Single Analyte Molecule Research Articles

Single-Molecule Surface-Enhanced Raman Scattering Measurements Enabled by Plasmonic DNA Origami Nanoantennas.

Surface-enhanced Raman scattering (SERS) has the capability to detect single molecules for which high field enhancement is required. Single-molecule (SM) SERS is able to provide molecule-specific spectroscopic information about individual molecules and therefore yields more detailed chemical information than other SM detection techniques. At the same time, there is the potential to unravel information from SM measurements that remain hidden in Raman measurements of bulk material. This protocol outlines the SM SERS measurements using a DNA origami nanoantenna (DONA) in combination with atomic force microscopy (AFM) and Raman spectroscopy. A DNA origami fork structure and two gold nanoparticles are combined to form the DONAs, with a 1.2-2.0 nm gap between them. This allows an up to 1011-fold SERS signal enhancement, enabling measurements of single molecules. The protocol further demonstrates the placement of a single analyte molecule in a SERS hot spot, the process of AFM imaging, and the subsequent overlaying of Raman imaging to measure an analyte in a single DONA.

A cryogenic ion trap for single molecule vibrational spectroscopy.

We report on an ion trapping system for performing a novel form of cryogenic messenger spectroscopy with single molecule sensitivity. The system features a cryogenic radio-frequency ion trap loaded with single analyte molecules via a quadrupole mass filter. We demonstrate the ability to controllably attach inert gas particles to buffer gas cooled, trapped molecular ions. Sympathetic cooling by co-trapped, laser cooled 88Sr+ further reduces the translational temperature of trapped molecules to the millikelvin regime. We verify the presence of cryogenic "tags" via non-destructive optical mass spectrometry and selectively remove these adducts by resonantly driving vibrational transitions in the tagged molecular ions. This enables us to derive the vibrational spectrum of a single analyte molecule from the frequency dependence of the tag detachment rate. We have demonstrated these capabilities by measuring transitions in the C-H stretching region for single cationic fragments of both indole (C8H7N) and 1,3-benzodioxole (C6H4O2CH2). These capabilities are not reliant on a specific molecular level structure and thus constitute a general, non-destructive method for vibrational spectroscopy of individual molecular ions.

What Digital Immunoassays Can Learn from Ambient Analyte Theory: A Perspective.

Immunoassays are important tools for clinical diagnosis as well as environmental and food analysis because they enable highly sensitive and quantitative measurements of analyte concentrations. In the 1980s, Roger Ekins suggested to improve the sensitivity of immunoassays by employing microspot assays, which are carried out under ambient analyte conditions and do not change the bulk analyte concentration of a sample during a measurement. More recently, the measurement of single analyte molecules has additionally attracted wide research interest. Although the ability to detect a single analyte molecule is not synonymous with the highest analytical sensitivity, single-molecule detection makes new routes accessible to avoiding background noise. This perspective follows the development of solid-phase immunoassays from the design of label techniques to single-molecule (digital) assays against the backdrop of Ekins's fundamental work on immunoassay theory. The essential aspects of both ambient analyte and digital assay approaches are presented as a guideline to finding a balance between the speed, sensitivity, and precision of immunoassays.

(Invited) Ultrasensitive Detection of Nucleic Acid Molecules with Interferometric Plasmonic Microscopy

The detection of nucleic acid molecules plays important role in clinical diagnosis of diseases and fundamental biomedical research. The widely used polymerized chain reaction technique requires hours of amplification process, and is prone to aerosol pollution. Here, we presented the amplification-free digital sensing of nucleic acid molecules with the interferometric plasmonic microscopy (iPM). A sandwich assay was performed with the primary DNA probes coated on the plasmonic sensing surface and the secondary DNA probes tethered Au nanoparticles. Hybridization between DNA probes and single analyte molecules was monitored by the imaging of single Au nanoparticle with iPM system. By digitally counting the events of hybridization, the detection limit at the fM level could be achieved. Without amplification, this assay could be done within one hour. Furthermore, by analyzing the real-time binding behaviro during single hybridization event, non-specific bindings could be excluded from the specific ones, resulting in the improved specificity. This technique could be further improving by a careful design of the kinetic binding properties between DNA probes and analyte molecules.

A Versatile DNA Origami-Based Plasmonic Nanoantenna for Label-Free Single-Molecule Surface-Enhanced Raman Spectroscopy.

DNA origami technology allows for the precise nanoscale assembly of chemical entities that give rise to sophisticated functional materials. We have created a versatile DNA origami nanofork antenna (DONA) by assembling Au or Ag nanoparticle dimers with different gap sizes down to 1.17 nm, enabling signal enhancements in surface-enhanced Raman scattering (SERS) of up to 1011. This allows for single-molecule SERS measurements, which can even be performed with larger gap sizes to accommodate differently sized molecules, at various excitation wavelengths. A general scheme is presented to place single analyte molecules into the SERS hot spots using the DNA origami structure exploiting covalent and noncovalent coupling schemes. By using Au and Ag dimers, single-molecule SERS measurements of three dyes and cytochrome c and horseradish peroxidase proteins are demonstrated even under nonresonant excitation conditions, thus providing long photostability during time-series measurement and enabling optical monitoring of single molecules.

Effects of Electrospray Droplet Size on Analyte Aggregation: Evidence for Serine Octamer in Solution.

Spraying solutions of serine under a wide variety of conditions results in unusually abundant gaseous octamer clusters that exhibit significant homochiral specificity, but the extent to which these clusters exist in solution or are formed by clustering during droplet evaporation has been debated. Electrospray ionization emitters with tip sizes between 210 nm and 9.2 μm were used to constrain the number of serine molecules that droplets initially contain. Protonated octamer was observed for all tip sizes with 10 mM serine solution, but the abundance decreases from 10% of the serine population at the largest tip size to ∼5.6% for the two smallest tip sizes. At 100 μM, the population abundance of the protonated serine octamer decreases from 1% to 0.6% from the largest to the smallest tip size, respectively. At 100 μM, fewer than 10% of the initial droplets should contain even a single analyte molecule with 210 nm emitter tips. These results indicate that the majority of protonated octamer observed in mass spectra under previous conditions is formed by clustering inside the electrospray droplet, but ≤5.6% and ∼0.6% of serine exists as an octamer complex in 10 mM and 100 μM solutions, respectively. These results show that aggregation occurs in large droplets, but this aggregation can be eliminated using emitters with sufficiently small tips. Use of these emitters with small tips is advantageous for clearly distinguishing between species that exist in solution and species formed by clustering inside droplets as solvent evaporation occurs.

Frontal Affinity Chromatography: A Highly Suitable Retardation Phenomenon-Based Research Tool for Analyzing Weak Interactions Between Biomolecules.

The greatest advantage of frontal affinity chromatography (FAC) is that the analyte concentration does not need to be taken into consideration, and this renders FAC an extremely favorable analytical tool for weak interactions. In this short review, we propose a straightforward explanation of the underlying mechanism. When FAC is performed using analyte solutions at relatively high concentrations, concentration-dependent retardation is observed due to competition among analyte molecules, and the elution volume changes depending on the degree of saturation of the immobilized ligand.However, when the analyte concentration is very low, no competition occurs among the analytes, and the elution volume reaches a constant value, which reflects the proportion of bound state to free state of a single analyte molecule. Therefore, the binding strength can be determined using a minimum analyte concentration.

Characterization of functionalized glass and indium tin oxide surfaces as substrates for super-resolution microscopy

Modern high-throughput biosensors with sensitivity down to a single analyte molecule may be possible with single-molecule localization microscopy (SMLM). Functionalized surfaces can be fabricated with self-assembly monolayer chemistry on indium tin oxide (ITO) substrates but not glass. However, characterizations of SMLM-compatible fluorophores are primarily performed on glass substrates. Here we collect single-molecule kinetics data of isolated Alexa Fluor 647 molecules on bare and functionalized glass and ITO surfaces. Extracting the photophysical dynamics of the fluorophores allows direct comparison of behavior of this dye on these substrates and fitting data to a model that accounts for multiple reversible dark states. All surfaces had sensitivity sufficient to image single fluorophore molecules. Photophysical kinetics observed are similar between the two substrates. The photon yield from individual fluorophores was greatest on bare glass, but functionalized ITO surfaces showed superior yield to functionalized glass surfaces and nearly matched the yield of bare glass. Together these results indicate functionalized ITO as a promising substrate for modern single-molecule biosensors.

Smart SERS Hot Spots: Single Molecules Can Be Positioned in a Plasmonic Nanojunction Using Host-Guest Chemistry.

Single-molecule surface-enhanced Raman spectroscopy (SERS) offers new opportunities for exploring the complex chemical and biological processes that cannot be easily probed using ensemble techniques. However, the ability to place the single molecule of interest reliably within a hot spot, to enable its analysis at the single-molecule level, remains challenging. Here we describe a novel strategy for locating and securing a single target analyte in a SERS hot spot at a plasmonic nanojunction. The "smart" hot spot was generated by employing a thiol-functionalized cucurbit[6]uril (CB[6]) as a molecular spacer linking a silver nanoparticle to a metal substrate. This approach also permits one to study molecules chemically reluctant to enter the hot spot, by conjugating them to a moiety, such as spermine, that has a high affinity for CB[6]. The hot spot can accommodate at most a few, and often only a single, analyte molecule. Bianalyte experiments revealed that one can reproducibly treat the SERS substrate such that 96% of the hot spots contain a single analyte molecule. Furthermore, by utilizing a series of molecules each consisting of spermine bound to perylene bisimide, a bright SERS molecule, with polymethylene linkers of varying lengths, the SERS intensity as a function of distance from the center of the hot spot could be measured. The SERS enhancement was found to decrease as 1 over the square of the distance from the center of the hot spot, and the single-molecule SERS cross sections were found to increase with AgNP diameter.

A stochastic view on column efficiency

A stochastic model of transcolumn eddy dispersion along packed beds was derived. It was based on the calculation of the mean travel time of a single analyte molecule from one radial position to another. The exchange mechanism between two radial positions was governed by the transverse dispersion of the analyte across the column. The radial velocity distribution was obtained by flow simulations in a focused-ion-beam scanning electron microscopy (FIB-SEM) based 3D reconstruction from a 2.1 mm × 50 mm column packed with 2 μm BEH-C18 particles. Accordingly, the packed bed was divided into three coaxial and uniform zones: (1) a 1.4 particle diameter wide, ordered, and loose packing at the column wall (velocity uw), (2) an intermediate 130 μm wide, random, and dense packing (velocity ui), and (3) the bulk packing in the center of the column (velocity uc).First, the validity of this proposed stochastic model was tested by adjusting the predicted to the observed reduced van Deemter plots of a 2.1 mm × 50 mm column packed with 2 μm BEH-C18 fully porous particles (FPPs). An excellent agreement was found for ui = 0.93uc, a result fully consistent with the FIB-SEM observation (ui = 0.95uc). Next, the model was used to measure ui = 0.94uc for 2.1 mm × 100 mm column packed with 1.6 μm Cortecs-C18 superficially porous particles (SPPs). The relative velocity bias across columns packed with SPPs is then barely smaller than that observed in columns packed with FPPs (+6% versus + 7%). uw=1.8ui is measured for a 75 μm × 1 m capillary column packed with 2 μm BEH-C18 particles. Despite this large wall-to-center velocity bias (+80%), the presence of the thin and ordered wall packing layer has no negative impact on the kinetic performance of capillary columns. Finally, the stochastic model of long-range eddy dispersion explains why analytical (2.1–4.6 mm i.d.) and capillary (<400 μm i.d.) columns can all be packed efficiently (1 <hmin< 2) with particles of size larger than 2 μm. In contrast, the model predicts that 0.4–1.2 mm i.d. columns and 2.1 mm i.d. columns cannot be packed well (hmin>3) with sub-2 μm particles and with 1 μm particles, respectively.

Supercharging Proteins: How Many Charges Can a Protein Carry?

Very highly charged proteins, so-called "supercharged" ions, can lose (excess) protons to background gases like N2 . It is remarkable that such extremely acidic species can be generated in electrospray ionization, in the presence of not just N2 but also much higher-basicity solvents. What mechanism(s) can explain such high charging, and what is the ultimate limit?

Implementation and evaluation of an analytical method for a novel derivatizing agent to measure 4,4'-methylene diphenyl diisocyanate atmospheres

ABSTRACTAccurate measurement of 4,4'-methylene diphenyl diisocyanate (MDI) atmospheres is a challenge since the molecule is both chemically reactive and likely to be present in aerosol form when heated and sprayed because of its low vapor pressure. Meeting this challenge requires optimizing both the sampling device used and the derivatization agent employed to stabilize the isocyanate functional group. This study describes the use of a novel derivatization reagent for isocyanate sampling to address the challenge of MDI aerosol exposure sampling. Like most conventional derivatizing agents for isocyanates, 1,8-diaminonapthalene (DAN) reacts with isocyanate functional groups to form a urea. However, unlike other isocyanate derivatizing agents, the sample workup procedure with DAN includes a second step which yields a single analyte molecule, perimidone, for each isocyanate group. This feature gives DAN the unique ability to assess exposure to “total reactive isocyanate group” (TRIG). The analytical method implemented to quantitate the perimidone uses liquid chromatography coupled with tandem mass spectrometry. Positive mode ionization led to LOD and LOQ of 10 ng/mL and 34 ng/mL, respectively. The dynamic range was from 50–2000 ng/mL (with R2 ≥ 0.990), which corresponds to TRIG concentrations in air from 0.07–3.04 µg/m3, assuming 60 min of sampling at 10 L/min (based on use of the CIP-10M sampler). The intra-day and inter-day analytical precisions were <4% for all of the concentration levels tested, and the accuracy was within an appropriate range of 98 ± 2%. Minimal matrix effect was observed, and a total recovery of 109% was obtained. The approach seems to be promising for TRIG measurements and further work is planned to establish DAN method behavior in samplers used for workplace monitoring.

Direct optical sensing of single unlabelled proteins and super-resolution imaging of their binding sites.

Detection of single analyte molecules without the use of any label would improve the sensitivity of current biosensors by orders of magnitude to the ultimate graininess of biological matter. Over two decades, scientists have succeeded in pushing the limits of optical detection to single molecules using fluorescence. However, restrictions in photophysics and labelling protocols make this technique less attractive for biosensing. Recently, mechanisms based on vibrational spectroscopy, photothermal detection, plasmonics and microcavities have been explored for fluorescence-free detection of single biomolecules. Here, we show that interferometric detection of scattering (iSCAT) can achieve this goal in a direct and label-free fashion. In particular, we demonstrate detection of cancer marker proteins in buffer solution and in the presence of other abundant proteins. Furthermore, we present super-resolution imaging of protein binding with nanometer localization precision. The ease of iSCAT instrumentation promises a breakthrough for label-free studies of interactions involving proteins and other small biomolecules.

Sensing through signal amplification

The naked eye detection of single molecules in a complex mixture is the ultimate detection limit. Since a single molecule is unable to generate a strong enough signal, sensing methodologies able to reach that limit by necessity need to rely on signal amplification. This tutorial review describes various molecular approaches towards signal amplification in which a single analyte molecule affects the properties of a multitude of reporter molecules. Sensing by advanced instrumentation or changes in the physical properties of materials are excluded. The review is divided into four parts (catalysts, macromolecules, metal surfaces and supramolecular aggregates) depending on the species responsible for generating reporter molecules. Although on first sight apparently very diverse in nature, the majority of approaches rely on two key concepts: catalysis and multivalency. The ability of a catalyst to convert a multitude of substrate molecules into product (defined by the turn over number) makes a catalyst an intrinsic signal amplifier in case the chemical conversion of the substrate is accompanied by a measurable change in physical properties. For sensing purposes, catalytic activity must depend on the interaction between the analyte and the catalyst. Sensing using multivalent structures such as polymers and functionalized nanoparticles relies on the ability of a single analyte molecule to affect the properties of a multitude of reporter molecules collected in the multivalent structure. Chemical sensing systems will be discussed with detection limits that indeed go down to a few molecules and can rival the best biological assays. It will be shown that the most sensitive methods rely on a cascade of amplification mechanisms.

Dendritic Chain Reaction

Signal amplification techniques are broadly used to improve the detection sensitivity of various analytes for diagnostic purposes. We have developed a novel, non-PCR-based modular technique for exponential amplification of diagnostic signals that is conveniently performed in an aqueous environment. The technique is based on a distinctive dendritic chain reaction (DCR); the diagnostic signal is generated upon disassembly of a self-immolative dendrimer that releases chromogenic molecules. Under ideal conditions, a single analyte molecule initiates a DCR that generates a strong diagnostic signal. When coupled with a protease diagnostic probe, the DCR technique detected the activity of penicillin-G-amidase with high sensitivity. This is the first example of exponential signal amplification performed under aqueous conditions that is not based on PCR.

Conversion of multiple analyte cation types to a single analyte anion type via ion/ion charge inversion

Charge inversion ion/ion reactions can convert several cation types associated with a single analyte molecule to a single anion type for subsequent mass analysis. Specifically, analyte ions present with one of a variety of cationizing agents, such as an excess proton, excess sodium ion, or excess potassium ion, can all be converted to the deprotonated molecule, provided that a stable anion can be generated for the analyte. Multiply deprotonated species that are capable of exchanging a proton for a metal ion serve as the reagent anions for the reaction. This process is demonstrated here for warfarin and for a glutathione conjugate. Examples for several other glutathione conjugates are provided as supplementary material to demonstrate the generality of the reaction. In the case of glutathione conjugates, multiple metal ions can be associated with the singly-charged analyte due to the presence of two carboxylate groups. The charge inversion reaction involves the removal of the excess cationizing agent, as well as any metal ions associated with anionic groups to yield a singly deprotonated analyte molecule. The ability to convert multiple cation types to a single anion type is analytically desirable in cases in which the analyte signal is distributed among several cation types, as is common in the electrospray ionization of solutions with relatively high salt contents. For analyte species that undergo efficient charge inversion, such as glutathione conjugates, there is the additional potential advantage for significantly improved signal-to-noise ratios when species that give rise to 'chemical noise' in the positive ion spectrum do not undergo efficient charge inversion.

Chapter Thirteen Identifying Small Pulsatile Signals within Noisy Data: A Fluorescence Application

One of the most challenging scientific data analysis quandaries is the identification of small intermittent irregularly spaced pulsatile signals in the presence of large amounts of heteroscedastic experimental measurement uncertainties. We present an application of the use of AutoDecon to a typical fluorescence and/or spectroscopic data sampling paradigm, which is to detect a single fluorophore in the presence of high background emission. Our calculations demonstrate that single events can be reliably detected by AutoDecon with a signal-to-noise ratio of 3/20. AutoDecon was originally developed for the analysis of pulsatile hormone-concentration time-series data measured in human serum. However, AutoDecon has applications within many other scientific fields, such as fluorescence measurements where the goal is to count single analyte molecules in clinical samples.

Transport across artificial membranes–an analytical perspective

Biosensors that make use of transport processes across lipid membranes are very rare even though a stimulus, the binding of a single analyte molecule, can enhance the sensor response manifold if the analyte leads to the transport of more than one ion or molecule across the membrane. Prerequisite for a proper function of such membrane based biosensors is the formation of lipid bilayers attached to a support that allow for the insertion of membrane peptides and proteins in a functional manner. In this review, the current state of the art technologies to obtain lipid membranes on various supports are described. Solid supported membranes on transparent and electrically conducting surfaces, lipid bilayers on micromachined apertures and on porous materials are discussed. The focus lies on the applicability of such membranes for the investigation of transport phenomena across lipid bilayers facilitated by membrane embedded peptides, channel proteins and transporters. Carriers and channel forming peptides, which are easy to handle and rather robust, are used frequently to build up membrane based biosensors. However, channel forming proteins and transporters are more difficult to insert functionally and thus, there are yet only few examples that demonstrate the applicability of such systems as biosensor devices.

The BARC biosensor applied to the detection of biological warfare agents

The Bead ARray Counter (BARC) is a multi-analyte biosensor that uses DNA hybridization, magnetic microbeads, and giant magnetoresistive (GMR) sensors to detect and identify biological warfare agents. The current prototype is a table-top instrument consisting of a microfabricated chip (solid substrate) with an array of GMR sensors, a chip carrier board with electronics for lock-in detection, a fluidics cell and cartridge, and an electromagnet. DNA probes are patterned onto the solid substrate chip directly above the GMR sensors, and sample analyte containing complementary DNA hybridizes with the probes on the surface. Labeled, micron-sized magnetic beads are then injected that specifically bind to the sample DNA. A magnetic field is applied, removing any beads that are not specifically bound to the surface. The beads remaining on the surface are detected by the GMR sensors, and the intensity and location of the signal indicate the concentration and identity of pathogens present in the sample. The current BARC chip contains a 64-element sensor array, however, with recent advances in magnetoresistive technology, chips with millions of these GMR sensors will soon be commercially available, allowing simultaneous detection of thousands of analytes. Because each GMR sensor is capable of detecting a single magnetic bead, in theory, the BARC biosensor should be able to detect the presence of a single analyte molecule.

Time-resolved detection and identification of single analyte molecules in microcapillaries by time-correlated single-photon counting (TCSPC)

A PC plug-in card for on-line time resolved fluorescence detection of single dye molecules based on a new time-correlated single photon counting (TCSPC) module is described. The module contains all electronic components constant fraction discriminators (CFDs), time-to-amplitude converter (TAC), analog-to-digital converter (ADC), multichannel analyzer (MCA timers) on board required for TCSPC. A fast TAC design in combination with a fast flash ADC and an error-correcting ADC/MCA principle results in a maximum count rate of 8 MHz (dead time 125 ns). A dual memory architecture allows for unlimited recording of decay curves with collection times down to 150 μs without time gaps between subsequent recordings. Applying a short-pulse diode laser emitting at 640 nm with a repetition rate of 60 MHz in combination with a confocal microscope, we studied bursts of fluorescence photons from individual dye labeled mononucleotide molecules (Cy5-dCTP) in a cone shaped microcapillary with an inner diameter of 0.5 μm at the end of the tip. The flow of the conjugates was controlled by electrokinetic forces. The presented technique permits the counting and identification of all labeled analyte molecules present in a given sample due to their characteristic velocities, burst sizes, and fluorescence decay times.