Implementing conventional logic unconventionally: photochromic molecular populations as registers and logic gates

In this paper we detail experimental methods to implement registers, logic gates and logic circuits using populations of photochromic molecules exposed to sequences of light pulses. Photochromic molecules are molecules with two or more stable states that can be switched reversibly between states by illuminating with appropriate wavelengths of radiation. Registers are implemented by using the concentration of molecules in each state in a given sample to represent an integer value. The register's value can then be read using the intensity of a fluorescence signal from the sample. Logic gates have been implemented using a register with inputs in the form of light pulses to implement 1-input/1-output and 2-input/1-output logic gates. A proof of concept logic circuit is also demonstrated; coupled with the software workflow describe the transition from a circuit design to the corresponding sequence of light pulses.     

Fluorescence Lifetime Imaging of Molecular Rotors in Living Cells

Diffusion is often an important rate-determining step in chemical reactions or biological processes and plays a role in a wide range of intracellular events. Viscosity is one of the key parameters affecting the diffusion of molecules and proteins, and changes in viscosity have been linked to disease and malfunction at the cellular level.^1-3 While methods to measure the bulk viscosity are well developed, imaging microviscosity remains a challenge. Viscosity maps of microscopic objects, such as single cells, have until recently been hard to obtain. Mapping viscosity with fluorescence techniques is advantageous because, similar to other optical techniques, it is minimally invasive, non-destructive and can be applied to living cells and tissues.Fluorescent molecular rotors exhibit fluorescence lifetimes and quantum yields which are a function of the viscosity of their microenvironment.^4,5 Intramolecular twisting or rotation leads to non-radiative decay from the excited state back to the ground state. A viscous environment slows this rotation or twisting, restricting access to this non-radiative decay pathway. This leads to an increase in the fluorescence quantum yield and the fluorescence lifetime. Fluorescence Lifetime Imaging (FLIM) of modified hydrophobic BODIPY dyes that act as fluorescent molecular rotors show that the fluorescence lifetime of these probes is a function of the microviscosity of their environment.^6-8 A logarithmic plot of the fluorescence lifetime versus the solvent viscosity yields a straight line that obeys the Förster Hoffman equation.⁹ This plot also serves as a calibration graph to convert fluorescence lifetime into viscosity.Following incubation of living cells with the modified BODIPY fluorescent molecular rotor, a punctate dye distribution is observed in the fluorescence images. The viscosity value obtained in the puncta in live cells is around 100 times higher than that of water and of cellular cytoplasm.^6,7 Time-resolved fluorescence anisotropy measurements yield rotational correlation times in agreement with these large microviscosity values. Mapping the fluorescence lifetime is independent of the fluorescence intensity, and thus allows the separation of probe concentration and viscosity effects. In summary, we have developed a practical and versatile approach to map the microviscosity in cells based on FLIM of fluorescent molecular rotors.     

pH敏感的荧光探针及在活细胞中的应用

细胞内的pH是细胞内多种酶活性和生理活动的重要调节因素,准确、动态的监测细胞内pH变化对研究细胞内的活动至关重要。一些荧光小分子可以感应pH的变化,同时具有较高的灵敏度和特异性,对细胞损伤较小且标记操作简单,已逐渐发展成为一种监测细胞内pH变化的有效方法。本文主要介绍目前常用pH敏感的荧光探针及其在活细胞研究中的进展。     

量子点荧光光谱学与生命科学

近年来,量子点(半导体纳米微晶体)的研究引起国内外研究者的广泛兴趣,其研究内容涉及物理学、化学、材料等多学科,已成为一门新兴的交叉学科。虽然量子点在生物学中的应用才刚刚起步,但是已经取得了有意义的进展,成为人们极为关注的一个热点。现就量子点的光学特性、制备方法,以及在生物学中的研究进展和应用前景作一简要综述。     

Enzyme logic gates for the digital analysis of physiological level upon injury

A biocomputing system composed of a combination of AND/IDENTITY logic gates based on the concerted operation of three enzymes: lactate oxidase, horseradish peroxidase and glucose dehydrogenase was designed to process biochemical information related to pathophysiological conditions originating from various injuries. Three biochemical markers: lactate, norepinephrine and glucose were applied as input signals to activate the enzyme logic system. Physiologically normal concentrations of the markers were selected as logic 0 values of the input signals, while their abnormally increased concentrations, indicative of various injury conditions were defined as logic 1 input. Biochemical processing of different patterns of the biomarkers resulted in the formation of norepi-quinone and NADH defined as the output signals. Optical and electrochemical means were used to follow the formation of the output signals for eight different combinations of three input signals. The enzymatically processed biochemical information presented in the form of a logic truth table allowed distinguishing the difference between normal physiological conditions, pathophysiological conditions corresponding to traumatic brain injury and hemorrhagic shock, and abnormal situations (not corresponding to injury). The developed system represents a biocomputing logic system applied for the analysis of biomedical conditions related to various injuries. We anticipate that such biochemical logic gates will facilitate decision-making in connection to an integrated therapeutic feedback-loop system and hence will revolutionize the monitoring and treatment of injured civilians and soldiers.     

Ultrasensitive DNA detection by cycle isothermal amplification based on nicking endonuclease and its application to logic gates

In recent years, an intense interest has grown in the DNA logic gates having high potential for computation at literally the “nano-size” level. A limitation of traditional DNA logic gates is that each target strand hybridizes with only a single copy of the probe. This 1:1 hybridization radio limits the gain of the approach and thus its sensitivity. The exponential amplification of nucleic acids has become a core technology in medical diagnostics and has been widely used for the construction of DNA sensor, DNA nanomachine and DNA sequencing. It would be of great interest to develop DNA-based logic systems with exponential amplification for the output signal. In the present study, a series of three-input DNA logic gates with the cycle isothermal amplification based on nicking endonuclease (NEase) are designed. Very low concentrations of the analytes were sufficient to initiate an autocatalytic cascade, achieving a significant improvement of the detection limit, 100-fold improvement compared to the non-autocatalytic system. This was achieved by engineering a simple and flexible biological circuit designed to initiate a cascade of events to detect and amplify a specific DNA sequence. This procedure has the potential to greatly simplify the logic operation because amplification can be performed in “one-pot”.     

条斑紫菜R-藻红蛋白荧光探针制备条件优化

通过化学方法使条斑紫菜R-藻红蛋白与抗体进行交联以制备荧光探针, 并对制备条件进行优化。首先采用异双功能试剂SPDP (N-琥珀酰亚氨基-3-2-吡啶基二硫丙酸醇)和DTT（二硫苏糖醇）分别使 R-PE(R-藻红蛋白)衍生化、IgG（单克隆抗体）巯基化, 其次测定了SPDP与R-PE不同摩尔比对R-PE衍生化的影响、DTT与IgG不同摩尔比对IgG巯基化的影响, 结果表明：SPDP与R-PE的最佳摩尔比为40：1, DTT与IgG的最佳摩尔比为500:1。在此基础上, 建立了R-PE与IgG交联的制备技术, 并应用全波长扫描吸收光谱、电泳分析和荧光显微镜观察等监测和分析技术, 证实了藻红蛋白与抗体已成功交联形成了复合物。     

Fluorescence‐based logic gate for sensing of Ca2+ and F− ions using PVP crowned chrysene nanoparticles in aqueous medium

Polyvinyl pyrrolidone (PVP) crowned chrysene nanoparticles (CHYNPs) were prepared by using a reprecipitation method. Dynamic light scattering (DLS) and scanning electron microscope (SEM) studies indicate that the monodispersed spherical nanoparticles bear a negative charge on their surfaces. The bathochromic spectral shift in the UV–visible and fluorescence spectrum of CHYNPs from chrysene (CHY) in acetone solution supports the J‐ type aggregation of nanoparticles. The aggregation‐induced enhanced emission of CHYNPs at 486 and 522 nm decreases by increasing the concentration of the Ca²⁺ ion solution. It can display an ON–OFF type fluorescence response with high selectivity towards Ca²⁺ ions aqueous medium. Furthermore, the in situ generated PVP–CHYNPs–Ca²⁺ ensemble could recover the quenched fluorescence upon the addition of fluoride anions resulting in an OFF–ON type sensor. The present method has a correlation coefficient R² = 0.988 with a detection limit of 1.22 μg/mL for Ca²⁺ in the aqueous medium. The fluorescence changes of PVP crowned CHYNPs upon the addition of Ca²⁺ and F^? can be utilized as an INHIBIT logic gate at the molecular level, using Ca²⁺ and F^? chemical inputs and the fluorescence intensity signal as output.     

Boradiazaindacene dyes for technology of biological microchips

A number of boradiazaindacene dyes containing a carboxyl group separated from a fluorophore by two methylene units were synthesized. The compounds have narrow spectral bands with absorption maxima at 480–530 nm and fluorescence maxima at 500–550 nm. Succinimide esters of these compounds and the corresponding fluorescent-labeled oligonucleotides were also prepared. Boradiazaindacene dyes can be used as fluorescent labels for oligonucleotides for analysis of melting curves of duplexes on microchips either by themselves or in combination with Texas Red. They can also be applied for labeling primers for polymerase chain reaction.     

Single molecule fluorescence spectroscopy for quantitative biological applications

Single molecule techniques emerge as powerful and quantitative approaches for scientific investigations in last decades. Among them, single molecule fluorescence spectroscopy (SMFS) is able to non-invasively characterize and track samples at the molecular level. Here, applications of SMFS to fundamental biological questions have been briefly summarized in catalogues of single-molecule counting, distance measurements, force sensors, molecular tracking, and ultrafast dynamics. In these SMFS applications, statistics and physical laws are utilized to quantitatively analyze the behaviors of biomolecules in cellular signaling pathways and the mechanisms of biological functions. This not only deepens our understanding of bio-systems, but also provides a fresh angle to those fundamental questions, leading to a more quantitative thinking in life science.     

New indodicarbocyanine dyes for the biological microchip technology

New indodicarbocyanine dyes with the carboxybutyl group in position-3 of the indolenine fragment bearing methyl and sulfonic groups in positions 5 and 7 of the cycle were synthesized in order to find the most effective fluorescent labels for the biological microchip technology. The position of absorption and fluorescence maxima, the total charge of the dye molecule, and water solubility depend on the location and the total amount of methyl and sulfonic groups. The spectral characteristics of the dyes synthesized were determined. The relative fluorescence efficiencies of the dyes at equal concentrations were measured at excitation wavelengths of 635 and 655 nm and emission wavelengths of 670 and 690 nm, respectively.     

本科生物技术专业分子医学课程教学的探讨

分子医学时代的开启给生命科学领域的本科教学带来了新的挑战。在针对本科生物技术专业所开设的分子医学课程教学中,从授课内容与形式、教学手段与方法、教学考核等方面进行了相关的分析与实践,有效地提高了教学质量。     

Fluorescence spectroscopic analysis on interaction of fleroxacin with pepsin

The interaction between fleroxacin (FLX) and pepsin was investigated by spectrofluorimetry. The effects of FLX on pepsin showed that the microenvironment of tryptophan residues and molecular conformation of pepsin were changed based on fluorescence quenching and synchronous fluorescence spectroscopy in combination with three‐dimensional fluorescence spectroscopy. Static quenching was suggested and it was proved that the fluorescence quenching of pepsin by FLX was related to the formation of a new complex and a non‐radiation energy transfer. The quenching constants K_SV, binding constants K and binding sites n were calculated at different temperatures. The molecular interaction distance (r = 6.71) and energy transfer efficiency (E = 0.216) between pepsin and FLX were obtained according to the Forster mechanism of non‐radiation energy transfer. Hydrophobic and electrostatic interaction played a major role in FLX–pepsin association. In addition, the hydrophobic interaction and binding free energy were further tested by molecular modeling study. Copyright © 2013 John Wiley & Sons, Ltd.     

Synthesis and Characterization of Time-resolved Fluorescence Probes for Evaluation of Competitive Binding to Melanocortin Receptors

Probes for use in time-resolved fluorescence competitive binding assays at melanocortin receptors based on the parental ligands MSH(4), MSH(7), and NDP-α-MSH were prepared by solid phase synthesis methods, purified, and characterized. The saturation binding of these probes was studied using HEK-293 cells engineered to overexpress the human melanocortin 4 receptor (hMC4R) as well as the human cholecystokinin 2 receptor (hCCK2R). The ratios of non-specific binding to total binding approached unity at high concentrations for each probe. At low probe concentrations, receptor-mediated binding and uptake was discernable, and so probe concentrations were kept as low as possible in determining K_d values. The Eu-DTPA-PEGO-MSH(4) probe exhibited low specific binding relative to non-specific binding, even at low nanomolar concentrations, and was deemed unsuitable for use in competition binding assays. The Eu-DTPA-PEGO probes based on MSH(7) and NDP-α-MSH exhibited K_d values of 27 ± 3.9 nM and 4.2 ± 0.48 nM, respectively, for binding with hMC4R. These probes were employed in competitive binding assays to characterize the interactions of hMC4R with monovalent and divalent MSH(4), MSH(7), and NDP-α-MSH constructs derived from squalene. Results from assays with both probes reflected only statistical enhancements, suggesting improper ligand spacing on the squalene scaffold for the divalent constructs. The K_i values from competitive binding assays that employed the MSH(7)-based probe were generally lower than the K_i values obtained when the probe based on NDP-α-MSH was employed, which is consistent with the greater potency of the latter probe. The probe based on MSH(7) was also competed with monovalent, divalent, and trivalent MSH(4) constructs that previously demonstrated multivalent binding in competitive binding assays against a variant of the probe based on NDP-α-MSH. Results from these assays confirm multivalent binding, but suggest a more modest increase in avidity for these MSH(4) constructs than was previously reported.     

虚拟生物实验室实例

虚拟生物实验室在生物课程资源中有巨大并且尚未开发的潜力。它对于不同级别学生的学习都是有利的。介绍了虚拟生物实验室的一些实例。并展望了其应用前景。     

荧光相关光谱在生物化学领域中的应用

荧光相关光谱(fluorescence correlation spectroscopy,FCS)是一种通过监测荧光涨落从而获得单分子水平的分子扩散行为信息的技术。FCS高灵敏度的优点使得它已发展成为一种可以在活体外与活体内检测分子浓度、扩散系数、结合和解离常数等参数的有力工具。荧光互相关光谱(fluorescence cross-correlation spectroscopy,FCCS)是FCS技术的进一步发展,其大大扩展了FCS技术的应用范围。本文介绍了FCS及其衍生技术的原理及其在生物化学领域的应用。     

Multiphoton microscopy for the in-situ investigation of cellular processes and integrity in cryopreservation

In this study we demonstrate a new noninvasive imaging method to monitor freezing processes in biological samples and to investigate life in the frozen state. It combines a laser scanning microscope with a computer-controlled cryostage. Nearinfrared (NIR) femtosecond laser pulses evoke the fluorescence of endogenous fluorophores and fluorescent labels due to multiphoton absorption.The inherent optical nonlinearity of multiphoton absorption allows 3D fluorescence imaging for optical tomography of frozen biological material in-situ. As an example for functional imaging we use fluorescence lifetime imaging (FLIM) to create images with chemical and physical contrast.     

血清白蛋白的生物学特性研究进展

人类血清白蛋白是单链、多结构域的大分子物质,是血浆中含量最丰富,也是人体中很重要的。一种蛋白质。白蛋白有77个结合配体的位点,能与一系列内源性和外源性物质相结合,起着存储和转运的作用。此外,白蛋白还具有维持血液正常的渗透压、抗氧化及参与炎症反应等一系列的生理和药理学功能。在临床上,白蛋白的应用已有50多年的历史,主要应用于中风、烧伤、低白蛋白血症等。回顾了近年来相关文献,就白蛋白的生物学特性作一阐述。     

Fluorescence in Situ Hybridization (FISH): DNA Probe Production and Hybridization Criteria

We describe methods for the production of fluorescence in situ hybridization (FISH) probes and the utilization of these probes for the detection of complementary DNA sequences with accuracy and sensitivity for application in both basic research and clinical diagnosis. Due to the frequent use of FISH in many laboratories, it is important to apply the most convenient and reproducible approach. This review describes some of the most recent techniques, and includes versatile, effective and simple methods of probe production and fluorescence in situ hybridization. We also describe methods for the production of region-specific and chromosome-specific DNA probes and hybridization techniques for the visualization of these probes.