An efficient and economic enhancer mix for PCR

Polymerase chain reaction (PCR) has become a fundamental technique in molecular biology. Nonetheless, further improvements of the existing protocols are required to broaden the applicability of PCR for routine diagnostic purposes, to enhance the specificity and the yield of PCRs as well as to reduce the costs for high-throughput applications. One known problem typically reported in PCR experiments is the poor amplification of GC-rich DNA sequences. Here we designed and tested a novel effective and low-cost PCR enhancer, a concentration-dependent combination of betaine, dithiothreitol, and dimethyl sulfoxide that broadly enhanced the quantitative and/or qualitative output of PCRs. Additionally, we showed that the performances of this enhancer mix are comparable to those of commercially available PCR additives and highly effective with different DNA polymerases. Thus, we propose the routine application of this PCR enhancer mix for low- and high-throughput experiments.     

A New Approach to Enhanced PCR Specificity

A new approach to enhanced specificity and product yield of polymerase chain reaction is proposed. It is based on control of DNA polymerase activity during PCR by changing the magnesium ion concentration, which depends on the temperature of the reaction mixture. A slightly soluble magnesium salt, magnesium oxalate, whose solubility depends on temperature, was used as a source of magnesium ions. During PCR, magnesium oxalate was maintained at saturating concentration by the presence of an insoluble excess of this salt, and the concentration of magnesium ions depended on the salt solubility: binding of magnesium ions at lower temperatures and their release at higher temperatures was shown to affect the DNA polymerase activity and to favor the specific PCR amplification of the target DNA fragment.     

A new approach to enhance PCR specificity

A new approach to enhanced specificity and product yield of polymerase chain reaction is proposed. It is based on control of DNA polymerase activity during PCR by changing the magnesium ion concentration, which depends on the temperature of the reaction mixture. A slightly soluble magnesium salt, magnesium oxalate, whose solubility depends on temperature, was used as a source of magnesium ions. During PCR, magnesium oxalate was maintained at saturating concentration by the presence of an insoluble excess of this salt, and the concentration of magnesium ions depended on the salt solubility: binding of magnesium ions at lower temperatures and their release at higher temperatures was shown to affect the DNA polymerase activity and to favor the specific PCR amplification of the target DNA fragment.     

PCR增强剂在核酸体外扩增检测技术的研究进展

在各种高致病性病原体、禽流感病毒、食源性微生物等引起的疾病随时大规模流行的背景下,利用聚合酶链式反应（polymerase chain reaction,PCR）技术对第一例或第一波病例的快速实验室诊断显得尤为重要,同时发展出多种以PCR技术为基础的检测技术以便更加快速、高通量、敏感地对疾病进行诊断、预防或预测。然而,在实际病原体检测中,常常出现灵敏度低、准确性差的结果。PCR增强剂是在PCR及PCR衍生技术中添加的一类物质,其可从产率、特异性、灵敏度等方面提高核酸扩增性能,从而优化核酸检测,解决病原体检测的应用瓶颈,为第一例病原体检出节约宝贵的时间。结合以PCR为基础的核酸体外扩增检测技术对PCR增强剂在其中的应用、优缺点、作用机理进行介绍,以期为病原体核酸检测的实际应用提供一些参考。     

Maximizing specificity and yield of PCR by the quantum dot itself rather than property of the quantum dot surface

We found that semiconductor quantum dots (QDs) dramatically improved both product yield and specificity of PCR. The concentration of QDs is important for improving PCR amplification. In the presence of appropriate concentration of mercaptoacetic acid (MAA)-coated QDs, specificity and yield of PCR were enhanced. Also, strong nonspecific bands and weaker smeared bands were eliminated. At lower annealing temperatures (25–45 °C), addition of MAA-coated QDs into the PCR reagent produced specific PCR products without nonspecific sequence amplification. MAA alone did not improve PCR amplification. Streptavidin (SA) surface modified QDs with different size also effectively improved the specificity of PCR, demonstrating that the observed effect was not due to property of the QD surface but instead due to the QD itself. Bovine Serum Albumin (BSA) could relieve Taq polymerase from MAA-coated QDs in PCR by interaction with QDs and therefore imply that QDs improve specificity of PCR by interaction with Taq polymerase. These results demonstrate that QDs, added to reaction mixes at appropriate concentrations, can increase PCR yield and improve PCR specificity, even at low annealing temperatures. We assume that many different surface modified polymeric nanoparticles might have similar effects.     

Evaluation of novel control elements by construction of eukaryotic expression vectors

A novel mammalian eukaryotic expression vector for the production of immunoglobulin heavy chain (IgH) genes has been designed. This expression vector contains the variable heavy chain (VH) promoter, the IgH intron enhancer (μE) and the IgH 3′ enhancer (3′E). This construct, designated pTIF-1, was stably transfected into the myeloma cell line J558L. A fivefold increase in the expression level of a rearranged IgH gene was observed when using the pTIF-1 vector containing the 3′E compared to an expression vector lacking this enhancer. Interestingly, this positive effect on the expression level of the 3′ enhancer appears to be position independent. The introduction of two recently identified Ig control elements, HS3 and HS4, to the vector cassette did not further elevate the expression level in the cell line tested. The pTIF-1 vector can be used for expression of any antibody specificity, using PCR amplification of the VDJ region of interest. Furthermore, the constant region can easily be exchanged, which further facilitates studies to dissect different effector functions of IgH constant genes.     

Inhibition of a thermophilic deoxyribonucleic acid polymerase by fullerene derivatives

Enzyme inhibition by fullerene derivatives has attracted much attention. In this communication, effects of two water-solube fullerene derivatives, fullerol and trimalonic acid C60 (TMA C60) on polymerase chain reaction (PCR) were investigated by using PCR of beta-actin cDNA derived from HeLa cells as an experimental model. Both fullerol and TMA C60 were found to inhibit PCR in a dose-dependent manner. PCR was ultimately inhibited while the concentrations of each compound were not less than 0.01 mM. In contrast, mannitol exerted no effects on PCR while its concentration increased up to 2 mM. Compensation experiments with Thermus aquaticus (Taq) DNA polymerase revealed that both fullerol and TMA C60 inhibited the enzymatic activity of Taq DNA polymerase, and the inhibitory potency of TMA C60 was slightly greater than that of fullerol. Our data provides some novel aspects on the enzyme inhibiting activities of fullerene derivatives.     

一种新的用于提高lea3基因扩增特异性和产量的增强剂（英文）

在对目的DNA序列尤其是高GC含量的片段进行PCR扩增的时候,经常需要对一些试验条件进行优化。在一定条件下,二甲基亚砜、甲酰胺、甘油、NP-40和Tween20等可以在某种程度上提高PCR的特异性和效率。我们在对禾本科lea3基因进行分离克隆时发现了一种新的可以提高PCR产量和特异性的物质——极高热稳定单链结合蛋白（ETSSB）,研究发现在每50μlPCR反应体系中加入200ng的ETSSB,可以有效地抑制DNA片段的非特异性条带的产生,并可以提高目的片段的产量。     

Bovine serum albumin further enhances the effects of organic solvents on increased yield of polymerase chain reaction of GC-rich templates

ABSTRACT: BACKGROUND: While being a standard powerful molecular biology technique, applications of the PCR to the amplification of high GC-rich DNA samples still present challenges which include limited yield and poor specificity of the reaction. Organic solvents, including DMSO and formamide, have been often employed as additives to increase the efficiency of amplification of high GC content (GC > 60%) DNA sequences. Bovine serum albumin (BSA) has been used as an additive in several applications, including restriction enzyme digestions as well as in PCR amplification of templates from environmental samples that contain potential inhibitors such as phenolic compounds. FINDINGS: Significant increase in PCR amplification yields of GC-rich DNA targets ranging in sizes from 0.4 kb to 7.1 kb were achieved by using BSA as a co-additive along with DMSO and formamide. Notably, enhancing effects of BSA occurs in the initial PCR cycles with BSA additions having no detrimental impact on PCR yield or specificity. When a PCR was set up such that the cycling parameters paused after every ten cycles to allow for supplementation of BSA, combining BSA and organic solvent produced significantly higher yields relative to conditions using the solvent alone. The co-enhancing effects of BSA in presence of organic solvents were also obtained in other PCR applications, including site-directed mutagenesis and overlap extension PCR. CONCLUSIONS: BSA significantly enhances PCR amplification yield when used in combination with organic solvents, DMSO or formamide. BSA enhancing effects were obtained in several PCR applications, with DNA templates of high GC content and spanning a broad size range. When added to the reaction buffer, promoting effects of BSA were seen in the first cycles of the PCR, regardless of the size of the DNA to amplify. The strategy outlined here provides a cost-effective alternative for increasing the efficiency of PCR amplification of GC-rich DNA targets over a broad size range.     

携带不同数量增强子的嵌合型肝脏特异性启动子的构建及其体外实验研究

通过PCR手段成功获得肝细胞特异性启动子人α1-抗胰蛋白酶启动子hAATp(human α1-antitrypsin promoter,hAATp)及具有增强子功能的肝脏特异的肝调控区HCR (hepatic control region,HCR)。在此基础上,通过分子克隆手段构建获得携带有不同数量的HCR增强子的嵌合型肝脏特异性hAAT启动子,并在下游连入报告基因Luciferase,然后将重组质粒转染人肝癌细胞系HepG2、小鼠肝癌细胞系Hepa1-6、人胚肾细胞系HEK293和人脑星形胶质母细胞瘤细胞系U87-MG,通过检测Luciferase表达活性分析携带不同数量增强子的肝脏特异性启动子的启动活性及其组织特异性。结果表明,携带有3个增强子的嵌合型肝脏特异性启动子活性及特异性最好,为肝脏类疾病的靶向性治疗研究奠定了基础。     

hMAM启动子／增强子调控表达载体构建和调控作用

目的构建人乳腺珠蛋白（human mammaglobin,hMAM）启动子／增强子调控报告基因表达载体,探讨hMAM启动子／增强子序列在乳腺癌细胞中的特异性调控作用。方法应用PCR技术,从基因组DNA中扩增出hMAM启动子／增强子DNA序列,构建于PGL3报告基因上游,分别转染体外培养的乳腺癌细胞MDA—MB-415、T47D及胃癌细胞7901,分析启动子和增强子序列对乳腺癌细胞的基因表达调控作用。结果酶切图谱分析、DNA序列测定表明成功构建hMAM启动子／增强子调控的表达载体;荧光素酶报告基因检测结果分析表明,hMAM启动子／增强子能够调控报告基因的表达。结论hMAM启动子／增强子,在MDA—MB-415乳腺癌细胞具有调控基因表达的作用;     

Enhancing PCR amplification and sequencing using DNA-binding proteins

The polymerase chain reaction (PCR) is a powerful core molecular biology technique, which when coupled to chain termination sequencing allows gene and DNA sequence information to be derived rapidly. A number of modifications to the basic PCR format have been developed in an attempt to increase amplification efficiency and the specificity of the reaction. We have applied the use of DNA-binding protein, gene 32 protein from bacteriophage T4 (T4gp32) to increase amplification efficiency with a number of diverse templates. In addition, we have found that using single-stranded DNA-binding protein (SSB) or recA protein in DNA sequencing reactions dramatically increases the resolution of sequencing runs. The use of DNA-binding proteins in amplification and sequencing may prove to be generally applicable in improving the yield and quality of a number of templates from various sources.     

Prevention of pre-PCR mis-priming and primer dimerization improves low-copy-number amplifications.

A Hot Start Polymerase Chain Reaction (PCR) entails the withholding of at least one reagent from the reaction mixture until the reaction tube temperature has reached 60-80 degrees C. Hot Start amplification with an AmpliWax vapor barrier uses a layer of solid wax to separate the retained reagent(s) and the test sample from the bulk of the reagents until the first heating step of automated thermal cycling melts the wax and convectively mixes the two aqueous layers. Wax-mediated Hot Start PCR greatly increases the specificity, yield, and precision of amplifying low copy numbers of three HIV targets. In the presence of 1 microgram of human placental DNA (1.6 x 10(5) diploid genomes) the specificity improvement entails considerable to complete reduction in the amplification of mis-primed sequences and putative primer oligomers. When mis-priming is negligible, the procedural improvement still suppresses putative primer oligomerization. Hot Start PCR with an AmpliWax vapor barrier permits routine amplification of a single target molecule with detection by ethidium stained gel electrophoresis; nonisotopically visualized probing suffices for confirmation. The improved amplification performance is evident for target copy numbers below approximately 10(3).     

高GC含量DNA模板的PCR扩增

目的：探索高GC含量DNA的PCR扩增条件,为扩增达托霉素生物合成基因簇及拼接奠定基础。方法：在PCR扩增体系中,使用高保真的聚合酶及添加不同浓度的DMSO、7-deaza-dGTP等增强剂,并选择合适的PCR循环程序,优化富含GC的DNA的PCR扩增条件。结果：向反应体系中额外添加1%~4%的DMSO可以显著提高富含GC的DNA的PCR扩增产物量,但会降低其特异性;7-deaza-dGTP可以提高扩增产物的特异性及保真度,但产量会有所下降。应用touch down PCR并在体系中添加7-deaza-dGTP能够提高扩增产物的特异性和产率,增加扩增的保真度。结论：应用优化的PCR扩增条件将所有达托霉素生物合成基因簇分段扩增出来,并可扩增出长达6 kb的片段,且序列完全正确,可以进行后续拼接。     

The role of Methanomassiliicoccales in trimethylamine metabolism in the rumen of dairy cows

A considerable amount of trimethylamine (TMA) is likely generated in the rumen; however, its metabolism is still unclear. This study aimed to investigate the role of Methanomassiliicoccales (Mmc) in TMA metabolism in the rumen of dairy cows. Three experiments, two rumen in vitro fermentation trials and one dairy cow in vivo trial, were conducted. Four groups were set in Experiment 1: control, nitroglycerin (NG, a methanogen inhibitor), TMA (7.2 mmol/L), and TMA + NG. The methanogenic activity was completely inhibited in the NG group, and no methane production was observed in the NG and TMA + NG groups. The TMA content hardly reduced in the TMA + NG group (6.9 mmol/L) following a 2 d-incubation; in contrast, it demonstrated a significant reduction by 47.2% in the TMA group. Methanogen 16S rRNA gene sequencing and real-time PCR showed that the relative abundance of Mmc increased in the TMA group (P = 0.005). The increase was mainly attributed to two species-level taxa, Group 9 sp. ISO4-G1 and Group 10 sp. Four groups were set in Experiment 2: control, NG, choline (choline chloride, 7.2 mmol/L), and choline + NG. Choline was completely degraded in 24 h, and the TMA content reached the peak point (7.3 mmol/L) in the fermentation culture. The TMA content remained relatively stable in the choline + NG group following the peak point. However, it started to decrease after 24 h in the choline group, corresponding to the rapid increase in methane production and the abundance of Mmc. Eight mid-lactating, rumen-fistulated Holstein cows were randomly assigned to the control (n = 4) or choline (n = 4) group in Experiment 3: In the choline group, cows were gradually supplemented with 100–250 g/(cow·d) of choline chloride over 4 weeks. Compared to the control group, TMA accumulated in the rumen fluid, and the abundance of Mmc 16S rRNA gene and choline-degrading bacterial cutC gene increased in the rumen content in the choline group (P < 0.050). The trimethylamine N-oxide content in the plasma and milk of the dairy cows was approximately 10 times higher in the choline group than that in the control at the end of the experiment. These findings revealed that Mmc played an important role in the elimination of TMA in the rumen. The accumulation of TMA in the rumen would lead to a large amount of TMA absorbed into the blood stream of the dairy cows.     

The Mechanism of σ-Crystallin Gene Regulation: Cooperation of Lens-Specific and Non-Specific Elements1

Employing δ-crystallin gene as a model, we have investigated tissue-specific gene regulation. Our approach was to analyze regulatory elements associated with the gene utilizing gene transfer techniques. Introduction of the chicken δ1-crystallin gene into the genome of developing mouse embryos resulted in lens-specific expression, indicating that the elements governing the tissue specificity are located in the DNA sequence introduced. Through analysis of various regions of the δ1-crystallin gene and the associated DNA sequences, we identified a lens-specific enhancer in the third intron of the gene. It was demonstrated that this enhancer alone is sufficient to account for lens specificity of the δ1-crystallin gene. Dissection of the δ1-crystallin enhancer and functional assessment by multiplication of enhancer fragments demonstrated the cooperative interaction of lens-specific and nonspecific elements in the enhancer. The mechanism by which heterologous elements cooperate in generating enhancer activity unquestionably provides great flexibility to the regulatory system, and may account for developmental modulation of gene activity superimposed on tissue specificity.