Effect of surface conjugation chemistry on the sensitivity of microcantilever sensors

Microcantilever sensors are an offshoot of atomic force microscopy and are useful tools for effectively detecting a target biomolecule. The recognition of the target molecule on the biosensor is based on the physical bending of the microcantilever, which is driven by a specific molecular interaction between the target molecule and the sensor surface. In this study, to enhance the sensitivity of the microcantilever sensor, the sensor surface was modified through a surface conjugation method using self-assembled monolayers (SAMs) and heterobifunctional cross-linkers. After the surface modification of the microcantilever sensor, the sensitivity for L-cysteine was recorded. The detection of L-cysteine was influenced by the active site and the molecular size of the cross-linked compound attached onto the surface of the microcantilever.     

Molecular recognition imaging using tuning fork-based transverse dynamic force microscopy

We demonstrate simultaneous transverse dynamic force microscopy and molecular recognition imaging using tuning forks as piezoelectric sensors. Tapered aluminum-coated glass fibers were chemically functionalized with biotin and anti-lysozyme molecules and attached to one of the prongs of a 32 kHz tuning fork. The lateral oscillation amplitude of the tuning fork was used as feedback signal for topographical imaging of avidin aggregates and lysozyme molecules on mica substrate. The phase difference between the excitation and detection signals of the tuning fork provided molecular recognition between avidin/biotin or lysozyme/anti-lysozyme. Aggregates of avidin and lysozyme molecules appeared as features with heights of 1–4 nm in the topographic images, consistent with single molecule atomic force microscopy imaging. Recognition events between avidin/biotin or lysozyme/anti-lysozyme were detected in the phase image at high signal-to-noise ratio with phase shifts of 1–2°. Because tapered glass fibers and shear-force microscopy based on tuning forks are commonly used for near-field scanning optical microscopy (NSOM), these results open the door to the exciting possibility of combining optical, topographic and biochemical recognition at the nanometer scale in a single measurement and in liquid conditions.     

High-resolution scanning tunneling microscopy for molecules

Scanning tunneling microscopy (STM) can detect individual molecular configuration with its high spatial resolution ability, but some intrinsical and extrinsic factors result in the complexities of STM imaging of single molecules. By combining STM experimental work and theoretical simulation with the local density approximation based on Bardeen perturbation method, we have explored the atomic-scale configuration of the following molecular systems: C(60) molecules adsorbed on Si(111)-(7x7); alkanethiol self-assembly monolayers on Au(111); C(60) molecule imaged by STM tip adsorbed with another C(60) molecule; O(2) molecule adsorbed on Ag(110) and CO molecule adsorbed on Cu(111) imaged by CO chemically modified STM tip. Some related problems including: molecule-substrate interactions, STM imaging mechanism, chemically modified STM tip, etc., are discussed.     

Dependence of tunneling current through a single molecule of phenylene oligomers on the molecular length

The electrical properties of single phenylene oligomers were studied in terms of the dependence of the tunneling current on the length of the oligomers using self-assembling techniques and scanning tunneling microscopy (STM). It is important to isolate single molecules in an insulating matrix for the measurement of the conductivity of the single molecule. We demonstrate here a novel self-assembled monolayer (SAM) matrix appropriate for isolation of the single molecules. A bicyclo[2.2.2]octane derivative was used for a SAM matrix, in which the single molecules were inserted at molecular lattice defects. The isolated single molecules of phenylene oligomers inserted in the SAM matrix were observed as protrusions in STM topography using a constant current mode. We measured the topographic heights of the molecular protrusions using STM and estimated the decay constant, beta, of the tunneling current through the single phenylene oligomers using a bilayer tunnel junction model.     

Hybridisation of short DNA molecules investigated with in situ atomic force microscopy

By introducing the complementary DNA (cDNA) strand to a molecular layer of short single stranded DNA (ssDNA), immobilised on a gold surface, we have investigated hybridisation between the two DNA strands through the technique of in situ atomic force microscopy (AFM). Before introduction of cDNA, the ssDNA molecular layer was modulated with the spacer molecule mercaptohexanol (MCH), which makes the ssDNA molecules more accessible for hybridisation.With in situ AFM, we have monitored the formation of a smooth, mixed molecular layer containing ssDNA and MCH. Furthermore, the hybridisation between the two DNA strands has been studied. Introduction of the cDNA strand resulted in an increase in smoothness and thickness of the molecular layer. Both the increase in order and thickness of the molecular layer can be expected if hybridisation occurs, since double stranded DNA molecules have a more rigid and elongated structure than ssDNA molecules.     

Single molecule mapping of the optical field distribution of probes for near-field microscopy

The most difficult task in near-field scanning optical microscopy (NSOM) is to make a high quality subwavelength aperture probe. Recently, we have developed high definition NSOM probes by focused ion beam (FIB) milling. These probes have a higher brightness, better polarization characteristics, better aperture definition and a flatter end face than conventional NSOM probes. We have determined the quality of these probes in four independent ways: by FIB imaging and by shear-force microscopy (both providing geometrical information), by far-field optical measurements (yielding throughput and polarization characteristics), and ultimately by single molecule imaging in the near-field. In this paper, we report on a new method using shear-force microscopy to study the size of the aperture and the end face of the probe (with a roughness smaller than 1.5 nm). More importantly, we demonstrate the use of single molecules to measure the full three-dimensional optical near-field distribution of the probe with molecular spatial resolution. The single molecule images exhibit various intensity patterns, varying from circular and elliptical to double arc and ring structures, which depend on the orientation of the molecules with respect to the probe. The optical resolution in the measurements is not determined by the size of the aperture, but by the high optical field gradients at the rims of the aperture. With a 70 nm aperture probe, we obtain fluorescence field patterns with 45 nm FWHM. Clearly, this unprecedented near-field optical resolution constitutes an order of magnitude improvement over far-field methods like confocal microscopy.     

核酸适配体在液相色谱和毛细管电泳中的应用

指数富集配体的系统进化(SELEX)技术是一种新的组合化学技术,应用人工合成的随机寡核苷酸文库,通过筛选、分离、富集获得能与氨基酸、蛋白、药物、有机小分子、无机离子等靶分子特异性结合的寡核苷酸适配子,对于靶分子具有高亲和力。本文从核酸适配体分子识别特性出发,综述了核酸适配体在液相色谱和毛细管电泳中应用的研究进展。     

Single molecule mapping of the optical field distribution of probes for near-field microscopy

The most difficult task in near-field scanning optical microscopy (NSOM) is to make a high quality subwavelength aperture probe. Recently, we have developed high definition NSOM probes by focused ion beam (FIB) milling. These probes have a higher brightness, better polarization characteristics, better aperture definition and a flatter end face than conventional NSOM probes. We have determined the quality of these probes in four independent ways: by FIB imaging and by shear-force microscopy (both providing geometrical information), by far-field optical measurements (yielding throughput and polarization characteristics), and ultimately by single molecule imaging in the near-field. In this paper, we report on a new method using shear-force microscopy to study the size of the aperture and the end face of the probe (with a roughness smaller than 1.5 nm). More importantly, we demonstrate the use of single molecules to measure the full three-dimensional optical near-field distribution of the probe with molecular spatial resolution. The single molecule images exhibit various intensity patterns, varying from circular and elliptical to double arc and ring structures, which depend on the orientation of the molecules with respect to the probe. The optical resolution in the measurements is not determined by the size of the aperture, but by the high optical field gradients at the rims of the aperture. With a 70 nm aperture probe, we obtain fluorescence field patterns with 45 nm FWHM. Clearly, this unprecedented near-field optical resolution constitutes an order of magnitude improvement over far-field methods like confocal microscopy.     

Total internal reflection fluorescence microscopy imaging-guided confocal single-molecule fluorescence spectroscopy

We have developed an integrated spectroscopy system combining total internal reflection fluorescence microscopy imaging with confocal single-molecule fluorescence spectroscopy for two-dimensional interfaces. This spectroscopy approach is capable of both multiple molecules simultaneously sampling and in situ confocal fluorescence dynamics analyses of individual molecules of interest. We have demonstrated the calibration with fluorescent microspheres, and carried out single-molecule spectroscopy measurements. This integrated single-molecule spectroscopy is powerful in studies of single molecule dynamics at interfaces of biological and chemical systems.     

A prism combination for near isotropic fluorescence excitation by total internal reflection

Total internal reflection fluorescence (TIRF) microscopy is finding increasing application for selectively detecting molecules at or near a glass–water surface. As with all fluorescence methods, the efficiency of excitation of a fluorophore is potentially sensitive to the polarization state of the source. In TIRF, s‐polarized excitation produces an evanescent field that is perpendicular to the incident plane (y direction), whereas p‐polarized light generates a more complex pattern but one dominated by a field that is vertical to the surface (z direction). Thus, fluorophores whose absorption dipoles are fixed in the x direction are not favourably aligned for excitation. Here we describe a beam‐splitting prism arrangement that allows excitation by two orthogonal beams, thus giving isotropic excitation in the x–y plane with s‐polarized light. With linearly polarized light at the magic angle, near isotropic excitation in three dimensions should be achieved. This prism design should find application in polarized fluorescence microscopy to investigate the rotational motions of macromolecules or to minimize flickering of fluorescence emission arising from molecular rotations in single molecule studies.     

Recognition and classification of structure by means of stereological methods in neurobiology

The problem of measuring fine structure of individual particles without losing information on largescale characteristics of particle arrangement is discussed. With the help of stereological and pattern recognition methods a possible solution of this important problem is introduced. The domain specimen for which the brain serves as an example is characterized by two main properties. One of them being the position dependent ‘aggregate characteristics’ (distribution of neurons within the specimen), the other position invariant ‘single cell characteristics’ (structural properties of single neurons). It is shown that by simultaneous observation both properties together cannot be detected with sufficient accuracy by conventional methods. This is the decisive problem of ‘correlation microscopy’. The method described in this paper is based on selection of the most informative variables and selection of subdomains (e.g. sections and reference planes). This results in a very general probabilistic concept in modern stereology, offering solutions to complex structure classification problems in biology.     

Comparison of different aminofunctionalization strategies for attachment of single antibodies to AFM cantilevers

Atomic force microscopy (AFM) has developed into a key technique for elucidation of biological systems on the single molecular level. In particular, molecular recognition force microscopy has proven to be a powerful tool for the investigation of biological interactions under near physiological conditions. For this purpose, ligands are tethered to AFM tips and the interaction forces with cognate receptors on the sample surface are measured with pico-Newton accuracy. In the first step of tip functionalization, amino groups are typically introduced on the initially inert AFM tip. Several methods have been developed to reproducibly adjust the desired low density of amino groups on the tip surface, i.e. esterification with ethanolamine, gas-phase silanization with aminopropyl-triethoxysilane (APTES), or treatment with aminophenyl-trimethoxysilane (APhS) in toluene solution. In the present study, the usefulness of these methods for attachments of antibodies to AFM tips was characterized by a standardized test system, in which biotinylated IgG was bound to the tip and a dense monolayer of avidin on mica served as test sample. All three methods of aminofunctionalization were found fully satisfactory for attachment of single antibodies to AFM tips, only in a parallel macroscopic assay on silicon nitride chips a minor difference was found in that APTES appeared to yield a slightly lower surface density of amino groups.     

Structure–property relationships of model chlorstrifluoroethylene oligomer compounds: Thermal stability

Low molecular weight chlorotrifluoroethylene (CTFE) oligomers have been the base fluid for an extensive DoD research and development programme for nonflammable hydraulic fluids, compatible elastomeric seals, components, and systems. To gain a more fundamental understanding of the effect of the specific isomers and other components of commercial CTFE fluids on the important fluid properties, model compounds were synthesised and their physical and chemical properties were determined. Thermal stability, in the presence of typical hardware system metals, is one of the more important properties and is discussed in relation to molecular structure. Two Microscale evaluation techniques were devised and validated. Optimum thermal stability is observed when the chlorines in the molecules are positioned as far apart as possible. In general, it was found that the compounds with larger amounts of chlorine were less stable and the positioning of the chlorine in the molecule had a lesser, but measurable effect.     

Quantitative X-ray imaging of labelled molecules in tissues and cells

Using cisplatin as a model system, we have been able to demonstrate the feasibility of studying the cellular and subcellular distribution of a labelled molecule containing a single atom of platinum per molecule in bone marrow. An X-ray imaging system consisting of a microcomputer, a 4pi system and a software package was interfaced with an electron microscope enabling the computer to control the beam movements as well as receive signals from the STEM and EDS X-ray detectors. X-ray imaging is useful for both tissue and samples in which the population of cells is not homogeneous. Imaging permits elemental distributions to be measured throughout the sample and not in just randomly selected areas as previously done in X-ray microanalysis. Images are created for not only the element labelling the molecule of interest but also other specified elements present.
Three types of maps for imaging labelled molecules are compared and discussed. When the original (collected) data are mapped, the elements of interest are obscured by the continuum. The maps calculated using an internal standard give a concentration distribution on the basis of volume (mmol L⁻¹ of packed cells). The maps calculated using the continuum normalization method according to Hall produces concentration distribution on the basis of mass (mmol kg⁻¹ dry weight). By recalculating using the 'Peak' or 'Hall' method the continuum problem is removed yielding quantitative images of the intracellular distribution of labelled molecules present in low concentrations.     

Single molecule microscopy methods for the study of DNA origami structures

Single molecule microscopy techniques play an important role in the investigation of advanced DNA structures such as those created by the DNA origami method. Three single molecule microscopy techniques are particularly interesting for the investigation of complex self-assembled three-dimensional (3D) DNA nanostructures, namely single molecule fluorescence microscopy, atomic force microscopy (AFM), and cryogenic transmission electron microscopy (cryo-EM). Here we discuss the strengths of these three techniques and demonstrate how their interplay can yield very important and unique new insights into the structure and conformation of advanced biological nanostructures. The applications of the three single molecule microscopy techniques are illustrated by focusing on a self-assembled DNA origami 3D box nanostructure. Its size and structure were studied by AFM and cryo-EM, while the lid opening, which can be controlled by the addition of oligonucleotide keys, was recorded by F?rster/fluorescence resonance energy transfer (FRET) spectroscopy.     

Terminal protein-induced stretching of bacteriophage φ29 DNA

Stretching of DNA molecules helps to resolve detail during the fluorescence microscopy of both single DNA molecules and single DNA–protein complexes. To make stretching occur, intricate procedures of specimen preparation and manipulation have been developed in previous studies. By contrast, the present study demonstrates that conventional procedures of specimen preparation cause DNA stretching to occur, if the specimen is the double‐stranded DNA genome of bacteriophage φ29. Necessary for this stretching is a protein covalently bound at both 5′ termini of φ29 DNA molecules. Some DNA molecules are attached to a cover glass only at the two ends. Others are attached at one end only with the other end free in solution. The extent of stretching varies from ～50% overstretched to ～50% understretched. The understretched DNA molecules are internally mobile to a variable extent. In addition to stretching, some φ29 DNA molecules also undergo assembly to form both linear and branched concatemers observed by single‐molecule fluorescence microscopy. The assembly also requires the terminal protein. The stretched DNA molecules are potentially useful for observing DNA biochemistry at the single molecule level.     

Antenna-based ultrahigh vacuum microwave frequency scanning tunneling microscopy system

The instrumental synthesis of high resolution scanning tunneling microscopy (STM) with the ability to measure differential capacitance with atomic scale resolution is highly desirable for fundamental metrology and for the study of novel physical characteristics. Microwave frequency radiation directed at the tip-sample junction in an STM system allows for such high-resolution differential capacitance information. This ability is particularly critical in ultrahigh vacuum environments, where the additional parameter space afforded by including a capacitance measurement would prove powerful. Here we describe the modifications made to a commercial scanning tunneling microscope to allow for broad microwave frequency alternating current scanning tunneling microscopy (ACSTM) in ultrahigh vacuum conditions using a relatively simple loop antenna and microwave difference frequency detection. The advantages of our system are twofold. First, the use of a removable antenna on a commercial STM prevents interference with other UHV processes while providing a simple method to retrofit any commercial UHV-STM with UHV-ACSTM capability. Second, mounting the microwave antenna on a translator allows for specific tuning of the system to replicate experimental conditions between samples, which is particularly critical in sensitive systems like organic thin films or single molecules where small changes in incident power can affect the results. Our innovation therefore provides a valuable approach to give nearly any commercial STM, be it an ambient or UHV system, the capability to measure atomic-scale microwave studies such as differential capacitance or even single molecule microwave response, and it ensures that experimental ACSTM conditions can be held constant between different samples.     

Atomic force microscopy to characterize the molecular size of prion protein

The conformational transition of α‐helix‐rich cellular prion protein (PrP^C) to an isomer with high β‐sheet content is associated with transmissible spongiform encephalopathies. With the ultimate long‐term goal of using imaging techniques to study PrP aggregation, we report the results of initial experiments to determine whether PrP molecules could be visualized as single molecules, and if the observed size corresponded to the calculated size for PrP. The investigation of single molecules, and not those embedded into larger aggregates, was the key in our experimental approach. Using atomic force microscopy (AFM) as an imaging method, the immobilization of recombinant histidine (His)₁₀‐tagged PrP on mica was performed in the presence of different heavy metal ions. The addition of Cu²⁺ resulted in an enhanced PrP immobilization, whereas Ni²⁺ reduced coverage of the surface by PrP. High‐resolution data from dried PrP preparations provided a first approximation to geometrical parameters of PrP precipitates, which indicated that the volume of a single PrP molecule was 30 nm³. Molecular dynamics simulations performed to complement the structural aspects of the AFM investigation yielded a calculated molecular volume of 33 nm³ for PrP. These experimentally observed and theoretically expected values provide basic knowledge for further studies on the size and composition of larger amyloidal PrP aggregates, PrP isoforms or mutants such as PrP molecules without octarepeats.     

Contrast definition and contour detection for logarithmic images

Logarithmic images, such as images obtained by transmitted light or those produced by the human visual system, differ from linear images. Their processing and analysis require consequently specific laws and structures. The latter have been developed in the concept of a logarithmic image processing (LIP) model (Jourlin & Pinoli, 1987, 1988; Pinoli, 1987a). This model permits the introduction of a well-justified contrast definition: from a physical point of view, it is closely linked with logarithmic images and from a mathematical point of view, it is set up in an algebraic structure. The applications presented at the end of this paper concern image preprocessing and segmentation. In particular, in the case of microscopic images, the proposed method of segmentation gives good results with transmitted light (thin foils in biology or transmitted electronic microscopy). However, images obtained by reflected light microscopy are not within the scope of this model.     

An improved microfluidics approach for monitoring real-time interaction profiles of ultrafast molecular recognition

Our study illustrates the development of a microfluidics (MF) platform combining fluorescence microscopy and femtosecond/picosecond-resolved spectroscopy to investigate ultrafast chemical processes in liquid-phase diffusion-controlled reactions. By controlling the flow rates of two reactants in a specially designed MF chip, sub-100 ns time resolution for the exploration of chemical intermediates of the reaction in the MF channel has been achieved. Our system clearly rules out the possibility of formation of any intermediate reaction product in a so-called fast ionic reaction between sodium hydroxide and phenolphthalein, and reveals a microsecond time scale associated with the formation of the reaction product. We have also used the developed system for the investigation of intermediate states in the molecular recognition of various macromolecular self-assemblies (micelles) and genomic DNA by small organic ligands (Hoechst 33258 and ethidium bromide). We propose our MF-based system to be an alternative to the existing millisecond-resolved "stopped-flow" technique for a broad range of time-resolved (sub-100 ns to minutes) experiments on complex chemical∕biological systems.