processes from the single-cell down to the single-molecule level. In this chapter, we provide an introduction on the use of optical tweezers in single-molecule approaches. We introduce the basic principles and methodology involved in optical trapping, force calibration, and force measurements. Next, we describe the components of an optical tweezers setup and their experimental relevance in single-molecule approaches. Finally, we provide a concise overview of commercial optical tweezers systems. Commercial systems are becoming increasingly available and provide access to single-molecule optical tweezers experiments without the need for a thorough background in physics.

An atomic force microscopy method for the detection of binding forces between bacteria and a lipid bilayer containing higher order gangliosides

We developed an atomic force microscopy (AFM) method to determine the binding forces between a model cell wall plasma membrane and Vibrio cholerae. V. cholerae cells were covalently attached to AFM probes and forces were determined against a lipid bilayer containing sialic acid (N-acetylneuraminic acid) molecules as well as several control surfaces.

Three dimensional nanoparticle trapping enhanced by surface plasmon resonance

We demonstrate a three dimensional nanoparticle trapping approach aided by the surface plasmon resonance of metallic nanostructures. The localized surface plasmon resonance effect provides strong electromagnetic field enhancement, which enables confinement of nanoparticles in the three-dimensional space. Numerical simulations indicate that the plasmonic structure provides approximately two orders of magnitude stronger optical forces for trapping nanoparticles, compared with that without nanostructures. The study of thermal effect of the plasmonic structure shows that the impact of the thermal force is significant, which may determine the outcome of the nanoparticle trapping.

Processive replication of single DNA molecules in a nanopore catalyzed by phi29 DNA polymerase

Coupling nucleic acid processing enzymes to nanoscale pores allows controlled movement of individual DNA or RNA strands that is reported as an ionic current/time series. Hundreds of individual enzyme complexes can be examined in single-file order at high bandwidth and spatial resolution. The bacteriophage phi29 DNA polymerase (phi29 DNAP) is an attractive candidate for this technology, due to its remarkable processivity and high affinity for DNA substrates. Here we show that phi29 DNAP-DNA complexes are stable when captured in an electric field across the α-hemolysin nanopore. DNA substrates were activated for replication at the nanopore orifice by exploiting the 3'-5' exonuclease activity of wild-type phi29 DNAP to excise a 3'-H terminal residue, yielding a primer strand 3'-OH. In the presence of deoxynucleoside triphosphates, DNA synthesis was initiated, allowing real-time detection of numerous sequential nucleotide additions that was limited only by DNA template length. Translocation of phi29 DNAP along DNA substrates was observed in real time at Ångstrom-scale precision as the template strand was drawn through the nanopore lumen during replication.

All-optical patterning of Au nanoparticles on surfaces using optical traps

The fabrication of nanoscale devices would be greatly enhanced by "nanomanipulators" that can position single and few objects rapidly with nanometer precision and without mechanical damage. Here, we demonstrate the feasibility and precision of an optical laser tweezer, or optical trap, approach to place single gold (Au) nanoparticles on surfaces with high precision (approximately 100 nm standard deviation). The error in the deposition process is rather small but is determined to be larger than the thermal fluctuations of single nanoparticles within the optical trap. Furthermore, areas of tens of square micrometers could be patterned in a matter of minutes. Since the method does not rely on lithography, scanning probes or a specialized surface, it is versatile and compatible with a variety of systems. We discuss active feedback methods to improve positioning accuracy and the potential for multiplexing and automation.

Replication of individual DNA molecules under electronic control using a protein nanopore

Nanopores can be used to analyse DNA by monitoring ion currents as individual strands are captured and driven through the pore in single file by an applied voltage. Here, we show that serial replication of individual DNA templates can be achieved by DNA polymerases held at the α-haemolysin nanopore orifice. Replication is blocked in the bulk phase, and is initiated only after the DNA is captured by the nanopore. We used this method, in concert with active voltage control, to observe DNA replication catalysed by bacteriophage T7 DNA polymerase (T7DNAP) and by the Klenow fragment of DNA polymerase I (KF). T7DNAP advanced on a DNA template against an 80-mV load applied across the nanopore, and single nucleotide additions were measured on the millisecond timescale for hundreds of individual DNA molecules in series. Replication by KF was not observed when this enzyme was held on top of the nanopore orifice at an applied potential of 80 mV. Sequential nucleotide additions by KF were observed upon applying controlled voltage reversals.

Atomic force microscopy study of DNA conformation in the presence of drugs

Binding of ligands to DNA gives rise to several relevant biological and biomedical effects. Here, through the use of atomic force microscopy (AFM), we studied the consequences of drug binding on the morphology of single DNA molecules. In particular, we quantitatively analyzed the effects of three different DNA-binding molecules (doxorubicin, ethidium bromide, and netropsin) that exert various pharmacologic and therapeutic effects. The results of this study show the consequences of intercalation and groove molecular binding on DNA conformation. These single-molecule measurements demonstrate morphological features that reflect the specific modes of drug-DNA interaction. This experimental approach may have implications in the design of therapeutically effective agents.

A primary hydrogen-deuterium isotope effect observed at the single-molecule level

The covalent chemistry of reactants tethered within a single protein pore can be monitored by observing the time-dependence of ionic current flow through the pore, which responds to bond making and breaking in individual reactant molecules. Here we use this 'nanoreactor' approach to examine the reaction of a quinone with a thiol to form a substituted hydroquinone by reductive 1,4-Michael addition. Remarkably, a primary hydrogen-deuterium isotope effect is readily detected at the single-molecule level during prototropic rearrangement of an initial adduct. The observation of individual reaction intermediates allows the measurement of an isotope effect whether or not the step involved is rate limiting, which would not be the case in an ensemble measurement.

Non-contact acoustic cell trapping in disposable glass capillaries

Non-contact trapping using acoustic standing waves has shown promising results in cell-based research lately. However, the devices demonstrated are normally fabricated using microfabrication or precision machining methods leading to a high unit cost. In e.g. clinical or forensic applications avoiding cross-contamination, carryover or infection is of outmost importance. In these applications disposable devices are key elements, thus making the cost per unit a critical factor. A solution is presented here where low-cost off-the-shelf glass capillaries are used as resonators for standing wave trapping. Single-mode as well as multi-node trapping is demonstrated with an excellent agreement between simulated and experimentally found operation frequencies. Single particle trapping is verified at 7.53 MHz with a trapping force on a 10 microm particle of up to 1.27 nN. The non-contact trapping is proved using confocal microscopy. Finally, an application is presented where the capillary is used as a pipette for aspirating, trapping and dispensing red blood cells.

Use of tapered amplifier diode laser for biological-friendly high-resolution optical trapping

A 1064 nm laser is commonly used for biological optical trapping. However, it has the problem of generating reactive oxygen species in the presence of a sensitizer, which leads to photo damage in biological samples. Here we constructed optical tweezers using a tapered amplifier diode laser that operates at 830 nm. Compared to a 1064 nm laser, this laser is friendly to live cells, eliminates photo damage associated with reactive oxygen species, and allows simultaneous two-photon fluorescence imaging of green fluorescent proteins in live mammalian cells. All these advantages could significantly benefit future application of this single molecule technique in biological studies.

Mechanistic constraints from the substrate concentration dependence of enzymatic fluctuations

The time it takes an enzyme to complete its reaction is a stochastic quantity governed by thermal fluctuations. With the advent of high-resolution methods of single-molecule manipulation and detection, it is now possible to observe directly this natural variation in the enzymatic cycle completion time and extract kinetic information from the statistics of its fluctuations. To this end, the inverse of the squared coefficient of variation, which we term n(min), is a useful measure of fluctuations because it places a strict lower limit on the number of kinetic states in the enzymatic mechanism. Here we show that there is a single general expression for the substrate dependence of n(min) for a wide range of kinetic models. This expression is governed by three kinetic parameters, which we term N(L), N(S), and alpha. These parameters have simple geometric interpretations and provide clear constraints on possible kinetic mechanisms. As a demonstration of this analysis, we fit the fluctuations in the dwell times of the packaging motor of the bacteriophage varphi29, revealing additional features of the nucleotide loading process in this motor. Because a diverse set of kinetic models display the same substrate dependence for their fluctuations, the expression for this general dependence may prove of use in the characterization and study of the dynamics of a wide range of enzymes.

Insight into helicase mechanism and function revealed through single-molecule approaches

Helicases are a class of nucleic acid (NA) motors that catalyze NTP-dependent unwinding of NA duplexes into single strands, a reaction essential to all areas of NA metabolism. In the last decade, single-molecule (sm) technology has proven to be highly useful in revealing mechanistic insight into helicase activity that is not always detectable via ensemble assays. A combination of methods based on fluorescence, optical and magnetic tweezers, and flow-induced DNA stretching has enabled the study of helicase conformational dynamics, force generation, step size, pausing, reversal and repetitive behaviors during translocation and unwinding by helicases working alone and as part of multiprotein complexes. The contributions of these sm investigations to our understanding of helicase mechanism and function will be discussed.

Optical path clearing and enhanced transmission through colloidal suspensions

We utilize advanced laser fields to clear a path through a dynamic turbid medium, a concept termed "Optical path clearing (OPC)." Particles are evacuated from a volume of the medium using the gradient and/or scattering forces due to an applied laser field with a suitably tailored spatial profile. Our studies encompass both an analytical model and proof-of-principle experiments where paths are cleared in dense bulk colloidal suspensions. Based on our results we suggest that high-performance and high efficiency OPC will be achieved by multiple-step clearing using dynamic laser fields based on Airy or inverted axicon beams.

Biopolymer organization upon confinement

Biopolymers in vivo are typically subject to spatial restraints, either as a result of molecular crowding in the cellular medium or of direct spatial confinement. DNA in living organisms provides a prototypical example of a confined biopolymer. Confinement prompts a number of biophysics questions. For instance, how can the high level of packing be compatible with the necessity to access and process the genomic material? What mechanisms can be adopted in vivo to avoid the excessive geometrical and topological entanglement of dense phases of biopolymers? These and other fundamental questions have been addressed in recent years by both experimental and theoretical means. A review of the results, particularly of those obtained by numerical studies, is presented here. The review is mostly devoted to DNA packaging inside bacteriophages, which is the best studied example both experimentally and theoretically. Recent selected biophysical studies of the bacterial genome organization and of chromosome segregation in eukaryotes are also covered.

Single-molecule studies of the replisome

Replication of DNA is carried out by the replisome, a multiprotein complex responsible for the unwinding of parental DNA and the synthesis of DNA on each of the two DNA strands. The impressive speed and processivity with which the replisome duplicates DNA are a result of a set of tightly regulated interactions between the replication proteins. The transient nature of these protein interactions makes it challenging to study the dynamics of the replisome by ensemble-averaging techniques. This review describes single-molecule methods that allow the study of individual replication proteins and their functioning within the replisome. The ability to mechanically manipulate individual DNA molecules and record the dynamic behavior of the replisome while it duplicates DNA has led to an improved understanding of the molecular mechanisms underlying DNA replication.

Single ribosome dynamics and the mechanism of translation

Our current understanding of the mechanism of translation is based on nearly fifty years of biochemical and biophysical studies. This mechanism, which requires the ribosome to manipulate tRNA and step repetitively along the mRNA, implies movement. High-resolution structures of the ribosome and its ligands have recently described translation in atomic detail, capturing the endpoints of large-scale rearrangements of the ribosome. Direct observation of the dynamic events that underlie the mechanism of translation is challenged by ensemble averaging in bulk solutions. Single-molecule methods, which eliminate these averaging effects, have emerged as powerful tools to probe the mechanism of translation. Single-molecule fluorescence experiments have described the dynamic motion of the ribosome and tRNA. Single-molecule force measurements have directly probed the forces stabilizing ribosomal complexes. Recent developments have allowed real-time observation of ribosome movement and dynamics during translation. This review covers the contributions of single-molecule studies to our understanding of the dynamic nature of translation.

Can common adhesion molecules and microtopography affect cellular elasticity? A combined atomic force microscopy and optical study

The phenomenon that cells respond to chemical and topographic cues in their surroundings has been widely examined and exploited in many fields ranging from basic life science research to biomedical therapeutics. Adhesion promoting molecules such as poly-L-lysine (PLL) and fibronectin (Fn) are commonly used for in vitro cell assays to promote cell spreading/proliferation on tissue culture plastic and to enhance the biocompatibility of biomedical devices. Likewise, engineered topography is often used to guide cell growth and differentiation. Little is known about how these cues affect the biomechanical properties of cells and subsequent cell function. In this study we have applied atomic force microscopy (AFM) to investigate these biomechanical properties. In the first stage of the study we formulated a rigorous approach to quantify cellular elasticity using AFM. Operational factors, including indentation depth and speed, and mathematical models for data fitting have been systematically evaluated. We then quantified how PLL, Fn and microtopography affected cellular elasticity and the organization of the cytoskeleton. Cellular elasticity after 1 day in culture was greater on a Fn-coated surface as compared to PLL or glass. These statistically significant differences disappeared after two more days in culture. In contrast, the significantly higher elasticity associated with cells grown on micrometric grooves remained for at least 3 days. This work sheds light on the apparently simple but debatable questions: "Are engineered chemical cues eventually masked by a cell's own matrix proteins and so only exert short-term influence? Does engineered topography as well as engineered chemistry affect cell elasticity?"

Magnetic tweezers measurements of the nanomechanical properties of DNA in the presence of drugs

Herein, we study the nanomechanical characteristics of single DNA molecules in the presence of DNA binders, including intercalating agents (ethidium bromide and doxorubicin), a minor groove binder (netropsin) and a typical alkylating damaging agent (cisplatin). We have used magnetic tweezers manipulation techniques, which allow us to measure the contour and persistence lengths together with the bending and torsional properties of DNA. For each drug, the specific variations of the nanomechanical properties induced in the DNA have been compared. We observed that the presence of drugs causes a specific variation in the DNA extension, a shift in the natural twist and a modification of bending dependence on the imposed twist. By introducing a naive model, we have justified an anomalous correlation of torsion data observed in the presence of intercalators. Finally, a data analysis criterion for discriminating between different molecular interactions among DNA and drugs has been suggested.

Power spectrum analysis with least-squares fitting: amplitude bias and its elimination, with application to optical tweezers and atomic force microscope cantilevers

Optical tweezers and atomic force microscope (AFM) cantilevers are often calibrated by fitting their experimental power spectra of Brownian motion. We demonstrate here that if this is done with typical weighted least-squares methods, the result is a bias of relative size between -2/n and +1/n on the value of the fitted diffusion coefficient. Here, n is the number of power spectra averaged over, so typical calibrations contain 10%-20% bias. Both the sign and the size of the bias depend on the weighting scheme applied. Hence, so do length-scale calibrations based on the diffusion coefficient. The fitted value for the characteristic frequency is not affected by this bias. For the AFM then, force measurements are not affected provided an independent length-scale calibration is available. For optical tweezers there is no such luck, since the spring constant is found as the ratio of the characteristic frequency and the diffusion coefficient. We give analytical results for the weight-dependent bias for the wide class of systems whose dynamics is described by a linear (integro)differential equation with additive noise, white or colored. Examples are optical tweezers with hydrodynamic self-interaction and aliasing, calibration of Ornstein-Uhlenbeck models in finance, models for cell migration in biology, etc. Because the bias takes the form of a simple multiplicative factor on the fitted amplitude (e.g. the diffusion coefficient), it is straightforward to remove and the user will need minimal modifications to his or her favorite least-squares fitting programs. Results are demonstrated and illustrated using synthetic data, so we can compare fits with known true values. We also fit some commonly occurring power spectra once-and-for-all in the sense that we give their parameter values and associated error bars as explicit functions of experimental power-spectral values.

Light forces the pace: optical manipulation for biophotonics

The biomedical sciences have benefited immensely from photonics technologies in the last 50 years. This includes the application of minute forces that enable the trapping and manipulation of cells and single molecules. In terms of the area of biophotonics, optical manipulation has made a seminal contribution to our understanding of the dynamics of single molecules and the microrheology of cells. Here we present a review of optical manipulation, emphasizing its impact on the areas of single-molecule studies and single-cell biology, and indicating some of the key experiments in the fields.

Monitoring ligand-receptor interactions by photonic force microscopy

We introduce a method for the acquisition of single molecule force measurements of ligand-receptor interactions using the photonic force microscope (PFM). Biotin-functionalized beads, manipulated with an optical trap, and a streptavidin-functionalized coverslip were used to measure the effect of different pulling forces on the lifetime of individual streptavidin-biotin complexes. By optimizing the design of the optical trap and selection of the appropriate bead size, pulling forces in excess of 50 pN were achieved. Based on the amplitude of three-dimensional (3D) thermal position fluctuations of the attached bead, we were able to select for a bead-coverslip interaction that was mediated by a single streptavidin-biotin complex. Moreover, the developed experimental system was greatly accelerated by automation of data acquisition and analysis. In force-dependent kinetic measurements carried out between streptavidin and biotin, we observed that the streptavidin-biotin complex exhibited properties of a catch bond, with the lifetime increasing tenfold when the pulling force increased from 10 to 20 pN. We also show that silica beads were more appropriate than polystyrene beads for the force measurements, as tethers, longer than 200 nm, could be extracted from polystyrene beads.

Chromatin fiber dynamics under tension and torsion

Genetic and epigenetic information in eukaryotic cells is carried on chromosomes, basically consisting of large compact supercoiled chromatin fibers. Micromanipulations have recently led to great advances in the knowledge of the complex mechanisms underlying the regulation of DNA transaction events by nucleosome and chromatin structural changes. Indeed, magnetic and optical tweezers have allowed opportunities to handle single nucleosomal particles or nucleosomal arrays and measure their response to forces and torques, mimicking the molecular constraints imposed in vivo by various molecular motors acting on the DNA. These challenging technical approaches provide us with deeper understanding of the way chromatin dynamically packages our genome and participates in the regulation of cellular metabolism.

Polarization gradient: exploring an original route for optical trapping and manipulation

We report a study of the capabilities of an optical tweezer based on polarization gradient. We use a light polarization pattern that is able to simultaneously exert forces and torques in opposite directions depending on the particle's position. It allows to perform oscillatory displacements and control the sense of rotation of several particles inside a uniformly illuminated region. Unconventional trapping of spinning particles in circularly polarized fringes has been observed, which suggests the involvement of hydrodynamic forces.

Tracking a molecular motor with a nanoscale optical encoder

Optical encoders are commonly used in macroscopic machines to make precise measurements of distance and velocity by translating motion into a periodic signal. Here we show how Forster resonance energy transfer can be used to implement this technique at the single-molecule scale. We incorporate a series of acceptor dye molecules into self-assembling DNA, and the periodic signal resulting from unhindered motion of a donor-labeled molecular motor provides nanometer-scale resolution in milliseconds.

Revealing the base pair stepping dynamics of nucleic acid motor proteins with optical traps

Nearly all aspects of nucleic acid metabolism involve motor proteins. This diverse group of enzymes, which includes DNA and RNA polymerases, the ribosome, helicases, and other translocases, converts chemical energy in the form of bond hydrolysis into concerted motion along nucleic acid filaments. The direct observation of this motion at its fundamental distance scale of one base pair has required the development of new ultrasensitive techniques. Recent advances in optical traps have now made these length scales, once the exclusive realm of crystallographic techniques, accessible. Several new studies using optical traps have revealed for the first time how motor proteins translocate along their substrates in a stepwise fashion. Though these techniques have only begun to be applied to biological problems, the unprecedented access into nucleic acid motor protein movement has already provided important insights into their mechanism. In this perspective, we review these advances and offer our view on the future of this exciting development.

Superresolution imaging in optical tweezers using high-speed cameras

High-speed cameras are reliable alternatives for the direct characterization of optical trap force and particle motion in optical tweezers setups, replacing indirect motion measurements often performed by quadrant detectors. In the present approach, subpixel motion data of the trapped particle is retrieved from a high-speed low-resolution video sequence. Due to the richness structure of motion diversity of microscopic trapped particles, which are subjected to a Brownian motion, we propose to also use the obtained motion information for tackling the inherent lack of resolution by applying superresolution algorithms on the low-resolution image sequence. The obtained results both for trapping calibration beads and for living bacteria show that the proposed approach allows the proper characterization of the optical tweezers by obtaining the real particle motion directly from the image domain, while still providing high resolution imaging.

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.

Robust transport by multiple motors with nonlinear force-velocity relations and stochastic load sharing

Transport by processive molecular motors plays an important role in many cell biological phenomena. In many cases, motors work together to transport cargos in the cell, so it is important to understand the mechanics of the multiple motors. Based on earlier modeling efforts, here we study effects of nonlinear force-velocity relations and stochastic load sharing on multiple motor transport. We find that when two or three motors transport the cargo, then the nonlinear and stochastic effects compensate so that the mechanical properties of the transport are robust. Similarly, the transport is insensitive to compliance of the cargo-motor links. Furthermore, the rate of movement against moderate loads is not improved by increasing the small number of motors. When the motor number is greater than 4, correlations between the motors become negligible, and the earlier analytical mean-field theory of the multiple motor transport holds. We predict that the effective diffusion of the cargo driven by the multiple motors under load increases by an order of magnitude compared to that for the single motor. Finally, our simulations predict that the stochastic effects are responsible for a significant dispersion of velocities generated by the 'tug-of-war' of the multiple opposing motors.

Rotational dynamics of optically trapped nanofibers

We report on the experimental evidence of tilted polymer nanofiber rotation, using a highly focused linear polarized Gaussian beam. Torque is controlled by varying trapping power or fiber tilt angle. This suggests an alternative strategy to previously reported approaches for the rotation of nano-objects, to test fundamental theoretical aspects. We compare experimental rotation frequencies to calculations based on T-Matrix formalism, which accurately reproduces measured data, thus providing a comprehensive description of trapping and rotation dynamics of the linear nanostructures.

Single-photon atomic force microscopy

In the last few years, an array of novel technologies, especially the big family of scanning probe microscopy, now often integrated with other powerful imaging tools such as laser confocal microscopy and total internal reflection fluorescence microscopy, have been widely applied in the investigation of biomolecular interactions and dynamics. But it is still a great challenge to directly monitor the dynamics of biomolecular interactions with high spatial and temporal resolution in living cells. An innovative method termed "single-photon atomic force microscopy" (SP-AFM), superior to existing techniques in tracing biomolecular interactions and dynamics in vivo, was proposed on the basis of the combination of atomic force microscopy with the technologies of carbon nanotubes and single-photon detection. As a unique tool, SP-AFM, capable of simultaneous topography imaging and molecular identification at the subnanometer level by synchronous acquisitions and analyses of the surface topography and fluorescent optical signals while scanning the sample, could play a very important role in exploring biomolecular interactions and dynamics in living cells or in a complicated biomolecular background.

Single-molecule dual-beam optical trap analysis of protein structure and function

Optical trapping is one of the most powerful single-molecule techniques. We provide a practical guide to set up and use an optical trap, applied to the molecular motor myosin as an example. We focus primarily on studies of myosin function using a dual-beam optical trap, a protocol to build such a trap, and the experimental and data analysis protocols to utilize it.

Force-fluorescence spectroscopy at the single-molecule level

During the past decade, various powerful single-molecule techniques have evolved and helped to address important questions in life sciences. Yet these techniques would be even more powerful if they would be combined, that is, single-molecule manipulation with an orthogonal single-molecule observation. Here, we present a recently developed approach to combine single-molecule optical tweezers with single-molecule fluorescence spectroscopy. Optical tweezers are used to manipulate and observe mechanical properties on the nanometer scale and piconewton force range. However, once the force range is in the low piconewton range or less, the spatial resolution of optical tweezers decreases significantly. In combination with fluorescence spectroscopy, like Förster resonance energy transfer (FRET), we are able to observe nanometer fluctuations and internal conformational changes in a low-force regime. The possibility to place fluorescent labels at nearly any desired position and a sophisticated design of the experiment increases the amount of information that can be extracted in contrast to pure mechanical or fluorescence experiments.

Single-molecule DNA analysis

The ability to detect single molecules of DNA or RNA has led to an extremely rich area of exploration of the single most important biomolecule in nature. In cases in which the nucleic acid molecules are tethered to a solid support, confined to a channel, or simply allowed to diffuse into a detection volume, novel techniques have been developed to manipulate the DNA and to examine properties such as structural dynamics and protein-DNA interactions. Beyond the analysis of the properties of nucleic acids themselves, single-molecule detection has enabled dramatic improvements in the throughput of DNA sequencing and holds promise for continuing progress. Both optical and nonoptical detection methods that use surfaces, nanopores, and zero-mode waveguides have been attempted, and one optically based instrument is already commercially available. The breadth of literature related to single-molecule DNA analysis is vast; this review focuses on a survey of efforts in molecular dynamics and nucleic acid sequencing.

Confocal Raman microscopy of optical-trapped particles in liquids

The in situ analysis of small, dispersed particles in liquids is a challenging problem, the successful solution to which influences diverse applications of colloidal particles in materials science, synthetic chemistry, and molecular biology. Optical trapping of small particles with a tightly focused laser beam can be combined with confocal Raman microscopy to provide molecular structure information about individual, femtogram-sized particles in liquid samples. In this review, we consider the basic principles of combining optical trapping and confocal Raman spectroscopy, then survey the applications that have been developed through the combination of these techniques and their use in the analysis of particles dispersed in liquids.