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View additional product information for GeneRacer™ Kit with SuperScript™ III RT and Zero Blunt™ TOPO™ PCR Cloning Kit for Sequencing - FAQs (L150202)
47 product FAQs found
请看下面的原因和建议：
-基因组DNA污染或者存在未知的剪切体： 采用扩增级DNase I（货号18068015）预处理RNA。设计退火到内含子两侧的外显子序列的引物，或者退火到mRNA的外显子/外显子边界处的序列的引物，以便区分扩增的cDNA和潜在的污染物基因组DNA。如需检测产物是否来自于DNA，设置一组不进行反转录的RNA对照组进行PCR。
-引物非特异性退火： 改变PCR的退火条件。使用热启动PCR聚合酶。针对各种模板和引物组合优化镁离子浓度。
-引物形成二聚体： 设计3′ 端不含互补序列的引物。
以下列出了各种原因和我们提供的建议：
-第一链cDNA合成过程中出错：请采用优质RNA作为对照，验证第一链反应的效率。
-存在RNase污染： 向样品中添加对照RNA，以判定在第一链反应体系中是否存在RNase。您可在第一链反应体系中使用RNase抑制剂。
-RNA出现多糖共沉淀： 采用氯化锂沉淀RNA，以便去除多糖，详见Sambrook等人所述。
-靶标mRNA含有较强的转录停顿因子： 在第一链合成中，使用随机六聚体引物替代oligo(dT)，提高温度，使用靠近靶标cDNA 3′末端的PCR引物。
-PCR使用的第一链产物过少： 在50 mL PCR反应之中，至多可使用10%的第一链反应产物
-第一链合成时使用了基因特异性引物： 可以试试其他的基因特异性引物，或者改用 oligo(dT)。请确保GSP为反义序列。
-存在反转录酶抑制剂： 可在第一链反应之前，通过对mRNA进行乙醇沉淀来去除抑制剂。可以使用70%（体积比）乙醇洗涤mRNA沉淀。注：反转录酶抑制剂包括SDS、EDAT、胍盐、甲酰胺、焦磷酸钠和亚精胺。
-RNA已降解： 确认使用高质量和完整的RNA。
-退火温度过高： 视必要降低温度和/或使用降落PCR。
3′端RACE利用了mRNA中自带的poly(A)尾作为通用的PCR反应的起始位点。在这一操作步骤中，mRNA通过反转录酶(RT)和oligo-dT接头引物反转录成cDNA。特异性的cDNA随后通过PCR反应，采用基因特异性引物（GSP，退火到已知外显子序列的区域）和接头引物（靶向poly(A)尾区域）进行扩增。这样一来，即可捕获处于外显子和poly(A)尾之间的未知的3′-mRNA序列。
以下为几条有助于您优化自己的RACE反应的建议：
•使用优质完整的RNA
•使用目标基因高表达丰度的RNA样品
•各个步骤上样量不要超过建议的量
•针对PCR反应优化退火温度
•加入推荐的对照
可变剪接或可变polyA位点以及可变的起始位点都会产生正常的多个条带。进行测序有助于帮助您解决不确定性问题。
如果该反应能够得到特异性的产物且对照反应没能得出特异性产物，则您的条带很可能是真实的。唯一的确证方法是对产物进行测序。
如果您进行5′ 端或3′端RACE，则需要一条基因特异性引物；如果您同时进行5′ 端和3′端RACE，则需要两条基因特异性引物。引物应符合下述规定：
•50–70% GC含量，以保证具有较高的退火温度 (>72°C)
•长度为23–28核苷酸，以增加特异性结合
•3′段具有较低的GC含量，以便最大程度的降低DNA聚合酶在非特异性位点的扩增（在最后五个碱基中含有不超过两个G或C残基）
•引物中不含有自身互补碱基序列或不含与试剂盒附带的引物互补的序列，尤其是在3′端
•退火温度超过 72°C—使用高退火温度的引物有助于提升您的PCR反应的特异性
在核查RNA的完整性时，对500 ng的RNA通过琼脂糖/溴化乙啶凝胶电泳方法进行分析。您可以使用常规的1%琼脂糖凝胶或者变性的琼脂糖凝胶。对于总RNA样品，您应观测到 28S和18S的 rRNA条带。 mRNA会形成0.5至12 kb的拖尾。 28S条带的强度应为18S条带的两倍。如果您上样的RNA不足，则28S条带可能显示为弥散状态。如果使用变性的凝胶，则rRNA条带会非常清晰且尖锐。28S条带对应于4.5 kb，而18S条带对应于1.9 kb。
RACE的含义为cDNA末端快速扩增技术。这是一种发现全长转录本的5′和/或 3′末端的方法。如果您所感兴趣的转录本的局部序列已知，可采用RACE技术获得完整的ORF、5′ UTR和3′ UTR序列。
仅使用载体进行转化不是推荐的阴性对照实验。拓扑异构酶改构过程不是一个效率100%的过程，因此，在您的混合物中将会存在“不含插入片段的载体”，因此会产生克隆。
磷酸化的产物可以进行TA克隆但不能进行TOPO克隆。这是因为所需的磷酸基团已经包含在载体DNA和拓扑异构酶形成的中间体复合物中。TOPO载体含有一个与拓扑异构酶共价结合的3' 磷酸基团和一个5'磷酸基团。非TOPO载体的线性载体（TA和Blunt）含有一个3' OH基团和一个5'磷酸基团。磷酸化产物在进行TOPO-克隆之前应该用磷酸酶（CIP）处理。
你可能克隆了一段假阳性序列。TA和TOPO克隆对于存在于某些PCR反应中的小片段（< 100 bp）非常高效。使用硅基DNA纯化系统对插入片段进行凝胶纯化或者电洗脱。确保所有溶液均不含核酸酶（例如避免共用溴化乙锭染色器皿）。
出现这一问题的原因可能有：
•插入片段没有破坏lacZ基因的读码框。如果你的插入序列较短（< 500 bp），则可能出现浅蓝色克隆。可以分析一些这类克隆，因为它们可能含有插入片段。
•使用了不能在3´ 末端加A的聚合酶。如果您使用的是具有校读活性的聚合酶，例如AccuPrime Pfx 或Platinum Pfx，您将需要进行一个后续Taq酶处理步骤以添加3’ A突出末端。
• PCR产物在连接之前进行了凝胶纯化。凝胶纯化可以去除单个的3’ A突出碱基。如果没有进行凝胶纯化，那么请优化您的PCR反应以便可以直接从PCR产物进入克隆步骤。
• PCR产物在进行连接反应前被存放了很长时间。请使用新鲜PCR产物。即使仅存放1天，连接效率也会下降。
•连接反应中加入了太多扩增反应的成分。PCR反应体系内的高盐成分会抑制连接反应。在连接反应中应使用不超过2-3 μl的PCR反应混合物。
•连接反应中的载体：插入片段摩尔比可能不正确。估计PCR产物的浓度。使连接反应中载体和插入片段的摩尔比大约为1:1或1:3。
通常平板上应该有少量不含插入片段的白色克隆。这些克隆通常比其它克隆大一些，是由于罕见的重组事件会导致质粒上部分序列缺失引起的（通常是从多克隆接头到F1起始点附近的一个位点）。为找到含有插入片段的克隆，最好挑选各种颜色和形态的克隆进行分析。同一插入片段经常会由于插入方向的不同而产生两种完全不同的克隆形态。
无克隆产生的原因可能是出现了下列问题：
•细菌不是感受态细胞。使用包含在One Shot模块内的pUC18载体检查感受态细胞的转化效率。
•平板的抗生素浓度不正确，或者平板过于陈旧。使用100 μg/mL的氨苄青霉素或50 µg/mL的卡那霉素。确保氨苄平板是新鲜的（储存时间小于1个月）。
•产物被磷酸化了（仅针对TOPO克隆而言）。磷酸化的产物可以进行TA-克隆但不能进行TOPO-克隆。这是因为连接所需的磷酸基团已经包含在载体DNA和拓扑异构酶-形成的中间体复合物中了。TOPO载体含有一个与拓扑异构酶共价结合的3' 磷酸基团和一个5'磷酸基团。非TOPO载体（TA和Blunt）含有一个3' OH基团和一个5'磷酸基团。磷酸化产物在进行TOPO-克隆之前应该用磷酸酶（CIP）处理。
请考虑以下可能原因：
• pH > 9：检查PCR扩增反应的pH值，并使用1 M Tris-HCl, pH 8的缓冲液进行调节。
• PCR产物过多（或过度稀释）：减少PCR产物的用量（或增加其浓度)
• PCR反应延伸不完全：确保PCR反应最后包含一个7到30分钟的延伸步骤。长的PCR产物将需要更长的延伸时间。
•克隆长插入片段（>1 kb）：请尝试以下一个或全部建议：提高插入片段用量。延长 TOPO克隆反应孵育时间。使用硅基DNA纯化系统（如PureLink系统）或者电洗脱法对插入片段进行凝胶纯化。确保所有溶液均不含核酸酶（例如避免共用溴化乙锭染色器皿）。
•尽管你使用了Taq聚合酶但是PCR产物仍然没有足够的3´ A突出：提高最后的延伸时间以确保所有的3´末端被腺苷化。Taq聚合酶在模板链的A后面再添加一个A时的效率较低。Taq聚合酶在模板链的C后边添加一个A时的效率最高。您可能需要重新设计引物以使它们包含一个5´ G而非一个5´ T。
请尝试以下建议以提高克隆数量。
•向反应中加入6X盐溶液后，提高TOPO反应在室温孵育的时间。
•电转化能显著提高克隆数量；通常能提高10到20倍。但是，如果进行电转化，重要的一点是TOPO反应混合物要包含稀释的盐溶液，或者，为获得最佳结果，在转化前进行沉淀。为获得高电转化效率，建议如下操作： ◦向 6 µL TOPO反应体系中加入100 µL双蒸水并在37度再孵育10分钟。
◦加入10 µL 3 M 醋酸钠，2 µL 20 µg/µL糖原，300 µL 100%乙醇进行沉淀。置于干冰上或–80摄氏度20分钟，4摄氏度最高速离心15分钟。使用800 µL 80%乙醇洗涤沉淀团块，最高速离心10分钟，倒去乙醇，离心1分钟，然后移除剩余乙醇，避免碰到沉淀团块。干燥沉淀团块（空气干燥或真空吸干）。
◦将沉淀重悬于10 µL ddH2O中并根据常用电转步骤使用3.3 µL 重悬的DNA进行电转化。该电转化将产生比使用同样的TOPO-反应体系进行化学转化时多出高达20倍的克隆。加入100 µL ddH2O并孵育10分钟并不是绝对必要，但是它能充分的稀释反应并可能有助于拓扑异构酶的失活，以使得电转化更容易进行。
我们建议您使用我们的TOPO TA cloning kit for sequencing，它包含pCR4 TOPO载体，或者使用我们的Zero Blunt TOPO PCR cloning kit for sequencing,，它包含pCR4Blunt-TOPO载体。
是的，但是您需要使用牛小肠磷酸酶(CIP)对其进行处理以除去5’磷酸基团才能用于TOPO克隆。
TA克隆
这种克隆方法最初是为配合纯Taq聚合酶（天然的、重组的、热启动）使用而设计的；然而，某些高保真Taq酶和Taq酶混合物通常也适合TA克隆。即使Taq与具有校正能力的聚合酶以10:1或15:1的比例，仍可以产生足够的3’ A突出端去做TA克隆。
推荐使用的我公司的聚合酶包括Platinum Taq、Accuprime Taq、Platinum或Accuprime Taq High Fidelity、AmpliTaq、AmpliTaq Gold或AmpliTaq Gold 360等。
平末端克隆
使用Platinum SuperFi DNA聚合酶等具有校对能力的酶。
定向TOPO克隆
Platinum SuperFi DNA聚合酶效果良好。
不，你不能用pCR-Blunt 或pCR-Blunt-TOPO载体克隆使用Taq DNA聚合酶扩增而来的PCR产物。 pCR-Blunt载体被制备为平末端以接受平末端片段。因为Taq DNA聚合酶的末端转移活性，该酶产生的PCR产物带有3’-A突起。为了将这些PCR产物克隆进pCR-Blunt，你需要将它们的末端抹平（这通常是一个低效的过程）。我们的TA Cloning试剂盒或TOPO TA Cloning试剂盒对于克隆Taq酶生成的PCR产物来说是更好的选择。 TA Cloning试剂盒包含带有3’-T突起的线性化载体用于高效连接Taq酶生成的PCR产物，无需额外操作。
You can store your cDNA at 2-6 degrees C for up to 24 hours. For long-term storage, store the cDNA at -15 to -25 degrees C and add EDTA to a final concentration of 1 mM to prevent degradation.
The GeneRacer method is designed to ensure that only full-length messages are ligated to the GeneRacer RNA Oligo and PCR amplified after cDNA synthesis. It is highly recommended that you clone your RACE products and analyze at least 10-12 colonies to ensure that you isolate the longest message. Many genes do not have only one set of transcription start sites but rather multiple transcription start sites spanning sometimes just a few or other times a hundred or even more bases. Cloning of the RACE products and analyzing multiple colonies ensues that you detect the diversity of the heterogeneous transcription start sites of your gene. It is also possible that you might obtain PCR products that may not represent the full-length message for your gene. PCR products that do not represent full-length message may be obtained because:
-RNA degradation after the CIP reaction creates new truncated substrates with a 5' phosphate for ligation to the GeneRacer RNA Oligo. Be sure to take precautions to ensure that the RNA is not degraded.
-CIP dephosphorylation was incomplete. Increase the amount of CIP in the reaction or decrease the amount of RNA.
-PCR yielded a PCR artifact and not true ligation product. Optimize your PCR using the suggestions described above.
RACE PCR artifacts or nonspecific PCR bands can result from one or more of the following:
-Nonspecific binding of GSPs to other cDNAs resulting in the amplification of unrelated products as well as desired products.
-Nonspecific binding of GeneRacer primers to cDNA resulting in PCR products with GeneRacer primer sequence on both ends of the PCR product.
-RNA degradation.
-Contamination of PCR tubes or reagents.
Note: Artifacts usually result from less than optimal PCR conditions and can be identified in negative control PCR.
Please see the following causes and suggestions:
Contamination by genomic DNA or an unexpected splice variant - Pretreat RNA with DNase I, amplification grade (Cat. No 18068015).
Design primers that anneal to sequences in exons on both sides of an intron or at the exon/exon boundary of the mRNA to differentiate between amplified cDNA and potential contaminating genomic DNA.
To test if products were derived from DNA, perform a minus RT control.
Nonspecific annealing of primers - Vary the PCR annealing conditions.
Use a hot-start PCR polymerase.
Optimize magnesium concentration for each template and primer combination.
Primers formed dimers - Design primers without complementary sequences at the 3' ends.
Please see the following causes and suggestions:
Procedural error in first-strand cDNA synthesis - Use high-quality RNA as a control to verify the efficiency of the first-strand reaction.
RNase contamination - Add control RNA to sample to determine if RNase is present in the first-strand reaction. Use an RNase inhibitor in the first-strand reaction.
Polysaccharide co-precipitation of RNA - Precipitate RNA with lithium chloride to remove polysaccharides, as described in Sambrook et al.
Target mRNA contains strong transcriptional pauses - Use random hexamers instead of oligo(dT) in the first-strand reaction, increase the temperature, and use PCR primers closer to the 3' terminus of the target cDNA.
Too little first-strand product was used in PCR - Use up to 10% of first-strand reaction per 50 mL PCR.
Gene-specific primer was used for first-strand synthesis - Try another set of GSP or switch to oligo(dT). Make sure the GSP is the antisense of the sequence.
Inhibitors of RT present - Remove inhibitors by ethanol precipitation of mRNA preparation before the first-strand reaction. Include a 70% (v/v) ethanol wash of the mRNA pellet. Note: inhibitors of RT include SDS, EDTA, guanidinium salts, formamide, sodium pyrophosphate, and spermidine.
RNA has been damaged or degraded - Ensure that high-quality, intact RNA is being used.
Annealing temperature is too high - Decrease temperature as necessary and/or use touchdown PCR.
3' RACE takes advantage of the natural poly(A) tail found in mRNA as a generic priming site for PCR. In this procedure, mRNAs are converted into cDNA using reverse transcriptase (RT) and an oligo-dT adapter primer. Specific cDNA is then amplified by PCR using a gene-specific primer (GSP) that anneals to a region of known exon sequences and an adapter primer that targets the poly(A) tail region. This permits the capture of unknown 3'-mRNA sequences that lie between the exon and the poly(A) tail.
Here are our suggestions to optimize your RACE reaction:
-Use high-quality, intact RNA
-Use an RNA sample in which your gene is expressed at high levels
-Do not exceed the recommended amount of input material in each step
-Optimize annealing temperatures for PCR
-Include recommended controls
Alternative splicing, an alternative polyadenylation site, and alternative start sites can yield legitimate multiple bands. Sequencing will help to resolve any uncertainty.
If the reaction gives a specific product and the control reaction does not, your band is probably real. The only way to be sure is to sequence the product.
If you are performing either 5' or 3' RACE, you will need one gene-specific primer and if you are performing both 5' and 3' RACE, you would need two gene-specific primers. The primers should follow the rules stated below:
-50-70% GC content to obtain a high annealing temp (>72 degrees C)
-23-28 nucleotides in length to increase specificity of binding
-Low-GC content at 3' ends to minimize extension by DNA polymerase at non-target sites (no more than two G or C residues in the last five bases)
-No self-complementary sequences within the primer or no sequence complementary to the primers supplied in the kit, especially at the 3' end
-Annealing temperature greater than 72 degrees C—using primers with a high annealing temperature will help to improve specificity of your PCR
To check the RNA for integrity, analyze 500 ng of your RNA by agarose/ethidium bromide gel electrophoresis. You may use a regular 1% agarose gel or a denaturing agarose gel. For total RNA you should see the 28S and 18S rRNA bands. mRNA will appear as a smear from 0.5 to 12 kb. The 28S band should be twice the intensity of the 18S band. If you do not load enough RNA, the 28S band may appear to be diffuse. If you are using a denaturing gel, the rRNA bands should appear very clear and sharp. The 28S band should run at 4.5 kb and the 18S band should run at 1.9 kb.
RACE stands for Rapid Amplification of cDNA Ends. It is a method used to discover the 5' and/or 3' end of full-length transcripts. If partial sequence is known for a transcript of interest, RACE can help to elucidate the full ORF, 5' UTR, and 3' UTR sequences.
Using the vector only for transformation is not a recommended negative control. The process of TOPO-adaptation is not a 100% process, therefore, there will be “vector only” present in your mix, and colonies will be obtained.
Phosphorylated products can be TA cloned but not TOPO cloned. This is because the necessary phosphate group is contained within the topoisomerase-DNA intermediate complex of the vector. TOPO vectors have a 3' phosphate to which topoisomerase is covalently bound and a 5' phosphate. Non-TOPO linear vectors (TA and Blunt) have a 3' OH and a 5' phosphate. Phosphorylated products should be phosphatased (CIP) before TOPO cloning.
You may be cloning in an artifact. TA and TOPO Cloning are very efficient for small fragments (< 100 bp) present in certain PCR reactions. Gel-purify your PCR product using either a silica-based DNA purification system or electroelution. Be sure that all solutions are free of nucleases (avoid communal ethidium bromide baths, for example.)
There could be a few possibilities for this:
- The insert does not interrupt the reading frame of the lacZ gene. If you have a small insert (< 500 bp), you may have light blue colonies. Analyze some of these blue colonies as they may contain insert.
- A polymerase that does not add 3' A-overhangs was used. If you used a proofreading enzyme, you will need to do a post-reaction treatment with Taq polymerase to add the 3' A-overhangs.
- PCR products were gel-purified before ligation. Gel purification can remove the single 3' A- overhangs. Otherwise, optimization of your PCR can be performed so that you can go directly from PCR to cloning.
- The PCR products were stored for a long period of time before ligation reaction. Use fresh PCR products. Efficiencies are reduced after as little as 1 day of storage.
- Too much of the amplification reaction was added to the ligation. The high salt content of PCR can inhibit ligation. Use no more than 2-3 µl of the PCR mixture in the ligation reaction.
- The molar ratio of vector:insert in the ligation reaction may be incorrect. Estimate the concentration of the PCR product. Set up the ligation reaction with a 1:1 or 1:3 vector:insert molar ratio.
On a typical plate there are a few white colonies which do not contain insert. These are usually larger than the other colonies and are due to a deletion of a portion of the plasmid sequence by a rare recombination event (usually from the polylinker to a site in the F1 origin). To find a colony with an insert it is best to pick clones of a variety of color and pattern for analysis. Often an insert will generate two distinct patterns according to its orientation.
No colonies may occur due to the following problems:
Bacteria were not competent. Use the pUC18 vector included with the One Shot module to check the transformation efficiency of the cells.
- Incorrect concentration of antibiotic on plates, or the plates are too old. Use 100 µg/mL of ampicillin or 50 µg/mL kanamycin. Be sure ampicillin plates are fresh (< 1 month old).
- The product was phosphorylated (TOPO cloning only). Phosphorylated products can be TA-cloned but not TOPO-cloned. This is because the necessary phosphate group is contained within the topoisomerase-DNA intermediate complex of the vector. The TOPO vector has a 3' phosphate to which topoisomerase is covalently bound and a 5' phosphate. The non- TOPO vectors (TA and Blunt) have a 3' OH and a 5' phosphate. Phosphorylated products should be phosphatased (CIP) before TOPO-cloning.
Please consider the following possible causes:
- pH > 9: Check the pH of the PCR amplification reaction and adjust with 1 M Tris-HCl, pH 8.
- Excess (or overly dilute) PCR product: Reduce (or concentrate) the amount of PCR product.
- Incomplete extension during PCR: Be sure to include a final extension step of 7 to 30 minutes during PCR. Longer PCR products will need a longer extension time.
- Cloning large inserts (>1 kb): Try one or all of the following suggestions: Increase amount of insert. Incubate the TOPO cloning reaction longer. Gel-purify the insert using either a silica-based DNA purification system (e.g., PureLink system) or electroelution. Be sure that all solutions are free of nucleases (avoid communal ethidium bromide baths, for example.)
- PCR product does not contain sufficient 3' A-overhangs even though you used Taq polymerase: Increase the final extension time to ensure all 3' ends are adenylated. Taq polymerase is less efficient at adding a nontemplate 3' A next to another A. Taq is most efficient at adding a nontemplate 3' A next to a C. You may have to redesign your primers so that they contain a 5' G instead of a 5´ T.
Please try the suggestions below to increase the number of colonies.
- Longer incubation of the TOPO cloning reaction at room temperature, provided that the 6X Salt solution is added to the reaction.
- Electroporation can give significant increases in colony numbers; often 10-20 fold higher. However, if doing electroporation, it is important that the TOPO reaction mix contains diluted Salt solution or, for best results, precipitated prior to transformation. For high primary transformants by electroporation it is recommended to:
- Add 100 µL double diH2O to the 6 µL TOPO reaction and incubate 10 more minutes at 37 degrees C.
- Precipitate by adding 10 µL 3 M Na-Acetate, 2 µL 20 µg/µL glycogen, 300 µL 100% ethanol. Place on dry ice or –80 degrees C for 20 min, spin at top speed in a microcentrifuge at 4 degrees C for 15 min. Wash pellet with 800 µL 80% ethanol, spin at top speed for 10 min, pour off ethanol, spin 1 min, and remove remaining ethanol without disturbing pellet. Dry pellet (air-dry or speed-vac).
- Resuspend pellet in 10 µL ddH2O and electroporate 3.3 µL of resuspended DNA according to a normal electroporation protocol. This electroporation protocol can yield up to 20 fold more colonies than chemical transformation of an equivalent TOPO-reaction. The addition of the 100 µL ddH2O followed by 10 mins incubation is not absolutely necessary, but it sufficiently dilutes the reaction and may help inactivate topoisomerase so that it is more easily electroporated.
We would suggest using our TOPO TA cloning kit for sequencing, which contains the pCR 4 TOPO vector, or our Zero Blunt TOPO PCR cloning kit for sequencing, which contains the pCR4Blunt-TOPO vector.
Yes, though you will need to treat it with calf intestinal phosphatase (CIP) to get rid of the 5' phosphate group for TOPO Cloning.
TA Cloning:
- This cloning method was designed for use with pure Taq polymerases (native, recombinant, hot start); however, High Fidelity or Taq blends generally work well with TA cloning. A 10:1 or 15:1 ratio of Taq to proofreader polymerase will still generate enough 3' A overhangs for TA cloning.
- Recommended polymerases include Platinum Taq, Accuprime Taq, Platinum or Accuprime Taq High Fidelity, AmpliTaq, AmpliTaq Gold, or AmpliTaq Gold 360.
Blunt cloning:
- Use a proofreading enzyme such as Platinum SuperFi DNA Polymerase.
Directional TOPO cloning:
- Platinum SuperFi DNA Polymerase works well.
Several factors are important for the best results.
(1) The key factor for success is the quality of the RNA. RNA degradation is the most likely reason for failure to obtain a correct RACE product. We strongly recommend that you analyze a sample of your RNA on an agarose gel before starting to confirm RNA integrity. The use of RNaseOUT RNase inhibitor ensures RNA stability during various enzymatic reactions. If you are concerned about RNA stability, you may check the stability of the RNA after each enzymatic reaction (CIP, TAP, and ligation reaction) using agarose gel electrophoresis. Resuspend the RNA in DEPC water after enzymatic treatment in an appropriate volume (see pages 7, 9 and 11 of GeneRacer kit manual) and check 1 µL on an agarose gel. Compare with the same amount of untreated RNA to check for degradation.
(2) RACE PCR artifacts or non-specific PCR bands can result from one or more of the following:
-Non-specific binding of GSPs to other cDNAs resulting in the amplification of unrelated products as well as desired products.
-Non-specific binding of GeneRacer primers to cDNA resulting in PCR products with GeneRacer primer sequence on one end.
-RNA degradation.
-Contamination of PCR tubes or reagents.
Note: Artifacts usually result from less-than-optimal PCR conditions and can be identified in negative control PCR.
(3) If a smear in GeneRacer 5' primer negative control is visible, then we recommend the following:
-Use a different 5' primer, called the GeneRacer 5' primer. It is homologous to the slightly different site at the RNA oligo but it generally gives less background compared to the original 5' primer. Here is the sequence of the GeneRacer 5' primer:
5' GCACGAGGACACTGACATGGACTGA
This primer can be synthesized and used in the 5' RACE PCR instead of the original 5' primer. It should reduce the background in RACE PCR.
(4) If you see smears when performing the negative control using 5' primer, the other negative controls (no template, GSP with template) were fine, and all reactions had the same PCR conditions, then:
-If there is background when using the 5' primer and template than you should subtract those bands/smear from the actual RACE reaction discarding it so that not to confuse with the real RACE bands. The smear in that negative control will always be there because every cDNA has the binding site for that primer. So there should not be any major concern about the smear. If the actual RACE PCR works then the RACE band would outweigh the smear background.
For the Directional TOPO Cloning Vectors, a PCR product must be generated by a proofreading enzyme to create a blunt product. Pfx50 or Accuprime Pfx and Accuprime Pfx Supermix from Thermo Fisher Scientific are recommended for use.
When cloning a Pfx-amplified PCR product, the insert to vector ratio is an important consideration. The PCR product generally needs to be diluted since Pfx generates a high concentration of product and using too much insert DNA can hamper the TOPO reaction. A 1:1 molar ratio of vector to insert (or about 2-10ng of insert) is recommended.
No you cannot use pCR-Blunt or pCR-Blunt-TOPO vector to clone PCR products amplified with Taq DNA polymerase. The pCR-Blunt vector is prepared with blunt ends to accept blunt-ended fragments. Due to the terminal transferase activity of Taq DNA polymerase, PCR products amplified with this enzyme have 3'-A overhangs. In order to clone these products into pCR-Blunt, you would need to polish the ends to make them blunt (which usually is not an efficient process). Our TA Cloning Kits or TOPO TA Cloning kits are a better choice for cloning Taq-generated PCR products. TA Cloning kits include a linearized vector with 3'-T overhangs for efficient ligation of Taq-generated PCR products without additional manipulation.
Assuming that the primer is at a 50 nM final concentration and 50 mM final salt concentration, the melting temperatures are: M13 Forward (-20) Primer = 52.7 and the M13 Reverse Primer = 45.3. For use in the control PCR reaction we recommend using an annealing temperature of 56C.
CIP will remove the 5' phosphates from DNA or RNA, acting on both protruding or recessed phosphates. In the GeneRacer kit, it is used to eliminate any background RNA, including non-mRNA or truncated mRNA that does not have the 5' Methyl Cap structure. CIP will not digest the Methyl Cap structure, allowing these capped transcripts to be further processed in the GeneRacer protocol and only allowing full length transcripts to be amplified by 5' RACE.