DNA origami-based single-molecule force spectroscopy elucidates RNA Polymerase III pre-initiation complex stability.

The TATA-binding protein (TBP) and a transcription factor (TF) IIB-like factor are important constituents of all eukaryotic initiation complexes. The reason for the emergence and strict requirement of the additional initiation factor Bdp1 in the RNA polymerase (RNAP) III system, however, remained elusive. A poorly studied aspect in this context is the effect of DNA strain arising from DNA compaction and transcriptional activity on initiation complex formation. We made use of a DNA origami-based force clamp to follow the assembly of human initiation complexes in the RNAP II and RNAP III systems at the single-molecule level under piconewton forces. We demonstrate that TBP-DNA complexes are force-sensitive and TFIIB is sufficient to stabilise TBP on a strained promoter. In contrast, Bdp1 is the pivotal component that ensures stable anchoring of initiation factors, and thus the polymerase itself, in the RNAP III system. Thereby, we offer an explanation for the crucial role of Bdp1 for the high transcriptional output of RNAP III.

Capturing transient antibody conformations with DNA origami epitopes.

Revealing antibody-antigen interactions at the single-molecule level will deepen our understanding of immunology. However, structural determination under crystal or cryogenic conditions does not provide temporal resolution for resolving transient, physiologically or pathologically relevant functional antibody-antigen complexes. Here, we develop a triangular DNA origami framework with site-specifically anchored and spatially organized artificial epitopes to capture transient conformations of immunoglobulin Gs (IgGs) at room temperature. The DNA origami epitopes (DOEs) allows programmed spatial distribution of epitope spikes, which enables direct imaging of functional complexes with atomic force microscopy (AFM). We establish the critical dependence of the IgG avidity on the lateral distance of epitopes within 3-20 nm at the single-molecule level. High-speed AFM imaging of transient conformations further provides structural and dynamic evidence for the IgG avidity from monovalent to bivalent in a single event, which sheds light on various applications including virus neutralization, diagnostic detection and cancer immunotherapy.

In vivo assessment of inflammation in carotid atherosclerosis by noninvasive photoacoustic imaging.

Objectives: The objective of this study was to demonstrate the feasibility of using noninvasive photoacoustic imaging technology along with novel semiconducting polymer nanoparticles for in vivo identifying inflammatory components in carotid atherosclerosis and assessing the severity of inflammation using mouse models. Methods and Results: Healthy carotid arteries and atherosclerotic carotid arteries were imaged in vivo by the noninvasive photoacoustic imaging system. Molecular probes PBD-CD36 were used to label the inflammatory cells to show the inflammation information by photoacoustic imaging. In in vivo imaging experiments, we observed the maximum photoacoustic signal enhancement of 4.3, 5.2, 8 and 16.3 times between 24 h post probe injection and that before probe injection in four carotid arteries belonging to three atherosclerotic mice models. In the corresponding carotid arteries stained with CD36, the ratio of 0.043, 0.061, 0.082 and 0.113 was found between CD36 positive (CD36(+)) expression area and intima-media area (P < 0.05). For the CD36(+) expression less than 0.008 in eight arteries, no photoacoustic signal enhancement was found due to the limited system sensitivity. The photoacoustic signal reflects CD36(+) expression in plaques, which shows the feasibility of using photoacoustic imaging for in vivo assessment of carotid atherosclerosis. Conclusion: This research demonstrates a semiconducting polymer nanoparticle along with photoacoustic technology for noninvasive imaging and assessment of inflammation of carotid atherosclerotic plaques in vivo.

A new molecular probe: An NRP-1 targeting probe for the grading diagnosis of glioma in nude mice.

Magnetic resonance molecular imaging, as a safe imaging technology, provides a new idea for the early qualitative and hierarchical diagnosis of gliomas. The purpose of this study was to design and evaluate the value of neuropilin-1 (NRP-1) targeting molecular probes in the hierarchical diagnosis of gliomas. First, we created an NRP-1 targeted magnetic resonance molecular probe (USPIO-PEG-tLyP-1) by combining the polypeptide tLyP-1 with ultra-small superparamagnetic iron oxide nanoparticles (USPIONs), detecting the physical properties by transmission electron microscopy (TEM) and dynamic light scattering (DLS). Second, in vivo experiments, we established two different degrees of malignant gliomas in-situ in nude mice by injecting U87 and CHG-5 cells. Then, to detect the binding ability of the probe with different grades of tumour tissues, we injected the probe into the tumour-bearing mice through the tail vein. Next, MRI was performed before injection, and 6 h, 12 h, 24 h after injection, and we found significantly more iron particles in the tumour tissues of U87 tumour-bearing mice than in tumour tissues of CHG-5 tumour-bearing mice. The signal intensities of the T2-weighted images of the tumour tissues of each group as well as microscopic observations by Prussian blue staining indicated that the binding ability of this molecular probe to U87 glioma (HGG) with high NRP-1 expression was significantly greater than that of CHG-5 glioma (LGG) with low NRP-1 expression (P < 0.01). Therefore, this study confirms that the novel molecular probe USPIO-PEG-tLyP-1 can be used for the grading diagnosis by MRI for gliomas of high and low grade with different NRP-1 expression levels.

Measuring the Conformation and Persistence Length of Single-Stranded DNA Using a DNA Origami Structure.

Measuring the mechanical properties of single-stranded DNA (ssDNA) is a challenge that has been addressed by different methods lately. The short persistence length, fragile structure, and the appearance of stem loops complicate the measurement, and this leads to a large variability in the measured values. Here we describe an innovative method based on DNA origami for studying the biophysical properties of ssDNA. By synthesizing a DNA origami structure that consists of two rigid rods with an ssDNA segment between them, we developed a method to characterize the effective persistence length of a random-sequence ssDNA while allowing the formation of stem loops. We imaged the structure with an atomic force microscope (AFM); the rigid rods provide a means for the exact identification of the ssDNA ends. This leads to an accurate determination of the end-to-end distance of each ssDNA segment, and by fitting the measured distribution to the ideal chain polymer model we measured an effective persistence length of 1.98 ± 0.72 nm. This method enables one to measure short or long strands of ssDNA, and it can cope with the formation of stem loops that are often formed along ssDNA. We envision that this method can be used for measuring stem loops for determining the effect of repetitive nucleotide sequences and environmental conditions on the mechanical properties of ssDNA and the effect of interacting proteins with ssDNA. We further noted that the method can be extended to nanoprobes for measuring the interactions of specific DNA sequences, because the DNA origami rods (or similar structures) can hold multiple fluorescent probes that can be easily detected.

[Characterization of Surface Interaction between Chitosan-modified Liposomes and Mucin Layer by Using CNT Probe AFM Method].

　In order to characterize the adhesion and deformation behavior between chitosan-modified liposomes and the mucin layer of the small intestine, mucin was coated on hydrophobic surface-modified carbon nanotube (CNT) probe of an atomic force microscope. The interaction between this mucin layer and the liposomes with or without chitosan modification in phosphoric acid buffer solution was determined by atomic force microscopy. The pH of the buffer solution was controlled at 2.8 and 7.0. The chitosan modification increased the attractive force between the liposomes and mucin layer during the separation process under both pH conditions. This result corresponded with that from a previous study about the liposome adhesion behavior on the surface of the small intestine of rats. By using the mucin-coated CNT probe, the long range and different types of attractive forces between the chitosan-modified liposomes and mucin layer was observed. Furthermore, the small-scaled deformation behavior change on the liposomal surfaces due to chitosan modification was also observed by the CNT probe. The detail deformation and adhesion behavior of the liposomes with or without chitosan modification was detected.

Non plasmonic semiconductor quantum SERS probe as a pathway for in vitro cancer detection.

Surface-enhanced Raman scattering (SERS)-based cancer diagnostics is an important analytical tool in early detection of cancer. Current work in SERS focuses on plasmonic nanomaterials that suffer from coagulation, selectivity, and adverse biocompatibility when used in vitro, limiting this research to stand-alone biomolecule sensing. Here we introduce a label-free, biocompatible, ZnO-based, 3D semiconductor quantum probe as a pathway for in vitro diagnosis of cancer. By reducing size of the probes to quantum scale, we observed a unique phenomenon of exponential increase in the SERS enhancement up to ~106 at nanomolar concentration. The quantum probes are decorated on a nano-dendrite platform functionalized for cell adhesion, proliferation, and label-free application. The quantum probes demonstrate discrimination of cancerous and non-cancerous cells along with biomolecular sensing of DNA, RNA, proteins and lipids in vitro. The limit of detection is up to a single-cell-level detection.

Mechanistic Studies on the Self-Assembly of PLGA Patchy Particles and Their Potential Applications in Biomedical Imaging.

Currently, several challenges prevent poly(lactic-co-glycolic acid) (PLGA) particles from reaching clinical settings. Among these is a lack of understanding of the molecular mechanisms involved in the formation of these particles. We have been studying in depth the formation of patchy polymeric particles. These particles are made of PLGA and lipid-polymer functional groups. They have unique patch-core-shell structural features: hollow or solid hydrophobic cores and a patchy surface. Previously, we identified the shear stress as the most important parameter in a patchy particle's formation. Here, we investigated in detail the role of shear stress in the patchy particle's internal and external structure using an integrative experimental and computational approach. By cross-sectioning the multipatch particles, we found lipid-based structures embedded in the entire PLGA matrix, which represents a unique finding in the PLGA field. By developing novel computational fluid dynamics and molecular dynamics simulations, we found that the shear stress determines the internal structure of the patchy particles. Equally important, we discovered that these particles emit a photoacoustic (PA) signal in the optical clinical imaging window. Our results show that particles with multiple patches emit a higher PA signal than single-patch particles. This phenomenon most likely is due to the fact that multipatchy particles absorb more heat than single-patchy particles as shown by differential scanning calorimetry analysis. Furthermore, we demonstrated the use of patchy polymeric particles as photoacoustic molecular probes both in vitro and in vivo studies. The fundamental studies described here will help us to design more effective PLGA carriers for a number of medical applications as well as to accelerate their medical translation.

A new hydrothermal refluxing route to strong fluorescent carbon dots and its application as fluorescent imaging agent.

Due to their unique optical and biochemical properties, the water-soluble fluorescent carbon dots (CDs) have attracted a lot of attention recently. Here, strong fluorescent carbon dots with excellent quality have been synthesized by the hydrothermal refluxing method using lactose as carbon source and tris(hydroxymethyl) aminomethane (i.e. Tris) as surface passivation reagent. This facile approach was simple, efficient, economical, green without pollution, and allows large-scale production of CDs without any post-treatment. TEM measurements showed that the resulting particles exhibited an average diameter of 1.5 nm. The obtained CDs possess small particle sizes, good stability in a wide range of pH values (pH 3.5-9.5), high tolerance of salt concentration, strong resistibility to photobleaching, and a fluorescent quantum yield up to 12.5%. The CDs were applied to optical bioimaging of HeLa cells, showing low cytotoxicity and excellent biocompatibility.

Development of siRNA-probes for studying intracellular trafficking of siRNA nanoparticles.

One important barrier facing the delivery of short interfering RNAs (siRNAs) via synthetic nanoparticles is the rate of nanoparticle disassembly. However, our ability to optimize the release kinetics of siRNAs from nanoparticles for maximum efficacy is limited by the lack of methods to track their intracellular disassembly. Towards this end, we describe the design of two different siRNA-based fluorescent probes whose fluorescence emission changes in response to the assembly state of the nanoparticle. The first probe design involves a redox-sensitive fluorescence-quenched probe that fluoresces only when the nanoparticle is disassembled in a reductive environment. The second probe design is based on a FRET-labeled siRNA pair that fluoresces due to the proximity of the siRNA pair when the nanoparticle is intact. In both approaches, the delivery vehicle need not be labeled. The utility of these probes was investigated with a lipidoid nanoparticle (LNP) as proof-of-concept in both extracellular and intracellular environments. Fluorescence kinetic data from both probes were fit to a two-phase release and decay curve and subsequently quantified to give intracellular disassembly rate constants. Quantitative analysis revealed that the rate constant of siRNA release measured via the fluorescence-quenched probe was almost identical to the rate constant for nanoparticle disassembly measured via the FRET-labeled probes. Furthermore, these probes were utilized to determine subcellular localization of LNPs with the use of automated high-resolution microscopy as they undergo dissociation. Interestingly, this work shows that large amounts of siRNA remain inside vesicular compartments. Altogether, we have developed new siRNA probes that can be utilized with multiple nanocarriers for quantitative and qualitative analysis of nanoparticle dissociation that may serve as a design tool for future delivery systems.

Preparation of 2-mercaptobenzothiazole-labeled immuno-Au aggregates for SERS-based immunoassay.

A detailed method for preparation of 2-mercaptobenzothiazole (MBT)-labeled immuno-Au aggregates as a novel Raman probe for SERS-based immunoassay has been proposed in this paper. The formation kinetics of gold aggregates induced by MBT and the impact of the amount of labeled reporter on the aggregation, as well as the fabrication of MBT-labeled immuno-Au aggregates were characterized comprehensively by UV-vis spectrophotometer. Meanwhile, a chain-like morphology of aggregates was monitored by TEM images. Experimental results show that this Raman tag can act as an efficient label and an enhanced Raman signal of SERS-based immunoassay can be obtained successfully with this novel probe. This work shows the method for the preparation of immune probe for SERS-based immunoassay using MBT as reporter and provides a reference for the preparation of immune probe with other Raman markers for multi-channel SERS-based immunoassay.

Biodegradable quantum dot nanocomposites enable live cell labeling and imaging of cytoplasmic targets.

Semiconductor quantum dots (QDs) offer great promise as the new generation of fluorescent probes to image and study biological processes. Despite their superior optical properties, QDs for live cell monitoring and tracking of cytoplasmic processes remain limited due to inefficient delivery methods available, altered state or function of cells during the delivery process and the requirement of surface-functionalized QDs for specific labeling of subcellular structures. Here, we present a noninvasive method to image subcellular structures in live cells using bioconjugated QD nanocomposites. By incorporating antibody-coated QDs within biodegradable polymeric nanospheres, we have designed a bioresponsive delivery system that undergoes endolysosomal to cytosolic translocation via pH-dependent reversal of nanocomposite surface charge polarity. Upon entering the cytosol, the polymer nanospheres undergo hydrolysis thus releasing the QD bioconjugates. This approach facilitates multiplexed labeling of subcellular structures inside live cells without the requirement of cell fixation or membrane permeabilization. As compared to conventional intracellular delivery techniques, this approach allows the high throughput cytoplasmic delivery of QDs with minimal toxicity to the cell. More importantly, this development demonstrates an important rational strategy for the design of a multifunctional nanosystem for biological applications.

Evaluation of interaction forces between profilin and designed peptide probes by atomic force microscopy.

We evaluated the binding affinity of peptide probes for profilin (protein) using force curve measurement techniques and atomic force microscopy (AFM). The peptide probes designed and synthesized for this investigation were H-A3GP5GP5GP5G-OH (1), H-A3GP5G-OH (2), H-A3G7-OH (3), and H-A3G-OH (4). Each peptide probe was immobilized on a cantilever tip, and the interaction force to profilin, immobilized on a mica substrate, was examined by force curve measurements. The retraction forces obtained showed a sequence-dependent affinity of the peptide probe for profilin. The retraction force for peptide probe 1 was the largest of the four probes examined, and it confirmed that peptide probe 1 has high affinity for profilin. The single molecular retraction force between peptide probe 1 and profilin was estimated to be 96 pN, as determined by Gaussian fitting to the histogram of the retraction forces.

Colorimetric bio-barcode amplification assay for cytokines.

The bio-barcode amplification assay has become a powerful tool in detecting tens to hundreds of biological targets such as proteins and nucleic acids in the entire sample. However, current bio-barcode detection schemes still require many experimental steps including microarrayer-based immobilization of oligonucleotides on a glass chip, silver enhancement of immobilized gold nanoparticles on a chip, and light-scattering measurement. Here, we report a colorimetric bio-barcode method that minimizes the above requirements while detecting 30 aM concentrations of cytokines (approximately 3 orders of magnitude more sensitive than conventional nonenzymatic cytokine detection assays). The assay is based on porous microparticles, which enable loading of a large number of barcode DNA per particle, and gold nanoparticle-based colorimetric barcode detection method.

A simple pen-spotting method for arraying biomolecules on solid substrates.

We describe a simple, relatively inexpensive method for depositing biomolecules on a solid substrate using Rapidograph drafting pens. The pens can be used without modification to accurately deposit spots between approximately 100 and 600 microm in diameter. When mounted on a suitable microtranslation stage, the pens can be used to easily deposit tens of spots aligned with underlying substrate features such as microfabricated sensors. The pens are particularly convenient because pre-mixed solutions can be stored in the pens for multiple uses. We demonstrate the use of this approach to deposit DNA probes on a microsensor array.

Leupeptin-induced appearance of partial fragment of betaine homocysteine methyltransferase during autophagic maturation in rat hepatocytes.

A cytosolic enzyme, betaine homocysteine methyltransferase (BHMT), and its partial fragments were discovered as autolysosomal membrane proteins from rat liver in the presence of leupeptin [Ueno et al. (1999) J. Biol. Chem. 274, 15222-15229]. The present study was undertaken to further characterize the transport and processing of BHMT from cytosol to autolysosome and to test if the fragment can be used as an in vitro probe for the maturation step of macroautophagy. Upon subcellular fractionation, BHMT (p44) was found in all fractions, while its 32-kDa fragment (p32) was found only in the mitochondrial-lysosomal (ML) fraction. Incubation of isolated hepatocytes with leupeptin induced time-dependent accumulation of p32 in the ML fraction from 30 to 90 min after the start of incubation. However, chloroquine completely inhibited the appearance of p32, indicating that the processing from p44 to p32 is lysosomal. Incubation with Bafilomycin A(1), a vacuolar H(+)-ATPase inhibitor, together with leupeptin, led to linear accumulation of p44, but not of p32. The p44 accumulation rate was calculated to be 4.9%/h, which was comparable to autophagic sequestration rate. The distribution of p44 within the ML fraction turned out to be dual, i.e., the membrane-surface attached and luminal/sedimentable forms. Amino acids and 3-methyladenine, both of which specifically suppress macroautophagy, inhibited the accumulation of p32 as well as of p44. Finally, energy-dependent appearance of p32 was demonstrated during incubation of postnucler supernatant fractions, making it possible to establish an in vitro assay system. All the results strongly support the idea that BHMT is taken up and degraded to p32 through the macroautophagic pathway, and that p32 could be a novel probe for the maturation of macroautophagy.

Molecular rotors as fluorescent probes for biological studies.

Molecular rotors, which structure can be 4-(N,N-dimethylamino)-benzene, -benzylidene and -cinnamylidene derivatives and, also, coumarine-like compounds, have photophysical characteristics which strongly depend on the environmental parameters (polarity, viscosity, temperature, etc.). In this paper, a basic knowledge on molecular fluorescent rotors will be reminded and two fields of applications using molecular fluorescent rotors as optical sensors will be described: firstly, in polymer and, more particularly to detect the formation of hydrophobic microdomains, in the case of the aggregation of amphiphilic polymers (as models for globular proteins and/or enzymes) and, secondly, in cell biology, especially in liposomes (as models for biological membranes) to follow their thermotropic behavior and in endothelial cells under 3D fluorescence microscopy.