Single-molecule detection of DNA hybridization

Ion-Regulated Signal Amplification Optical Microfiber Interferometric DNA Sensor

Genetic information sensors play a pivotal role in the biomedical field. The detection of deoxyribonucleic acid (DNA) is achieved experimentally using an optical microfiber interferometric sensor, which operates based on an ion-regulation sensitivity enhancement mechanism. The optical microfiber is fabricated by drawing optical fiber into a diameter of less than 10 μm via the melting and tapering technique. Leveraging the characteristics of monovalent cations can effectively promote the folding of G-rich single-stranded DNA (ssDNA) into stable G-quadruplex structures, enabling the detection of specific sequences of ssDNA at low concentrations. The results show an improvement of the linear detection range by 3 orders of magnitude, and with the introduction of the ion-regulation sensitivity enhancement mechanism, the limit of detection (LOD) value is 1.07 × 10-15 M. This optical microfiber interferometric sensing architecture is characterized by its simplicity and high sensitivity, positioning it as a formidable tool for diverse biosensing and analytical applications.

Silver-Coordinated Watson-Crick Pairing-Driven Three-Dimensional DNA Walker for Locus-Specific Detection of Genomic N6-Methyladenine and N4-Methylcytosine at the Single-Molecule Level

N6-Methyladenine (6mdA) and N4-methylcytosine (4mdC) are the two most dominant DNA modifications in both prokaryotes and eukaryotes, but standard hybridization-based techniques cannot be applied for the 6mdA/4mdC assay. Herein, we demonstrate the silver-coordinated Watson-Crick pairing-driven three-dimensional (3D) DNA walker for locus-specific detection of genomic 6mdA/4mdC at the single-molecule level. 6mdA-DNA and 4mdC-DNA can selectively hybridize with the binding probes (BP1 and BP2) to form 6mdA-DNA-BP1 and 4mdC-DNA-BP2 duplexes. The 6mdA-C/4mdC-A mismatches cannot be stabilized by AgI, and thus, 18-nt BP1/BP2 cannot be extended by the catalysis of KF exonuclease. Through toehold-mediated strand displacement (TMSD), the signal probe (SP1/SP2) functionalized on the gold nanoparticles (AuNPs) can competitively bind to BP1/BP2 in 6mdA-DNA-BP1/4mdC-DNA-BP2 duplex to obtain SP1-18-nt BP1 and SP2-18-nt BP2 duplexes. The resulting DNA duplexes can act as the substrates of lambda exonuclease, leading to the cleavage of SP1/SP2 and the release of Cy3/Cy5 and 18-nt BP1/BP2. The released 18-nt BP1/BP2 can subsequently serve as the walker DNA, moving along the surface of the AuNP to activate dynamic 3D DNA walking and releasing abundant Cy3/Cy5. The released Cy3/Cy5 can be quantified by single-molecule imaging. This nanosensor exhibits high sensitivity with a limit of detection (LOD) of 9.80 × 10-15 M for 6mdA-DNA and 9.97 × 10-15 M for 4mdC-DNA. It can discriminate 6mdA-/4mdC-DNA from unmodified genomic DNAs, distinguish 0.01% 6mdA-/4mdC-DNA from excess unmethylated DNAs, and quantify 6mdA-/4mdC-DNA at specific sites in genomic DNAs of liver cancer cells and Escherichia coli plasmid cloning vector, providing a new platform for locus-specific analysis of 6mdA/4mdC in genomic DNAs.

Multi intercalators FRET enhanced detection of minute amounts of DNA

A novel approach is presented that increases sensitivity and specificity for detecting minimal traces of DNA in liquid and on solid samples. Förster Resonance Energy Transfer (FRET) from YOYO to Ethidium Bromide (EtBr) substantially increases the signal from DNA-bound EtBr highly enhancing sensitivity and specificity for DNA detection. The long fluorescence lifetime of the EtBr acceptor, when bound to DNA, allows for multi-pulse pumping with time gated (MPPTG) detection, which highly increases the detectable signal of DNA-bound EtBr. A straightforward spectra/image subtraction eliminates sample background and allows for a huge increase in the overall detection sensitivity. Using a combination of FRET and MPPTG detection an amount as small as 10 pg of DNA in a microliter sample can be detected without any additional sample purification/manipulation or use of amplification technologies. This amount of DNA is comparable to the DNA content of a one to two human cells. Such a detection method based on simple optics opens the potential for robust, highly sensitive DNA detection/imaging in the field, quick evaluation/sorting (i.e., triaging) of collected DNA samples, and can support various diagnostic assays.

N protein-based ultrasensitive SARS-CoV-2 antibody detection in seconds via 3D nanoprinted, microarchitected array electrodes

Rapid detection of antibodies to SARS-CoV-2 is critical for COVID-19 diagnostics, epidemiological research, and studies related to vaccine evaluation. It is known that the nucleocapsid (N) is the most abundant protein of SARS-CoV-2 and can serve as an excellent biomarker due to its strong immunogenicity. This paper reports a rapid and ultrasensitive 3D biosensor for quantification of COVID-19 antibodies in seconds via electrochemical transduction. This sensor consists of an array of three-dimensional micro-length-scale electrode architecture that is fabricated by aerosol jet 3D printing, which is an additive manufacturing technique. The micropillar array is coated with N proteins via an intermediate layer of nano-graphene and is integrated into a microfluidic channel to complete an electrochemical cell that uses antibody-antigen interaction to detect the antibodies to the N protein. Due to the structural innovation in the electrode geometry, the sensing is achieved in seconds, and the sensor shows an excellent limit of detection of 13 fm and an optimal detection range of 100 fm to 1 nm. Furthermore, the sensor can be regenerated at least 10 times, which reduces the cost per test. This work provides a powerful platform for rapid screening of antibodies to SARS-CoV-2 after infection or vaccination.

Förster Resonance Energy Transfer-Enhanced Detection of Minute Amounts of DNA

This article presents a novel approach to increase the detection sensitivity of trace amounts of DNA in a sample by employing Förster resonance energy transfer (FRET) between intercalating dyes. Two intercalators that present efficient FRET were used to enhance sensitivity and improve specificity in detecting minute amounts of DNA. Comparison of steady-state acceptor emission spectra with and without the donor allows for simple and specific detection of DNA (acceptor bound to DNA) down to 100 pg/μL. When utilizing as an acceptor a dye with a significantly longer lifetime (e.g., ethidium bromide bound to DNA), multipulse pumping and time-gated detection enable imaging/visualization of picograms of DNA present in a microliter of an unprocessed sample or DNA collected on a swab or other substrate materials.

Breaking the barrier to biomolecule limit-of-detection via 3D printed multi-length-scale graphene-coated electrodes

Sensing of clinically relevant biomolecules such as neurotransmitters at low concentrations can enable an early detection and treatment of a range of diseases. Several nanostructures are being explored by researchers to detect biomolecules at sensitivities beyond the picomolar range. It is recognized, however, that nanostructuring of surfaces alone is not sufficient to enhance sensor sensitivities down to the femtomolar level. In this paper, we break this barrier/limit by introducing a sensing platform that uses a multi-length-scale electrode architecture consisting of 3D printed silver micropillars decorated with graphene nanoflakes and use it to demonstrate the detection of dopamine at a limit-of-detection of 500 attomoles. The graphene provides a high surface area at nanoscale, while micropillar array accelerates the interaction of diffusing analyte molecules with the electrode at low concentrations. The hierarchical electrode architecture introduced in this work opens the possibility of detecting biomolecules at ultralow concentrations.

Cytosine-5 methylation-directed construction of a Au nanoparticle-based nanosensor for simultaneous detection of multiple DNA methyltransferases at the single-molecule level

DNA methylation at cytosine/guanine dinucleotide islands (CpGIs) is the most prominent epigenetic modification in prokaryotic and eukaryotic genomes. DNA methyltransferases (MTases) are responsible for genomic methylation, and their aberrant activities are closely associated with various diseases including cancers. However, the specific and sensitive detection of multiple DNA MTases has remained a great challenge due to the specificity of the methylase substrate and the rareness of methylation-sensitive restriction endonuclease species. Here, we demonstrate for the first time the cytosine-5 methylation-directed construction of a Au nanoparticle (AuNP)-based nanosensor for simultaneous detection of multiple DNA MTases at the single-molecule level. We used the methyl-directed endonuclease GlaI to cleave the site-specific 5-methylcytosine (5-mC). In the presence of CpG and GpC MTases (i.e., M.SssI and M.CviPI), their hairpin substrates are methylated at cytosine-5 to form the catalytic substrates for GlaI, respectively, followed by simultaneous cleavage by GlaI to yield two capture probes. These two capture probes can hybridize with the Cy5/Cy3-signal probes which are assembled on the AuNPs, respectively, to form the double-stranded DNAs (dsDNAs). Each dsDNA with a guanine ribonucleotide can act as the catalytic substrate for ribonuclease (RNase HII), inducing recycling cleavage of signal probes to liberate large numbers of Cy5 and Cy3 molecules from the AuNPs. The released Cy5 and Cy3 molecules can be simply quantified by total internal reflection fluorescence (TIRF)-based single-molecule imaging for simultaneous measurement of M.SssI and M.CviPI MTase activities. This method exhibits good specificity and high sensitivity with a detection limit of 2.01 × 10-3 U mL-1 for M.SssI MTase and 3.39 × 10-3 U mL-1 for M.CviPI MTase, and it can be further applied for discriminating different kinds of DNA MTases, screening potential inhibitors, and measuring DNA MTase activities in human serum and cell lysate samples, holding great potential in biomedical research, clinical diagnosis, drug discovery and cancer therapeutics.

Selective Manipulation of Biomolecules with Insulator-Based Dielectrophoretic Tweezers

Insulator-based dielectrophoretic (iDEP) trapping, separating, and concentrating nanoscale objects is carried out using a non-metal, unbiased, mobile tip acing as a tweezers. The spatial control and manipulation of fluorescently-labeled polystyrene particles and DNA were performed to demonstrate the feasibility of the iDEP tweezers. Frequency-dependent iDEP tweezers' strength and polarity were quantitatively determined using two theoretical approaches to DNA, which resulted in a factor of 2 ~ 40 differences between them. In either approach, the strength of iDEP was at least 4-order of magnitude stronger than the thermal force, indicating iDEP was a dominant force for trapping, holding, and separating DNA. The trapping strength and volume of the iDEP tweezers were also determined, which further supports direct capture and manipulation of DNA at the tip end.

Probing Multiple Binding Modes of DNA Hybridization: A Comparison between Single-Molecule Observations and Ensemble Measurements

Interactions between biomolecules are generally analyzed by ensemble measurements, assuming that the interactions occur in a single binding manner. However, such interactions may occur via multiple binding modes. We investigated the kinetics of DNA hybridization as a multiple dynamic model of biomolecular interactions. Two kinetic analyses were performed with a single-molecule observation using total internal reflection fluorescence microscopy (TIRFM) and with ensemble measurements using a quartz-crystal microbalance (QCM) biosensor. We observed the DNA hybridization of 8 and 12 bp DNAs with random sequences and dA₁₂-dT₁₂ and calculated the kinetic parameters, including the dissociation rate constant (k_off). Hybridization of 8 bp DNA proceeded mainly via a single binding mode. However, hybridization of 12 bp DNA indicated at least two different binding modes and dA₁₂-dT₁₂ hybridization showed multiple binding modes. For the multiple binding interactions, the kinetic parameters obtained from TIRFM and QCM were different because kinetic parameters obtained from QCM indicate average number of molecules, whereas those from TIRFM indicate average association time. The present study revealed the details of multiple interactions, which can be utilized for better understanding of not only DNA hybridization but also biomolecular interaction mechanisms.

Measuring Microtubule Supertwist and Defects by Three-Dimensional-Force-Clamp Tracking of Single Kinesin-1 Motors

Three-dimensional (3D) nanometer tracking of single biomolecules provides important information about their biological function. However, existing microscopy approaches often have only limited spatial or temporal precision and do not allow the application of defined loads. Here, we developed and applied a high-precision 3D-optical-tweezers force clamp to track in vitro the 3D motion of single kinesin-1 motor proteins along microtubules. To provide the motors with unimpeded access to the whole microtubule lattice, we mounted the microtubules on topographic surface features generated by UV-nanoimprint lithography. Because kinesin-1 motors processively move along individual protofilaments, we could determine the number of protofilaments the microtubules were composed of by measuring the helical pitches of motor movement on supertwisted microtubules. Moreover, we were able to identify defects in microtubules, most likely arising from local changes in the protofilament number. While it is hypothesized that microtubule supertwist and defects can severely influence the function of motors and other microtubule-associated proteins, the presented method allows for the first time to fully map the microtubule lattice in situ. This mapping allows the correlation of motor-filament interactions with the microtubule fine-structure. With the additional ability to apply loads, we expect our 3D-optical-tweezers force clamp to become a valuable tool for obtaining a wide range of information from other biological systems, inaccessible by two-dimensional and/or ensemble measurements.

Single-Molecule Detection of Polynucleotide Kinase Based on Phosphorylation-Directed Recovery of Fluorescence Quenched by Au Nanoparticles

5'-Polynucleotide kinase such as T4 polynucleotide kinase (T4 PNK) may catalyze the phosphorylation of 5'-hydroxyl termini in nucleic acids, playing a crucial role in DNA replication, DNA recombination, and DNA damage repair. Here, we demonstrate for the first time single-molecule detection of PNK based on phosphorylation-directed recovery of fluorescence quenched by Au nanoparticle (AuNP) in combination with lambda exonuclease-mediated cleavage reaction. In the presence of PNK, the γ-phosphate group from adenosine triphosphate (ATP) is transferred to 5'-hydroxyl terminus, resulting in 5'-phosphorylation of the hairpin probe. The phosphorylated hairpin probes may function as the substrates of lambda exonuclease and enable the removal of 5' mononucleotides from the stem, leading to the unfolding of hairpin structure and the formation of binding probes. The resultant binding probes may specifically hybridize with the AuNP-modified capture probes, forming double-strand DNA (dsDNA) duplexes with 5'-phosphate groups as the substrates of lambda exonuclease and subsequently leading to the cleavage of capture probes and the liberation of Cy5 molecules and the binding probes. The released binding probes may further hybridize with new capture probes, inducing cycles of digestion-release-hybridization and consequently the release of numerous Cy5 molecules. Through simply monitoring Cy5 molecules with total internal reflection fluorescence (TIRF)-based imaging, PNK activity can be quantitatively measured. This assay is very sensitive with a limit of detection of 9.77 × 10^-8 U/μL, and it may be further used to screen the PNK inhibitors and measure PNK in cancer cell extracts.

Programmable DNA Nanosystem for Molecular Interrogation

We describe a self-assembling DNA-based nanosystem for interrogating molecular interactions. The nanosystem contains a rigid supporting dumbbell-shaped frame, a cylindrical central core, and a mobile ring that is coaxial with the core. Motion of the ring is influenced by several control elements whose force-generating capability is based on the transition of single-stranded DNA to double-stranded DNA. These forces can be directed to act in opposition to adhesive forces between the ring and the frame thereby providing a mechanism for molecular detection and interrogation at the ring-frame interface. As proof of principle we use this system to evaluate base stacking adhesion and demonstrate detection of a soluble nucleic acid viral genome mimic.

Nanoscale characterization of DNA conformation using dual-color fluorescence axial localization and label-free biosensing

Quantitative determination of the density and conformation of DNA molecules tethered to the surface can help optimize and understand DNA nanosensors and nanodevices, which use conformational or motional changes of surface-immobilized DNA for detection or actuation. We present an interferometric sensing platform that combines (i) dual-color fluorescence spectroscopy for precise axial co-localization of two fluorophores attached at different nucleotides of surface-immobilized DNA molecules and (ii) independent label-free quantification of biomolecule surface density at the same site. Using this platform, we examined the conformation of DNA molecules immobilized on a three-dimensional polymeric surface and demonstrated simultaneous detection of DNA conformational change and binding in real-time. These results demonstrate that independent quantification of both surface density and molecular nanoscale conformation constitutes a versatile approach for nanoscale solid-biochemical interface investigations and molecular binding assays.

Probing DNA Stiffness through Optical Fluctuation Analysis of Plasmon Rulers

The distance-dependent plasmon coupling between biopolymer tethered gold or silver nanoparticles forms the foundation for the so-called plasmon rulers. While conventional plasmon ruler applications focus on the detection of singular events in the far-field spectrum, we perform in this Letter a ratiometric analysis of the continuous spectral fluctuations arising from thermal interparticle separation variations in plasmon rulers confined to fluid lipid membranes. We characterized plasmon rulers with different DNA tethers and demonstrate the ability to detect and quantify differences in the plasmon ruler potential and tether stiffness. The influence of the nature of the tether (single-stranded versus double-stranded DNA) and the length of the tether is analyzed. The characterization of the continuous variation of the interparticle separation in individual plasmon rulers through optical fluctuation analysis provides additional information about the conformational flexibility of the tether molecule(s) located in the confinement of the deeply subdiffraction limit interparticle gap and enhances the versatility of plasmon rulers as a tool in Biophysics and Nanotechnology.

An active one-particle microrheometer: incorporating magnetic tweezers to total internal reflection microscopy

We present a novel microrheometer by incorporating magnetic tweezers in the total internal reflection microscopy (TIRM) that enables measuring of viscoelastic properties of materials near solid surface. An evanescent wave generated by a solid∕liquid interface in the TIRM is used as the incident light source in the microrheometer. When a probe particle (of a few micrometers diameter) moves near the interface, it can interact with the evanescent field and reflect its position with respect to the interface by the scattered light intensity. The exponential distance dependence of the evanescent field, on the one hand, makes this technique extremely sensitive to small changes from z-fluctuations of the probe (with a resolution of several nanometers), and on the other, it does not require imaging of the probe with high lateral resolution. Another distinct advantage is the high sensitivity in determining the z position of the probe in the absence of any labeling. The incorporated magnetic tweezers enable us to effectively manipulate the distance of the embedded particle from the interface either by a constant or an oscillatory force. The force ramp is easy to implement through a coil current ramp. In this way, the local viscous and elastic properties of a given system under different confinements can therefore be measured by resolving the near-surface particle motion. To test the feasibility of applying this microrheology to soft materials, we measured the viscoelastic properties of sucrose and poly(ethylene glycol) solutions and compared the results to bulk rheometry. In addition, we applied this technique in monitoring the structure and properties of deformable microgel particles near the flat surface.

Electrochemical detection of individual DNA hybridization events

We report on real-time electrochemical detection of individual DNA hybridization events at an electrode surface. The experiment is carried out in a microelectrochemical device configured with a working electrode modified with single-stranded DNA probe molecules. When a complementary DNA strand labelled with a catalyst hybridizes to the probe, an easily detectable electrocatalytic current is observed. In the experiments reported here, the catalyst is a platinum nanoparticle and the current arises from electrocatalytic oxidation of hydrazine. Two types of current transients are observed: short bursts and longer-lived steps. At low concentrations of hydrazine, the average size of the current transients is proportional to the amount of hydrazine present, but at higher concentrations the hydrazine oxidation reaction interferes with hybridization.

Single-molecule mechanical identification and sequencing

High-throughput, low-cost DNA sequencing has emerged as one of the challenges of the postgenomic era. Here we present the proof of concept for a single-molecule platform that allows DNA identification and sequencing. In contrast to most present methods, our scheme is not based on the detection of the fluorescent nucleotides but on DNA hairpin length. By pulling on magnetic beads tethered by a DNA hairpin to the surface, the molecule can be unzipped. In this open state it can hybridize with complementary oligonucleotides, which transiently block the hairpin rezipping when the pulling force is reduced. By measuring from the surface to the bead of a blocked hairpin, one can determine the position of the hybrid along the molecule with nearly single-base precision. Our approach can be used to identify a DNA fragment of known sequence in a mix of various fragments and to sequence an unknown DNA fragment by hybridization or ligation.

Scanning evanescent fields using a pointlike light source and a nanomechanical DNA gear

The characterization of three-dimensional inhomogeneous illumination fields is a challenge in modern microscopy. Here we use a four-arm DNA junction as a nanomechanical translation stage to move a single fluorescent quantum dot through an exponentially decaying evanescent field. Recording the emission of the quantum dot within the evanescent field as well as under homogeneous illumination allows one to directly obtain the intensity distribution of the excitation field without additional deconvolution. Our method will allow the characterization of a broad range of illumination fields and to study near-field effects between small optical probes.

Viscoelastic transition and yield strain of the folded protein

For proteins, the mechanical properties of the folded state are directly related to function, which generally entails conformational motion. Through sub-Angstrom resolution measurements of the AC mechanical susceptibility of a globular protein we describe a new fundamental materials property of the folded state. For increasing amplitude of the forcing, there is a reversible transition from elastic to viscoelastic response. At fixed frequency, the amplitude of the deformation is piecewise linear in the force, with different slopes in the elastic and viscoelastic regimes. Effectively, the protein softens beyond a yield point defined by this transition. We propose that ligand induced conformational changes generally operate in this viscoelastic regime, and that this is a universal property of the folded state.

Distance-dependent metal-enhanced quantum dots fluorescence analysis in solution by capillary electrophoresis and its application to DNA detection

Here the distance dependence of metal-enhanced quantum dots (QDs) fluorescence in solution is studied systematically by capillary electrophoresis (CE). Complementary DNA oligonucleotides-modified CdSe/ZnS QDs and gold nanoparticles (Au NPs) were connected together in solution by the hybridization of complementary oligonucleotides, and a model system (QD-Au) for the study of metal-enhanced QDs fluorescence was constructed, in which the distance between the QDs and Au NPs was controlled by adjusting the base number of the oligonucleotide. In our CE experiments, the metal-enhanced fluorescence of the QDs solution was only observed when the distance between the QDs and Au NPs ranged from 6.8 to 18.7 nm, and the maximum enhancement by a factor of 2.3 was achieved at 11.9 nm. Furthermore, a minimum of 19.6 pg of target DNA was identified in CE based on its specific competition with the QD-DNA in the QD-Au system. This work provides an important reference for future study of metal-enhanced QDs fluorescence in solution and exhibits potential capability in nucleic acid hybridization analysis and high-sensitivity DNA detection.

Quantitative High-Resolution Sensing of DNA Hybridization Using Magnetic Tweezers with Evanescent Illumination

We applied the combined approach of evanescent nanometry and force spectroscopy using magnetic tweezers to quantify the degree of hybridization of a single synthetic single-stranded DNA oligomer to a resolution approaching a single-base. In this setup, the 200 nucleotide long DNA was covalently attached to the surface of an optically transparent solid support at one end and to the surface of a superparamagnetic fluorescent microsphere (force probe) at the other end. The force was applied to the probes using an electromagnet. The end-to-end molecular distance (i.e. out-of-image-plane position of the force probe) was determined from the intensity of the probe fluorescent image observed with total-internal reflectance microscopy. An equation of state for single stranded DNA molecules under tension (extensible freely jointed chain) was used to derive the penetration depth of the evanescent field and to calibrate the magnetic properties of the force probes. The parameters of the magnetic response of the force probes obtained from the equation of state remained constant when changing the penetration depth, indicating a robust calibration procedure. The results of such a calibration were also confirmed using independently measured probe-surface distances for probes mounted onto cantilevers of an atomic force microscope. Upon hybridization of the complementary 50 nucleotide-long oligomer to the surface-bound 200-mer, the changes in the force-distance curves were consistent with the quantitative conversion of 25% of the original single-stranded DNA to its double-stranded form, which was modeled as an elastic rod. The method presented here for quantifying the hybridization state of the single DNA molecules has potential for determining the degree of hybridization of individual molecules in a single molecule array with high accuracy.

Elasticity of globular proteins measured from the ac susceptibility

We introduce a new method to measure the elastic constants of globular proteins. Gold nanoparticles, tethered to a gold surface by the protein, are driven by an ac electric field while their displacement is synchronously detected by evanescent wave scattering, yielding the mechanical response function of the macromolecular sample in the frequency domain. We apply the method to measure the stiffening of an enzyme upon binding its substrate.

Conformational diversity of short DNA duplex

Two 25 base-pair cDNA strands are encapsulated within an optically trapped nanodroplet, and we observe the kinetics of their hybridization in dynamic equilibrium via single-molecule fluorescence resonance energy transfer (FRET) as a function of temperature and of the solution's NaCl concentration. We have observed the duplex unfolding and refolding, and we have observed quasistable partially unfolded states under low salinity conditions. Furthermore, our measurements reveal that, even in conditions under which the duplex is stable, it undergoes conformational fluctuations in solution.

Probing DNA conformational changes with high temporal resolution by tethered particle motion

The tethered particle motion (TPM) technique informs about conformational changes of DNA molecules, e.g. upon looping or interaction with proteins, by tracking the Brownian motion of a particle probe tethered to a surface by a single DNA molecule and detecting changes of its amplitude of movement. We discuss in this context the time resolution of TPM, which strongly depends on the particle-DNA complex relaxation time, i.e. the characteristic time it takes to explore its configuration space by diffusion. By comparing theory, simulations and experiments, we propose a calibration of TPM at the dynamical level: we analyze how the relaxation time grows with both DNA contour length (from 401 to 2080 base pairs) and particle radius (from 20 to 150 nm). Notably we demonstrate that, for a particle of radius 20 nm or less, the hydrodynamic friction induced by the particle and the surface does not significantly slow down the DNA. This enables us to determine the optimal time resolution of TPM in distinct experimental contexts which can be as short as 20 ms.

DNA-nanoparticle micelles as supramolecular fluorogenic substrates enabling catalytic signal amplification and detection by DNAzyme probes

Catalytic DNA molecules have tremendous potential in propagating detection events via nucleic acid sequence selective signal amplification. However, they suffer from product inhibition limiting their widespread utility. Herein, this limitation is overcome utilizing a novel fluorogenic substrate design consisting of cooperatively assembled DNA-nanoparticle micelles.

Optical response of magnetic fluorescent microspheres used for force spectroscopy in the evanescent field

Force spectroscopy based on magnetic tweezers is a powerful technique for manipulating single biomolecules and studying their interactions. The resolution in magnetic probe displacement, however, needs to be commensurate with molecular sizes. To achieve the desirable sensitivity in tracking displacements of the magnetic probe, some recent approaches have combined magnetic tweezers with total internal reflection fluorescence microscopy. In this situation, a typical force probe is a polymer microsphere containing two types of optically active components: a pure absorber (magnetic nanoparticles for providing the pulling force) and a luminophore (semiconducting nanoparticles or organic dyes for fluorescent imaging). To assess the system's capability fully with regard to tracking the position of the force probe with subnanometer accuracy, we developed a body-of-revolution formulation of the method of auxiliary sources (BOR-MAS) to simulate the absorption, scattering, and fluorescence of microscopic spheres in an evanescent electromagnetic field. The theoretical formulation uses the axial symmetry of the system to reduce the dimensionality of the modeling problem and produces excellent agreement with the reported experimental data on forward scattering intensity. Using the BOR-MAS numerical model, we investigated the probe detection sensitivity for a high numerical aperture objective. The analysis of both backscattering and fluorescence observation modes shows that the total intensity of the bead image decays exponentially with the distance from the surface (or the length of a biomolecule). Our investigations demonstrate that the decay lengths of observable optical power are smaller than the penetration depth of the unperturbed excitation evanescent wave. In addition, our numerical modeling results illustrate that the expected sensitivity for the decay length changes with the angle of incidence, tracking the theoretical penetration depth for a two-media model, and is sensitive to the bead size. The BOR-MAS methodology developed in this work for near-field modeling of bead-tracking experiments fully describes the fundamental photonic response of microscopic BOR probes at the subwavelength level and can be used for future improvements in the design of these probes or in the setup of bead-tracking experiments.

Enhanced Single-Molecule Detection using Porous Silver Membrane

We evaluated a commercial porous silver membrane as a support substrate for direct localization and visualization of single molecule events. We characterized the fluorescence behaviors of fluorescently labeled DNA oligonucleotides on the silver membranes. The fluorescence from the fluorescent probes that were immobilized on the porous silver is greatly enhanced. Additionally, correlated to reflectance contour image, it appears that enhanced fluorescence came from location close to the "valley" of the pore channels (or in the voids). These results are of great interest to increase the effectiveness of fluorescence-based single molecule DNA analysis.

Parallax: high accuracy three-dimensional single molecule tracking using split images

Three-dimensional (3D) tracking can provide valuable biological insights that are missing in conventional microscopy. Here we developed a single molecule 3D tracking microscopy technique, named Parallax, with high localization precision and temporal resolution. We demonstrated its capabilities by studying the 3D trafficking of glucose-transporter-4 containing vesicles in living adipocytes as well as the walking path of single myosin VI molecules along actin filaments.

Imaging biomolecular interactions by fast three-dimensional tracking of laser-confined carrier particles

The quantitative study of the near-equilibrium structural behavior of individual biomolecules requires high-resolution experimental approaches with longtime stability. We present a new technique to explore the dynamics of weak intramolecular interactions. It is based on the analysis of the 3D Brownian fluctuations of a laser-confined glass bead that is tethered to a flat surface by the biomolecule of interest. A continuous autofocusing mechanism allows us to maintain or adjust the height of the optical trap with nanometer accuracy over long periods of time. The resulting remarkably stable trapping potential adds a well-defined femto-to-piconewton force bias to the energy landscape of molecular configurations. A combination of optical interferometry and advanced pattern-tracking algorithms provides the 3D bead positions with nanometer spatial and >120 Hz temporal resolution. The analysis of accumulated 3D positions has allowed us not only to identify small single biomolecules but also to characterize their nanomechanical behavior, for example, the force-extension relations of short oligonucleotides and the unfolding/refolding transitions of small protein tethers.

Diffusive hidden Markov model characterization of DNA looping dynamics in tethered particle experiments

In many biochemical processes, proteins bound to DNA at distant sites are brought into close proximity by loops in the underlying DNA. For example, the function of some gene-regulatory proteins depends on such 'DNA looping' interactions. We present a new technique for characterizing the kinetics of loop formation in vitro, as observed using the tethered particle method, and apply it to experimental data on looping induced by lambda repressor. Our method uses a modified ('diffusive') hidden Markov analysis that directly incorporates the Brownian motion of the observed tethered bead. We compare looping lifetimes found with our method (which we find are consistent over a range of sampling frequencies) to those obtained via the traditional threshold-crossing analysis (which can vary depending on how the raw data are filtered in the time domain). Our method does not involve any time filtering and can detect sudden changes in looping behavior. For example, we show how our method can identify transitions between long-lived, kinetically distinct states that would otherwise be difficult to discern.

Opening rates of DNA hairpins: experiment and model

We present single-molecule measurements of the opening rate of DNA hairpins under mechanical tension and compare with the results obtained from a reduced-degrees-of-freedom statistical mechanics model. We extract the apparent position of the transition state s and find that the model, with no fitting parameters, reproduces the experimental measurements surprisingly well. Our values for s are different from the ones obtained in previous experiments, where, however, the experimental conditions were different (different force fields, different salt concentrations). Thus it appears that the values of s measured for relatively short hairpins are strongly affected by these experimental conditions.

Quantification of protein based on single-molecule counting by total internal reflection fluorescence microscopy with adsorption equilibrium

We developed a sensitive single-molecule imaging method for quantification of protein by total internal reflection fluorescence microscopy with adsorption equilibrium. In this method, the adsorption equilibrium of protein was achieved between solution and glass substrate. Then, fluorescence images of protein molecules in a evanescent wave field were taken by a highly sensitive electron multiplying charge coupled device. Finally, the number of fluorescent spots corresponding to the protein molecules in the images was counted. Alexa Fluor 488-labeled goat anti-rat IgG(H+L) was chosen as the model protein. The spot number showed an excellent linear relationship with protein concentration. The concentration linear range was 5.4 x 10(-11) to 8.1 x 10(-10) mol L(-1).

Use of plasmon coupling to reveal the dynamics of DNA bending and cleavage by single EcoRV restriction enzymes

Pairs of Au nanoparticles have recently been proposed as "plasmon rulers" based on the dependence of their light scattering on the interparticle distance. Preliminary work has suggested that plasmon rulers can be used to measure and monitor dynamic distance changes over the 1- to 100-nm length scale in biology. Here, we substantiate that plasmon rulers can be used to measure dynamical biophysical processes by applying the ruler to a system that has been investigated extensively by using ensemble kinetic measurements: the cleavage of DNA by the restriction enzyme EcoRV. Temporal resolutions of up to 240 Hz were obtained, and the end-to-end extension of up to 1,000 individual dsDNA enzyme substrates could be simultaneously monitored for hours. The kinetic parameters extracted from our single-molecule cleavage trajectories agree well with values obtained in bulk through other methods and confirm well known features of the cleavage process, such as DNA bending before cleavage. Previously unreported dynamical information is revealed as well, for instance, the degree of softening of the DNA just before cleavage. The unlimited lifetime, high temporal resolution, and high signal/noise ratio make the plasmon ruler a unique tool for studying macromolecular assemblies and conformational changes at the single-molecule level.