普通Taq DNA聚合酶扩增幽门螺杆菌尿素酶基因长片段

ＰＣＲ反应扩增较长的ＤＮＡ片段比较困难。本实验对幽门螺杆菌染色体ＤＮＡ上的２７Ｋｂ尿素酶基因用普通ＴａｑＤＮＡ聚合酶进行扩增,扩增结果以琼脂糖凝胶电泳证实,得到所需的２７Ｋｂ的片段。该实验为今后幽门螺杆菌工作的进一步研究提供了经济,有效,简捷的条件。     

大肠杆菌表达的TaqDNA聚合酶的纯化

Taq DNA聚合酶是分子生物学研究中最常用的热稳定DNA聚合酶之一,与其他热稳定DNA聚合酶具有相似的特征,其纯化策略不但有潜在的应用前景,也对同类聚合酶的分离具有指导意义。已报道的适宜大量制备Taq酶的方案所需成本较高,而文章介绍了一种利用国产阳离子交换树脂廉价制备Taq酶的方案。在本方案中,采用热变性、(NH4)SO4沉淀与724离子交换层析分离大肠杆菌表达的Taq酶,约18 g Na型树脂干粉一次可回收比活约8 131.98 U/mg、总酶活2.2×105U、近27.07 mg Taq酶。纯化的产率可达48.92%,纯化倍数约59.35。所制酶SDS-PAGE电泳只检测到94 kDa单一蛋白条带,未检测到DNA核酸酶污染,与商品酶的PCR扩增能力无区别。此纯化方法成本低,适合实验室一般性的制备和生产应用。     

One-step purification of Taq DNA polymerase using nucleotide-mimetic affinity chromatography

The thermostable Thermus aquaticus DNA polymerase (Taq Pol) has been the key factor in transforming the initial PCR method into one with huge impact in molecular biology and biotechnology. Therefore, the development of effective affinity adsorbents for the purification of Taq Pol, as well as other DNA polymerases, attracts the attention of the enzyme manufacturers and the research laboratories. In this report we describe a simple protocol for the purification of Taq Pol from E. coli lysates, leading to enzymes of high specific activity and purity. The protocol is based on a single affinity chromatography step, featuring an immobilized ligand selected from a structure-biased combinatorial library of dNTP-mimetic synthetic ligands. The ligand library was screened for its ability to bind and purify Taq Pol from E. coli lysates. One immobilized ligand (mABSGu) of the general formula X-Trz-Y, bearing 9-aminoethylguanine (AEGu) and aniline-2-sulfonic acid (mABS) linked on the triazine scaffold (Trz), displayed the highest purifying ability. Adsorption equilibrium studies with this affinity ligand and Taq Pol determined a dissociation constant (KD) of 0.12 mM for the respective complex, whereas ATP prevented the formation of the mABSGu-Taq Pol complex. The mABSGu affinity adsorbent was exploited in the development of a facile Taq Pol purification protocol, affording homogeneous enzyme (>99% purity, approximately 61 500 U/mg) in a single chromatography step. Quality control tests showed that Taq Pol purified on the mABSGu affinity adsorbent is free of nucleic acids and contaminating nuclease activities.     

Inhibition of Taq DNA polymerase by seaweed extracts from British Columbia, Canada and Korea

Fifty-nine species of marine macrophytes from the coasts of British Columbia, Canada and Korea have been screened for the presence of PCR inhibitors, namely inhibitors of Taq DNA polymerase. Eleven of the species displayed some inhibitor activity. At the concentration of 5 μg of methanol extract in 25μL reaction mixture of PCR containing 1.5 unit of Taq DNA polymerase, one (Ulva sp.) of 8 Chlorophyta, eight (Colpomenia bullosa, Ecklonia cava, Endarachne binghamiae, Fucus distichus, Hizikia fusiformis, Sargassum confusum, Sargassum sagamianum, and Sargassum thunbergii) of 28 Phaeophyta, and one (Symphyocladia latiuscula) of 34 Rhodophyta showed inhibition in PCR amplification. In the case of the water extract, two (Cladophora columbiana, Ulva sp.) Chlorophyta, seven (Endarachne binghamiae, Fucus distichus, Hizikia fusiformis, Sargassum confusum, Sargassum sagamianum, Sargassum horneri, Scytosiphon dotyi) Phaeophyta, no Rhodophyta and one (Phyllospadix scouleri) seagrass showed inhibition in PCR amplification. the methanol fraction of Sargassum confusum and the water fraction of Fucus gardneri (mid–intertidal) have been found to inhibit PCR at level as low as 0.5 μg in 25μL of PCR reaction mixture. This revised version was published online in August 2006 with corrections to the Cover Date.     

Taq DNA聚合酶功能区域的定位

通过参Ｕ法定点突变产生了ＴａｑＤＮＡ聚合酶Ｎ端分别缺失３个,２３５个,２８７个和４４３个氨基酸的４个缺失体,利用Ｂａｌ－３１连续缺失法产生了ＴａｑＤＮＡ聚合酶的Ｃ端分别缺失了２个、１６个、２９个、３２个、３４个氨基酸的５个缺失体．经ＤＮＡ聚合酶活性测定表明Ｎ端缺失３个,２３５个,２８７个氨基酸后活力和完整的Ｔａｑ相近,而缺失４４３个氨基酸后则失去了ＤＮＡ聚合酶活力;Ｃ端的５个缺失体都失去了ＤＮＡ聚合酶活性．据此ＴａｑＤＮＡ聚合酶的功能区域被定位在２８７～８３２氨基酸之间．     

DNA damage reduces Taq DNA polymerase fidelity and PCR amplification efficiency

DNA damage blocks DNA polymerase progression and increases miscoding. In this study, we assessed the effects of specific lesions on Taq DNA polymerase fidelity and amplification efficiency. In the presence of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG), Taq DNA polymerase inserted dCMP and to a lesser extent dAMP. 8-Oxo-7,8-dihydro-2'-deoxyadenosine (8-oxodA) instructed the incorporation of dTMP and caused a pronounced n-1 deletion not observed in other systems. The presence of an abasic lesion led to dAMP incorporation and n-1 deletions. In addition, we introduce the mean modified efficiency (MME) as a more precise method for determining PCR amplification efficiency of damaged templates. Using this method, we were able to quantify reductions in amplification efficiency of templates containing 8-oxodG (single or multiple), 8-oxodA, or abasic sites. Because the MME method can detect small reductions in amplification efficiency, it may be useful in comparing the extent of damage in environmentally degraded or archival DNA specimens.     

利用Taq DNA聚合酶对PCR产物直接进行顺序分析

Taq DNA聚合酶具有反应速度快、温度作用范围广及良好的续进性等特点,可视为一种理想的DNA顺序分析酶。本文首先对非对称性PCR扩增过程中单、双链DNA产物的积累情况进行了分析,然后采用标记延伸二步法,对Taq DNA聚合酶的性质及影响因素进行分析。为进一步改进Taq DNA聚合酶测序的方法,本反应建立了“Klenow-型”的直接掺入标记同位素测序法,即在反应液中加入与标记核苷酸相应的一定浓度的冷dNTP。此法不但解决了二步法中引物后部分DNA顺序无法读出的缺点,而且简化了反应步骤,亦能得到令人满意的顺序分析结果,每次可读出至少400碱基的序列。     

一种利用Taq酶快速标记DNA探针的方法

目的：探索低成本、高效、快速的DNA探针标记方法。方法：以特定引物和16nler的随机引物作为延伸引物,利用Taq酶标记DNA探针。以大肠杆菌Klenow片断随机引物延伸标记法作为对照。点杂交方法检测探针标记效果。结果与结论：Taq酶标记法和大肠杆菌Klenow片段随机引物延伸标记法同样有较好的标记效果,且随机引物或特定引物作为延伸引物均可以合成足够有效的探针。Taq酶标记法是一种低成本、高效、快速的DNA探针标记方法。     

The stability of Taq DNA polymerase results from a reduced entropic folding penalty; identification of other thermophilic proteins with similar folding thermodynamics

The thermal stability of Taq DNA polymerase is well known, and is the basis for its use in PCR. A comparative thermodynamic characterization of the large fragment domains of Taq (Klentaq) and E. coli (Klenow) DNA polymerases has been performed by obtaining full Gibbs‐Helmholtz stability curves of the free energy of folding (ΔG) versus temperature. This analysis provides the temperature dependencies of the folding enthalpy and entropy (ΔH and ΔS), and the heat capacity (ΔC_p) of folding. If increased or enhanced non‐covalent bonding in the native state is responsible for enhanced thermal stabilization of a protein, as is often proposed, then an enhanced favourable folding enthalpy should, in general, be observed for thermophilic proteins. However, for the Klenow–Klentaq homologous pair, the folding enthalpy (ΔH_fold) of Klentaq is considerably less favorable than that of Klenow at all temperatures. In contrast, it is found that Klentaq's extreme free energy of folding (ΔG_fold) originates from a significantly reduced entropic penalty of folding (ΔS_fold). Furthermore, the heat capacity changes upon folding are similar for Klenow and Klentaq. Along with this new data, comparable extended analysis of available thermodynamic data for 17 other mesophilic–thermophilic protein pairs (where enough applicable thermodynamic data exists) shows a similar pattern in seven of the 18 total systems. When analyzed with this approach, the more familiar “reduced ΔC_p mechanism” for protein thermal stabilization (observed in a different six of the 18 systems) frequently manifests as a temperature dependent shift from enthalpy driven stabilization to a reduced‐entropic‐penalty model. Proteins 2014; 82:785–793. © 2013 Wiley Periodicals, Inc.     

一种移码差错率大幅度下降的聚合酶N端缺失体的研究

采用双引物定变法,构建了以２３６位氨基酸为起始密码子的Ｔａｑ酶的高表达质粒,并以－１移码突变质粒ｐＦＤＰＭ１１８作为模板,建立了测定ＤＮＡ聚合酶的体外合成精确性的Ｇａｐｐｅｄ－ＤＮＡ系统。通过转化大肠杆菌ＴＧ１菌株皇计数Ｘ－ｇａｌ平板上蓝白菌落的比例,测定了Ｔａｑ和ＴａｑＮＤ２３６两种ＤＮＡ聚合酶在ＤＮＡ体外合成中的称码突变率,发现缺失后的ＴａｑＮＤ２３６复制精确性提高了１０倍以上。     

Influence of DNA aptamer structure on the specificity of binding to Taq DNA polymerase

The secondary structure of DNA aptamer to Taq DNA polymerase was established as a hairpin. Both stem and loop structures of DNA ligand were shown to be involved in the interaction with Taq DNA polymerase. Moreover, the structure and sequence of DNA aptamer that was the most effective inhibitor of DNA polymerase activity were established. This crucial structure was evaluated as a GC-rich stem longer than 17 bp, and a loop consisting of 12 bases with strictly determined nucleotide sequence. It was demonstrated that nucleotide in position 23 counting from the 5"-end of DNA ligand was involved in direct contact with Taq DNA polymerase. The ability of optimized DNA aptamer TQ21-11 to form a complex with the enzyme was increased 5-fold in comparison to the initial aptamer.     

DNA ligases from thermophilic bacteria enhance PCR amplification of long DNA sequences

Bacterial NAD-dependent Taq and Tth DNA ligases are capable of significantly increasing the yield of long PCR products when the amplification is carried out using bacterial family A DNA polymerases, e.g. Taq or Tth DNA polymerases, or with enzymatic blends containing these polymerases. We also show that Taq and Tth DNA ligases improve the results of PCR in the absence of NAD and therefore in the absence of DNA ligase activity. These observations suggest that bacterial DNA ligases can interact with these DNA polymerases, presumably as accessory proteins, thereby enhancing the efficiency of DNA polymerization. Published in Russian in Biokhimiya, 2009, Vol. 74, No. 5, pp. 685–690.     

A hot start alternative for high-fidelity DNA polymerase amplification mediated by quantum dots

Quantum dots （QDs） are of great interest due to their unique chemical and physical properties. Recently, a hot start （HS） polymerase chain reaction （PCR） amplification performance based on QDs with a high-fidelity Pfu DNA polymerase has been reported. However, whether QDs can trigger HS effects with other high-fidelity or conventional DNA polymerases is yet to be understood. In the present study, we studied the QD-triggered HS effects with four high-fidelity and three conventional DNA polymerases, and the HS effect comparisons among them were also made. It was found that QDs could trigger a distinct HS PCR amplification performance with all the four tested high,fidelity DNA polymerases, and specific target DNA could be well amplified even if the PCR mixture was preincubated for 2 h at 50℃. On the contrary, the HS effects were not prominent with all the three conventional Taq DNA polymerases. Specifically, the fidelity of Pfu is not sacrificed in the presence of QDs, even after a 1 h pre-incu- bation at 50℃ before PCR. Furthermore, the electrophoresis results preliminarily demonstrated that QDs prefer to adsorb high-fidelity polymerases rather than conventional ones, which might result in the QD-triggered HS effects on PCR performance by using high-fidelity DNA poly- merases.     

Temperature-dependent downhill unfolding of ubiquitin. II. Modeling the free energy surface

To provide evidence for the interpretation of temperature‐dependent unfolding kinetics and the downhill unfolding scenario presented in the accompanying experimental article (Part I), the free energy surface of ubiquitin unfolding is calculated using statistical mechanical models of the Muñoz‐Eaton (ME) form. The models allow only two states for each amino acid residue, folded or unfolded, and permutations of these states generate an ensemble of microstates. One‐dimensional free energy curves are calculated using the number of folded residues as a reaction coordinate. The proposed sequential unfolding of ubiquitin's β‐sheet is tested by mapping the free energy onto two reaction coordinates inspired by the experiment as follows: the number of folded residues in ubiquitin's stable β‐strands I and II and those of the less stable strands III–V. Although the original ME model successfully captures folding features of zipper‐like one‐dimensional folders, it misses important tertiary interactions between residues that are far from each other in primary sequence. To take tertiary contacts into account, partially folded microstates based on a spherical growth model are included in the calculation and compared with the original model. By calculating the folding probability of each residue for a given point on the free energy surface, the unfolding pathway of ubiquitin is visualized. At low temperature, thermal unfolding occurs along a sequential unfolding pathway as follows: disruption of the β‐strands III–V followed by unfolding of the strands I and II. At high temperature, multiple unfolding routes are formed. The heterogeneity of the transition state explains the global nonexponential unfolding observed in the T‐jump experiment at high temperature. The calculation also reports a high stability for the α‐helix of ubiquitin. Proteins 2008. © 2008 Wiley‐Liss, Inc.     

耐热DNA聚合酶基因的克隆及在大肠杆菌中的表达

用PCR法从水生栖热菌菌株YT－1中扩增耐热DNA聚合酶基因,得到2．5kb的DNA片段t扩增片段重组到pUCl8中测序证实为Taq DNA聚合酶基因,将该片段重组到pBV221温控表达质粒中,在大肠杆菌中表达出94kDa的重组蛋白,100ml培养物的细胞产酶为1．5×10⁵u,表达的蛋白能催化PCR反应的进行。     

Empirical free energy calculation: comparison to calorimetric data.

An effective free energy potential, developed originally for binding free energy calculation, is compared to calorimetric data on protein unfolding, described by a linear combination of changes in polar and nonpolar surface areas. The potential consists of a molecular mechanics energy term calculated for a reference medium (vapor or nonpolar liquid), and empirical terms representing solvation and entropic effects. It is shown that, under suitable conditions, the free energy function agrees well with the calorimetric expression. An additional result of the comparison is an independent estimate of the side-chain entropy loss, which is shown to agree with a structure-based entropy scale. These findings confirm that simple functions can be used to estimate the free energy change in complex systems, and that a binding free energy evaluation model can describe the thermodynamics of protein unfolding correctly. Furthermore, it is shown that folding and binding leave the sum of solute-solute and solute-solvent van der Waals interactions nearly invariant and, due to this invariance, it may be advantageous to use a nonpolar liquid rather than vacuum as the reference medium.     

Partial destabilization of native structure by a combination of heat and denaturant facilitates cold denaturation in a hyperthermophile protein

Cold denaturation is a phenomenon seen in many different proteins. However, there have been no reports so far of its occurrence in hyperthermophile proteins. Here, using a recombinant triosephosphate isomerase (PfuTIM) from the hyperthermophile archaeon, Pyrococcus furiosus, we show that the heating of this protein through the low temperature side of its thermal unfolding transition in the presence of guanidinium hydrochloride (GdmCl) results in the formation of partially-disordered conformational ensembles that retain considerable native-like secondary and tertiary structure. Unlike PfuTIM itself, these thermochemically obtained partially-disordered PfuTIM ensembles display cold denaturation as they are cooled to room temperature. The protein thus shows hysteresis, adopting different structural states in a manner dependent upon the nature of the heating and cooling treatment, rather than upon the initial and final conditions of temperature and GdmCl concentration, indicating that some sort of a kinetic effect influences structure adoption and retention. The structure lost through cooling of partially-disordered PfuTIM is found to be regained through heating. The ability of GdmCl to thus apparently destabilize the highly thermodynamically and kinetically stable structure of PfuTIM (sufficiently, to cause it to display observable cold-denaturation and heat-renaturation transitions, in real-time, with cooling and heating) offers support to current ideas concerning the how hyperthermophile proteins achieve their high kinetic stabilities, and suggests that desolvation-solvation barriers may be responsible for high kinetic stability.     

Thermally reversible inactivation of Taq polymerase in an organic solvent for application in hot start PCR

In the past, Taq polymerase was reversibly inactivated by modification with a dicarboxylic acid anhydride in aqueous media, to enable ‘hot start PCR’. However, there are various constraints in using such a method including temperature and concentration. Here we describe an alternative method whereby Taq polymerase may be reversibly inactivated following incubation with an excess of citraconic anhydride at elevated temperatures, in an anhydrous non-protic organic solvent – tert-butyl methyl ether – by first drying the enzyme with a salt or carbohydrate excipient to form an amorphous powder. Reactivation of the enzyme is due to the instability of the chemical modification at low pH following a short incubation in a suitable buffer.     

Using a second‐order differential model to fit data without baselines in protein isothermal chemical denaturation

In vitro protein stability studies are commonly conducted via thermal or chemical denaturation/renaturation of protein. Conventional data analyses on the protein unfolding/(re)folding require well‐defined pre‐ and post‐transition baselines to evaluate Gibbs free‐energy change associated with the protein unfolding/(re)folding. This evaluation becomes problematic when there is insufficient data for determining the pre‐ or post‐transition baselines. In this study, fitting on such partial data obtained in protein chemical denaturation is established by introducing second‐order differential (SOD) analysis to overcome the limitations that the conventional fitting method has. By reducing numbers of the baseline‐related fitting parameters, the SOD analysis can successfully fit incomplete chemical denaturation data sets with high agreement to the conventional evaluation on the equivalent completed data, where the conventional fitting fails in analyzing them. This SOD fitting for the abbreviated isothermal chemical denaturation further fulfills data analysis methods on the insufficient data sets conducted in the two prevalent protein stability studies.