Real-Time analysis of exosome secretion of single cells with single molecule imaging

The exosome-mediated response can promote or restrain the diseases by regulating the intracellular pathways,making the exosome become an effective marker for diagnosis and therapeutic control at the single-cell level.However,real-time analysis is hard to be achieved with traditional approaches because the exosomes usually need to be enriched by ultracentrifugation for a measurable signal-to-noise ratio.Recently developed label-free single-molecule imaging approaches may become an real-time quantitative tool for the analysis of single exosomes and related secretion behaviors of single living cells owing to their extreme sensitivity.

Real-Time PCR Technique and Its Application in Quantification of Plant Nucleic Acid Molecules

Real-time PCR is a closed DNA amplification system that skillfully integrates biochemical, photoelectric and computer techniques. Fluorescence data acquired once per cycle provides rapid absolute quantification of initial template copy numbers as PCR products are generated. This technique significantly simplifies and accelerates the process of producing reproducible quantification of nucleic acid molecules. It not only is a sensitive, accurate and rapid quantitative method, but it also provides an easier way to calculate the absolute starting copy number of nucleic acid molecules to be tested. Together with molecular bio-techniques, like microarray, real-time PCR will play a very important role in many aspects of molecular life science such as functional gene analysis and disease molecular diagnostics. This review introduces the detailed principles and application of the real-time PCR technique, describes a recently developed system for exact quantification of AUX/IAA genes In Arabidopsis, and discusses the problems with the real-time PCR process.

Interaction Study between DNA and Histone Proteins on Single-molecule Level using Atomic Force Microscopy

DNA and histone protein are important in the formation of nucleosomal arrays, which are the first packaging level of DNA into a more compact chromatin structure. To characterize the interactions of DNA and histone proteins, we reconstitute nucleosomes using lambda DNA and whole histone proteins by dialysis and perform direct atomic force microscopy （AFM） imaging. Compared with non-specific DNA and histone binding, nucleosomes are formed within the assembled “beads-on-a-string” nucleosomal array by dialysis. These observations facilitate the establishment of the molecular mechanisms of nucleosome and demonstrate the capability of AFM for protein-DNA interaction analysis.

Improvement of the Lewis-Abegg-Octet Rule Using an “Even-Odd” Rule in Chemical Structural Formulas: Application to Hypo and Hyper-Valences of Stable Uncharged Gaseous Single-Bonded Molecules with Main Group Elements

As Lewis proposed his octet rule, itself inspired by Abegg’s rule, that a molecule is stable when all its composing atoms have eight electrons in their valence shell, it perfectly applied to the vast majority of known stable molecules. Only a few stable molecules were known that didn’t fall under this rule, such as PCl5 and SF6, and Lewis chose to leave them aside at the time of his research. With further advances in chemistry, more exceptions to this rule of eight have been found, usually with the central atom of the structure having more or less than eight electrons in its valence shell. Theories have been developed in order to modify the octet rule to suit these molecules, defining these as hyper- or hypo-valent molecules and using other configurations for the electrons. The present paper aims to propose a representation rule for gaseous single-bonded molecules that makes it possible to reconcile both;molecules following the octet theory and those which do not. In this representation rule, each element of the molecule is subscripted with two numbers that follow a set of simple criteria. The first represents the number of valence electrons of the element;while the second is calculated by adding the first number to the number of the element’s covalent bonds within the molecule. The latter is equal to eight for organic molecules following the octet rule. Molecules being exceptions to the octet rule are now encompassed by this new even-odd rule: they have a valid chemical structural formula in which the second number is even but not always equal to eight. Both rules—octet and even-odd—are discussed and compared, using several well-known gaseous molecules having one or several single-bonded elements. A future paper will discuss the application of the even-odd rule to charged molecules.

Exploring the hepatitis C virus genome using single molecule realtime sequencing

Single molecular real-time(SMRT)sequencing,also called third-generation sequencing,is a novel sequencing technique capable of generating extremely long contiguous sequence reads.While conventional short-read sequencing cannot evaluate the linkage of nucleotide substitutions distant from one another,SMRT sequencing can directly demonstrate linkage of nucleotide changes over a span of more than 20 kbp,and thus can be applied to directly examine the haplotypes of viruses or bacteria whose genome structures are changing in real time.In addition,an error correction method(circular consensus sequencing)has been established and repeated sequencing of a single-molecule DNA template can result in extremely high accuracy.The advantages of long read sequencing enable accurate determination of the haplotypes of individual viral clones.SMRT sequencing has been applied in various studies of viral genomes including determination of the full-length contiguous genome sequence of hepatitis C virus(HCV),targeted deep sequencing of the HCV NS5A gene,and assessment of heterogeneity among viral populations.Recently,the emergence of multi-drug resistant HCV viruses has become a significant clinical issue and has been also demonstrated using SMRT sequencing.In this review,we introduce the novel third-generation PacBio RSII/Sequel systems,compare them with conventional next-generation sequencers,and summarize previous studies in which SMRT sequencing technology has been applied for HCV genome analysis.We also refer to another long-read sequencing platform,nanopore sequencing technology,and discuss the advantages,limitations and future perspectives in using these thirdgeneration sequencers for HCV genome analysis.

MORPHOLOGY EVOLUTION IN PTFE AS A FUNCTION OF MELT TIME AND TEMPERATURE——Ⅰ.HIGH MOLECULAR WEIGHT SINGLE-AND MULTI-MOLECULE FOLDED CHAIN SINGLE CRYSTALS AND BAND STRUCTURES

The effect of sintering dispersed dispersion and nano-emulsion particles of high molecular weightpolytetrafluoroethylene(PTFE)on a substrate as a function of“melt”time and temperature is described.Folded chain singlecrystals parallel to the substrate and as ribbons on-edge(with double striations),as well as bands,are produced for longersintering times;particle merger and diffusion of individual molecules,crystallizing as folded chain,single(or few)molecule,single crystals when“trapped”on the substrate by cooling occur for shorter sintering times.It is suggested the observedstructures develop with sintering time,in a mesomorphic melt.The structure of the nascent particles is also discussed.

The Even-Odd Rule on Single Covalent-Bonded Structural Formulas as a Modification of Classical Structural Formulas of Multiple-Bonded Ions and Molecules

In organic chemistry, as defined by Abegg, Kossel, Lewis and Langmuir, compounds are normally represented using structural formulas called Lewis structures. In these structures, the octet rule is used to define the number of covalent bonds that each atom forms with its neighbors and multiple bonds are frequent. Lewis’ octet rule has unfortunately shown limitations very early when applied to non-organic compounds: most of them remain incompatible with the “rule of eight” and location of charges is uncertain. In an attempt to unify structural formulas of octet and non-octet molecules or single-charge ions, an even-odd rule was recently proposed, together with a procedure to locate charge precisely. This even-odd rule has introduced a charge-dependent effective-valence number calculated for each atom. With this number and the number of covalent bonds of each element, two even numbers are calculated. These numbers are both used to understand and draw structuralformulas of single-covalent-bonded compounds. In the present paper, a procedure is proposed to adjust structural formulas of compounds that are commonly represented with multiple bonds. In order to keep them compatible with the even-odd rule, they will be represented using only single covalent bonds. The procedure will then describe the consequences of bond simplification on charges locations. The newly obtained representations are compared to their conventional structural formulas, i.e. single-bond representation vs. multiple-bond structures. Throughout the comparison process, charges are precisely located and assigned to specific atoms. After discussion of particular cases of compounds, the paper finally concludes that a rule limiting representations of multiplecovalent bonds to single covalent bonds, seems to be suitable for numerous known compounds.

A glass nanopore electrode for single molecule detection

We have developed a simple method for fabricating robust and low noise glass nanopore electrodes with pore size 10±5 nm to detect single molecules.β-Cyclodextrin was used as model compound for characterization.In 1.0 mol/L NaCl solution,the molecules generated current pulses of 2-5 pA with noise level less than 0.8 pA.A slide mode and a plug mode were suggested for the way ofβ-cyclodextrin single molecule moving into the glass nanopores.

Detailed investigation on single water molecule entering carbon nanotubes

The behavior of a water molecule entering carbon nanotubes （CNTs） is stud- ied. The Lennaxd-Jones potential function together with the continuum approximation is used to obtain the van der Waals interaction between a single-walled CNT （SWCNT） and a single water molecule. Three orientations are chosen for the water molecule as the center of mass is on the axis of nanotube. Extensive studies on the variations of force, energy, and velocity distributions axe performed by vaxying the nanotube radius and the orientations of the water molecule. The force and energy distributions are validated by those obtained from molecular dynamics （MD） simulations. The acceptance radius of the nanotube for sucking the water molecule inside is derived, in which the limit of the radius is specified so that the nanotube is favorable to absorb the water molecule. The velocities of a single water molecule entering CNTs axe calculated and the maximum entrance and the interior velocity for different orientations axe assigned and compared.

Visualized SERS Imaging of Single Molecule by Ag/ Black Phosphorus Nanosheets

Single-molecule detection and imaging are of great value in chemical analysis,biomarker identification and other trace detection fields.However,the localization and visualization of single molecule are still quite a challenge.Here,we report a special-engineered nanostructure of Ag nanoparticles embedded in multi-layer black phosphorus nanosheets(Ag/BP-NS)synthesized by a unique photoreduction method as a surfaceenhanced Raman scattering(SERS)sensor.Such a SERS substrate features the lowest detection limit of 10^(–20) mol L^(−1) for R6G,which is due to the three synergistic resonance enhancement of molecular resonance,photoinduced charge transfer resonance and electromagnetic resonance.We propose a polarization-mapping strategy to realize the detection and visualization of single molecule.In addition,combined with machine learning,Ag/BP-NS substrates are capable of recognition of different tumor exosomes,which is meaningful for monitoring and early warning of the cancer.This work provides a reliable strategy for the detection of single molecule and a potential candidate for the practical bio-application of SERS technology.

Density Functional Theory Study of MoO_3 Molecule Encapsulated inside Single-walled Carbon Nanotubes

The binding energies, geometric structures and electronic properties of molybde- num trioxide （MOO3） molecule encapsulated inside （8, 0）, （9, 0）, （10, 0） and （14, 0） single-walled carbon nanotubes （SWNTs） have been investigated using density functional theory （DFT） method. Due to curvature effect, the calculated binding energy values are different, the variation of which indicated that the stability of MoO3/SWNT systems increases with increasing the radius of SWNTs. At the same time, owing to the presence of MoO3 molecule, the band gap of MoO3/SWNTs systems decreases. The analysis of density of states （DOS） reveals hybridization between C-2p and Mo-4d and between C-2p and O-2p orbitals near the Fermi level, which results in electron transfer from SWNTs to MoO3 molecule. The present computations suggest that electronic properties of SWNTs can be modified by doping MoO3 molecule.

Simultaneous, hybrid single-molecule method by optical tweezers and fluorescence

As studies on life sciences progress toward the single-molecule level,new experiments have put forward more requirements for simultaneously displaying the mechanical properties and conformational changes of biomolecules.Optical tweezers and fluorescence microscopy have been combined to solve this problem.The combination of instruments forms a new generation of hybrid single-molecule technology that breaks through the limitations of traditional biochemical analysis.Powerfulmanipulation and fluorescence visualization have beenwidely used,and these techniques provide new possibilities for studying complex biochemical reactions at the singlemolecule level.This paper explains the features of this combined technique,including the application characteristics of single-trap and dual-traps,the anti-bleaching method,and optical tweezers combined with epifluorescence,confocal fluorescence,total internal reflection fluorescence,and other fluorescence methods.Using typical experiments,we analyze technical solutions and explain the factors and principles that instrument designers should consider.This review aims to give an introduction to this novel fusion technology process and describe important biological results.

Surface-enhanced resonance Raman scattering spectroscopy of single R6G molecules

Surface-enhanced resonance Raman scattering （SERRS） of Rhodamine 6G （R6G） adsorbed on colloidal silver clusters has been studied. Based on the great enhancement of the Raman signal and the quench of the fluorescence, the SERRS spectra of R6G were recorded for the samples of dye colloidal solution with different concentrations. Spectral inhomogeneity behaviours from single molecules in the dried sample films were observed with complementary evidences, such as spectral polarization, spectral diffusion, intensity fluctuation of vibrational lines and even ＂breathing＂ of the molecules. Sequential spectra observed from a liquid sample with an average of 0.3 dye molecules in the probed volume exhibited the expected Poisson distribution for actually measuring 0, 1 or 2 molecules. Difference between the SERRS spectra of R6G excited by linearly and circularly polarized light were experimentally measured.

Theoretical study on the lasing plasmon of a split ring for label-free detection of single molecules and single nanoparticles

This paper reports the plasmonic lasing of a split ring filled with gain material in water. The lasing mode（1500 nm）is far from the pump mode（980 nm）, which can depress the detection noise from the pump light. The laser intensities of the two modes simultaneously increase by more than 10^3 in amplitude, which can intensify the absorption efficiency of the pumping light and enhance the plasmonic lasing. The plasmonic lasing is a sensitive sensor. When a single protein nanoparticle（n = 1.5, r = 1.25 nm） is trapped in the gap of the split ring, the lasing spectrum moves by 0.031 nm, which is much larger than the detection limit of 10^-5 nm. Moreover, the lasing intensity is also very sensitive to the trapped nanoparticle. It reduces to less than 1/600 when a protein nanoparticle（n = 1.5, r = 1.25 nm） is trapped in the gap.

Improved data analysis method of single-molecule experiments based on probability optimization

To extract the dynamic parameters from single molecule manipulation experiments, usually lots of data at different forces need to be recorded. But the measuring time of a single molecule is limited due to breakage of the tether or degradation of the molecule. Here we propose a data analysis method based on probability maximizalion of the recorded time trace to extract the dynamic parameters from a single measurement. The feasibility of this method was verified by dealing with the simulation data of a two-state system. We also applied this method to estimate the parameters of DNA hairpin folding and unfolding dynamics measured by a magnetic tweezers experiment.

Combination of Micro-fluidic Chip with Fluorescence Correlation Spectroscopy for Single Molecule Detection

A single molecule detection technique was developed by the combination of a single channel poly （dimethylsiloxane）/glass micro-fluidic chip and fluorescence correlation spectroscopy （FCS）. This method was successfully used to determine the proportion of two model components in the mixture containing fluorescein and the rhodamine-green succinimidyl ester.

Single Molecule FRET Study of DNAG Quadruplex

The DNA G quadruplex formed by the human telomeric sequence is a potential target for novel anticancer drugs. We have investigated an intramolecular DNA G quadruplex using single molecule fluorescence resonance energy transfer and shown that individual folded quadruplexes can be identified. The mean proximity ratio measured at the single molecule level was consistent with ensemble measurement

Preferable Orientations of Interacting C_(60) Molecules inside Single Wall Boron Nitride Nanotubes

This work focuses on the preferable orientation analysis of the hybrid system where the C60 molecules are encap- sulated inside the boron nitride nanotubes by using the two-molecule model. The low-energy state can be acquired in the contour map, which provides the visual information of the systematical van der Waals interaction potential for the C60 molecules adopting different orientations. Our results show that the C60 molecules exhibit the pre- ferred pentagon and hexagon orientations with the tube＇s diameter smaller and larger than 13.55A, respectively. The preferred two-bond orientation obtained in the single-molecule model is absent in this study, indicating that the intermolecular interaction of adjacent C60 molecules plays an important role in the orientational behaviors of this peapod structure.

Deterministic Generation of Quantum State Transfer Between Spatially Separated Single Molecule Magnets

We propose a new scheme for realizing deterministic quantum state transfer （QST） between two spatially separated single molecule magnets （SMMs） with the framework of cavity quantum eleetrodynamics （QED）. In the present scheme, two SMMs are trapped in two spatially separated optical cavities coupled by an optical fiber. Through strictly numerically simulating, we demonstrate that our scheme is robust with respect to the SMMs＇ spontaneous decay and fiber loss under the conditions of dispersive SMMs-field interaction and strong coupling of cavity fiber. In addition, we also discuss the influence of photon leakage out of cavities and show that our proposal is good enough to demonstrate the generation of QST with high fidelity utilizing the current experimental technology. The present investigation provides research opportunities for realizing QST between solid-state qubits and may result in a substantial impact on the progress of solid-state-based quantum communications network.