The structure of DNA by direct imaging

Atomic Force Microscopy: Mechanosensor and Mechanotransducer for Probing Biological System from Molecules to Tissues

Atomic Force Microscopy (AFM) is a powerful technique with widespread applications in various scientific fields, including biology. It operates by precisely detecting the interaction between a sharp tip and a sample surface, providing high-resolution topographical information and mechanical properties at a nanoscale. Through the years, a deeper understanding of this tip-sample interaction and the mechanisms by which it can be more precisely regulated have invariably led to improvements in AFM imaging. Additionally, AFM can serve not only as a sensor but also as a tool for actively manipulating the mechanical properties of biological systems. By applying controlled forces to the sample surface, AFM allows for a deeper understanding of mechanotransduction pathways, the intricate signaling cascades that convert physical cues into biochemical responses. This review, is an extensive overview of the current status of AFM working either as a mechanosensor or a mechanotransducer to probe biological systems across diverse scales, from individual molecules to entire tissues is presented. Challenges are discussed and potential future research directions are elaborated.

Angle between DNA linker and nucleosome core particle regulates array compaction revealed by individual-particle cryo-electron tomography

The conformational dynamics of nucleosome arrays generate a diverse spectrum of microscopic states, posing challenges to their structural determination. Leveraging cryogenic electron tomography (cryo-ET), we determine the three-dimensional (3D) structures of individual mononucleosomes and arrays comprising di-, tri-, and tetranucleosomes. By slowing the rate of condensation through a reduction in ionic strength, we probe the intra-array structural transitions that precede inter-array interactions and liquid droplet formation. Under these conditions, the arrays exhibite irregular zig-zag conformations with loose packing. Increasing the ionic strength promoted intra-array compaction, yet we do not observe the previously reported regular 30-nanometer fibers. Interestingly, the presence of H1 do not induce array compaction; instead, one-third of the arrays display nucleosomes invaded by foreign DNA, suggesting an alternative role for H1 in chromatin network construction. We also find that the crucial parameter determining the structure adopted by chromatin arrays is the angle between the entry and exit of the DNA and the corresponding tangents to the nucleosomal disc. Our results provide insights into the initial stages of intra-array compaction, a critical precursor to condensation in the regulation of chromatin organization.

Conformational Change of Nucleosome Arrays prior to Phase Separation

Chromatin phase transition serves as a regulatory mechanism for eukaryotic transcription. Understanding this process requires the characterization of the nucleosome array structure in response to external stimuli prior to phase separation. However, the intrinsic flexibility and heterogeneity hinders the arrays' structure determination. Here we exploit advances in cryogenic electron tomography (cryo-ET) to determine the three-dimensional (3D) structure of each individual particle of mono-, di-, tri-, and tetranucleosome arrays. Statistical analysis reveals the ionic strength changes the angle between the DNA linker and nucleosome core particle (NCP), which regulate the overall morphology of nucleosome arrays. The finding that one-third of the arrays in the presence of H1 contain an NCP invaded by foreign DNA suggests an alternative function of H1 in constructing nucleosomal networks. The new insights into the nucleosome conformational changes prior to the intermolecular interaction stage extends our understanding of chromatin phase separation regulation.

Activation/Inhibition of Gene Expression Caused by Alcohols: Relationship with the Viscoelastic Property of a DNA Molecule

Alcohols are used in the life sciences because they can condense and precipitate DNA. Alcohol consumption has been linked to many diseases and can alter genetic activity. In the present report, we carried out experiments to make clear how alcohols affect the efficiency of transcription-translation (TX-TL) and translation (TL) by adapting cell-free gene expression systems with plasmid DNA and RNA templates, respectively. In addition, we quantitatively analyzed intrachain fluctuations of single giant DNA molecules based on the fluctuation-dissipation theorem to gain insight into how alcohols affect the dynamical property of a DNA molecule. Ethanol (2-3%) increased gene expression levels four to five times higher than the control in the TX-TL reaction. A similar level of enhancement was observed with 2-propanol, in contrast to the inhibitory effect of 1-propanol. Similar alcohol effects were observed for the TL reaction. Intrachain fluctuation analysis through single DNA observation showed that 1-propanol markedly increased both the spring and damping constants of single DNA in contrast to the weak effects observed with ethanol, whereas 2-propanol exhibits an intermediate effect. This study indicates that the activation/inhibition effects of alcohol isomers on gene expression correlate with the changes in the viscoelastic mechanical properties of DNA molecules.

Biomolecular histology as a novel proxy for ancient DNA and protein sequence preservation

Researchers' ability to accurately screen fossil and subfossil specimens for preservation of DNA and protein sequences remains limited. Thermal exposure and geologic age are usable proxies for sequence preservation on a broad scale but are of nominal use for specimens of similar depositional environments. Cell and tissue biomolecular histology is thus proposed as a novel proxy for determining sequence preservation potential of ancient specimens with improved accuracy. Biomolecular histology as a proxy is hypothesized to elucidate why fossils/subfossils of some depositional environments preserve sequences while others do not and to facilitate selection of ancient specimens for use in molecular studies.

Nuclear-targeted carbon quantum dot mediated CRISPR/Cas9 delivery for fluorescence visualization and efficient editing

Nuclear targeted delivery has great potential in improving the efficiency of non-viral carrier mediated genome editing. However, direct and efficient delivery of CRISPR/Cas9 plasmid into the nucleus remains a challenge. In this study, a nuclear targeted gene delivery platform based on fluorescent carbon quantum dots (CQDs) was developed. Polyethylenimine (PEI) and polyethylene glycol (PEG) synergistically passivated the surface of CQDs, providing an excitation-independent green-emitting fluorescent CQDs-PEI-PEG conjugate (CQDs-PP) with an ultra-small size and positive surface charge. Here we show that CQDs-PP could bind CRISPR/Cas9 plasmid to form a nano-complex by electrostatic attraction, which can bypass lysosomes and enter the nucleus by passive diffusion, and thereby improve the transfection efficiency. Also, CQDs-PP could deliver CRISPR/Cas9 plasmid into HeLa cells, resulting in the insertion/deletion mutation of the target EFHD1 gene. More importantly, CQDs-PP exhibited a considerably higher gene editing efficiency as well as comparable or lower cytotoxicity relative to Lipo2000 and PEI-passivated CQDs-PEI (CQDs-P). Thus, the nuclear-targeted CQDs-PP is expected to constitute an efficient CRISPR/Cas9 delivery carrier in vitro with imaging-trackable ability.

Scanning Tunneling Microscopy of Biological Structures: An Elusive Goal for Many Years

Scanning tunneling microscopy (STM) is a technique that can be used to directly observe individual biomolecules at near-molecular scale. Within this framework, STM is of crucial significance because of its role in the structural analysis, the understanding the imaging formation, and the development of relative techniques. Four decades after its invention, it is pertinent to ask how much of the early dream has come true. In this study, we aim to overview different analyses for DNA, lipids, proteins, and carbohydrates. The relevance of STM imaging is exhibited as an opportunity to assist measurements and biomolecular identification in nanobiotechnology, nanomedicine, biosensing, and other cutting-edge applications. We believe STM research is still an entire science research ecosystem for joining several areas of expertise towards a goal settlement that has been elusive for many years.

Direct imaging of polymer filaments pulled from rebounding drops

Polymer filaments form the foundation of biology from cell scaffolding to DNA. Their study and fabrication play an important role in a wide range of processes from tissue engineering to molecular machines. We present a simple method to deposit stretched polymer fibers between micro-pillars. This occurs when a polymeric drop impacts on and rebounds from an inclined superhydrophobic substrate. It wets the top of the pillars and pulls out liquid filaments which are stretched and can attach to adjacent pillars leaving minuscule threads, with the solvent evaporating to leave the exposed polymers. We use high-speed video at the microscale to characterize the most robust filament-forming configurations, by varying the impact velocity, substrate structure and inclination angle, as well as the PEO-polymer concentration. Impacts onto plant leaves or a randomized nano-structured surface leads to the formation of a branched structure, through filament mergers at the free surface of the drop. SEM shows the deposition of filament bundles which are thinner than those formed by evaporation or rolling drops. Raman spectroscopy identifies the native mode B stretched DNA filaments from aqueous-solution droplets.

Direct Visualization and Identification of Membrane Voltage-Gated Sodium Channels from Human iPSC-Derived Neurons by Multiple Imaging and Light Enhanced Spectroscopy

In this study, transmission electron microscopy atomic force microscopy, and surface enhanced Raman spectroscopy are combined through a direct imaging approach, to gather structural and chemical information of complex molecular systems such as ion channels in their original plasma membrane. Customized microfabricated sample holder allows to characterize Na_v channels embedded in the original plasma membrane extracted from neuronal cells that are derived from healthy human induced pluripotent stem cells. The identification of the channels is accomplished by using two different approaches, one of them widely used in cryo-EM (the particle analysis method) and the other based on a novel Zernike Polynomial expansion of the images bitmap. This approach allows to carry out a whole series of investigations, one complementary to the other, on the same sample, preserving its state as close as possible to the original membrane configuration.

Micro/Nanopatterned Superhydrophobic Surfaces Fabrication for Biomolecules and Biomaterials Manipulation and Analysis

Superhydrophobic surfaces display an extraordinary repulsion to water and water-based solutions. This effect emerges from the interplay of intrinsic hydrophobicity of the surface and its morphology. These surfaces have been established for a long time and have been studied for decades. The increasing interest in recent years has been focused towards applications in many different fields and, in particular, biomedical applications. In this paper, we review the progress achieved in the last years in the fabrication of regularly patterned superhydrophobic surfaces in many different materials and their exploitation for the manipulation and characterization of biomaterial, with particular emphasis on the issues affecting the yields of the fabrication processes and the quality of the manufactured devices.

DNA Studies: Latest Spectroscopic and Structural Approaches

This review looks at the different approaches, techniques, and materials devoted to DNA studies. In the past few decades, DNA nanotechnology, micro-fabrication, imaging, and spectroscopies have been tailored and combined for a broad range of medical-oriented applications. The continuous advancements in miniaturization of the devices, as well as the continuous need to study biological material structures and interactions, down to single molecules, have increase the interdisciplinarity of emerging technologies. In the following paragraphs, we will focus on recent sensing approaches, with a particular effort attributed to cutting-edge techniques for structural and mechanical studies of nucleic acids.

A droplet reactor on a super-hydrophobic surface allows control and characterization of amyloid fibril growth

Methods to produce protein amyloid fibrils, in vitro, and in situ structure characterization, are of primary importance in biology, medicine, and pharmacology. We first demonstrated the droplet on a super-hydrophobic substrate as the reactor to produce protein amyloid fibrils with real-time monitoring of the growth process by using combined light-sheet microscopy and thermal imaging. The molecular structures were characterized by Raman spectroscopy, X-ray diffraction and X-ray scattering. We demonstrated that the convective flow induced by the temperature gradient of the sample is the main driving force in the growth of well-ordered protein fibrils. Particular attention was devoted to PHF6 peptide and full-length Tau441 protein to form amyloid fibrils. By a combined experimental with the molecular dynamics simulations, the conformational polymorphism of these amyloid fibrils were characterized. The study provided a feasible procedure to optimize the amyloid fibrils formation and characterizations of other types of proteins in future studies.

Zhang et al present an integrated real-time imaging and flow field control platform based on water droplet evaporation on super-hydrophobic substrate (SHS) to enable amyloid fibril aggregation. They apply this methodology to observe structural polymorphism in PHF6 peptide and full length Tau441.

Bent DNA Bows as Sensing Amplifiers for Detecting DNA-Interacting Salts and Molecules

Due to the central role of DNA, its interactions with inorganic salts and small organic molecules are important. For example, such interactions play important roles in various fundamental cellular processes in living systems and are involved in many DNA-damage related diseases. Strategies to improve the sensitivity of existing techniques for studying DNA interactions with other molecules would be appreciated in situations where the interactions are too weak. Here we report our development and demonstration of bent DNA bows for amplifying, sensing, and detecting the interactions of 14 inorganic salts and small organic molecules with DNA. With the bent DNA bows, these interactions were easily visualized and quantified in gel electrophoresis, which were difficult to measure without bending. In addition, the strength of the interactions of DNA with the various salts/molecules were quantified using the modified Hill equation. This work highlights the amplification effects of the bending elastic energy stored in the DNA bows and the potential use of the DNA bows for quantitatively measuring DNA interactions with small molecules as simple economic methods; it may also pave the way for exploiting the bent DNA bows for other applications such as screening DNA-interacting molecules and drugs.

Dynamic Detection of Active Enzyme Instructed Supramolecular Assemblies In Situ via Super-Resolution Microscopy

Inspired by the self-assembly phenomena in nature, the instructed self-assembly of exogenous small molecules in a biological environment has become a prevalent process to control cell fate. Despite mounting examples of versatile bioactivities, the underlying mechanism remains less understood, which is in large hindered by the difficulties in the identification of those dynamic assemblies in situ. Here, with direct stochastic optical reconstruction microscopy, we are able to elucidate the dynamic morphology transformation of the enzyme-instructed supramolecular assemblies in situ inside cancer cells with a resolution below 50 nm. It indicates that the assembling molecules endure drastically different pathways between cell lines with different phosphatase activities and distribution. In HeLa cells, the direct formation of intracellular supramolecular nanofibers showed slight cytotoxicity, which was due to the possible cellular secretory pathway to excrete those exogenous molecules assemblies. In contrast, in Saos-2 cells with active phosphatase on the cell surface, assemblies with granular morphology first formed on the cell membranes, followed by a transformation into nanofibers and accumulation in cells, which induced Saos-2 cell death eventually. Overall, we provided a convenient method to reveal the in situ dynamic nanomorphology transformation of the supramolecular assemblies in a biological environment, in order to decipher their diverse biological activities.

Visualization of unstained homo/heterogeneous DNA nanostructures by low-voltage scanning transmission electron microscopy

Three-dimensional (3D) homo/heterogeneous DNA nanostructures were studied with low-voltage scanning transmission electron microscopy (LV-STEM). Four types of 3D DNA nanostructures were designed and fabricated by the origami method including newly proposed protocols. The low-energy electron probe and optimized dark-field STEM detector enabled individual unstained DNA nanostructures to be clearly imaged by the single acquisition without the averaging process. For the vertically stacked double structures, assembled through modified single-stranded domains, and the structures containing a square opening (i.e., a hole) in the center, the LV-STEM successfully reveals the vertical information of these 3D structures as the contrast differences compared to the reference. For the heterogeneous structures, the LV-STEM visualized both regions of the functionalized gold nanoparticles and the DNA base structure with distinct contrasts. This study introduces a straightforward method to fabricate stackable DNA nanostructures or nanoparticles by replacing a relatively small number of incumbent DNA strands, which could realize the simple and sophisticated fabrication of higher-order 3D DNA homo/hetero nanostructures. Together with these design techniques of DNA nanostructures, this study has demonstrated that the LV-STEM is the swift and simple method for visualizing the 3D DNA nanostructures and certifying the fabricated products as the specified design, which is applicable to various research fields on soft materials including DNA nanotechnology.

Visualization of unstained DNA nanostructures with advanced in-focus phase contrast TEM techniques

Over the last few years, tremendous progress has been made in visualizing biologically important macromolecules using transmission electron microscopy (TEM) and understanding their structure-function relation. Yet, despite the importance of DNA in all forms of life, TEM visualization of individual DNA molecules in its native unlabeled form has remained extremely challenging. Here, we present high-contrast images of unstained single-layer DNA nanostructures that were obtained using advanced in-focus phase contrast TEM techniques. These include sub-Ångstrom low voltage electron microscopy (SALVE), the use of a volta-potential phase plate (VPP), and dark-field (DF) microscopy. We discuss the advantages and drawbacks of these techniques for broad applications in structural biology and materials science.

Nanomechanical DNA resonators for sensing and structural analysis of DNA-ligand complexes

The effect of direct or indirect binding of intercalant molecules on DNA structure is of fundamental importance in understanding the biological functioning of DNA. Here we report on self-suspended DNA nanobundles as ultrasensitive nanomechanical resonators for structural studies of DNA-ligand complexes. Such vibrating nanostructures represent the smallest mechanical resonator entirely composed of DNA. A correlative analysis between the mechanical and structural properties is exploited to study the intrinsic changes of double strand DNA, when interacting with different intercalant molecules (YOYO-1 and GelRed) and a chemotherapeutic drug (Cisplatin), at different concentrations. Possible implications of our findings are related to the study of interaction mechanism of a wide category of molecules with DNA, and to further applications in medicine, such as optimal titration of chemotherapeutic drugs and environmental studies for the detection of heavy metals in human serum.

Structural Modification of DNA Studied by Scanning Tunneling Microscopy

In addition to the well-known double-helix structure of deoxyribonucleic acid (DNA), theoretical simulations have predicted structural variants, such as cross and T-shaped formations. The direct visualization of individual DNA molecules by scanning probe microscopy should be able to identify these structures. In this study, we examine various structures of DNA deposited on Au(111) by using an electrospray method and analyzing with a low-temperature scanning tunneling microscope. We could identify in detail several interesting structures. In particular, we found that double-stranded DNAs are partially unraveled into single-stranded DNAs and we confirmed the presence of T-shaped DNA structures.

Radiation damage during in situ electron microscopy of DNA-mediated nanoparticle assemblies in solution

Oligonucleotide-nanoparticle conjugates, also called programmable atom equivalents, carry promise as building blocks for self-assembled colloidal crystals, reconfigurable or stimuli responsive functional materials, as well as bio-inspired hierarchical architectures in wet environments. In situ studies of the DNA-mediated self-assembly of nanoparticles have so far been limited to reciprocal space techniques. Liquid-cell electron microscopy could enable imaging such systems with high resolution in their native environment but to realize this potential, radiation damage to the oligonucleotide linkages needs to be understood and conditions for damage-free electron microscopy identified. Here, we analyze in situ observations of DNA-linked two-dimensional nanoparticle arrays, along with control experiments for different oligonucleotide configurations, to identify the mechanisms of radiation damage for ordered superlattices of DNA-nanoparticle conjugates. In a biological context, the results point to new avenues for studying direct and indirect radiation effects for small ensembles of DNA in solution by tracking conjugated nanoparticles. By establishing low-dose conditions suitable for extended in situ imaging of programmable atom equivalents, our work paves the way for real-space observations of DNA-mediated self-assembly processes.

Imaging and structural studies of DNA-protein complexes and membrane ion channels

In bio-imaging by electron microscopy, damage of the sample and limited contrast are the two main hurdles for reaching high image quality. We extend a new preparation method based on nanofabrication and super-hydrophobicity to the imaging and structural studies of nucleic acids, nucleic acid-protein complexes (DNA/Rad51 repair protein complex) and neuronal ion channels (gap-junction, K⁺ and GABA_A channels) as paradigms of biological significance and increasing complexity. The preparation method is based on the liquid phase and is compatible with physiological conditions. Only in the very last stage, samples are dried for TEM analysis. Conventional TEM and high-resolution TEM (HRTEM) were used to achieve a resolution of 3.3 and 1.5 Å, respectively. The EM dataset quality allows the determination of relevant structural and metrological information on the DNA structure, DNA-protein interactions and ion channels, allowing the identification of specific macromolecules and their structure.

Circulating free DNA in the era of precision oncology: Pre- and post-analytical concerns

Cancer treatment has entered the era of precision medicine, where knowledge of a patient's genetic profile is used to facilitate early diagnosis, drug selection, prognosis, prediction of drug responsiveness, the onset of secondary resistance, and relapse. Circulating free DNA (cfDNA) has emerged as an ideal source of genetic information for cancer patients, and numerous studies have explored its validity in various clinical applications. However, clinical implementation of cfDNA-based tests has been slow. In this review, we addressed some of the pre- and post-analytical issues regarding cfDNA tests. First, we summarized the characteristics of cfDNA and reviewed the methods used to identify tumor-derived cfDNA from the pool of total cfDNA. Second, we described the procedures used to extract cfDNA, which have a great impact on representativeness and yield. Finally, we discussed our thoughts on the validation of cfDNA-based tests and the reporting of test results amid drastic limitations.

Effect of testosterone and its aliphatic and aromatic dimers on DNA morphology

Conjugation of DNA with testosterone and it aliphatic dimer (alip) and aromatic dimer (arom) was investigated in aqueous solution at pH 7.4. Multiple spectroscopic methods, transmission electron microscopy (TEM) and molecular modeling were used to characterize steroid-DNA binding and DNA morphology. Spectroscopic analysis showed that testosterone binds DNA via A7, A16, A17, T8, T15 and T18 nucleobases with overall binding constants K_test-DNA=1.8 (±0.4)×10⁴M^-1, K_{test-dimeralip-DNA}=5.7 (±0.7)×10⁴M^-1 and K_{test-dimer-arom-DNA}=7.3 (±0.9)×10⁴M^-1. The binding affinity increases in this order: testosterone dimer-aromatic>testosterone dimer-aliphatic>testosterone. The steroid loading efficacy was 40-50%. Transmission electron microscopy showed major changes in DNA morphology as testosterone-DNA interaction occurred with increase in the diameter of the DNA aggregate, indicating encapsulation of testosterone by DNA. Modeling showed the presence of several nucleobases attached to testosterone with the free binding energy of -4.93Kcal/mol.