PCR产物末端性质的分析研究

利用PCR、UT-PCR、克隆及测序等技术,对强直性肌营养不良基因（MT-PK）3′-非翻译区分别用Taq,Taq＋Pwo DNA聚合酶进行了扩增、克隆和测序,研究了PCR产物末端组成情况,并比较了上述两种DNA聚合酶对PCR产物末端的影响.结果在用Taq DNA聚合酶扩增的PCR产物主要得到3′端突出1个A（占67.3％,35/52）;在Taq＋Pwo DNA聚合酶扩增的PCR产物末端中得到3′端+A的仅占17.4％,而－1的占34.8％,与前者显著不同.表明PCR扩增产物的末端是复杂多样的.     

耐热DNA聚合酶基因双元载体的初步构建

Taq DNA聚合酶是PCR反应中的重要试剂,它具有结构性稳定和耐高温的特性,有能在90℃以上合成DNA的能力,因此被广泛使用于DNA扩增技术当中,但是国内尚未报道有关Taq DNA聚合酶基因用于转基因的研究.若将此耐热基因转入某些经济作物中培育耐热新品种,将会有很好的前景和实用价值.本试验将初步构建Taq DNA聚合酶的基因表达双元载体.通过引物设计,用PCR法从含有Thermus aquaticus DNA polymerase克隆基因的散装Taq DNA 聚合酶中扩增耐热DNA 聚合酶基因,得到约2.5 kb的DNA片段.扩增片段连接到质粒pUC19中测序证实是Taq DNA聚合酶基因,再将该片段重组到双元载体pBin19中,通过蓝白筛选选择重组子,构建耐热DNA聚合酶的基因双元载体pBin19-Taq.对其作进一步的加工,即插入植物启动子和增强子等后,可通过土壤农癌杆菌的介导作用,用作植物转基因之用.     

海南特有极小种群植物文昌锥的SCoT-PCR体系建立及有效引物评价

为了应用SCoT分子标记研究文昌锥种质资源,通过单因素试验和正交试验2种方法,分析DNA、引物、dNTPs、Taq DNA聚合酶这4种因素对文昌锥SCoT-PCR扩增结果的影响,优化建立文昌锥SCoT-PCR体系,并对文昌锥SCoT标记引物进行有效性评价。结果表明：各个因子对SCoT-PCR扩增影响大小依次为：DNA > dNTPs > 引物 > Taq DNA聚合酶;最优反应体系为：总体系为20 μL,DNA含量为2.5 ng,引物浓度为0.8 μmol·L^-1,dNTPs浓度为0.2 mmol·L^-1,Taq DNA聚合酶的含量1 U;经验证,该体系获得的扩增产物清晰、稳定;应用该体系筛选出15条多态性好且适合文昌锥扩增的引物,为今后利用SCoT分子标记技术对文昌锥及其他壳斗科植物进行相关研究提供技术支持。     

水稻RAPD反应体系的正交优化

以焦旱1号总DNA为材料,首先对影响RAPD-PCR反应的模板DNA、Mg~(2+)、dNTP、引物和Taq DNA聚合酶浓度等因素进行了初步优化,分析了各因素对RAPD-PCR扩增结果的影响.在此基础上对影响RAPD-PCR反应的Mg~(2+)、dNTP、引物和Taq DNA聚合酶浓度等4个主要因素进行正交优化,研究结果表明:在25 μl RAPD-PCR反应体系中,模板DNA 20 ng;Mg~(2+)浓度1.5mmol/L;dNTP的浓度0.2mmol/L;引物量15 pmol;Taq DNA聚合酶1.0 U.在此最佳条件下,利用引物B8对18个北方粳稻品种进行了成功的扩增.     

马铃薯SRAP-PCR反应体系优化及验证

为建立马铃薯最佳的SRAP-PCR反应体系,以马铃薯基因组DNA为模板,采用单因素和正交试验相结合的方法,对影响SRAP-PCR反应体系的5个因素(引物浓度、Mg2+浓度、模板DNA用量、d NTPs浓度和Taq DNA聚合酶用量)进行优化,建立马铃薯优化的SRAP-PCR反应体系。结果表明:马铃薯SRAP-PCR最佳反应体系中模板DNA用量为60 ng,Mg2+浓度为1.5 mmol/L,d NTPs浓度为0.25 mmol/L,引物浓度为0.60μmol/L,Taq DNA聚合酶用量为0.75 U。各因素对扩增结果影响依次是:Mg2+浓度Taq DNA聚合酶用量模板DNA用量引物浓度d NTPs浓度。用6份马铃薯样品DNA对优化体系进行验证,扩增结果清晰稳定,可用于马铃薯遗传多样性分析和遗传图谱构建等研究。     

银杏ISSR-PCR扩增反应体系的建立与优化

目的:为了对银杏进行分子鉴定和遗传关系的分析,建立银杏ISSR-PCR的最佳扩增反应体系。方法:采用正交设计和单因素梯度实验,对影响ISSR-PCR反应体系的5个主要因素(Mg2+、dNTP、引物、模板DNA及Taq DNA聚合酶)进行筛选及优化。结果:银杏25μL ISSR最佳扩增反应体系包含10×Taq反应缓冲液、2.5 mmol/L MgCl2、0.45 mmol/L dNTP、1.2μmol/L引物(UBC861)、10 ng模板DNA及0.9 U Taq DNA聚合酶,使用此ISSR扩增反应体系,获得了10株不同性别银杏DNA的清晰条带,验证了该体系的稳定性。结论:优化的反应体系为采用ISSR分子标记技术对银杏进行遗传多样性分析、遗传育种和转基因等研究奠定了一定的理论基础。     

菊花SRAP-PCR反应体系的优化与确立

采用L16(45)正交实验设计,对SRAP-PCR反应体系中Mg2+ 、 dNTPs和引物浓度以及Taq DNA聚合酶和模板DNA用量等5个因素进行了优化,并确立了适合菊花[Dendranthema×grandiflorum (Ramat.) Kitamura]SRAP-PCR的反应体系.菊花的SRAP-PCR最佳反应体系为:反应体系总体积20 μL,含3.125 mmol·L-1 Mg2+ 、187.5 μmol·L-1 dNTPs、10.0 μmol·L-1引物、50 ng模板DNA、0.5 U Taq DNA 聚合酶及1×PCR buffer.各因素对菊花基因组DNA SRAP-PCR扩增结果的影响程度不同,其中dNTPs浓度影响最大,Taq DNA聚合酶用量的影响最小.运用菊花品种'奥运含笑'和'雨花落英'及二者的F1杂交后代单株的基因组DNA对优化的SRAP-PCR反应体系进行验证,均获得了多态性丰富、条带清晰的扩增图谱,表明所确立的菊花SRAP-PCR反应体系稳定可靠.     

黄皮SRAP反应体系优化正交实验研究

以黄皮(Clausena lansium)‘甜黄皮’品种为试材,利用正交设计L₁₆(4⁵)对黄皮SRAP-PCR反应体系中的5因素(Taq聚合酶、Mg²⁺、模板DNA、dNTPs、引物)在4个水平上进行优化试验。结果表明,不同因素对黄皮SRAP反应体系影响从大到小的顺序为:Mg²⁺和Taq聚合酶> 模板DNA> 引物> dNTPs;初步确立了适合黄皮的SRAP-PCR扩增体系为:在25 μl反应体系中,包括10×PCR buffer 2.5 μl、Taq DNA聚合酶0.75U、Mg²⁺ 2.0 mmol/L、模板DNA 60 ng、dNTPs 0.2 mmol/L、引物0.2 μmol/L。     

荔枝SRAP-PCR反应体系的优化

SRAP(sequence-related amplified polymorphism)是基于基因的内含子和外显子区域进行检测的新型分子标记技术,具有多态性高、重复性好、易测序、便于克隆目标片段等特点,在荔枝(Litchi chinensis Sonn)中还没有相关的研究报道.为了建立适合荔枝的SRAP反应体系,对反应体系中的DNA模板、Mg2+、dNTP、引物、Taq DNA聚合酶诸因子的用量进行了探索,确立了适合荔枝的SRAP反应体系为:在20 μL反应体系中,模板DNA为40 ng,Mg2+浓度2.5 mmol/L,dNTP 0.3 mmol/L,引物5 mmol/L,Taq DNA聚合酶1.0 U.扩增程序为:94℃预变性3 min,反应前5个循环在94℃1 min、35℃1 min、72℃ 1 min的条件下运行;随后的35个循环退火温度提高到50℃;最后72℃延伸10 min.利用该反应体系对荔枝10个不同品系进行SRAP反应,用5%的变性聚丙烯酰胺凝胶电泳检测,结果显示:不同品系间DNA谱带多态性丰富.证实该体系稳定可靠,可以用于荔枝的分子标记研究.     

罗汉果SRAP反应体系的建立与优化

建立适合罗汉果的SRAP-PCR扩增体系,为罗汉果的遗传图谱构建及基因定位奠定基础。实验对罗汉果SRAP-PCR反应体系的影响因素(引物,dNTP,Taq酶,Mg~(2+),模板DNA)在多个水平上进行优化试验,筛选出各反应因素的最佳水平,建立了罗汉果SRAP-PCR反应的最佳体系(10μL):引物0.6μmol/L、dNTP0.25 mmol/L、Taq DNA聚合酶0.5U、Mg~(2+)2.0 mmol/L和模板DNA 30 ng。该体系的建立能很好的满足罗汉果基因组DNA的扩增要求,SRAP标记应用于罗汉果遗传研究是可行的。     

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。     

Synthesis of 5-substituted 2'-deoxycytidine 5'-(alpha-P-borano)triphosphates, their incorporationinto DNA and effects on exonuclease

Direct PCR sequencing with boronated nucleotides provides an alternative to current PCR sequencing methods. The positions of boranophosphate-modified nucleotides incorporated randomly into DNA during PCR can be revealed directly by exonuclease digestion to give sequencing ladders. Cytosine nucleotides, however, are especially sensitive to exonuclease digestion and provide suboptimal sequencing ladders. Therefore, a series of 5-substituted analogs of 2'-deoxycytidine 5'-(alpha-P-borano)triphosphates (dCTPalphaB) were synthesized with the hope of increasing the nuclease resistance of deoxycytosine residues and thereby enhancing the deoxycytosine band intensities. These dCTP analogs contain a boranophosphate modification at the alpha-phosphate group in 2'-deoxycytidine 5'-triphosphate (dCTP) as well as a 5-methyl, 5-ethyl, 5-bromo or 5-iodo substitution for the 5-hydrogen of cytosine. The two diastereomers of each new dCTP derivative were separated by reverse phase HPLC. The first eluted diastereomer (putatively Rp) of each dCTP analog was a substrate for T7 DNA polymerase (Sequenase) and had an incorporation efficiency similar to normal dCTP and dCTPalphaB, with the 5-iodo-dCTPalphaB analog being the least efficient. Substitution at the C-5 position of cytosine by alkyl groups (ethyl and methyl) markedly enhanced the dCTPalphaB resistance towards exonuclease III (5-Et-dCTPalphaB >5-Me-dCTPalphaB >dCTPalphaB approximately 5-Br-dCTPalphaB >5-I-dCTPalphaB), thereby generating DNA sequences that better define the deoxycytosine positions. The introduction of modified dCTPalphaB should increase the utility of direct DNA sequencing with boronated nucleoside 5'-triphosphates.     

A Non-radioactive DNA Sequencing Method Using Biotinylated Dideoxynucleoside Triphosphates and {Delta}Tth DNA Polymerase

We synthesized a set of four biotinylated dideoxynucleosidetriphosphates (biotin-9-ddNTPs) and optimized the reaction conditionsfor non-radioactive cycle sequencing using modified Tth DNApolymerase (Tth) and a chemiluminescent detection system. Theresulting sequencing ladders showed lower background comparedto those with the conventional non-radioactive sequencing methodwhich uses 5'-biotinylated primers, especially when PCR productswere analysed. With our method, DNA sequences can be determinedat any primer positions without preparing 5'-biotinylated primersfor dideoxy chaintermination.     

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．     

利用Taq DNA聚合酶反转录cDNA第一链的研究

应用Taq DNA聚合酶(Thermus aquaticus DNA polymerase)直接对RNA进行反转录成cDNA第一链,然后用特异引物进行PCR扩增,结果表明,反转录达到AMV逆转录酶的效果,且可能得到比AMV逆转录酶更完整的cDNA第一链。     

Elimination of band compression in sequencing gels by the use of N4-methyl-2'-deoxycytidine 5'-triphosphate.

Taq DNA polymerase, Sequenase, and the large fragment of E.coli polymerase I effectively utilize N4-methyl-2'-deoxycytidine 5'-triphosphate (N4-methyl-dCTP) in the place of dCTP in dideoxynucleotide terminator sequencing reactions on single-stranded templates. When the resulting fragment mixtures are resolved on sequencing gels, they are found to be free of band compressions even in cases where such compressions remain unresolved by the substitution of 7-deaza-dGTP for dGTP. Sequencing reactions using N4-methyl-dCTP instead of dCTP are somewhat more prone to false stops than are sequencing reactions using 7-deaza-dGTP instead of dGTP; this difference is more pronounced when sequencing with Sequenase at 37 degrees C than when sequencing with Taq DNA polymerase at 72 degrees C. For the three polymerases investigated, replacement of dCTP by N4-methyl-dCTP does not fundamentally change the characteristic variations in band intensities seen in the C-lane. N4-methyl-dCTP can also be used for sequencing double-stranded DNA and for DNA amplification by the polymerase chain reaction.     

Application of N-terminally Truncated DNA Polymerase from Thermus thermophilus ({Delta}Tth Polymerase) to DNA Sequencing and Polymerase Chain Reactions: Comparative Study of {Delta}Tth and Wild-Type Tth Polymerases

N-Terminally truncated DNA polymerase from Thermus thermophilus(Tth polymerase) lacking 5'-3' exonuclease activity was usedfor DNA sequencing and polymerase chain reaction (PCR). In contrastto the high background of the sequencing ladder observed withthe wild-type Tth polymerase, Tth polymerase gave readable sequencingpatterns which extend up to more than 500 bases from the primersite on cycle sequencing and automated sequencing. The Tth polymerasewas used for the standard and mutagenic PCR, and net amplificationof the DNA and the mutations accumulated during PCR were analyzed.Under mutagenic PCR, the mutation rates were 7.0 x 10^–4(Tth) and 8.3 x 10^–4 (Tth) per nucleotide per cycle ofamplification, which were 4–9 times higher than the ratesunder standard PCR.     

Thermostable DNA Polymerase from Thermus thermophilus B35: Preparation and Study of a Modified Form of the Enzyme with High Affinity to ddNTP

The hybrid protein consisting of Tte DNA polymerase fragment and mutant Taq DNA polymerase (F667Y) fragment in the ratio 20 : 1 was constructed. Affinity of the modified enzyme (substitutions F669Y, V667I, and S692Q) to ddNTP was two orders higher than that of the wild type enzyme. The modified enzyme was used for sequencing DNA fragment with total deoxyguanosine and deoxycytidine content of 68%. In the polymerase chain reaction, the modified enzyme exhibits properties typical of the wild type Tte DNA polymerase.     

A New Solid-Phase Chemical DNA Sequencing Method Which Uses Streptavidin-Coated Magnetic Beads

To simplify the chemical DNA sequencing protocol, we developeda new solid-phase method which uses streptavidin-coated magneticbeads. This method is based on the finding that the biotinylatedDNA-streptavidin complex was stable under the conditions forsome chemical sequencing reactions. The 5'-biotinylated DNAgenerated by the polymerase chain reaction was first capturedby streptavidin-coated magnetic beads and then subjected toa set of simplified chemical sequencing reactions on the beadsat room temperature. Followed by the piperidine cleavage reaction,the products were resolved by gel electrophoresis, transferredonto a nylon membrane and visualized by chemiluminescent detection.As a consequence, highquality sequencing ladders were obtained,due to complete removal of contaminating chemicals, withoutthe time-consuming precipitation/centrifugation steps used inthe conventional chemical sequencing protocol     

DNA聚合酶与引物/模板的相互作用对PCR效率的影响

PCR是体外酶促合成特异DNA片段的一种方法,引物的优劣直接关系到PCR的特异性与成功与否。传统的PCR引物设计软件基本上忽略了DNA聚合酶与引物/模板的亲和性对PCR效率的影响。为揭示DNA聚合酶与引物/模板的相互作用是否对PCR的效率有影响,通过构建Taq DNA 聚合酶与不同序列引物/模板DNA相互作用的三维结构模型,采用MM/GBSA方法计算复合物的结合自由能,以结合自由能为参数,为人血清白蛋白基因(Human Serum Albumin gene,HSA gene)和结核杆菌pyrF基因(Mycobacterium tuberculosis pyrF gene)设计了PCR引物。PCR实验结果表明,引物的PCR效率与结合自由能相关：引物与聚合酶的结合自由能越低,PCR实验的效率相对越高。这说明DNA聚合酶与引物/模板的相互作用对PCR效率有重要影响。因此,引物/模板DNA与聚合酶的结合自由能可以作为PCR引物设计的新参数。