Surface biology of DNA by atomic force microscopy

Fourier transform-based post-processing drift compensation and calibration method for scanning probe microscopy

Scanning probe microscopy (SPM) is ubiquitous in nanoscale science allowing the observation of features in real space down to the angstrom resolution. The scanning nature of SPM, wherein a sharp tip rasters the surface during which a physical setpoint is maintained via a control feedback loop, often implies that the image is subject to drift effects, leading to distortion of the resulting image. While there are in-operando methods to compensate for the drift, correcting the residual linear drift in obtained images is often neglected. In this paper, we present a reciprocal space-based technique to compensate the linear drift in atomically-resolved scanning probe microscopy images without distinction of the fast and slow scanning directions; furthermore this method does not require the set of SPM images obtained for the different scanning directions. Instead, the compensation is made possible by the a priori knowledge of the lattice parameters. The method can also be used to characterize and calibrate the SPM instrument.

Approaches for Determining DNA Persistence Length Using Atomic Force Microscopy

Atomic force microscopy (AFM) is widely used to image and study biological molecules. As an example, we have utilized AFM to investigate how the mechanical properties of DNA polymers depend on electrostatics and the strength of DNA base stacking by studying double-stranded DNA molecules incorporating several different neutral and charged base modifications. Here we describe ten complementary approaches for determining DNA persistence length by AFM imaging. The combination of different approaches provides increased confidence and statistical reliability over existing methods utilizing only a single approach.

Adsorbing DNA to Mica by Cations: Influence of Valency and Ion Type

Ion-mediated attraction between DNA and mica plays a crucial role in biotechnological applications and molecular imaging. Here, we combine molecular dynamics simulations and single-molecule atomic force microscopy experiments to characterize the detachment forces of single-stranded DNA at mica surfaces mediated by the metal cations Li+, Na+, K+, Cs+, Mg2+, and Ca2+. Ion-specific adsorption at the mica/water interface compensates (Li+ and Na+) or overcompensates (K+, Cs+, Mg2+, and Ca2+) the bare negative surface charge of mica. In addition, direct and water-mediated contacts are formed between the ions, the phosphate oxygens of DNA, and mica. The different contact types give rise to low- and high-force pathways and a broad distribution of detachment forces. Weakly hydrated ions, such as Cs+ and water-mediated contacts, lead to low detachment forces and high mobility of the DNA on the surface. Direct ion-DNA or ion-surface contacts lead to significantly higher forces. The comprehensive view gained from our combined approach allows us to highlight the most promising cations for imaging in physiological conditions: K+, which overcompensates the negative mica charge and induces long-ranged attractions. Mg2+ and Ca2+, which form a few specific and long-lived contacts to bind DNA with high affinity.

Analytical Models for Measuring the Mechanical Properties of Yeast

The mechanical properties of yeast play an important role in many biological processes, such as cell division and growth, maintenance of internal pressure, and biofilm formation. In addition, the mechanical properties of cells can indicate the degree of damage caused by antifungal drugs, as the mechanical parameters of healthy and damaged cells are different. Over the past decades, atomic force microscopy (AFM) and micromanipulation have become the most widely used methods for evaluating the mechanical characteristics of microorganisms. In this case, the reliability of such an estimate depends on the choice of mathematical model. This review presents various analytical models developed in recent years for studying the mechanical properties of both cells and their individual structures. The main provisions of the applied approaches are described along with their limitations and advantages. Attention is paid to the innovative method of low-invasive nanomechanical mapping with scanning ion-conductance microscopy (SICM), which is currently starting to be successfully used in the discovery of novel drugs acting on the yeast cell wall and plasma membrane.

Atomic Force Microscopy of DNA and DNA-Protein Interactions

Atomic force microscopy (AFM) is a microscopy technique that uses a sharp probe to trace a sample surface at nanometer resolution. For biological applications, one of its key advantages is its ability to visualize the substructure of single molecules and molecular complexes in an aqueous environment. Here, we describe the application of AFM to determine the secondary and tertiary structure of surface-bound DNA, and its interactions with proteins.

Self-Suppression of the Giant Coherent Anti-Stokes Raman Scattering Background for Detection of Buried Interfaces with Submonolayer Sensitivity

Despite its success in many fields, the implementation of coherent anti-Stokes Raman spectroscopy (CARS) in tackling the problems at interfaces was hindered by the enormous resonant and nonresonant background from the bulk. In this work, we have developed a novel CARS scheme that can probe a buried interface via ≥10⁵-fold suppression of the nonresonant and resonant bulk contribution. The method utilizes self-destructive interference between the forward and backward CARS generated in the bulk near the Brewster angle. As a result, we can resolve the vibrational spectrum of submonolayer interfacial polar/apolar species immersed in the surrounding medium with huge CARS responses. We expect that our approach opens up the opportunity to interrogate the interfaces involving apolar molecules and benefits other nonlinear optical spectroscopic techniques, e.g., sum-frequency spectroscopy and four-wave mixing spectroscopy in general, to promote the signal-to-background noise ratio.

Biosensing, Characterization of Biosensors, and Improved Drug Delivery Approaches Using Atomic Force Microscopy: A Review

Since its invention, atomic force microscopy (AFM) has come forth as a powerful member of the “scanning probe microscopy” (SPM) family and an unparallel platform for high-resolution imaging and characterization for inorganic and organic samples, especially biomolecules, biosensors, proteins, DNA, and live cells. AFM characterizes any sample by measuring interaction force between the AFM cantilever tip (the probe) and the sample surface, and it is advantageous over other SPM and electron micron microscopy techniques as it can visualize and characterize samples in liquid, ambient air, and vacuum. Therefore, it permits visualization of three-dimensional surface profiles of biological specimens in the near-physiological environment without sacrificing their native structures and functions and without using laborious sample preparation protocols such as freeze-drying, staining, metal coating, staining, or labeling. Biosensors are devices comprising a biological or biologically extracted material (assimilated in a physicochemical transducer) that are utilized to yield electronic signal proportional to the specific analyte concentration. These devices utilize particular biochemical reactions moderated by isolated tissues, enzymes, organelles, and immune system for detecting chemical compounds via thermal, optical, or electrical signals. Other than performing high-resolution imaging and nanomechanical characterization (e.g., determining Young’s modulus, adhesion, and deformation) of biosensors, AFM cantilever (with a ligand functionalized tip) can be transformed into a biosensor (microcantilever-based biosensors) to probe interactions with a particular receptors of choice on live cells at a single-molecule level (using AFM-based single-molecule force spectroscopy techniques) and determine interaction forces and binding kinetics of ligand receptor interactions. Targeted drug delivery systems or vehicles composed of nanoparticles are crucial in novel therapeutics. These systems leverage the idea of targeted delivery of the drug to the desired locations to reduce side effects. AFM is becoming an extremely useful tool in figuring out the topographical and nanomechanical properties of these nanoparticles and other drug delivery carriers. AFM also helps determine binding probabilities and interaction forces of these drug delivery carriers with the targeted receptors and choose the better agent for drug delivery vehicle by introducing competitive binding. In this review, we summarize contributions made by us and other researchers so far that showcase AFM as biosensors, to characterize other sensors, to improve drug delivery approaches, and to discuss future possibilities.

Self-Assembly of DNA molecules in magnetic Fields

In this work, a rich variety of self-assembled DNA patterns were obtained in the magnetic field. Herein, atomic force microscopy (AFM) was utilized to investigate the effects of the concentration of DNA solution, intensity and direction of magnetic field and modification of mica surface by different cations on the self-assembly of DNA molecules. It was found that owning to the change of the DNA concentration, even under the same magnetic field, the DNA self-assembly results were different. Thein situtest results showed that the DNA self-assembly in an magnetic field was more likely to occur in liquid phase than in gas phase. In addition, whether in a horizontal or vertical magnetic field, a single stretched dsDNA was obtained in a certain DNA concentration and magnetic field intensity. Besides, the modification of cations on the mica surface significantly increased the force between the DNA molecules and mica surface, and further changed the self-assembly of DNA molecules under the action of magnetic field.

Atomic force microscopy-A tool for structural and translational DNA research

Atomic force microscopy (AFM) is a powerful imaging technique that allows for structural characterization of single biomolecules with nanoscale resolution. AFM has a unique capability to image biological molecules in their native states under physiological conditions without the need for labeling or averaging. DNA has been extensively imaged with AFM from early single-molecule studies of conformational diversity in plasmids, to recent examinations of intramolecular variation between groove depths within an individual DNA molecule. The ability to image dynamic biological interactions in situ has also allowed for the interaction of various proteins and therapeutic ligands with DNA to be evaluated-providing insights into structural assembly, flexibility, and movement. This review provides an overview of how innovation and optimization in AFM imaging have advanced our understanding of DNA structure, mechanics, and interactions. These include studies of the secondary and tertiary structure of DNA, including how these are affected by its interactions with proteins. The broader role of AFM as a tool in translational cancer research is also explored through its use in imaging DNA with key chemotherapeutic ligands, including those currently employed in clinical practice.

DNA Knot Malleability in Single-Digit Nanopores

Knots in long DNA molecules are prevalent in biological systems and serve as a model system for investigating static and dynamic properties of biopolymers. We explore the dynamics of knots in double-stranded DNA in a new regime of nanometer-scale confinement, large forces, and short time scales, using solid-state nanopores. We show that DNA knots undergo isomorphic translocation through a nanopore, retaining their equilibrium morphology by swiftly compressing in a lateral direction to fit the constriction. We observe no evidence of knot tightening or jamming, even for single-digit nanopores. We explain the observations as the malleability of DNA, characterized by sharp buckling of the DNA in nanopores, driven by the transient disruption of base pairing. Our molecular dynamics simulations support the model. These results are relevant not only for the understanding of DNA packing and manipulation in living cells but also for the polymer physics of DNA and the development of nanopore-based sequencing technologies.

Mechanical Flexibility of DNA: A Quintessential Tool for DNA Nanotechnology

The mechanical properties of DNA have enabled it to be a structural and sensory element in many nanotechnology applications. While specific base-pairing interactions and secondary structure formation have been the most widely utilized mechanism in designing DNA nanodevices and biosensors, the intrinsic mechanical rigidity and flexibility are often overlooked. In this article, we will discuss the biochemical and biophysical origin of double-stranded DNA rigidity and how environmental and intrinsic factors such as salt, temperature, sequence, and small molecules influence it. We will then take a critical look at three areas of applications of DNA bending rigidity. First, we will discuss how DNA's bending rigidity has been utilized to create molecular springs that regulate the activities of biomolecules and cellular processes. Second, we will discuss how the nanomechanical response induced by DNA rigidity has been used to create conformational changes as sensors for molecular force, pH, metal ions, small molecules, and protein interactions. Lastly, we will discuss how DNA's rigidity enabled its application in creating DNA-based nanostructures from DNA origami to nanomachines.

Modeling of eccentric nanoneedle in trolling-mode atomic force microscope

Limitations on installation of a standard TR-AFM nanoneedle can have unpredictable effects on dynamics of system. Therefore, it is crucial to pay close attention to the position and geometry of mounted nanoneedle when deriving the mathematical model. During TR-AFM fabrication process, the nanoneedle may not always deposit precisely at the middle of AFM tip, which would result in coupled bending-torsion modes in the dynamical operation of system. In this paper, we investigate the effect of eccentric nanoneedle in dynamic response of TR-AFM. To address this issue, a continuous mathematical model is developed. This model accounts for eccentric nanoneedle which can address the couplings in nonlinear vibration. Hamilton's principle is used to derive equations of motion and then assumed mode method (AMM) is utilized. This model is capable of simulating the cantilever dynamics under complicated nanoneedle tip-sample interactions. Displacements of different components of system for various eccentricity are determined. It is found that nanoneedle eccentricity has noticeable effects on microbeam torsion angle and out of plane nanoneedle tip displacement.

Tuning the Topological Landscape of DNA-Cyclodextrin Nanocomplexes by Molecular Design

Original molecular vectors that ensure broad flexibility to tune the shape and surface properties of plasmid DNA (pDNA) condensates are reported herein. The prototypic design involves a cyclodextrin (CD) platform bearing a polycationic cluster at the primary face and a doubly linked aromatic module bridging two consecutive monosaccharide units at the secondary face that behaves as a topology-encoding element. Subtle differences at the molecular level then translate into disparate morphologies at the nanoscale, including rods, worms, toroids, globules, ellipsoids, and spheroids. In vitro evaluation of the transfection capabilities revealed marked selectivity differences as a function of nanocomplex morphology. Remarkably high transfection efficiencies were associated with ellipsoidal or spherical shapes with a lamellar internal arrangement of pDNA chains and CD bilayers. Computational studies support that the stability of such supramolecular edifices is directly related to the tendency of the molecular vector to form noncovalent dimers upon DNA templating. Because the stability of the dimers depends on the protonation state of the polycationic clusters, the coaggregates display pH responsiveness, which facilitates endosomal escape and timely DNA release, a key step in successful transfection. The results provide a versatile strategy for the construction of fully synthetic and perfectly monodisperse nonviral gene delivery systems uniquely suited for optimization schemes.

Complex DNA knots detected with a nanopore sensor

Equilibrium knots are common in biological polymers-their prevalence, size distribution, structure, and dynamics have been extensively studied, with implications to fundamental biological processes and DNA sequencing technologies. Nanopore microscopy is a high-throughput single-molecule technique capable of detecting the shape of biopolymers, including DNA knots. Here we demonstrate nanopore sensors that map the equilibrium structure of DNA knots, without spurious knot tightening and sliding. We show the occurrence of both tight and loose knots, reconciling previous contradictory results from different experimental techniques. We evidence the occurrence of two quantitatively different modes of knot translocation through the nanopores, involving very different tension forces. With large statistics, we explore the complex knots and, for the first time, reveal the existence of rare composite knots. We use parametrized complexity, in concert with simulations, to test the theoretical assumptions of the models, further asserting the relevance of nanopores in future investigation of knots.

Polymer Patterning with Self-Heating Atomic Force Microscope Probes

Scanning probe-assisted patterning methods already demonstrated a high degree of capabilities on submicrometer scales. However, the throughput is still far from its potential because of complexity or fragility of the probes for exploiting thermal effects, chemical reactions, and voltage-induced processes in various patterning operations. Here, we present a new approach to thermomechanical patterning by implementing a multitasking atomic force microscopy (AFM) probe: the functionalized planar probes. In this method, we can generate a tunable thermal gradient between the tip and the sample, wherein they remain in the noncontact regime. In principle, the capillary instability provoked by the van der Waals interaction yields a pull-off force toward the tip. Hence, locally rising protrusions form features at any selected position on a polymer surface without any chemical reaction or irreversible transformation. These multitasking probe-integrated AFMs can pave the way for a remarkable freedom in determining the operation regime on submicrometer surface-patterning applications.

Single-molecule visualization of the effects of ionic strength and crowding on structure-mediated interactions in supercoiled DNA molecules

DNA unwinding is an important cellular process involved in DNA replication, transcription and repair. In cells, molecular crowding caused by the presence of organelles, proteins, and other molecules affects numerous internal cellular structures. Here, we visualize plasmid DNA unwinding and binding dynamics to an oligonucleotide probe as functions of ionic strength, crowding agent concentration, and crowding agent species using single-molecule CLiC microscopy. We demonstrate increased probe–plasmid interaction over time with increasing concentration of 8 kDa polyethylene glycol (PEG), a crowding agent. We show decreased probe–plasmid interactions as ionic strength is increased without crowding. However, when crowding is introduced via 10% 8 kDa PEG, interactions between plasmids and oligos are enhanced. This is beyond what is expected for normal in vitro conditions, and may be a critically important, but as of yet unknown, factor in DNA’s proper biological function in vivo. Our results show that crowding has a strong effect on the initial concentration of unwound plasmids. In the dilute conditions used in these experiments, crowding does not impact probe–plasmid interactions once the site is unwound.

Further Insights into the Architecture of the PN Promoter That Controls the Expression of the bzd Genes in Azoarcus

The anaerobic degradation of benzoate in bacteria involves the benzoyl-CoA central pathway. Azoarcus/Aromatoleum strains are a major group of anaerobic benzoate degraders, and the transcriptional regulation of the bzd genes was extensively studied in Azoarcus sp. CIB. In this work, we show that the bzdR regulatory gene and the P_N promoter can also be identified upstream of the catabolic bzd operon in all benzoate-degrader Azoarcus/Aromatoleum strains whose genome sequences are currently available. All the P_N promoters from Azoarcus/Aromatoleum strains described here show a conserved architecture including three operator regions (ORs), i.e., OR1 to OR3, for binding to the BzdR transcriptional repressor. Here, we demonstrate that, whereas OR1 is sufficient for the BzdR-mediated repression of the P_N promoter, the presence of OR2 and OR3 is required for de-repression promoted by the benzoyl-CoA inducer molecule. Our results reveal that BzdR binds to the P_N promoter in the form of four dimers, two of them binding to OR1. The BzdR/P_N complex formed induces a DNA loop that wraps around the BzdR dimers and generates a superstructure that was observed by atomic force microscopy. This work provides further insights into the existence of a conserved BzdR-dependent mechanism to control the expression of the bzd genes in Azoarcus strains.

Measurement of nanomechanical properties of DNA molecules by PeakForce atomic force microscopy based on DNA origami

Characterization of the stiffness of thin DNA strands remains difficult. By constructing bilayer DNA molecules, we investigated their mechanical properties using AFM. Increased DNA thickness through DNA origami greatly reduced the substrate effect when measuring Young's modulus, thus providing a more accurate picture of the inherent nanomechanical properties of DNA.

Static and time-dependent mechanical response of organic matrix of bone

Bone derives its mechanical strength from the complex arrangement of collagen fibrils (type-I primarily) reinforced with hydroxy-apatite (HAp) mineral crystals in extra- and intra-fibrillar compartments. This study demonstrates a novel approach to obtain organic matrix of bone through its demineralization as well as mechanically characterize it at small length scales using static and dynamic indentation techniques. Sample surface preparation protocol used in the present work maintained the surface integrity of demineralized bone samples which resulted sample surface of roughness (RMS) magnitude of approximately 14 nm (averaged over 1 × 1 μm² area duly verified by atomic force microscope (AFM)). Elemental composition analysis via energy dispersive X-ray spectroscopy (EDX) (for probed depth upto 2 μm) confirmed the complete removal of HAp mineral from bone samples during their demineralization using EDTA leaving collagen molecule assemblies unaffected as represented by Second Harmonic Generation (SHG) imaging. The modulus magnitudes of organic matrix obtained using from quasistatic as well as dynamic indentations (at constant frequency of 30 Hz) as ∼2.6 GPa and 4.5 GPa respectively, demonstrated the influence of loading rate on the estimated mechanical properties. For indentation depth to surface roughness ratio greater than ∼5:1, interestingly, measured material properties of organic matrix were found to depend on increasing magnitude of indentation depth of up to ∼500 nm value which probed from few collagen fibrils to next level of hierarchy i.e. collagen fibers. These findings are very useful to accurately determine the elastic and visco-elastic response of organic matrices of mineralized tissues for various applications including tissue engineering, bio-mimetics, etc.

Nanoparticles in tissue engineering: applications, challenges and prospects

Tissue engineering (TE) is an interdisciplinary field integrating engineering, material science and medical biology that aims to develop biological substitutes to repair, replace, retain, or enhance tissue and organ-level functions. Current TE methods face obstacles including a lack of appropriate biomaterials, ineffective cell growth and a lack of techniques for capturing appropriate physiological architectures as well as unstable and insufficient production of growth factors to stimulate cell communication and proper response. In addition, the inability to control cellular functions and their various properties (biological, mechanical, electrochemical and others) and issues of biomolecular detection and biosensors, all add to the current limitations in this field. Nanoparticles are at the forefront of nanotechnology and their distinctive size-dependent properties have shown promise in overcoming many of the obstacles faced by TE today. Despite tremendous progress in the use of nanoparticles over the last 2 decades, the full potential of the applications of nanoparticles in solving TE problems has yet to be realized. This review presents an overview of the diverse applications of various types of nanoparticles in TE applications and challenges that need to be overcome for nanotechnology to reach its full potential.

Approaches for Determining DNA Persistence Length Using Atomic Force Microscopy

Atomic force microscopy (AFM) is widely used to image and study biological molecules. As an example, we have utilized AFM to investigate how the mechanical properties of DNA polymers depend on electrostatics and the strength of DNA base stacking by studying double-stranded DNA molecules incorporating several different neutral and charged base modifications. Here, we describe ten complementary approaches for determining DNA persistence length by AFM imaging. The combination of different approaches provides increased confidence and statistical reliability over existing methods utilizing only a single approach.

On-Surface Synthesis of Adenine Oligomers via Ullmann Reaction

Despite the fact that DNA bases have been well-studied on surface, the on-surface synthesis of one-dimensional DNA analogs through in situ reactions is still an interesting topic to be investigated. Herein, from the interplay of high-resolution scanning tunneling microscopy (STM) imaging and density functional theory (DFT) calculations, we have delicately designed a halogenated derivative of adenine as precursor to realize the combination of DNA bases and Ullmann reaction, and then successfully synthesized adenine oligomers on Au(111) via Ullmann coupling. This model system provides a possible bottom-up strategy of fabricating adenine oligomers on surface, which may further give access to man-made DNA strands with multiple bases.

Nanoscale imaging and force probing of biomolecular systems using atomic force microscopy: from single molecules to living cells

Due to the lack of adequate tools for observation, native molecular behaviors at the nanoscale have been poorly understood. The advent of atomic force microscopy (AFM) provides an exciting instrument for investigating physiological processes on individual living cells with molecular resolution, which attracts the attention of worldwide researchers. In the past few decades, AFM has been widely utilized to investigate molecular activities on diverse biological interfaces, and the performances and functions of AFM have also been continuously improved, greatly improving our understanding of the behaviors of single molecules in action and demonstrating the important role of AFM in addressing biological issues with unprecedented spatiotemporal resolution. In this article, we review the related techniques and recent progress about applying AFM to characterize biomolecular systems in situ from single molecules to living cells. The challenges and future directions are also discussed.

Nonviral gene-delivery by highly fluorinated gemini bispyridinium surfactant-based DNA nanoparticles

Biological and thermodynamic properties of a new homologous series of highly fluorinated bispyridinium cationic gemini surfactants, differing in the length of the spacer bridging the pyridinium polar heads in 1,1' position, are reported for the first time. Interestingly, gene delivery ability is closely associated with the spacer length due to a structural change of the molecule in solution. This conformation change is allowed when the spacer reaches the right length, and it is suggested by the trends of the apparent and partial molar enthalpies vs molality. To assess the compounds' biological activity, they were tested with an agarose gel electrophoresis mobility shift assay (EMSA), MTT proliferation assay and Transient Transfection assays on a human rhabdomyosarcoma cell line. Data from atomic force microscopy (AFM) allow for morphological characterization of DNA nanoparticles. Dilution enthalpies, measured at 298K, enabled the determination of apparent and partial molar enthalpies vs molality. All tested compounds (except that with the longest spacer), at different levels, can deliver the plasmid when co-formulated with 1,2-dioleyl-sn-glycero-3-phosphoethanolamine (DOPE). The compound with a spacer formed by eight carbon atoms gives rise to a gene delivery ability that is comparable to that of the commercial reagent. The compound with the longest spacer compacts DNA in loosely condensed structures by forming bows, which are not suitable for transfection. Regarding the compounds' hydrogenated counterparts, the tight relationship between the solution thermodynamics data and their biological performance is amazing, making "old" methods the foundation to deeply understanding "new" applications.

Preparation of Well-Defined DNA Samples for Reproducible Nanospectroscopic Measurements

Due to its well-defined topology and chemical structure, DNA could become a biological standard sample in the field of nanospectroscopy. Tip-enhanced Raman spectroscopy (TERS) provides new insights into individual DNA molecules immobilized on flat mica crystals. The high sensitivity of TERS is used to assess the chemical changes that appear in DNA upon different surface immobilization protocols.

Discriminating Intercalative Effects of Threading Intercalator Nogalamycin, from Classical Intercalator Daunomycin, Using Single Molecule Atomic Force Spectroscopy

DNA threading intercalators are a unique class of intercalating agents, albeit little biophysical information is available on their intercalative actions. Herein, the intercalative effects of nogalamycin, which is a naturally-occurring DNA threading intercalator, have been investigated by high-resolution atomic force microscopy (AFM) and spectroscopy (AFS). The results have been compared with those of the well-known chemotherapeutic drug daunomycin, which is a non-threading classical intercalator bearing structural similarity to nogalamycin. A comparative AFM assessment revealed a greater increase in DNA contour length over the entire incubation period of 48 h for nogalamycin treatment, whereas the contour length increase manifested faster in case of daunomycin. The elastic response of single DNA molecules to an externally applied force was investigated by the single molecule AFS approach. Characteristic mechanical fingerprints in the overstretching behaviour clearly distinguished the nogalamycin/daunomycin-treated dsDNA from untreated dsDNA—the former appearing less elastic than the latter, and the nogalamycin-treated DNA distinguished from the daunomycin-treated DNA—the classically intercalated dsDNA appearing the least elastic. A single molecule AFS-based discrimination of threading intercalation from the classical type is being reported for the first time.

Imaging DNA Structure by Atomic Force Microscopy

Atomic force microscopy (AFM) is a microscopy technique that uses a sharp probe to trace a sample surface at nanometre resolution. For biological applications, one of its key advantages is its ability to visualize substructure of single molecules and molecular complexes in an aqueous environment. Here, we describe the application of AFM to determine superstructure and secondary structure of surface-bound DNA. The method is also readily applicable to probe DNA-DNA interactions and DNA-protein complexes.

Nanomechanics of Cells and Biomaterials Studied by Atomic Force Microscopy

The behavior and mechanical properties of cells are strongly dependent on the biochemical and biomechanical properties of their microenvironment. Thus, understanding the mechanical properties of cells, extracellular matrices, and biomaterials is key to understanding cell function and to develop new materials with tailored mechanical properties for tissue engineering and regenerative medicine applications. Atomic force microscopy (AFM) has emerged as an indispensable technique for measuring the mechanical properties of biomaterials and cells with high spatial resolution and force sensitivity within physiologically relevant environments and timescales in the kPa to GPa elastic modulus range. The growing interest in this field of bionanomechanics has been accompanied by an expanding array of models to describe the complexity of indentation of hierarchical biological samples. Furthermore, the integration of AFM with optical microscopy techniques has further opened the door to a wide range of mechanotransduction studies. In recent years, new multidimensional and multiharmonic AFM approaches for mapping mechanical properties have been developed, which allow the rapid determination of, for example, cell elasticity. This Progress Report provides an introduction and practical guide to making AFM-based nanomechanical measurements of cells and surfaces for tissue engineering applications.

Single-molecule reconstruction of oligonucleotide secondary structure by atomic force microscopy

Based on soft-touch atomic force microscopy, a method is described to reconstruct the secondary structure of single extended biomolecules, without the need for crystallization. The method is tested by accurately reproducing the dimensions of the B-DNA crystal structure. Importantly, intramolecular variations in groove depth of the DNA double helix are resolved, which would be inaccessible for methods that rely on ensemble-averaging.

Effective pulmonary delivery of an aerosolized plasmid DNA vaccine via surface acoustic wave nebulization

BACKGROUND

Pulmonary-delivered gene therapy promises to mitigate vaccine safety issues and reduce the need for needles and skilled personnel to use them. While plasmid DNA (pDNA) offers a rapid route to vaccine production without side effects or reliance on cold chain storage, its delivery to the lung has proved challenging. Conventional methods, including jet and ultrasonic nebulizers, fail to deliver large biomolecules like pDNA intact due to the shear and cavitational stresses present during nebulization.

METHODS

In vitro structural analysis followed by in vivo protein expression studies served in assessing the integrity of the pDNA subjected to surface acoustic wave (SAW) nebulisation. In vivo immunization trials were then carried out in rats using SAW nebulized pDNA (influenza A, human hemagglutinin H1N1) condensate delivered via intratracheal instillation. Finally, in vivo pulmonary vaccinations using pDNA for influenza was nebulized and delivered via a respirator to sheep.

RESULTS

The SAW nebulizer was effective at generating pDNA aerosols with sizes optimal for deep lung delivery. Successful gene expression was observed in mouse lung epithelial cells, when SAW-nebulized pDNA was delivered to male Swiss mice via intratracheal instillation. Effective systemic and mucosal antibody responses were found in rats via post-nebulized, condensed fluid instillation. Significantly, we demonstrated the suitability of the SAW nebulizer to administer unprotected pDNA encoding an influenza A virus surface glycoprotein to respirated sheep via aerosolized inhalation.

CONCLUSION

Given the difficulty of inducing functional antibody responses for DNA vaccination in large animals, we report here the first instance of successful aerosolized inhalation delivery of a pDNA vaccine in a large animal model relevant to human lung development, structure, physiology, and disease, using a novel, low-power (<1 W) surface acoustic wave (SAW) hand-held nebulizer to produce droplets of pDNA with a size range suitable for delivery to the lower respiratory airways.

A new building block for DNA network formation by self-assembly and polymerase chain reaction

The predictability of DNA self-assembly is exploited in many nanotechnological approaches. Inspired by naturally existing self-assembled DNA architectures, branched DNA has been developed that allows self-assembly to predesigned architectures with dimensions on the nanometer scale. DNA is an attractive material for generation of nanostructures due to a plethora of enzymes which modify DNA with high accuracy, providing a toolbox for many different manipulations to construct nanometer scaled objects. We present a straightforward synthesis of a rigid DNA branching building block successfully used for the generation of DNA networks by self-assembly and network formation by enzymatic DNA synthesis. The Y-shaped 3-armed DNA construct, bearing 3 primer strands is accepted by Taq DNA polymerase. The enzyme uses each arm as primer strand and incorporates the branched construct into large assemblies during PCR. The networks were investigated by agarose gel electrophoresis, atomic force microscopy, dynamic light scattering, and electron paramagnetic resonance spectroscopy. The findings indicate that rather rigid DNA networks were formed. This presents a new bottom-up approach for DNA material formation and might find applications like in the generation of functional hydrogels.

Semiquinone glucoside derivative (SQGD) isolated from Bacillus sp. INM-1 protects against gamma radiation-induced oxidative stress

In the present study, radioprotective potential of Semiquinone glucoside derivative (SQGD) isolated from radioresistant bacterium Bacillus sp. INM-1 was evaluated. γ-Radiation induced protein carbonylation, plasmid DNA damage, enzyme functional impairment, lipid peroxidation, HO radicals generation and their protection by SQGD was assessed. As a result of SQGD treatment, significant inhibition (p<0.05) in protein carbonylation was observed with BSA. SQGD treatment was found to restore supercoiled (~70±3.21%) form of irradiated plasmid DNA against γ-irradiation. SQGD protects enzymes (EcoR1 and BamH1) against radiation-induced dysfunctioning. SQGD significantly inhibited (p<0.05) lipid peroxidation in liposomes, brain and liver homogenate. Higher HO(•) radicals-averting activity of SQGD was observed in the serum and liver homogenate of C57BL/6 mice against H2O2-induced oxidative stress. In conclusion, SQGD demonstrates excellent radical-scavenging activity towards bio-macromolecules in irradiated environment and can be developed as an ideal radioprotector against radiation-induced oxidative stress in future.

Patchiness of ion-exchanged mica revealed by DNA binding dynamics at short length scales

The binding of double-stranded (ds) DNA to mica can be controlled through ion-exchanging the mica with divalent cations. Measurements of the end-to-end distance of linear DNA molecules discriminate whether the binding mechanism occurs through 2D surface equilibration or kinetic trapping. A range of linear dsDNA fragments have been used to investigate length dependences of binding. Mica, ion-exchanged with Ni(II) usually gives rise to kinetically trapped DNA molecules, however, short linear fragments (<800 bp) are seen to deviate from the expected behaviour. This indicates that ion-exchanged mica is heterogeneous, and contains patches or domains, separating different ionic species. These results correlate with imaging of dsDNA under aqueous buffer on Ni(II)-mica and indicate that binding domains are of the order of 100 nm in diameter. Shorter DNA fragments behave intermediate to the two extreme cases of 2D equilibration and kinetic trapping. Increasing the incubation time of Ni(II) on mica, from minutes to hours, brings the conformations of the shorter DNA fragments closer to the theoretical value for kinetic trapping, indicating that long timescale kinetics play a role in ion-exchange. X-ray photoelectron spectroscopy (XPS) was used to confirm that the relative abundance of Ni(II) ions on the mica surface increases with time. These findings can be used to enhance spatial control of binding of DNA to inorganic surfaces with a view to patterning high densities arrays.

Nanoscale spatial distribution of thiolated DNA on model nucleic acid sensor surfaces

The nanoscale arrangement of the DNA probe molecules on sensor surfaces has a profound impact on molecular recognition and signaling reactions on DNA biosensors and microarrays. Using electrochemical atomic force microscopy, we have directly determined the nanoscale spatial distribution of thiolated DNA that are attached to gold via different methods. We discovered significant heterogeneity in the probe density and limited stability for DNA monolayers prepared by the backfilling method, that is, first exposing the surface to thiolated DNA then "backfilling" with a passivating alkanethiol. On the other hand, the monolayers prepared by "inserting" thiolated DNA into a preformed alkanethiol monolayer lead to a more uniformly distributed layer of DNA. With high-resolution images of single DNA molecules on the surface, we have introduced spatial statistics to characterize the nanoscale arrangement of DNA probes. The randomness of the spatial distribution has been characterized. By determining the local densities surrounding individual molecules, we observed subpopulations of probes with dramatically different levels of "probe crowding". We anticipate that the novel application of spatial statistics to DNA monolayers can enable a framework to understand heterogeneity in probe spatial distributions, interprobe interactions, and ultimately probe activity on sensor surfaces.

Biopolymer-based nanoparticles for drug/gene delivery and tissue engineering

There has been a great interest in application of nanoparticles as biomaterials for delivery of therapeutic molecules such as drugs and genes, and for tissue engineering. In particular, biopolymers are suitable materials as nanoparticles for clinical application due to their versatile traits, including biocompatibility, biodegradability and low immunogenicity. Biopolymers are polymers that are produced from living organisms, which are classified in three groups: polysaccharides, proteins and nucleic acids. It is important to control particle size, charge, morphology of surface and release rate of loaded molecules to use biopolymer-based nanoparticles as drug/gene delivery carriers. To obtain a nano-carrier for therapeutic purposes, a variety of materials and preparation process has been attempted. This review focuses on fabrication of biocompatible nanoparticles consisting of biopolymers such as protein (silk, collagen, gelatin, β-casein, zein and albumin), protein-mimicked polypeptides and polysaccharides (chitosan, alginate, pullulan, starch and heparin). The effects of the nature of the materials and the fabrication process on the characteristics of the nanoparticles are described. In addition, their application as delivery carriers of therapeutic drugs and genes and biomaterials for tissue engineering are also reviewed.

Electric-field dependent conformations of single DNA molecules on a model biosensor surface

Despite the variety of nucleic acid sensors developed, we still do not have definite answers to some questions that are important to the molecular binding and, ultimately, the sensitivity and reliability of the sensors. How do the DNA probes distribute on the surface at the nanoscale? As the functionalized surfaces are highly heterogeneous, how are the conformations affected when the probe molecules interact with defects? How do DNA molecules respond to electric fields on the surface, which are applied in a variety of detection methods? With in situ electrochemical atomic force microscopy and careful tailoring of nanoscale surface interactions, we are able to observe the nanoscale conformations of individual DNA molecules on a model biosensor surface: thiolated DNA on a gold surface passivated with a hydroxyl-terminated alkanethiol self-assembled monolayer. We find that under applied electric fields, the conformations are highly sensitive to the choice of the alkanethiol molecule. Depending on the monolayer and the nature of the defects, the DNA molecules may either adopt a highly linear or a highly curved conformation. These unusual structures are difficult to observe through existing "ensemble" characterizations of nucleic acid sensors. These findings provide a step toward correlating target-binding affinity, selectivity, and kinetics to the nanoscale chemical structure of and around the probe molecules in practical nucleic acid devices.

Possible origin of life between mica sheets: does life imitate mica?

The mica hypothesis for the origin of life proposes that life originated between the sheets of muscovite mica. This paper elaborates on two ways that life resembles what might have originated between mica sheets. First, enzymes: The configurations and dynamics of enzymes, with their substrates, cofactors, and sometimes transition metal ions, often resemble mica sheets, with their open-and-shut motions, acting on small molecules between them, sometimes assisted by transition metal ions. Second, organisms: Mica world had the potential to be a community or ecosystem of prebiotic organisms in a way unlike other models for the origin of life.

Atomic force microscopy with nanoscale cantilevers resolves different structural conformations of the DNA double helix

Structural variability and flexibility are crucial factors for biomolecular function. Here we have reduced the invasiness and enhanced the spatial resolution of atomic force microscopy (AFM) to visualize, for the first time, different structural conformations of the two polynucleotide strands in the DNA double helix, for single molecules under near-physiological conditions. This is achieved by identifying and tracking the anomalous resonance behavior of nanoscale AFM cantilevers in the immediate vicinity of the sample.

Single-stranded loops as end-label polarity markers for double-stranded linear DNA templates in atomic force microscopy

Visualization of DNA-protein interactions by atomic force microscopy (AFM) has deepened our understanding of molecular processes such as DNA transcription. Interpretation of systems where more than one protein acts on a single template, however, is complicated by protein molecules migrating along the DNA. Single-molecule AFM imaging experiments can reveal more information if the polarity of the template can be determined. A nucleic acid-based approach to end-labelling is desirable because it does not compromise the sample preparation procedures for biomolecular AFM. Here, we report a method involving oligonucleotide loop-primed synthesis for the end labelling of double-stranded DNA to discriminate the polarity of linear templates at the single-molecule level. Single-stranded oligonucleotide primers were designed to allow loop formation while retaining 3'-single-strand extensions to facilitate primer annealing to the template. Following a DNA polymerase extension, the labelled templates were shown to have the ability to form open promoter complexes on a model nested gene template using two Escherichia coli RNA polymerases in a convergent transcription arrangement. Analysis of the AFM images indicates that the added loops have no effect on the ability of the promoters to recruit RNA polymerase. This labelling strategy is proposed as a generic methodology for end-labelling linear DNA for studying DNA-protein interactions by AFM.