Herb Extracellular Vesicle-Chitosan-PEGylated Graphene Oxide Conjugate Delivers Estrogen Receptor α Targeting siRNA to Breast Cancer Cells

Herb-based extracellular vesicles (EV), inherently replete with bioactive proteins, RNA, lipids, and other medicinal compounds, are noncytotoxic and uniquely capable of cellular delivery to meet the ever-stringent challenges of ongoing clinical applications. EVs are abundant in nature, affordable, and scalable, but they are also incredibly fragile and stuffed with many biomolecules. To address the low drug binding abilities and poor stability of EVs, we demonstrated herb-based EVs (isolated from neem, mint, and curry leaves) conjugated with chitosan (CS) and PEGylated graphene oxide (GP) that led to their transformation into robust and efficient vectors. The designed conjugates successfully delivered estrogen receptor α (ERα1)-targeting siRNA to breast cancer MCF7 cells. Our data revealed that neem-based EV-CS-GP conjugates were most efficient in cellular siRNA delivery, which could be attributed to hyaluronic acid-mediated recognition of neem EVs by MCF7 cells via CD44 receptors. Our approach shows a futuristic direction in designing clinically viable, sustainable, nontoxic EV-based vehicles that can deliver a variety of functional siRNA cargos.

E-Protein Protonation Titration-Induced Single-Particle Chemical Force Spectroscopy for Microscopic Understanding and pI Estimation of Infectious DENV

The ionization state of amino acids on the outer surface of a virus regulates its physicochemical properties toward the sorbent surface. Serologically different strains of the dengue virus (DENV) show different extents of infectivity depending upon their interactions with a receptor on the host cell. To understand the structural dependence of E-protein protonation over its sequence dependence, we have followed E-protein titration kinetics both experimentally and theoretically for two differentially infected dengue serotypes, namely, DENV-2 and DENV-4. We have performed E-protein protonation titration-induced single-particle chemical force spectroscopy using an atomic force microscope (AFM) to measure the surface chemistry of DENV in physiological aqueous solutions not only to understand the charge distribution dynamics on the virus surface but also to estimate the isoelectric point (pI) accurately for infectious dengue viruses. Cryo-EM structure-based theoretical pI calculations of the DENV-2 surface protein were shown to be consistent with the evaluated pI value from force spectroscopy measurements. We also highlighted here the role of the microenvironment around the titrable residues (in the 3D-folded structure of the protein) in altering the pKa. This is a comprehensive study to understand how the cumulative charge distribution on the outer surface of a specific serotype of DENV regulates a prominent role of infectivity over minute changes at the genetic level.

Extracellular Vesicles for Drug Delivery and Theranostics In Vivo

Extracellular vesicles (EVs) are lipid bilayer-enclosed nanopouches generated by all cells and are abundant in various body fluids. Depending on the parent and recipient cells, EVs exchange diverse constituents including nucleic acids, proteins, carbohydrates, and metabolites. Morphologically, EVs suffer from low zeta potentials and short circulation times, but they also offer low intrinsic immunogenicity and inherent stability. Some crucial factors for the effective clinical application of EVs include controlling immune system clearance, achieving the large-scale production of EVs with efficient quality control, and determining the dominant mechanism of the in vivo action of EVs. In this Perspective, we shed light on how these intriguing nano-objects are utilized in cellular imaging and drug delivery for disease therapeutics. We also discuss potential strategies for overcoming the associated limitations.

Probing Aberrantly Glycosylated Mucin 1 in Breast Cancer Extracellular Vesicles

Aberrantly glycosylated mucin 1 is a critical prognostic biomarker in breast epithelial cancers. Hypoglycosylated mucin 1 coats the surface of the cancer cells, where O-glycans are predominantly linked via an N-acetylgalactosamine moiety (GalNAc). Cancer cell-derived extracellular vesicles (EVs) carry biomarkers from parent cancer cells to the recipient cells and, therefore, could potentially be leveraged for diagnostics and noninvasive disease monitoring. We devised a label-free approach for identifying glycoprotein mucin 1 overexpression on breast cancer EVs. While exploring a plethora of biochemical (enzyme-linked immunosorbent assay, flow cytometry, and SDS-PAGE) and label-free biophysical techniques (circular dichroism and infrared spectroscopy (IR)) along with multivariate analysis, we discovered that mucin 1 is significantly overexpressed in breast cancer EVs and aberrant glycosylation in mucin 1 could be critically addressed using IR and multivariate analysis targeting the GalNAc sugar. This approach emerges as a convenient and comprehensive method of distinguishing cancer EVs from normal samples and holds potential for nonintrusive breast cancer liquid biopsy screening.

Single molecule analysis of CENP-A chromatin by high-speed atomic force microscopy

Chromatin accessibility is modulated in a variety of ways to create open and closed chromatin states, both of which are critical for eukaryotic gene regulation. At the single molecule level, how accessibility is regulated of the chromatin fiber composed of canonical or variant nucleosomes is a fundamental question in the field. Here, we developed a single-molecule tracking method where we could analyze thousands of canonical H3 and centromeric variant nucleosomes imaged by high-speed atomic force microscopy. This approach allowed us to investigate how changes in nucleosome dynamics in vitro inform us about transcriptional potential in vivo. By high-speed atomic force microscopy, we tracked chromatin dynamics in real time and determined the mean square displacement and diffusion constant for the variant centromeric CENP-A nucleosome. Furthermore, we found that an essential kinetochore protein CENP-C reduces the diffusion constant and mobility of centromeric nucleosomes along the chromatin fiber. We subsequently interrogated how CENP-C modulates CENP-A chromatin dynamics in vivo. Overexpressing CENP-C resulted in reduced centromeric transcription and impaired loading of new CENP-A molecules. From these data, we speculate that factors altering nucleosome mobility in vitro, also correspondingly alter transcription in vivo. Subsequently, we propose a model in which variant nucleosomes encode their own diffusion kinetics and mobility, and where binding partners can suppress or enhance nucleosome mobility.

Glucose-Responsive Chitosan Nanoparticle/Poly(vinyl alcohol) Hydrogels for Sustained Insulin Release In Vivo

Stimuli-responsive hydrogels (HGs) with a controlled drug release profile are the current challenge for advanced therapeutic applications. Specifically, antidiabetic drug-loaded glucose-responsive HGs are being investigated for closed-loop insulin delivery in insulin-dependent diabetes patients. In this direction, new design principles must be exploited to create inexpensive, naturally occurring, biocompatible glucose-responsive HG materials for the future. In this work, we developed chitosan nanoparticle/poly(vinyl alcohol) (PVA) hybrid HGs (CPHGs) for controlled insulin delivery for diabetes management. In this design, PVA and chitosan nanoparticles (CNPs) are cross-linked with a glucose-responsive formylphenylboronic acid (FPBA)-based cross-linker in situ. Leveraging the structural diversity of FPBA and its pinacol ester-based cross-linkers, we fabricate six CPHGs (CPHG1-6) with more than 80% water content. Using dynamic rheological measurements, we demonstrate elastic solid-like properties of CPHG1-6, which are dramatically reduced under low-pH and high-glucose environments. An in vitro drug release assay reveals size-dependent glucose-responsive drug release from the CPHGs under physiological conditions. It is important to note that the CPHGs show appreciable self-healing and noncytotoxic properties. Promisingly, we observe a significantly slower insulin release profile from the CPHG matrix in the type-1 diabetes (T1D) rat model. We are actively pursuing scaling up of CPHGs and the in vivo safety studies for clinical trial in the near future.

Label-Free Physical-Analytical Techniques Reveal Epigenetic Modifications of Breast Cancer Chromosomes

Epigenetic dysregulation including DNA methylation and histone modifications is being increasingly recognized as a promising biomarker for the diagnosis and prognosis of cancer. Herein, we devised a label-free analytical toolbox comprising IR, UV-vis, CD spectroscopy, and cyclic voltammetry, which is capable to differentiate significantly hyper-methylated breast cancer chromosomes from the normal breast epithelial counterparts.

In Situ-Forming Protein-Polymer Hydrogel for Glucose-Responsive Insulin Release

Phenylboronic acid (PBA)-containing hydrogels (HGs), capable of glucose-responsive insulin release, have shown promise in diabetes management in preclinical studies. However, sustainable material usage and attaining an optimum insulin release profile pose a significant challenge in such HG design. Herein, we present the development of a straightforward fabrication strategy for glucose-responsive protein-polymer hybrid HGs (PPHGs). We prepare PPHGs by crosslinking polyvinyl alcohol (PVA) with various nature-abundant proteins, such as bovine serum albumin (BSA), egg albumin, casein, whey protein, and so forth, using formylphenylboronic acid (FPBA)-based crosslinkers. We showcase PPHGs with diverse bulk rheological properties that are appropriately modulated by the positions of aldehyde, boronic acid, and fluorine substitutions in the FPBA-crosslinker. The orthogonal imine and boronate ester bonds formed by FPBAs are susceptible to the acidic pH environment and glucose concentrations, leading to the glucose-responsive dissolution of the PPHGs. We further demonstrate that by an appropriate selection of FPBAs, glucose-responsive insulin release profiles of the PPHGs can be precisely engineered at the molecular level. Importantly, PPHGs are injectable, incur no cytotoxicity, and, therefore, hold great potential as smart insulin for in vivo applications in the near future.

A Mechanoelastic Glimpse on Hyaluronan-Coated Extracellular Vesicles

Cancer cells secrete extracellular vesicles (EVs) covered with a carbohydrate polymer, hyaluronan (HA), linked to tumor malignancy. Herein, we have unravelled the contour lengths of HA on a single cancer cell-derived EV surface using single-molecule force spectroscopy (SMFS), which divulges the presence of low molecular weight HA (LMW-HA < 200 kDa). We also discovered that these LMW-HA-EVs are significantly more elastic than the normal cell-derived EVs. This intrinsic elasticity of cancer EVs could be directly allied to the LMW-HA abundance and associated labile water network on EV surface as revealed by correlative SMFS, hydration dynamics with fluorescence spectroscopy, and molecular dynamics simulations. This method emerges as a molecular biosensor of the cancer microenvironment.

Importance of Extracellular Vesicle Derived RNAs as Critical Colorectal Cancer Biomarkers

Colorectal cancer typically begins from a nonmalignant polyp formation in the large intestine that, over time, develops into colorectal cancer. The growth of benign polyps can be checked if detected in the early stages of the disease. Doctors usually recommend colonoscopy to average and high-risk individuals for colorectal cancer screening. Elevated carcinoembryonic antigen (CEA) is a broadly used biomarker for colorectal cancer. The genetic and epigenetic alteration of genes such as p53, BRAF, APC, and PIK3CA is also correlated with colorectal cancer in various clinical studies. In general, tissue biopsy is most frequently used for colorectal cancer diagnosis, but the whole tumor heterogeneity cannot be accessed by this technique. Furthermore, such a highly invasive technique is not suitable for repeated testing. Recently, extracellular vesicles (EVs), lipid bilayer enclosed sacs secreted from colorectal cancer cells, are emerging as a diagnostic tool for colon cancer detection. The major advantages of using EVs for colon cancer diagnosis are (i) EVs can be isolated in a noninvasive manner from the body fluid and (ii) EV incorporated cargoes (mostly RNAs) reveal various aspects of colorectal cancer. EV-RNAs are also implicated in tumor invasion and influence the immune system for the further spread of tumors. However, due to the lack of standardized EV detection strategies, diagnostic applicability is limited. Herein, we review the recent literature on the pathobiological dependence of colorectal cancer on EV-RNAs. Further, we present the advantages of identification and characterization of EV-RNAs to explore the connection between differential expression of extracellular vesicle incorporated RNAs and colorectal cancer. How this approach may potentially translate into point of care colorectal cancer diagnostics is also discussed.

Repurposing Pinacol Esters of Boronic Acids for Tuning Viscoelastic Properties of Glucose-responsive Polymer Hydrogels: Effects on Insulin Release Kinetics

In the era of the diabetes pandemic, Injectable hydrogels (HGs) capable of releasing the desired amount of insulin under hyperglycemic conditions will significantly advance smart insulin development. Several smart boronic...

Polyethylene Glycol-Mediated Fusion of Extracellular Vesicles with Cationic Liposomes for the Design of Hybrid Delivery Systems

To realize a customizable biogenic delivery platform, herein we propose combining cell-derived extracellular vesicles (EVs) derived from breast cancer cell line MCF-7 with synthetic cationic liposomes using a fusogenic agent, polyethylene glycol (PEG). We performed a fluorescence resonance energy transfer (FRET)-based lipid-mixing assay with varying PEG 1000 concentrations (0%, 15%, and 30%) correlated with flow cytometry-based analysis and supported by dimensional analysis by dynamic light scattering (DLS), transmission electron microscopy (TEM), and atomic force microscopy (AFM) to validate our fusion strategy. Our data revealed that these hybrid vesicles at a particular concentration of PEG (∼15%) improved the cellular delivery efficiency of a model siRNA molecule to the EV parental breast cancer cells, MCF-7, by factors of 2 and 4 compared to the loaded liposome and EV precursors, respectively. The critical rigidity/pliability balance of the hybrid systems fused by PEG seems to be playing a pivotal role in improving their delivery capability. This approach can provide clinically viable delivery solutions using EVs.

Folate-Functionalized DNA Origami for Targeted Delivery of Doxorubicin to Triple-Negative Breast Cancer

DNA origami has emerged as a versatile platform for diverse applications, namely, photonics, electronics, (bio) sensing, smart actuator, and drug delivery. In the last decade, DNA origami has been extensively pursued for efficient anticancer therapy. However, challenges remain to develop strategies that improve the targeting efficiency and drug delivery capability of the DNA origami nanostructures. In this direction, we developed folate-functionalized DNA origami that effectively targets and delivers doxorubicin (DOX), a well-known anticancer drug to the folate receptor alpha (FOLR1) expressing triple-negative breast cancer (TNBC) cells in vitro. We show that folate-functionalized DNA origami structure targets and kills FOLR1 overexpressing cells with better efficacy than nontargeted origami. We envision that this study will open up the possibility of target specific delivery of anticancer drug combinations using the versatile DNA origami nanostructures to the drug resistant cancer cells.

Mechanical properties of nucleoprotein complexes determined by nanoindentation spectroscopy

The interplay between transcription factors, chromatin remodelers, 3-D organization, and mechanical properties of the chromatin fiber controls genome function in eukaryotes. Besides the canonical histones which fold the bulk of the chromatin into nucleosomes, histone variants create distinctive chromatin domains that are thought to regulate transcription, replication, DNA damage repair, and faithful chromosome segregation. Whether histone variants translate distinctive biochemical or biophysical properties to their associated chromatin structures, and whether these properties impact chromatin dynamics as the genome undergoes a multitude of transactions, is an important question in biology. Here, we describe single-molecule nanoindentation tools that we developed specifically to determine the mechanical properties of histone variant nucleosomes and their complexes. These methods join an array of cutting-edge new methods that further our quantitative understanding of the response of chromatin to intrinsic and extrinsic forces which act upon it during biological transactions in the nucleus.

Intriguing Biomedical Applications of Synthetic and Natural Cell-Derived Vesicles: A Comparative Overview

The significant role of a vesicle is well recognized; however, only lately has the advancement in biomedical applications started to uncover their usefulness. Although the concept of vesicles originates from cell biology, it later transferred to chemistry and material science to develop nanoscale artificial vesicles for biomedical applications. Herein, we examine different synthetic and biological vesicles and their applications in the biomedical field in general. As our understanding of biological vesicles increases, more suitable biomimicking synthetic vesicles will be developed. The comparative discussion between synthetic and natural vesicles for biomedical applications is a relevant topic, and we envision this could enable the development of a proper approach to realize the next-generation treatment goals.

Identification of Biomarker Hyaluronan on Colon Cancer Extracellular Vesicles Using Correlative AFM and Spectroscopy

Extracellular vesicles (EVs), naturally occurring nanosized vesicles secreted from cells, are essential for intercellular communication. They carry unique biomolecules on the surface or interior that are of great interest as biomarkers for various pathological conditions such as cancer. In this work, we use high-resolution atomic force microscopy (AFM) and spectroscopy (AFS) techniques to demonstrate differences between EVs derived from colon cancer cells and colon epithelial cells at the single-vesicle level. We observe that EV populations are significantly increased in the cancer cell media compared to the normal cell EVs. We show that both EVs display an EV marker, CD9, while EVs derived from the cancer cells are slightly higher in density. Hyaluronan (HA) is a nonsulfated glycosaminoglycan linked to malignant tumor growth according to recent reports. Interestingly, at the single-vesicle level, colon cancer EVs exhibit significantly increased HA surface densities compared to the normal EVs. Spectroscopic measurements such as Fourier transform infrared (FT-IR), circular dichroism (CD), and Raman spectroscopy unequivocally support the AFM and AFS measurements. To our knowledge, it represents the first report of detecting HA-coated EVs as a potential colon cancer biomarker. Taken together, this sensitive approach will be useful in identifying biomarkers in the early stages of detection and evaluation of cancer.

Role of Hyaluronan in Inflammatory Effects on Human Articular Chondrocytes

Hyaluronan (HA) fragments have been proposed to elicit defensive or pro-inflammatory responses in many cell types. For articular chondrocytes in an inflammatory environment, studies have failed to reach consensus on the endogenous production or effects of added HA fragments. The present study was undertaken to resolve this discrepancy. Cultured primary human articular chondrocytes were exposed to the inflammatory cytokine IL-1β, and then tested for changes in HA content/size in conditioned medium, and for the expression of genes important in HA binding/signaling or metabolism, and in other catabolic/anabolic responses. Changes in gene expression caused by enzymatic degradation of endogenous HA, or addition of exogenous HA fragments, were examined. IL-1β increased the mRNA levels for HA synthases HAS2/HAS3 and for the HA-binding proteins CD44 and TSG-6. mRNA levels for TLR4 and RHAMM were very low and were little affected by IL-1β. mRNA levels for catabolic markers were increased, while type II collagen (α1(II)) and aggrecan were decreased. HA concentration in the conditioned medium was increased, but the HA was not degraded. Treatment with recombinant hyaluronidase or addition of low endotoxin HA fragments did not elicit pro-inflammatory responses. Our findings showed that HA fragments were not produced by IL-1β-stimulated human articular chondrocytes in the absence of other sources of reactive oxygen or nitrogen species, and that exogenous HA fragments from oligosaccharides up to about 40 kDa in molecular mass were not pro-inflammatory agents for human articular chondrocytes, probably due to low expression of TLR4 and RHAMM in these cells.

Deciphering the response of asymmetry in the hydrophobic chains of novel cationic lipids towards biological function

Cationic liposomes, a type of non-viral vectors, often play the important biological function of delivering nucleic acids during cell transfection. Variations in the molecular architecture of di-alkyl dihydroxy ethyl ammonium chloride-based cationic lipids involving hydrophobic tails have been found to influence their biological function in terms of cell transfection efficiency. For example, liposomes based on a cationic lipid (Lip1814) with asymmetry in the hydrophobic chains were found to display higher transfection efficacy in cultured mammalian cell lines than those comprising of symmetric Lip1818 or asymmetric Lip1810. The effect of variations in the molecular architecture of the cationic lipids on the biological activity of liposomes has been explored here via the photophysical studies of 8-anilino-1-naphthalenesulphonate (ANS) and Nile Red (NR) in three cationic liposomes, namely Lip1810, Lip1814 and Lip1818. Time-resolved fluorescence of ANS revealed reduced hydration at the lipid-water interface and enhanced relaxation dynamics of surface water (lipid headgroup bound water molecules) in Lip1810- and Lip1814-based liposomes in the presence of cholesterol. As the probe ANS failed to be incorporated into the lipid-water interface of Lip1818 due to the significantly high rigidity of these liposomes, no information concerning the extent of hydration of the lipid-water interface or the interfacial water dynamics could be obtained. Time-resolved polarization-gated anisotropy measurements of NR in the presence of cholesterol revealed the rigidity of the cationic liposomes to be increasing in the order of Lip1810 < Lip1814 < Lip1818. In the presence of cholesterol, moderately higher rigidity, reduced membrane hydration and enhanced relaxation dynamics of the interfacial water molecules gave rise to the superior cell transfection efficacy of Lip1814-based cationic liposomes than those of the highly flexible Lip1810 or the highly rigid Lip1818.

Intrinsic elasticity of nucleosomes is encoded by histone variants and calibrated by their binding partners

Histone variants fine-tune transcription, replication, DNA damage repair, and faithful chromosome segregation. Whether and how nucleosome variants encode unique mechanical properties to their cognate chromatin structures remains elusive. Here, using in silico and in vitro nanoindentation methods, extending to in vivo dissections, we report that histone variant nucleosomes are intrinsically more elastic than their canonical counterparts. Furthermore, binding proteins, which discriminate between histone variant nucleosomes, suppress this innate elasticity and also compact chromatin. Interestingly, when we overexpress the binding proteins in vivo, we also observe increased compaction of chromatin enriched for histone variant nucleosomes, correlating with diminished access. Taken together, these data suggest a plausible link between innate mechanical properties possessed by histone variant nucleosomes, the adaptability of chromatin states in vivo, and the epigenetic plasticity of the underlying locus.

DNA-enabled rational design of fluorescence-Raman bimodal nanoprobes for cancer imaging and therapy

Recently, surface-enhanced Raman scattering nanoprobes have shown tremendous potential in oncological imaging owing to the high sensitivity and specificity of their fingerprint-like spectra. As current Raman scanners rely on a slow, point-by-point spectrum acquisition, there is an unmet need for faster imaging to cover a clinically relevant area in real-time. Herein, we report the rational design and optimization of fluorescence-Raman bimodal nanoparticles (FRNPs) that synergistically combine the specificity of Raman spectroscopy with the versatility and speed of fluorescence imaging. DNA-enabled molecular engineering allows the rational design of FRNPs with a detection limit as low as 5 × 10⁻¹⁵ M. FRNPs selectively accumulate in tumor tissue mouse cancer models and enable real-time fluorescence imaging for tumor detection, resection, and subsequent Raman-based verification of clean margins. Furthermore, FRNPs enable highly efficient image-guided photothermal ablation of tumors, widening the scope of the NPs into the therapeutic realm.

Currently available Raman scanners are limited in speed to acquire images of clinically relevant sizes in cancer imaging. Here, the authors developed a DNA based design principle for Raman-Fluorescence bimodal nanoparticles and demonstrate real-time, high precision image-guided tumor resections and photothermal ablation of cancer.

Negative Differential Resistance Behavior of the Iron Storage Protein Ferritin

Realization of useful nanometer length scale devices in which metalloproteins are junction-confined in a distinct molecular arrangement for generating practical electronic signals (e.g., in bioelectronic switch configuration) is elusive till date. This is mostly due to difficulties in observing an electronically appropriate signal (i.e., reproducible and controllable), when studied under junction-assembled condition. A useful "ON"-"OFF" behavior, based on the negative differential resistance (NDR) peak characteristics in the current-voltage response curves, acquired using metal-insulator-metal (MIM) configuration, has been observed only in the case of a few proteins, namely, azurin, cytochrome c, bacteriorhodopsin, so far. The case of NDR in ferritin, an iron storage protein having a semiconducting iron core consisting of few thousands of iron atoms connected in an oxide network, has not been studied in the MIM configuration where single (or a few) molecule(s) are junction-trapped, for example, as in the case of local probe configuration of scanning probe microscopy. The present study by scanning tunneling microscopy (STM), using the naturally occurring iron-containing ferritin (human liver), as well as different iron-loaded ferritins, provides clear indication of the capability of ferritins to be NDR capable, at varying sweep conditions. As ferritin can be tailor-made in a structurally conserved manner, metal core-reconstituted ferritins, that is, Mn(III)-ferritin, Cu(II)-ferritin, and Ag-ferritin, were prepared. A correlation between the NDR peak signatures, as observed in the respective current-voltage response curves of these reconstituted ferritins, and the nature of the metal core is demonstrated. In support of our earlier proposition, here, we affirm that the ferritin protein behaves as a conductor-insulator (metal core-polypeptide shell) composite, where the overall electronic structure of the material can alter as a function of the nature of the conducting filler placed inside the insulated matrix.

Adaptations in rod outer segment disc membranes in response to environmental lighting conditions

The light-sensing rod photoreceptor cell exhibits several adaptations in response to the lighting environment. While adaptations to short-term changes in lighting conditions have been examined in depth, adaptations to long-term changes in lighting conditions are less understood. Atomic force microscopy was used to characterize the structure of rod outer segment disc membranes, the site of photon absorption by the pigment rhodopsin, to better understand how photoreceptor cells respond to long-term lighting changes. Structural properties of the disc membrane changed in response to housing mice in constant dark or light conditions and these adaptive changes required output from the phototransduction cascade initiated by rhodopsin. Among these were changes in the packing density of rhodopsin in the membrane, which was independent of rhodopsin synthesis and specifically affected scotopic visual function as assessed by electroretinography. Studies here support the concept of photostasis, which maintains optimal photoreceptor cell function with implications in retinal degenerations.

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.

Interactions of Histone Acetyltransferase p300 with the Nuclear Proteins Histone and HMGB1, As Revealed by Single Molecule Atomic Force Spectroscopy

One of the important properties of the transcriptional coactivator p300 is histone acetyltransferase (HAT) activity that enables p300 to influence chromatin action via histone modulation. p300 can exert its HAT action upon the other nuclear proteins too--one notable example being the transcription-factor-like protein HMGB1, which functions also as a cytokine, and whose accumulation in the cytoplasm, as a response to tissue damage, is triggered by its acetylation. Hitherto, no information on the structure and stability of the complexes between full-length p300 (p300FL) (300 kDa) and the histone/HMGB1 proteins are available, probably due to the presence of unstructured regions within p300FL that makes it difficult to be crystallized. Herein, we have adopted the high-resolution atomic force microscopy (AFM) approach, which allows molecularly resolved three-dimensional contour mapping of a protein molecule of any size and structure. From the off-rate and activation barrier values, obtained using single molecule dynamic force spectroscopy, the biochemical proposition of preferential binding of p300FL to histone H3, compared to the octameric histone, can be validated. Importantly, from the energy landscape of the dissociation events, a model for the p300-histone and the p300-HMGB1 dynamic complexes that HAT forms, can be proposed. The lower unbinding forces of the complexes observed in acetylating conditions, compared to those observed in non-acetylating conditions, indicate that upon acetylation, p300 tends to weakly associate, probably as an outcome of charge alterations on the histone/HMGB1 surface and/or acetylation-induced conformational changes. To our knowledge, for the first time, a single molecule level treatment of the interactions of HAT, where the full-length protein is considered, is being reported.

Impact of reduced rhodopsin expression on the structure of rod outer segment disc membranes

Rhodopsin is the light receptor embedded in rod outer segment (ROS) disc membranes of photoreceptor cells that initiates vision via phototransduction. The relationship between rhodopsin expression and the formation of membrane structures in the ROS is unclear but important to better understand both normal function and pathological conditions. To determine the impact of reduced rhodopsin expression on the structure of ROS discs and the supramolecular organization of rhodopsin, ROS disc membrane samples from heterozygous rhodopsin knockout mice were examined by atomic force microscopy. Similar to rhodopsin in wild-type mice, rhodopsin formed nanodomains in ROS disc membranes of heterozygous knockout mice. The reduced rhodopsin expression in heterozygous knockout mice resulted in ROS disc membranes that were smaller compared to those in wild-type mice at all ages tested. Changes in ROS disc membrane properties were observed between 4 and 6 weeks of age in heterozygous knockout mice that were not present in age-matched wild-type mice. In 4 week old mice, the number and density of rhodopsin in ROS disc membranes was lower than that in age-matched wild-type mice. In contrast, 6 and 8 week old mice had more rhodopsin molecules present in disc membranes compared to 4 week old mice, which resulted in rhodopsin densities similar to those found in age-matched wild-type mice. Thus, mechanisms appear to be present that maintain a constant density of rhodopsin within ROS disc membranes even when reducing the expression of the light receptor by about half. These adaptive mechanisms, however, only occur after 4 weeks of age.

Nanoscale mechano-electronic behavior of a metalloprotein as a variable of metal content

In this work, we have explored an approach to finding a correlation between the mechanical response of a metalloprotein against a range of applied force (by force curve analysis) and its electrical response under pressure stimulation (by current sensing atomic force spectroscopy) at the nanoscale. Iron-storage protein ferritin has been chosen as an experimental model system because it naturally contains a semiconducting iron core. This core consists of a large number of iron atoms and is therefore expected to exert a clear influence on the overall mechanical response of the protein structure. Four different ferritins (apoferritin, Fe(III)-ferritins containing ~750 and ~1400 iron atoms, and holoferritin containing ~2600 iron atoms) were chosen in order to identify any relation between the mechano-electronic behavior of the ferritins and their metal content. We report the measurement of Young's modulus values of the ferritin proteins as applicable in a nanoscale environment, for the first time, and show that these values are directly linked to the iron content of the individual ferritin type. The greater the iron content, the greater the Young's modulus and in general the slower the rate of deformation against the application of force. When compressed, all the four ferritins exhibited increased electronic conductivity. A correlation between the iron content of the ferritins and the current values observed at certain bias voltages could be made at higher bias values (beyond 0.7 V), but no such discrimination among the four compressed ferritins could be made at the lower voltages. We propose that only at higher voltages can the iron atoms that reside deeper inside the core of the ferritins be accessed. The iron atoms that could be situated at the inner wall of the protein shell appear to make a general contribution to the electronic conductivity of the four ferritin systems.

Nanostructures of Sr2+ doped BiFeO3 multifunctional ceramics with tunable photoluminescence and magnetic properties

Careful tuning of formation (calcination) temperature of Sr(2+) doped BiFeO(3) multiferroic ceramics results in tailorable particle morphologies ranging from spherical to pillar-like. Based on the minimization of Gibb's free energy approach, the dominant homogeneous mechanism for particle growth is suggested. The chemical substitution of a trivalent ion (Bi(3+)) by a divalent ion (Sr(2+)) causes the transformation of certain fraction of Fe(3+) to Fe(4+) and/or the appearance of oxygen vacancies. This has been respectively proved by the analysis of XPS and refinement of neutron diffraction data. Although significant modification in the particle morphology is observed, the crystal unit cell remains rhombohedral with a R3c space group but interesting variations in physical properties are achieved. O-vacancies induced strong and sharp photoluminescence activity in the IR region, similar to ZnO, is reported for the first time. This observation opens up a new application for multiferroic ceramics. SQUID M-H data confirms the straightening of the canted spin structure of BiFeO(3), which in turn results in magnetism similar to ferromagnetic materials. Findings of the magneto-dielectric effect are also discussed to claim the multiferroic nature of the sample.

Optical and bio-sensing characteristics of ZnO nanotubes grown by hydrothermal method

ZnO nanostructures were fabricated on copper substrates by hydrothermal method at an optimized growth temperature of -95 degrees C. Structural properties were investigated by field emission scanning electron and transmission electron microscopy. Distinct morphologies were found to be formed at different growth times. The formation of nanotubes mainly involved the initial nucleation followed by the growth of nanorods at 95 degrees C, and then with the increase of dissolution time at room temperature, the preferential chemical dissolution of the metastable Zn-rich [0001] polar surfaces resulted in removing the atoms from the surfaces, thus leading to the thinning of the wall of the nanostructures. Completely hollow ZnO nanotubes could be obtained at a high dissolution time. The room temperature photoluminescence and optical absorption properties of ZnO nanotubes have been studied as a function of dissolution time. The efficacy of ZnO nanotubes for glucose sensing applications has been studied.

Tuning band gap of holoferritin by metal core reconstitution with Cu, Co, and Mn

Utility of ferritin in molecular electronics, especially in single molecule electronics based devices, has recently been proposed, since the iron core of holoferritin is semiconducting in nature. However, the practical aspects, e.g., how its electronic properties can be varied/tuned, need to be better addressed. In this direction, we have performed direct tunneling experiments using scanning tunneling microscopy (STM) and scanning tunneling spectroscopy (STS) on several metal core reconstituted ferritins, where the reconstitution has been carried out using biocompatible metals like copper, cobalt, and manganese that are found naturally in the human body. We show, for the first time, that, by metal core reconstitution of the ferritin protein, the band gap of the protein can be tuned to different values (here, within the range 1.17-0.00 eV, considering iron-containing holoferritin and apoferritin as well). From the respective current-voltage curves and the well-defined band gaps, clear distinction can be made among the five different ferritins indicating that the metal core has direct contribution in the observed electrical conductivities of ferritins. It is further revealed that the electrical conductivities of the reconstituted ferritins are of the same order as that for the free metal conductivities, meaning that the relative changes in the free metal conductivities are reflected in the contributions of the metals in protein shell-confinement (i.e., the ∼8 nm core of ferritin). This finding could lead to a strategy for fine-tuning ferritin band gap by preselecting a metal on the basis of the free metal conductivity values.

Near-metallic behavior of warm holoferritin molecules on a gold(111) surface

Ferritin, the iron-storage protein, holds great potential for bioelectronic applications because of the presence of an electronically conducting iron core. We have applied scanning tunneling microscopy (STM), a high-resolution imaging method based on direct tunneling, to visualize the ferritin molecules both in the iron-containing holo form and in the iron-free apo form, and we have probed the electron flow through the two forms of this protein by measuring the current-voltage response using scanning tunneling spectroscopy (STS). Clear distinctions could be made among the current-voltage responses of the metallic gold(111) substrate surface, holoferritin molecules, and apoferritin molecules at room temperature. When warmed to the near-physiological temperature of 40 °C, the current-voltage response of the holoferritin molecules exhibited no band gap resembling near-metallic behavior, and the apoferritin molecules exhibited only a reduced band gap.