Single-molecule detection of DNA hybridization

Diffusing colloidal probes of protein and synthetic macromolecule interactions

A new approach is described for measuring kT and nanometer scale protein-protein and protein-synthetic macromolecule interactions. The utility of this method is demonstrated by measuring interactions of bovine serum albumin (BSA) and copolymers with exposed polyethyleneoxide (PEO) moieties adsorbed to hydrophobically modified colloids and surfaces. Total internal reflection and video microscopy are used to track three-dimensional trajectories of many single diffusing colloids that are analyzed to yield interaction potentials, mean-square displacements, and colloid-surface association lifetimes. A criterion is developed to identify colloids as being levitated, associated, or deposited based on energetic, spatial, statistical, and temporal information. Whereas levitation and deposition occur for strongly repulsive or attractive potentials, association is exponentially sensitive to weak interactions influenced by adsorbed layer architectures and surface heterogeneity. Systematic experiments reveal how BSA orientation and PEO molecular weight produce adsorbed layers that either conceal or expose substrate heterogeneities to generate a continuum of colloid-surface association lifetimes. These measurements provide simultaneous access to a broad range of information that consistently indicates purely repulsive BSA and PEO interactions and a role for surface heterogeneity in colloid-surface association. The demonstrated capability to measure nonspecific protein interactions provides a basis for future measurements of specific protein interactions.

Electronic deoxyribonucleic acid (DNA) microarray detection of viable pathogenic Escherichia coli, Vibrio cholerae, and Salmonella typhi

An electronic deoxyribonucleic acid (DNA) microarray technique was developed for detection and identification of viable Escherichia coli O157:H7, Vibrio cholerae O1, and Salmonella typhi. Four unique genes, the E. coli O157 lipopolysaccharide (LPS) gene (rfbE) and H7 flagellin gene (fliC), the V. cholerae O1 LPS gene (rfbE), and the S. typhi LPS gene (tyv), were chosen as the targets for detection. These targets were selectively amplified from mRNA of viable cells using reverse transcription polymerase chain reaction (RT-PCR) and detected using the electronic DNA microarray technique. Specific captures and reporters were designed and examined for selective detection and correct identification of the target pathogens. The technique was able to detect as few as 2-150 cells of E. coli O157:H7. The co-presence of six other common bacteria and a parasite at 10- and 1000-fold higher concentrations than the target E. coli O157:H7 did not interfere with the specific detection. Comparative analysis of live and heat-killed E. coli O157:H7 cells showed that the technique only responded to the viable cells and not to the dead cells. Thus, the integration of RT-PCR of specific mRNA with the electronic DNA microarray technique enables specific and sensitive detection of viable target cells. This technique is potentially useful for high throughput screening of multiple pathogenic bacteria in different samples.

Inference of DNA sequences from mechanical unzipping: an ideal-case study

The performances of Bayesian inference to predict the sequence of DNA molecules from fixed-force unzipping experiments are investigated. We show that the probability of misprediction decreases exponentially with the amount of collected data. The decay rate is calculated as a function of biochemical parameters (binding free energies), the sequence content, the applied force, the elastic properties of a DNA single strand, and time resolution.

Recent developments in bio-molecular electronics techniques for food pathogens

Food borne illnesses contribute to the majority of infections caused by pathogenic microorganisms. Detection of these pathogens originating from different sources has led to increased interest of researchers. New bio-molecular techniques for food pathogen detection are being developed to improve the sensor characteristics such as sensitivity, reusability, simplicity and economic viability. Present article deals with the various methods of food pathogen detection with special emphasis on bio-molecular electronics techniques such as biosensors, microarrays, electronic nose, and nano-materials based methods.

Volume-exclusion effects in tethered-particle experiments: bead size matters

We give a theoretical analysis of bead motion in tethered-particle experiments, a single-molecule technique that has been used to explore the dynamics of a variety of macromolecules of biological interest. Our analysis reveals that the proximity of the tethered bead to a nearby surface gives rise to a volume-exclusion effect, resulting in an entropic stretching-force on the molecule that changes its statistical properties. In addition, volume exclusion brings about intriguing scaling relations between key observables (statistical moments of the bead) and parameters such as bead size and contour length of the molecule. We present analytic and numerical results for these effects in both flexible and semiflexible tethers. Finally, our results give a precise, experimentally testable prediction for the probability distribution of the bead center measured from the polymer attachment point.

Analytical Assays Based on Detecting Conformational Changes of Single Molecules

One common strategy for the detection of biomolecules is labeling either the target itself or an antibody that binds to it. Herein, a different approach, based on detecting the conformational change of a probe molecule induced by binding of the target is discussed. That is, what is being detected is not the presence of the target or the probe, but the conformational change of the probe. Recently, a single-molecule sensor has been developed that exploits this mechanism to detect hybridization of a single DNA oligomer to a DNA probe, as well as specific binding of a single protein to a DNA probe. Biomolecular recognition often involves large conformational changes of the molecules involved, and therefore this strategy may be applicable to other assays.

Mg2+-induced compaction of single RNA molecules monitored by tethered particle microscopy

We have applied tethered particle microscopy (TPM) as a single molecule analysis tool to studies of the conformational dynamics of poly-uridine(U) messenger (m)RNA and 16S ribosomal (r)RNA molecules. Using stroboscopic total internal reflection illumination and rigorous selection criteria to distinguish from nonspecific tethering, we have tracked the nanometer-scale Brownian motion of RNA-tethered fluorescent microspheres in all three dimensions at pH 7.5, 22 degrees C, in 10 mM or 100 mM NaCl in the absence or presence of 10 mM MgCl(2). The addition of Mg(2+) to low-ionic strength buffer results in significant compaction and stiffening of poly(U) mRNA, but not of 16S rRNA. Furthermore, the motion of poly(U)-tethered microspheres is more heterogeneous than that of 16S rRNA-tethered microspheres. Analysis of in-plane bead motion suggests that poly(U) RNA, but less so 16S rRNA, can be modeled both in the presence and absence of Mg(2+) by a statistical Gaussian polymer model. We attribute these differences to the Mg(2+)-induced compaction of the relatively weakly structured and structurally disperse poly(U) mRNA, in contrast to Mg(2+)-induced reinforcement of existing secondary and tertiary structure contacts in the highly structured 16S rRNA. Both effects are nonspecific, however, as they are dampened in the presence of higher concentrations of monovalent cations.

Homogenous rapid detection of nucleic acids using two-color quantum dots

We report a homogenous method for rapid and sensitive detection of nucleic acids using two-color quantum dots (QDs) based on single-molecule coincidence detection. The streptavidin-coated quantum dots functioned as both a nano-scaffold and as a fluorescence pair for coincidence detection. Two biotinylated oligonucleotide probes were used to recognize and detect specific complementary target DNA through a sandwich hybridization reaction. The DNA hybrids were first caught and assembled on the surface of 605 nm-emitting QDs (605QDs) through specific streptavidin-biotin binding. The 525 nm-emitting QDs (525QDs) were then added to bind the other end of DNA hybrids. The coincidence signals were observed only when the presence of target DNA led to the formation of 605QD/DNA hybrid/525QD complexes. In comparison with a conventional QD-based assay, this assay provided high detection efficiency and short analysis time due to its high hybridization efficiency resulting from the high diffusion coefficient and no limitation of temperature treatment. This QD-based single-molecule coincidence detection offers a simple, rapid and ultra sensitive method for genomic DNA analysis in a homogenous format.

Three-dimensional characterization of tethered microspheres by total internal reflection fluorescence microscopy

Tethered particle microscopy is a powerful tool to study the dynamics of DNA molecules and DNA-protein complexes in single-molecule experiments. We demonstrate that stroboscopic total internal reflection microscopy can be used to characterize the three-dimensional spatiotemporal motion of DNA-tethered particles. By calculating characteristic measures such as symmetry and time constants of the motion, well-formed tethers can be distinguished from defective ones for which the motion is dominated by aberrant surface effects. This improves the reliability of measurements on tether dynamics. For instance, in observations of protein-mediated DNA looping, loop formation is distinguished from adsorption and other nonspecific events.

A molecular ruler based on plasmon coupling of single gold and silver nanoparticles

Forster Resonance Energy Transfer has served as a molecular ruler that reports conformational changes and intramolecular distances of single biomolecules. However, such rulers suffer from low and fluctuating signal intensities, limited observation time due to photobleaching, and an upper distance limit of approximately 10 nm. Noble metal nanoparticles have plasmon resonances in the visible range and do not blink or bleach. They have been employed as alternative probes to overcome the limitations of organic fluorophores, and the coupling of plasmons in nearby particles has been exploited to detect particle aggregation by a distinct color change in bulk experiments. Here we demonstrate that plasmon coupling can be used to monitor distances between single pairs of gold and silver nanoparticles. We followed the directed assembly of gold and silver nanoparticle dimers in real time and studied the kinetics of single DNA hybridization events. These "plasmon rulers" allowed us to continuously monitor separations of up to 70 nm for >3,000 s.

Detection limits for nanoscale biosensors

We examine through analytical calculations and finite element simulations how the detection efficiency of disk and wire-like biosensors in unmixed fluids varies with size from the micrometer to nanometer scales. Specifically, we determine the total flux of DNA-like analyte molecules on a sensor as a function of time and flow rate for a sensor incorporated into a microfluidic system. In all cases, sensor size and shape profoundly affect the total analyte flux. The calculations reveal that reported femtomolar detection limits for biomolecular assays are very likely an analyte transport limitation, not a signal transduction limitation. We conclude that without directed transport of biomolecules, individual nanoscale sensors will be limited to picomolar-order sensitivity for practical time scales.

Mechanics of binding of a single integration-host-factor protein to DNA

We report on a single-molecule experiment where we directly observe local bending of a 76 base pair DNA oligomer caused by specific binding of a single integration-host-factor (IHF) protein. The conformational change of the DNA is detected by optically monitoring the displacement of a micron size bead tethered to a surface by the DNA. Since in the bound state the DNA loops around the IHF, a mechanical tension on the DNA tends to eject the protein. We measure how the rate for the protein to fall off the DNA depends on the mechanical tension in the DNA, gaining insight into the energy landscape for this molecular bond. Our method further demonstrates a new paradigm of molecular detection, where ligand binding is detected through the conformational change induced in the probe molecule. Here this allows the detection of single, unlabeled proteins.

Artificial allosteric control of maltose binding protein

We demonstrate the allosteric control of a protein based on mechanical tension. When substrate binding is accompanied by a significant change of conformation of the protein, a mechanical tension favoring one or the other conformation will alter the binding affinity for the substrate. We have constructed a chimera where the two lobes of the maltose-binding protein are covalently coupled to the ends of a DNA oligomer. The mechanical tension on the protein is controlled externally by exploiting the difference in stiffness between single stranded and double stranded DNA. We report that the binding affinity of the protein for its substrates is significantly altered by the tension.

Simultaneous atomic force microscope and fluorescence measurements of protein unfolding using a calibrated evanescent wave

Fluorescence techniques for monitoring single-molecule dynamics in the vertical dimension currently do not exist. Here we use an atomic force microscope to calibrate the distance-dependent intensity decay of an evanescent wave. The measured evanescent wave transfer function was then used to convert the vertical motions of a fluorescent particle into displacement (SD = < 1 nm). We demonstrate the use of the calibrated evanescent wave to resolve the 20.1 +/- 0.5-nm step increases in the length of the small protein ubiquitin during forced unfolding. The experiments that we report here make an important contribution to fluorescence microscopy by demonstrating the unambiguous optical tracking of a single molecule with a resolution comparable to that of an atomic force microscope.

Picometer-scale dynamical observations of individual membrane proteins: the case of bacteriorhodopsin

In vivo measurements of dynamical conformational changes in single biomolecules under functional conditions have had a tremendous impact on molecular and cell biology. However, even single-molecule fluorescent resonance energy transfer cannot easily monitor the intramolecular dynamics in cell systems due to shortcomings in monitoring precision. Here, we report dynamical observations of irreversible intramolecular conformational changes in a single-membrane protein [bacteriorhodopsin (BR)] using diffracted x-ray tracking. The light-driven proton pump BR is the best-characterized membrane protein. The position of BR's 35th amino acid, which is located farthest from retinal, exhibits a momentary positional jump of 0.73+/-0.48 A due to the expression of its function. Following that, we observed Brownian motion without the diffracted spots returning to their initial positions. The average width of this jump is about 14 times larger than that of thermal Brownian motion and agrees with estimated movements from known x-ray crystallography data. This result is an important step toward realizing in vivo observations of single-molecular conformational changes in membrane proteins.

Homogeneous detection of unamplified genomic DNA sequences based on colorimetric scatter of gold nanoparticle probes

Nucleic acid diagnostics is dominated by fluorescence-based assays that use complex and expensive enzyme-based target or signal-amplification procedures. Many clinical diagnostic applications will require simpler, inexpensive assays that can be done in a screening mode. We have developed a 'spot-and-read' colorimetric detection method for identifying nucleic acid sequences based on the distance-dependent optical properties of gold nanoparticles. In this assay, nucleic acid targets are recognized by DNA-modified gold probes, which undergo a color change that is visually detectable when the solutions are spotted onto an illuminated glass waveguide. This scatter-based method enables detection of zeptomole quantities of nucleic acid targets without target or signal amplification when coupled to an improved hybridization method that facilitates probe-target binding in a homogeneous format. In comparison to a previously reported absorbance-based method, this method increases detection sensitivity by over four orders of magnitude. We have applied this method to the rapid detection of mecA in methicillin-resistant Staphylococcus aureus genomic DNA samples.