Applications of synchrotron-based spectroscopic techniques in studying nucleic acids and nucleic acid-functionalized nanomaterials

Measuring full-field strain of the muscle-tendon junction using confocal microscopy combined with digital volume correlation

The muscle-tendon junction (MTJ) is a specialized interface that facilitates the transmission of force from the muscle to the tendon which has been implicated in muscle strains and tears. Understanding the transmission of forces and the strain generated in the MTJ is therefore important. For the first time, we report the 3D full-field strain distribution across the muscle-tendon junction (MTJ) using in-situ tensile testing and confocal microscopy coupled with digital volume correlation (DVC). This approach allowed us to measure the mechanical behaviour of the MTJ at the fibre/fascicle level. Acridine orange (AO) in 70% ethanol was used to enhance the contrast of the mouse Achilles-gastrocnemius MTJ, and the specimens were rehydrated prior to the tensile testing, which was performed using custom made tensile rig that fitted under the confocal microscopy. The 3D full-field strain distribution was obtained using DVC, where the strain changes were measured from confocal images taken with the MTJ under preload (0.4 N) and loaded (0.8 N and 1.2 N) representing 2.7- and 4-times body weight. High strain concentration was observed at the junction for both 0.8 N and 1.2 N loads. At the junction, the first principal stain (εp1), shear strain (γ) and von Mises strain (εVM) reached 15.2, 34.2 and 19.2% respectively. This study allowed us to measure fascicle level strain distribution at the MTJ. Using histology, microtears at the MTJ were seen in specimens loaded with 1.2 N which were associated with von Mises strain concentration in the adjacent region. The microtears occurred in regions where the strain level was between 8 and 15%. This study developed a methodology to determine high-resolution strain distribution at the MTJ and has the potential to be used to analyse the strain at the cellular level using higher magnification objectives.

Persistent Targeting DNA Nanocarrier Made of 3D Structural Unit Assembled from Only One Basic Multi-Palindromic Oligonucleotide for Precise Gene Cancer Therapy

Construction of a simple, reconfigurable, and stimuli-responsive DNA nanocarrier remains a technical challenge. In this contribution, by designing three palindromic fragments, a simplest four-sticky end-contained 3D structural unit (PS-unit) made of two same DNA components is proposed. Via regulating the rotation angle of central longitudinal axis of PS-unit, the oriented assembly of one-component spherical architecture is accomplished with high efficiency. Introduction of an aptamer and sticky tail warehouse into one component creates a size-change-reversible targeted siRNA delivery nanovehicle. Volume swelling of 20 nm allows one carrier to load 1987 siPLK1s. Once entering cancer cells and responding to glutathione (GSH) stimuli, siPLK1s are almost 100% released and original size of nanovehicle is restored, inhibiting the expression of PLK1 protein and substantially suppressing tumor growth (superior to commercial transfection agents) in tumor-bearing mice without systemic toxicity.

Full-Field Strain Measurements of the Muscle-Tendon Junction Using X-ray Computed Tomography and Digital Volume Correlation

We report, for the first time, the full-field 3D strain distribution of the muscle-tendon junction (MTJ). Understanding the strain distribution at the junction is crucial for the treatment of injuries and to predict tear formation at this location. Three-dimensional full-field strain distribution of mouse MTJ was measured using X-ray computer tomography (XCT) combined with digital volume correlation (DVC) with the aim of understanding the mechanical behavior of the junction under tensile loading. The interface between the Achilles tendon and the gastrocnemius muscle was harvested from adult mice and stained using 1% phosphotungstic acid in 70% ethanol. In situ XCT combined with DVC was used to image and compute strain distribution at the MTJ under a tensile load (2.4 N). High strain measuring 120,000 µε, 160,000 µε, and 120,000 µε for the first principal stain (εp1), shear strain (γ), and von Mises strain (εVM), respectively, was measured at the MTJ and these values reduced into the body of the muscle or into the tendon. Strain is concentrated at the MTJ, which is at risk of being damaged in activities associated with excessive physical activity.

Hybridization chain reaction and its applications in biosensing

To pursue the sensitive and efficient detection of informative biomolecules for bioanalysis and disease diagnosis, a series of signal amplification techniques have been put forward. Among them, hybridization chain reaction (HCR) is an isothermal and enzyme-free process where the cascade reaction of hybridization events is initiated by a target analyte, yielding a long nicked dsDNA molecule analogous to alternating copolymers. Compared with conventional polymerase chain reaction (PCR) that can proceed only with the aid of polymerases and complicated thermal cycling, HCR has attracted increasing attention because it can occur under mild conditions without using enzymes. As a powerful signal amplification tool, HCR has been employed to construct various simple, sensitive and economic biosensors for detecting nucleic acids, small molecules, cells, and proteins. Moreover, HCR has also been applied to assemble complex nanostructures, some of which even act as the carriers to execute the targeted delivery of anticancer drugs. Recently, HCR has engendered tremendous progress in RNA imaging applications, which can not only achieve endogenous RNA imaging in living cells or even living animals but also implement imaging-guided photodynamic therapy, paving a promising path to promote the development of theranostics. In this review, we begin with the fundamentals of HCR and then focus on summarizing the recent advances in HCR-based biosensors for biosensing and RNA imaging strategies. Further, the challenges and future perspective of HCR-based signal amplification in biosensing and theranostic application are discussed.

Rational design of guiding elements to control folding topology in i-motifs with multiple quadruplexes

Nucleic acids are versatile scaffolds that accommodate a wide range of precisely defined operational characteristics. Rational design of sensing, molecular computing, nanotechnology, and other nucleic acid devices requires precise control over folding conformations in these macromolecules. Here, we report a new approach that empowers well-defined conformational transitions in DNA molecular devices. Specifically, we develop tools for precise folding of multiple DNA quadruplexes (i-motifs) within the same oligonucleotide strand. To accomplish this task, we modify a DNA strand with kinetic control elements (hairpins and double stranded stems) that fold on a much faster timescale and consequently guide quadruplexes toward the targeted folding topology. To demonstrate that such guiding elements indeed facilitate formation of the targeted folding topology, we thoroughly characterize the folding/unfolding transitions through a combination of thermodynamic techniques, size exclusion chromatography (SEC) and small-angle X-ray scattering (SAXS). Furthermore, we extend SAXS capabilities to produce a direct insight on the shape and dimensions of the folded quadruplexes by computing their electron density maps from solution scattering data.

Multifunctionality of gold nanoparticles: Plausible and convincing properties

In a couple of decades, nanotechnology has become a trending area in science due to it covers all subject that combines diverse range of fields including but not limited to chemistry, physics and medicine. Various metal and metal oxide nanomaterials have been developed for wide range applications. However, the application of gold nanostructures and nanoparticles has been received more attention in various biomedical applications. The unique property of gold nanoparticles (AuNPs) is surface plasmon resonance (SPR) that determine the size, shape and stability. The wide surface area of AuNPs eases the proteins, peptides, oligonucleotides, and many other compounds to tether and enhance the biological activity of AuNPs. AuNPs have multifunctionality including antimicrobial, anticancer, drug and gene delivery, sensing applications and imaging. This state-of-the-art review is focused on the role of unique properties of AuNPs in multifunctionality and its various applications.

Small-Angle Scattering as a Structural Probe for Nucleic Acid Nanoparticles (NANPs) in a Dynamic Solution Environment

Nucleic acid-based technologies are an emerging research focus area for pharmacological and biological studies because they are biocompatible and can be designed to produce a variety of scaffolds at the nanometer scale. The use of nucleic acids (ribonucleic acid (RNA) and/or deoxyribonucleic acid (DNA)) as building materials in programming the assemblies and their further functionalization has recently established a new exciting field of RNA and DNA nanotechnology, which have both already produced a variety of different functional nanostructures and nanodevices. It is evident that the resultant architectures require detailed structural and functional characterization and that a variety of technical approaches must be employed to promote the development of the emerging fields. Small-angle X-ray and neutron scattering (SAS) are structural characterization techniques that are well placed to determine the conformation of nucleic acid nanoparticles (NANPs) under varying solution conditions, thus allowing for the optimization of their design. SAS experiments provide information on the overall shapes and particle dimensions of macromolecules and are ideal for following conformational changes of the molecular ensemble as it behaves in solution. In addition, the inherent differences in the neutron scattering of nucleic acids, lipids, and proteins, as well as the different neutron scattering properties of the isotopes of hydrogen, combined with the ability to uniformly label biological macromolecules with deuterium, allow one to characterize the conformations and relative dispositions of the individual components within an assembly of biomolecules. This article will review the application of SAS methods and provide a summary of their successful utilization in the emerging field of NANP technology to date, as well as share our vision on its use in complementing a broad suite of structural characterization tools with some simulated results that have never been shared before.

Synchrotron-radiation vacuum-ultraviolet circular dichroism spectroscopy in structural biology: an overview

Circular dichroism spectroscopy is widely used for analyzing the structures of chiral molecules, including biomolecules. Vacuum-ultraviolet circular dichroism (VUVCD) spectroscopy using synchrotron radiation can extend the short-wavelength limit into the vacuum-ultraviolet region (down to ~160 nm) to provide detailed and new information about the structures of biomolecules in combination with theoretical analysis and bioinformatics. The VUVCD spectra of saccharides can detect the high-energy transitions of chromophores such as hydroxy and acetal groups, disclosing the contributions of inter- or intramolecular hydrogen bonds to the equilibrium configuration of monosaccharides in aqueous solution. The roles of hydration in the fluctuation of the dihedral angles of carboxyl and amino groups of amino acids can be clarified by comparing the observed VUVCD spectra with those calculated theoretically. The VUVCD spectra of proteins markedly improves the accuracy of predicting the contents and number of segments of the secondary structures, and their amino acid sequences when combined with bioinformatics, for not only native but also nonnative and membrane-bound proteins. The VUVCD spectra of nucleic acids confirm the contributions of the base composition and sequence to the conformation in comparative analyses of synthetic poly-nucleotides composed of selected bases. This review surveys these recent applications of synchrotron-radiation VUVCD spectroscopy in structural biology, covering saccharides, amino acids, proteins, and nucleic acids.

Tapping into Synchrotron and Benchtop Circular Dichroism Spectroscopy for Expanding Studies of Complex Polysaccharides and their Interactions in Anoxic Archaeological Wood

Circular dichroism (CD) (and synchrotron circular dichroism (SCD)) spectroscopy is a rapid, highly sensitive technique used to investigate structural conformational changes in biomolecules in response to interactions with ligands in solution and in film. It is a chiroptical method and at least one of the interacting molecules must possess optical activity (or chirality). In this review, we compare the capabilities of CD and SCD in the characterisation of celluloses and lignin polymers in archaeological wood. Cellulose produces a range of spectral characteristics dependent on environment and form; many of the reported transitions occur in the vacuum-ultraviolet region (< 180 nm) most conveniently delivered using a synchrotron source. The use of induced CD in which achiral dyes are bound to celluloses to give shifted spectra in the visible region is also discussed, together with its employment to identify the handedness of the chiral twists in nanocrystalline cellulose. Lignin is one target for the design of future consolidants that interact with archaeological wood to preserve it. It is reportedly achiral, but here we review several studies in which CD spectroscopy has successfully revealed lignin interactions with chiral enzymes, highlighting the potential usefulness of the technique in future research to identify new generation consolidants.

Incorporation of mRNA in Lamellar Lipid Matrices for Parenteral Administration

Insertion of high molecular weight messenger RNA (mRNA) into lyotropic lipid phases as model systems for controlled release formulations for the mRNA was investigated. Low fractions of 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP) were used as an anchor to load the mRNA into a lamellar lipid matrix. Dispersions of zwitterionic lipid in the aqueous phase in the presence of increasing fractions of mRNA and cationic lipid were prepared, and the molecular organization was investigated as a function of mRNA and cationic lipid fraction. Insertion of both cationic lipid and mRNA was clearly proven from the physicochemical characteristics. The d-spacing of the lipid bilayers, as determined by small-angle X-ray scattering (SAXS) measurements, responded sensitively to the amount of inserted DOTAP and mRNA. A concise model of the insertion of the mRNA in the lipid matrices was derived, indicating that the mRNA was accommodated in the aqueous slab between lipid bilayers. Depending on the DOTAP and mRNA fraction, a different excess of water was present in this slab. Results from further physicochemical characterization, including determination of free and bound mRNA, zeta potential, and calorimetry data, were in line with this assumption. The structure of these concentrated lipid/mRNA preparations was maintained upon dilution. The functionality of the inserted mRNA was proven by cell culture experiments using C2C12 murine myoblast cells with the luciferase-encoding mRNA. The described lipid phases as carriers for the mRNA may be applicable for different routes of local administration, where control of the release kinetics and the form of the released mRNA (bound or free) is required.