AFM-Based Quantification of Conformational Changes in DNA Caused by Reactive Oxygen Species

Ultra-Tough Graphene Oxide/DNA 2D Hydrogel with Intrinsic Sensing and Actuation Functions

Hydrogel devices with mechanical toughness and tunable functionalities are highly desirable for practical long-term applications such as sensing and actuation elements for soft robotics. However, existing hydrogels have poor mechanical properties, slow rates of response, and low functionality. In this work, two-dimensional hydrogel actuators are proposed and formed on the self-assembly of graphene oxide (GO) and deoxynucleic acid (DNA). The self-assembly process is driven by the GO-induced transition of double stranded DNA (dsDNA) into single stranded DNA (ssDNA). Thus, the hydrogel's structural unit consists of two layers of GO covered by ssDNA and a layer of dsDNA in between. Such heterogeneous architectures stabilized by multiple hydrogen bondings have Young's modulus of up to 10 GPa and rapid swelling rates of 4.0 × 10-3 to 1.1 × 10-2 s-1, which surpasses most types of conventional hydrogels. It is demonstrated that the GO/DNA hydrogel actuators leverage the unique properties of these two materials, making them excellent candidates for various applications requiring sensing and actuation functions, such as artificial skin, wearable electronics, bioelectronics, and drug delivery systems.

Optimization and validation of ultrasensitive GC-MS/MS method to measure oxidatively induced DNA damage products and role of antioxidants in oxidation mechanism

Oxidation of DNA due to exposure to reactive oxygen species (ROS) is a major source of DNA damage. ROS induced damage to DNA plays an important role in some diseases such as various cancers, aging and neurodegenerative diseases. The detection of DNA oxidation products plays a major role in assessing the mutagenicity potential of specific exposure. The GC-MS/MS method was developed for the ultrasensitive determination of individual DNA damage products. The validation results revealed that the proposed method was reliable and sensitive. Multiple response surface methodology (MRSM) was used to optimize derivatization conditions of oxidatively DNA base damage products before GC-MS/MS analysis. The optimum derivatization conditions were determined as 40 min for derivatization time, 120 °C for derivatization temperature and 1.4 for BSTFA/pyridine ratio under nitrogen atmosphere. The effects of thymol, carvacrol and thymoquinone as antioxidants were investigated on oxidative DNA damage. The determination of the oxidatively induced DNA damage products was performed after adding DNA and antioxidants with different concentrations under oxidative stress. Eighteen DNA base damage products were analyzed simultaneously using GC-MS/MS. This study showed a significant decrease in the amount of DNA base damage products when the antioxidants were present in the medium.

The Effect of Gold Nanoparticle Concentration and Laser Fluence on the Laser-Induced Water Decomposition

This Article covers the influence of the concentration of gold nanoparticles on laser-induced water decomposition. It was established that addition of gold nanoparticles intensifies laser-induced water decomposition by almost 2 orders of magnitude. The water decomposition rate was shown to be maximal at a nanoparticle concentration around 10¹⁰ NP/mL, whereas a decrease or increase of nanoparticle concentration leads to a decrease of water decomposition rate. It was demonstrated that, if the concentration of nanoparticles in water-based colloid was less than 10¹⁰ NP/mL, laser irradiation of the colloid caused formation of molecular hydrogen, hydrogen peroxide, and molecular oxygen. If the concentration of nanoparticles exceeded 10¹¹ NP/mL, only two products, molecular hydrogen and hydrogen peroxide, were formed. Correlations between the water decomposition rate and the main optical and acoustic parameters of optical breakdown-generated plasma were investigated. Variants of laser-induced decomposition of colloidal solutions of nanoparticles based on organic solvents (ethanol, propanol-2, butanol-2, diethyl ether) were also analyzed.

New Algorithm to Enable Construction and Display of 3D Structures from Scanning Probe Microscopy Images Acquired Layer-by-Layer

Scanning probe microscopy (SPM), such as atomic force microscopy (AFM), is widely known for high-resolution imaging of surface structures and nanolithography in two dimensions (2D), providing important physical insights into surface science and material science. This work reports a new algorithm to enable construction and display of layer-by-layer 3D structures from SPM images. The algorithm enables alignment of SPM images acquired during layer-by-layer deposition and removal of redundant features and faithfully constructs the deposited 3D structures. The display uses a "see-through" strategy to enable the structure of each layer to be visible. The results demonstrate high spatial accuracy as well as algorithm versatility; users can set parameters for reconstruction and display as per image quality and research needs. To the best of our knowledge, this method represents the first report to enable SPM technology for 3D imaging construction and display. The detailed algorithm is provided to facilitate usage of the same approach in any SPM software. These new capabilities support wide applications of SPM that require 3D image reconstruction and display, such as 3D nanoprinting and 3D additive and subtractive manufacturing and imaging.

Ascent of atomic force microscopy as a nanoanalytical tool for exosomes and other extracellular vesicles

Over the last 30 years, atomic force microscopy (AFM) has made several significant contributions to the field of biology and medicine. In this review, we draw our attention to the recent applications and promise of AFM as a high-resolution imaging and force sensing technology for probing subcellular vesicles: exosomes and other extracellular vesicles. Exosomes are naturally occurring nanoparticles found in several body fluids such as blood, saliva, cerebrospinal fluid, amniotic fluid and urine. Exosomes mediate cell-cell communication, transport proteins and genetic content between distant cells, and are now known to play important roles in progression of diseases such as cancers, neurodegenerative disorders and infectious diseases. Because exosomes are smaller than 100 nm (about 30-120 nm), the structural and molecular characterization of these vesicles at the individual level has been challenging. AFM has revealed a new degree of complexity in these nanosized vesicles and generated growing interest as a nanoscale tool for characterizing the abundance, morphology, biomechanics, and biomolecular make-up of exosomes. With the recent interest in exosomes for diagnostic and therapeutic applications, AFM-based characterization promises to contribute towards improved understanding of these particles at the single vesicle and sub-vesicular levels. When coupled with complementary methods like optical super resolution STED and Raman, AFM could further unlock the potential of exosomes as disease biomarkers and as therapeutic agents.

Functional peptide-based nanoparticles for photodynamic therapy

Photodynamic therapy as a non-invasive approach has obtained great research attention during the last decade.

Reversible and Irreversible Mechanical Damaging of Large Double-Stranded DNA upon Electrospraying

Electrohydrodynamic spraying (or electrospaying, ES) of DNA solutions is an attractive technique for applications in mass spectrometry, in microarray fabrication, and in generation of DNA nanoaerosols. Here we report how ES affects DNA structure and evaluate possible ways to reduce DNA damage upon ES. It is shown that under any ES conditions, linear λ-phage DNA is subjected to intensive rupture producing a mixture of fragments. In addition to such fragmentation, notable reversible changes in the DNA structure were revealed by a slight increase in DNA electrophoretic mobility. The degree of fragmentation was shown to decrease with decreased DNA length and with increased flow rate through the ES capillary. Fragments shorter than 5 kbp did not show any notable damage upon ES. Both experimental data and theoretical estimations of the forces acting on DNA during ES indicate that DNA is damaged by mechanical forces, and the damage takes place in the vicinity of the Taylor cone tip, presumably due to the high shear stress or/and viscous drag forces operating there. Condensation of λ-DNA with hexamminecobalt(III) ions completely protected it from any damage upon ES.

AFM-based force spectroscopy for bioimaging and biosensing

AFM-based force spectroscopy shows wide bio-related applications especially for bioimaging and biosensing.

Single-molecule visualization of ROS-induced DNA damage in large DNA molecules

We present a single molecule visualization approach for the quantitative analysis of reactive oxygen species (ROS) induced DNA damage, such as base oxidation and single stranded breaks in large DNA molecules. We utilized the Fenton reaction to generate DNA damage with subsequent enzymatic treatment using a mixture of three types of glycosylases to remove oxidized bases, and then fluorescent labeling on damaged lesions via nick translation. This single molecule analytical platform provided the capability to count one or two damaged sites per λ DNA molecule (48.5 kb), which were reliably dependent on the concentrations of hydrogen peroxide and ferrous ion at the micromolar level. More importantly, the labeled damaged sites that were visualized under a microscope provided positional information, which offered the capability of comparing DNA damaged sites with the in silico genomic map to reveal sequence specificity that GTGR is more sensitive to oxidative damage. Consequently, single DNA molecule analysis provides a sensitive analytical platform for ROS-induced DNA damage and suggests an interesting biochemical insight that the genome primarily active during the lysogenic cycle may have less probability for oxidative DNA damage.