Millisecond analysis of double stranded DNA with fluorescent intercalator by micro-thermocontrol-device

Study of interaction between DNA and intercalator at molecular level is important to understand the mechanisms of DNA replication and repair. A micro-fabricated local heating thermodevice was adapted to perform denaturation experiments of DNA with fluorescent intercalator on millisecond time scale. Response time of complete unzipping of double stranded DNA, 16 μm in length, was measured to be around 5 min by commercial thermocycler. Response time of quenching of double stranded DNA with fluorescent intercalator SYBR Green was measured to be 10 ms. Thus, quenching properties owing to strand unzipping and denaturation at base pair level were distinguished. This method has provided easy access to measure this parameter and may be a powerful methodology in analyzing biomolecules on millisecond time scale.     

二硫键的氧化还原状态对Trx融合赤霉酸诱导富含半胱氨酸蛋白内源荧光及变性过程影响

在采用亲和层析、SDS-聚丙烯酰胺凝胶电泳(SDS-PAGE)对原核表达的赤霉酸诱导的富含半胱氨酸蛋白(Trx-GcGASA)进行纯化、鉴定的基础上,运用稳态荧光光谱手段研究了二硫苏糖醇(DTT)、氧化型谷胱甘肽(GSSG)、过氧化氢、盐酸胍(GdnHCl)对Trx-GcGASA内源荧光及变性过程的影响,发现(1)在中性缓冲体系中融合蛋白的内源荧光以305 nm的酪氨酸的荧光发射为主;(2)伴随着二硫键还原,融合蛋白中色氨酸和酪氨酸的相对荧光强度比值从0.7变化至1.8倍左右;(3)经过0.5 mmol.L-1GSSG、5 mmol.L-1过氧化氢处理后,酪氨酸和色氨酸的荧光强度下降约12~21%;(4)无论是否采用1 mmol.L-1DTT处理,6 mol.L-1盐酸胍均不能诱导融合蛋白彻底变性;(5)二硫键的存在与否影响了盐酸胍诱导的变性过程。通过两态模型拟合获得Trx-GcGASA变性过程Gibbs自由能变化ΔG约为3.7 kJ.mol-1。相关工作不仅为深入研究融合伴侣Trx对GcGASA变性热力学、动力学及复性过程影响奠定了基础;同时,也为通过光谱手段获取GcGASA的结构信息提供了基础的数据。     

Collagen absorption bands in heated and rehydrated dentine

The objective of this work is identifying changes in the collagen bands in heated and rehydrated dentine. We use bovine dentine slices that were heated in oven between 100 and 300 degrees C. The sample hydration was conducted in sodium chloride solution at 0.9 wt.%; the spectra were acquired by a Fourier transform infrared spectrometer in the spectral range of 4000-400 cm-1. Our results show a temperature range (T225 degrees C) where the collagen is denatured and no reversion is observed after rehydration. This work identifies an important characteristic that dentinal collagen can assume when the tissue is heated and rehydrated; these results indicate the denaturation temperature of dentinal collagen to be near 175-200 degrees C.     

A distinct intermediate of RNase A is induced by sodium dodecyl sulfate at its pK(a)

The chemical denaturation of RNase A was found to be mediated by sodium dodecyl sulfate (SDS) at various pH. The characterization of the unfolding pathway was investigated by spectrophotometry and differential scanning calorimetry (DSC), and was analyzed by multivariate curve resolution (MCR) as a chemometric method. The spectrophotometric titration curve of RNase A upon interaction with SDS indicated a distinct complex intermediate in glycine buffer at pH 3.3. This was accompanied with the catalytic activation of the enzyme and was concurrent with maximum population of the intermediate, determined by MCR. This was confirmed by the DSC profile of RNase A in the presence of SDS, indicated by two transitions in thermal unfolding. The kinetic data on the unfolding process of RNase A upon addition of SDS showed a two-phase pathway under the same conditions. The intermediate appeared at low pH especially at the pK_a of SDS (pH 3.3). These results provide strong evidence of the influence of low pH (around the pK_a of SDS) on the existence of an intermediate upon interaction of RNase A with SDS.     

盐酸胍/Ⅰ型胶原分散体系的流变性

采用胃蛋白酶降解法从猪皮中提取了胶原蛋白,用十二烷基硫酸钠-聚丙烯酰胺凝胶电泳(SDSPAGE)确定为Ⅰ型胶原;红外及紫外光谱表明胶原分子中存在三螺旋结构.分别采用小幅振荡剪切法、恒定剪切速率法及滞后环法研究了盐酸胍浓度及作用时间对Ⅰ型胶原蛋白体系流变性的影响.研究表明,随盐酸胍浓度的增大及作用时间的延长,盐酸胍/胶原分散体系由假塑性流体逐渐接近于牛顿流体.在所研究的盐酸胍浓度范围(0~6.0 mol/L)内,盐酸胍/胶原分散体系的触变性类型随盐酸胍浓度的增大发生正触变性-复合触变性-负触变性的转变;随盐酸胍作用时间的延长(6~48 h),盐酸胍浓度为1.0 mol/L的胶原分散体系的触变性类型发生复合触变性-负触变性的转变.本文的研究结果有助于加深对触变性产生机理的认识.     

DNA温度效应的Raman光谱研究

测定了不同温度下DNA纤维和溶液的拉曼光谱。结果表明: 当温度变化时, 碱基、磷酸根等特征振动都不同程度的受到影响, 谱线强度、频率随温度呈非线性变化。在所有的振动模式中, 腺嘌呤A的特征振动受到温度的影响最大。除了磷酸根的谱线1 101 cm-1以外, 其余谱线的波数变化均随温度的升高向低波数移动, 而且波数的移动主要集中在变性峰的起始点70 ℃左右。另外还讨论了拉曼谱线强度随温度的变化关系, 得到了38,82 ℃(纤维为85 ℃)2个峰, 其中38 ℃与DNA的功能活跃区有关, 82 ℃(和85 ℃)为DNA的变性点, 与DSC(差示扫描量热法)的测量结果一致。     

The effects of urea and n-propanol on collagen denaturation: using DSC, circular dicroism and viscosity

The effect of urea and n-propanol on circular dichroism (CD) and viscosity of purified type1 collagen solution at various temperatures and differential scanning calorimetry (DSC) of rat-tail tendon (RTT) collagen fibre have been studied. CD reveals a spectrum with a positive peak at around 220 nm and a negative peak at 200 nm characteristics of collagen triple helix. The molar ellipticity decreases as the concentration of urea increases up to particular concentration (collagen solution treated with 265 μM of urea) and after that it increases (collagen solution treated with 500 μM of urea). There is a linear decrease in molar ellipticity as the concentration of n-propanol increases. Denaturation temperature of urea and n-propanol treated with purified collagen solution has been studied using viscosity method. Additives such as urea and n-propanol decrease the thermal stability of collagen triple helix in solution and in RTT collagen fibre. Thermal helix to coil transition of urea and n-propanol treated collagen depends on the degree of hydration and the concentration of these additives. Thermodynamic parameters such as the peak temperature, enthalpy of activation, and energy of activation for collagen-gelatin transition for native, urea and n-propanol treated RTT collagen fibre has been calculated using DSC. The change in the thermodynamic parameters has been observed for native, urea and n-propanol treated RTT collagen fibres. The experimental results show that the change in the water structure, dehydration and desolvation induced by different additives such as urea and n-propanol on RTT may vary with the type of denaturation.     

Phase diagram of mechanically stretched DNA: The salt effect

The cations, in the form of salt, present in a solution containing DNA play a crucial role in the opening of the two strands of DNA. We use a simple non-linear model and investigate the role of these cations on the mechanical unzipping of DNA. The Hamiltonian is modified to incorporate the solvent effect and the presence of these cations in the solution. We calculate the melting temperature as well as the critical force that is required to unzip the DNA molecule as a function of salt concentration of the solution. The phase diagrams are found to be in close agreement with the experimental phase diagrams.     

Comparative Studies of Two Araceous Lectins by Steady State and Time-Resolved Fluorescence and CD Spectroscopy

Transitions in the tryptophan microenvironment and secondary structure of two monocot lectins from Sauromatum guttatum and Arisaema tortuosum under different denaturing conditions were studied by steady state and time resolved fluorescence and CD spectroscopy. The lectins exist as tetramers with a single tryptophan residue estimated per monomer, present in a polar environment. Quenching with ionic quenchers showed predominantly electropositive environment for tryptophan residues. Acrylamide had maximum quenching effect. A decrease in KI quenching due to lectin denaturation indicated redistribution of charges as a result of possible conformational change. The two values for lifetimes of tryptophanyl population (1.2–1.4 and 6.3–6.4 ns) reduced substantially on quenching or denaturation. Similarly, both the lectins showed a drastic loss of secondary structure in 5 M Gdn-HCl or 6 M Urea or at pH 2.0 and below. For the first time araceous lectins, like legume lectins are shown to bind adenine. The presence of a compact structure at alkaline pH 10.0–12.0 was observed in CD spectra.     

Hydrophilic lecithins protect milk proteins against heat-induced aggregation

In the present study, the heat-induced interaction between whey proteins and casein micelles was studied. To that end, the particle size distribution of 5.5% (w/w) casein micellar dispersions was determined by photon correlation spectroscopy as a function of both the whey protein concentration and heating time at 80 °C. The results clearly indicated that heat-induced aggregation of the casein micelles only occurred in the presence of whey proteins.

In an effort to overcome the heat-induced interactions between whey proteins and casein micelles, the influence of different soybean lecithins was investigated. Comparing native to hydrolysed, as well as hydroxylated soybean lecithin, it was observed that the heat-stabilising effect of the lecithins was directly related to their hydrophilicity: whereas native soybean lecithin had hardly any beneficial effect, highly hydrolysed as well as hydroxylated soybean lecithin largely prevented heat-induced casein micelle aggregation in the presence of whey proteins.

From experimental observations on the heat-induced decrease of whey protein solubility both in the absence and presence of hydrolysed lecithin, it was deduced that the latter may stabilise the exposed hydrophobic surface sites of heat-denatured whey proteins. Dynamic surface tension measurements indicated that the heat-stabilising properties of lecithins were mainly determined by their critical aggregation concentration.