Structural biology with carbon nanotube AFM probes

Three-Way DNA Junction as an End Label for DNA in Atomic Force Microscopy Studies

Atomic Force Microscopy (AFM) is widely used for topographic imaging of DNA and protein-DNA complexes in ambient conditions with nanometer resolution. In AFM studies of protein-DNA complexes, identifying the protein’s location on the DNA substrate is one of the major goals. Such studies require distinguishing between the DNA ends, which can be accomplished by end-specific labeling of the DNA substrate. We selected as labels three-way DNA junctions (3WJ) assembled from synthetic DNA oligonucleotides with two arms of 39–40 bp each. The third arm has a three-nucleotide overhang, GCT, which is paired with the sticky end of the DNA substrate generated by the SapI enzyme. Ligation of the 3WJ results in the formation of a Y-type structure at the end of the linear DNA mole cule, which is routinely identified in the AFM images. The yield of labeling is 69%. The relative orientation of arms in the Y-end varies, such dynamics were directly visualized with time-lapse AFM studies using high-speed AFM (HS-AFM). This labeling approach was applied to the characterization of the nucleosome arrays assembled on different DNA templates. HS-AFM experiments revealed a high dynamic of nucleosomes resulting in a spontaneous unraveling followed by disassembly of nucleosomes.

CNTs mediated CD44 targeting; a paradigm shift in drug delivery for breast cancer

The breast cancer is one of the most common cancer affecting millions of lives worldwide. Though the prevalence of breast cancer is worldwide; however, the developing nations are having a comparatively higher percentage of breast cancer cases and associated complications. The molecular etiology behind breast cancer is complex and involves several regulatory molecules and their downstream signaling. Studies have demonstrated that the CD44 remains one of the major molecule associated not only in breast cancer but also several other kinds of tumors. The complex structure and functioning of CD44 posed a challenge to develop and deliver precise anti-cancerous drugs against targeted tissue. There are more than 20 isoforms of CD44 reported till date associated with several kinds of tumor in the using breast cancer. The success of any anti-cancerous therapy largely depends on the precise drug delivery system, and in modern days nanotechnology-based drug delivery vehicles are the first choice not only for cancer but several other chronic diseases as well. The Carbon nanotubes (CNTs) have shown tremendous scope in delivering the drug by targeting a particular receptor and molecules. Functionalized CNTs including both SWCNTs and MWCNTs are a pioneer in drug delivery with higher efficacy. The present work emphasized mainly on the potential of CNTs including both SWCNTs and MWCNTs in drug delivery for anti-cancerous therapy. The review provides a comprehensive overview of the development of various CNTs and their validation for effective drug delivery. The work focus on drug delivery approaches for breast cancer, precisely targeting CD44 molecule.

Improved Application of Carbon Nanotube Atomic Force Microscopy Probes Using PeakForce Tapping Mode

In this work PeakForce tapping (PFT) imaging was demonstrated with carbon nanotube atomic force microscopy (CNT-AFM) probes; this imaging mode shows great promise for providing simple, stable imaging with CNT-AFM probes, which can be difficult to apply. The PFT mode is used with CNT-AFM probes to demonstrate high resolution imaging on samples with features in the nanometre range, including a Nioprobe calibration sample and gold nanoparticles on silicon, in order to demonstrate the modes imaging effectiveness, and to also aid in determining the diameter of very thin CNT-AFM probes. In addition to stable operation, the PFT mode is shown to eliminate “ringing” artefacts that often affect CNT-AFM probes in tapping mode near steep vertical step edges. This will allow for the characterization of high aspect ratio structures using CNT-AFM probes, an exercise which has previously been challenging with the standard tapping mode.

Tip Pressure on Semicircular Specimens in Tapping Mode Atomic Force Microscopy in Viscous Fluid Environments

Tapping mode (TM) atomic force microscopy (AFM) in a liquid environment is widely used to measure the contours of biological specimens. The TM triggers the AFM probe approximately at the resonant frequencies and controls the tip such that it periodically touches the specimen along the scanning path. The AFM probe and its tip produce a hydrodynamic pressure on the probe itself and press the specimen. The tip to specimen size ratio is known to affect the measurement accuracy of AFM, however, few studies have focused on the hydrodynamic pressure caused by the effects of specimen size. Such pressure affects the contour distortion of the biological specimen. In this study, a semi-analytical method is employed for a semicircular specimen to analyze the vorticity and pressure distributions for specimens of various sizes and at various tip locations. Changes in pressure distribution, fluid spin motion, and specimen deformation are identified as the tip approaches the specimen. The results indicate the following: the specimen surface experiences the highest pressure when the specimen diameter equals the tip width; the vorticity between tip and specimen is complex when the tip is close to the specimen center line; and the specimen inflates when the tip is aligned with the specimen center line.

Tip Effect of the Tapping Mode of Atomic Force Microscope in Viscous Fluid Environments

Atomic force microscope with applicable types of operation in a liquid environment is widely used to scan the contours of biological specimens. The contact mode of operation allows a tip to touch a specimen directly but sometimes it damages the specimen; thus, a tapping mode of operation may replace the contact mode. The tapping mode triggers the cantilever of the microscope approximately at resonance frequencies, and so the tip periodically knocks the specimen. It is well known that the cantilever induces extra liquid pressure that leads to drift in the resonance frequency. Studies have noted that the heights of protein surfaces measured via the tapping mode of an atomic force microscope are ~25% smaller than those measured by other methods. This discrepancy may be attributable to the induced superficial hydrodynamic pressure, which is worth investigating. In this paper, we introduce a semi-analytical method to analyze the pressure distribution of various tip geometries. According to our analysis, the maximum hydrodynamic pressure on the specimen caused by a cone-shaped tip is ~0.5 Pa, which can, for example, pre-deform a cell by several nanometers in compression before the tip taps it. Moreover, the pressure calculated on the surface of the specimen is 20 times larger than the pressure without considering the tip effect; these results have not been motioned in other papers. Dominating factors, such as surface heights of protein surface, mechanical stiffness of protein increasing with loading velocity, and radius of tip affecting the local pressure of specimen, are also addressed in this study.

Computational mechanics of viral capsids

Viral capsids undergo significant mechanical deformations during their assembly, maturation, and infective life-span. In order to characterize the mechanics of viral capsids, their response to applied external forces is analyzed in several experimental studies using, for instance, Atomic Force Microscope (AFM) indentation experiments. In recent years, a broader approach to study the mechanics of viral capsids has leveraged the theoretical tools proper of continuum mechanics. Even though the theory of continuum elasticity is most commonly used to study deformable bodies at larger macroscopic length scales, it has been shown that this very rich theoretical field can still offer useful insights into the mechanics of viral structures at the nanometer scale. Here we show the construction of viral capsid continuum mechanics models starting from different forms of experimental data. We will discuss the kinematics assumptions, the issue of the reference configuration, the material constitutive laws, and the numerical discretization necessary to construct a complete Finite Element capsid mechanical model. Some examples in the second part of the chapter will show the predictive capabilities of the constructed models and underline useful practical aspects related to efficiency and accuracy. We conclude each example by collecting several key findings discovered by simulating AFM indentation experiments using the constructed numerical models.

Combined atomic force microscopy and fluorescence microscopy

The atomic force microscope (AFM) is a high-resolution scanning-probe instrument which has become an important tool for cellular and molecular biophysics in recent years, but lacks the time resolution and functional specificities offered by fluorescence microscopic techniques. The advantages of both methods may be exploited by combining and synchronizing them. In this paper, the biological applications of AFM, fluorescence, and their combinations are briefly reviewed, and the assembly and utilization of a spatially and temporally synchronized AFM and total internal reflection fluorescence microscope are described. The application of the method is demonstrated on a fluorescently labeled cell culture.

A six degree of freedom nanomanipulator design based on carbon nanotube bundles

Scanning probe imaging and manipulation of matter is of crucial importance for nanoscale science and technology. However, its resolution and ability to manipulate matter at the atomic scale is limited by rather poor control over the fine structure of the probe. In the present paper, a strategy is proposed to construct a molecular nanomanipulator from ultrathin single-walled carbon nanotubes. Covalent modification of a nanotube cap at predetermined atomic sites makes the nanotube act as a support for a functional 'tooltip' molecule. Then, a small bundle of nanotubes (three or four) with aligned ends can act as an extremely high aspect ratio parallel nanomanipulator for a suspended molecule, where protraction or retraction of individual nanotubes results in controlled tilting of the tooltip in two dimensions. Together with the usual scanning probe microscopy three degrees of freedom and augmented with rotation of the system as a whole, the design offers six degrees of freedom for imaging and manipulation of matter with the precision and freedom so much needed for advanced nanotechnology. A similar design might be possible to implement with other high aspect ratio nanostructures, such as oxide nanowires.

A tripod molecular tip for single molecule ligand-receptor force spectroscopy by AFM

Tripod-shaped molecules were designed for chemical modification of the surface of probes used for atomic force microscopy (AFM). These chemically functionalized tips were used for chemical force spectroscopy (CFS) measurements of the ligand-protein receptor interaction in a biotin-NeutrAvidin model system. We demonstrate that by using this unique tripodal system, we can achieve significantly lower density of ligand on the AFM tip apex, which is optimal for true single molecule measurements. Furthermore, the molecular tripods form highly stable bonds to the AFM probes, leading to more robust and reproducible unbinding force data, thereby addressing one of the challenges in CFS studies. Histogram analysis of the hundreds of collected unbinding forces showed a specific distribution with a peak force maximum at approximately 165 pN, in good agreement with the previously reported data of single rupture events of biotin-avidin. We compared these molecular tripod tips with a molecular monopod. The results showed that the molecular tripods are more robust for repeated measurements. The distinct biotin-avidin force maximum was not observed in the control experiments. This indicated that the force distribution observed for molecular tripods corresponds to the specific rupture force between biotin and avidin. The improved robustness of molecular tripods for CFS will provide benefits in other ligand-receptor unbinding studies, including those of transmembrane receptor systems, which require high resolution, sensitivity, and reproducibility in force spectroscopy measurements.

Single-photon atomic force microscopy

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

Carbon nanotube tips for atomic force microscopy

The development of atomic force microscopy (AFM) over the past 20 years has had a major impact on materials science, surface science and various areas of biology, and it is now a routine imaging tool for the structural characterization of surfaces. The lateral resolution in AFM is governed by the shape of the tip and the geometry of the apex at the end of the tip. Conventional microfabrication routes result in pyramid-shaped tips, and the radius of curvature at the apex is typically less than 10 nm. As well as producing smaller tips, AFM researchers want to develop tips that last longer, provide faithful representations of complex surface topographies, and are mechanically non-invasive. Carbon nanotubes have demonstrated considerable potential as AFM tips but they are still not widely adopted. This review traces the history of carbon nanotube tips for AFM, the applications of these tips and research to improve their performance.

Peptide-coated nanotube-based biosensor for the detection of disease-specific autoantibodies in human serum

We demonstrate a label-free peptide-coated carbon nanotube-based immunosensor for the direct assay of human serum. A rheumatoid arthritis (RA)-specific (cyclic citrulline-containing) peptide, was immobilized to functionalized single-walled carbon nanotubes deposited on a quartz crystal microbalance (QCM) sensing crystal. Serum from RA patients was used to probe these nanotube-based sensors, and antibody binding was detected by QCM sensing. Specific antibody binding was also determined by comparing the assay of two serum control groups (normal and diseased sera), and the native unmodified peptide. The sensitivity of the nanotube-based sensor (detection in the femtomol range) was higher than that of the established ELISA and recently described microarray assay systems, detecting 34.4 and 37.5% more RA patients with anti-citrullinated peptide antibodies than those found by ELISA and microarray, respectively. There was also an 18.4 and 19.6% greater chance of a negative test being a true indicator of a person not having RA than by either ELISA or microarray, respectively. The performance of our label-free biosensor enables its application in the direct assay of sera in research and diagnostics.

Applications of nanoparticles to diagnostics and therapeutics in colorectal cancer

Nanotechnology has considerable promise for the detection, staging and treatment of cancer. Here, we outline one such promising application: the use of nanostructures with surface-bound ligands for the targeted delivery and ablation of colorectal cancer (CRC), the third most common malignancy and the second most common cause of cancer-related mortality in the US. Normal colonic epithelial cells as well as primary CRC and metastatic tumors all express a unique surface-bound guanylyl cyclase C (GCC), which binds the diarrheagenic bacterial heat-stable peptide enterotoxin ST. This makes GCC a potential target for metastatic tumor ablation using ST-bound nanoparticles in combination with thermal ablation with near-infrared or radiofrequency energy absorption. Furthermore, the incorporation of iron or iron oxide into such structures would provide advantages for magnetic resonance imaging (MRI). Although the scenarios outlined in this article are hypothetical, they might stimulate ideas about how other cancers could be attacked using nanotechnology.

Cantilever dynamics and quality factor control in AC mode AFM height measurements

We show that inconsistent-imaging dynamics, in which the cantilever oscillates in the attractive regime on substrate background but in the repulsive regime on sample, leads to artifacts in apparent height in AC mode Atomic force microscopy. Active Q control can be used to effectively tune the imaging dynamics. Increased effective Q promotes the attractive regime, improves imaging sensitivity, and results in less invasive imaging of soft biological molecules.

Single Biomolecule Imaging with Frequency and Force Modulation in Tapping-Mode Atomic Force Microscopy

A new intermittent-contact atomic force microscopy (AFM) mode (frequency and force modulation AFM, FFM-AFM) has been recently proposed to characterize soft samples. This method uses excitation force frequency and amplitude modulation to eliminate bistability and reduce the tip-sample forces. This letter describes theoretical modeling of FFM-AFM applied to a single bacteriorhodopsin molecule on a substrate, showing that its cross section can be measured without damage, in contrast to conventional tapping-mode AFM. Speculations are made regarding nonideal conditions and the ability of FFM-AFM to perform quantitative nanoelasticity measurements.

Miniaturized detection technology in molecular diagnostics

Miniaturization of genetic tests represents the convergence of molecular biology and engineering and is leading to a new class of small analyzers and test systems for genetic testing with improved analytical characteristics. Miniaturization initially focused on devices that contained micrometer-sized features designed for a particular analytical purpose (e.g., filters for cell isolation and chips for capillary electrophoresis). Now, the focus is shifting to analytical applications based on nano-sized objects such as nanotubes, nanochannels, nanoparticles, nanopores and nanocapacitors. These nanofabricated objects provide new tools for sequencing of nucleic acids and rapid, multiplexed, nucleic acid detection.

Global Tuning of Local Molecular Phenomena: An Alternative Approach to Bionanoelectronics

We have applied simultaneous horizontal and vertical bias to a single molecule (2 nm(2)) in an ordered and disordered matrix to virtually isolate and tune its property without taking it out physically from its environment. Using a dedicated electrode system, we have locally tuned nanoscale properties vertically by STM, while stabilizing its environment by applying a global electric field horizontally. Using this technique, we report tuning of molecular conformations in room temperature, whose evolution of states has been statistically investigated. We have also shown control on switching of a few selected conformations by applying dual bias simultaneously. As we avoid any direct injection of charge into the system via electrode contact, this technique could be used as a generalized method to tune phenomena evolved in an environment of weak interaction from a large distance without destroying the property.

Influence of the Carbon Nanotube Probe Tilt Angle on the Effective Probe Stiffness and Image Quality in Tapping-Mode Atomic Force Microscopy

Previous studies have shown that when using carbon nanotubes (CNTs) as tapping-mode AFM probes, their tilt angle with respect to vertical (denoted phi) must be close to 0 degrees to obtain high-quality images and that very poor images are obtained for phi > 30 degrees . Here we present a quantitative theoretical investigation of the effect of phi on tapping-mode AFM imaging for single-wall and multiwall nanotube (SWNT and MWNT, respectively) probes of diameters 3.4-5.5 nm and aspect ratio 7.5, which have been found ideal for imaging via TEM. Using molecular and classical dynamics, we investigate the effect of phi on CNT probe stiffness (quantified through the maximum gradient of the tip-sample interaction force) and show that it decreases linearly with increasing phi, becoming negligible at around phi approximately 40 degrees , thus confirming the conclusions of previous studies. We find that MWNT probe stiffness is proportional to the number of walls, but that the difference in stiffness between SWNTs and MWNTs also decreases linearly with increasing phi and becomes negligible at around phi approximately 40 degrees . The simulated cross-sectional scans of a sample SWNT using two different values of phi show that the image can be distorted and shifted laterally when phi is large, in some cases giving measured heights appreciably greater than the sample dimensions. We show analytically that the tip-sample forces that occur during imaging can be significantly lower when CNT probes are used instead of conventional probes, even in the absence of buckling, and that they can be further reduced by increasing phi. On the basis of this result, we propose the design of free-standing kinked probes for the characterization of sensitive samples, whereby the probe approaches the sample at a vertical orientation and possesses a tilted section that regulates the tip-sample interaction forces.

Visualizing and manipulating individual protein molecules

Single-molecule imaging and manipulation techniques have evolved in the past decade from mere jaw-dropping attractions to essential laboratory tools. By applying single-molecule methods important insights otherwise unavailable have been obtained on various biomolecular systems. Constantly improving single-molecule imaging techniques keep expanding the scale of the explorable spatial detail, thereby providing possible solutions to getting around the debilitating diffraction limit present in physiological-condition structural investigations. In some areas, such as motor protein studies, single-molecule methods have become part of the routine and essential research toolkit. Entire research fields, such as single-molecule force spectroscopy, have been born. In the present review single-molecule visualization and manipulation methods are reviewed with a focus on proteins. Relevant signals and prominent applications are discussed along with experimental examples and recent important results. Finally, the perspectives of the single-molecule field are explored.

Applications of Carbon Nanotubes in Biotechnology and Biomedicine

Due to their electrical, chemical, mechanical and thermal properties, carbon nanotubes are one of the most promising materials for the electronics, computer and aerospace industries. Here, we discuss their properties in the context of future applications in biotechnology and biomedicine. The purification and chemical modification of carbon nanotubes with organic, polymeric and biological molecules are discussed. Additionally we review their uses in biosensors, assembly of structures and devices, scanning probe microscopy and as substrates for neuronal growth. We note that additional toxicity studies of carbon nanotubes are necessary so that exposure guidelines and safety regulations can be established in a timely manner.

An overview of the biophysical applications of atomic force microscopy

The potentialities of the atomic force microscopy (AFM) make it a tool of undeniable value for the study of biologically relevant samples. AFM is progressively becoming a usual benchtop technique. In average, more than one paper is published every day on AFM biological applications. This figure overcomes materials science applications, showing that 17 years after its invention, AFM has completely crossed the limits of its traditional areas of application. Its potential to image the structure of biomolecules or bio-surfaces with molecular or even sub-molecular resolution, study samples under physiological conditions (which allows to follow in situ the real time dynamics of some biological events), measure local chemical, physical and mechanical properties of a sample and manipulate single molecules should be emphasized.

Macromolecular crystal growth as revealed by atomic force microscopy

Direct visualization of macromolecular crystal growth using atomic force microscopy (AFM) has provided a powerful tool in the delineation of mechanisms and the kinetics of the growth process. It has further allowed us to evaluate the wide variety of impurities that are incorporated into crystals of proteins, nucleic acids, and viruses. We can, using AFM, image the defects and imperfections that afflict these crystals, the impurity layers that poison their surfaces, and the consequences of various factors on morphological development. All of these can be recorded under normal growth conditions, in native mother liquors, over time intervals ranging from minutes to days, and at the molecular level.

Direct visualization of a DNA glycosylase searching for damage

DNA glycosylases preserve the integrity of genetic information by recognizing damaged bases in the genome and catalyzing their excision. It is unknown how DNA glycosylases locate covalently modified bases hidden in the DNA helix amongst vast numbers of normal bases. Here we employ atomic-force microscopy (AFM) with carbon nanotube probes to image search intermediates of human 8-oxoguanine DNA glycosylase (hOGG1) scanning DNA. We show that hOGG1 interrogates DNA at undamaged sites by inducing drastic kinks. The sharp DNA bending angle of these non-lesion-specific search intermediates closely matches that observed in the specific complex of 8-oxoguanine-containing DNA bound to hOGG1. These findings indicate that hOGG1 actively distorts DNA while searching for damaged bases.