
Description
Mannose receptor targeting by mannosylated liposomes has been demonstrated for a variety of mannosylated lipid conjugates in a variety of liposome morphologies and compositions in several different in vitro and in vivo models. A very large number of publications is about using a hydrophobic derivative of mannose (4-aminophenyl alpha-D-mannopyranoside) rather than using a mannosylated lipid in clodronate liposomes. This is mainly due to the high cost and complexity of synthesizing and conjugating mannose to lipid. 4-aminophenyl alpha-D-mannopyranoside is commercially available and far less expensive than synthesizing mannose conjugated lipid.
Why mannose? Mannose is one of the carbohydrate components of many bacterial and viral cell surfaces; therefore, the ever-efficient, highly redundant immune system has evolved multiple mechanisms for identifying pathogens based on mannose recognition. The animal and plant kingdoms likewise utilize carbohydrate recognition signaling mechanisms including mannose residues. Many publications evaluate other carbohydrates as targeting mechanisms for various cell types, however mannose targeting to phagocytes appears to be one of the more specific mechanisms identified to date. Mammalian cell surface identification molecules based on mannose binding, such as the ICAM family of leukocyte adhesion molecules, target the SIGN family of mannose receptors to accomplish self-recognition in vivo.
A well-known and cited study by Umezawa & Eto [1] demonstrates that liposomes containing aminophenyl mannoside were most efficiently incorporated into the mouse brain across the blood brain barrier. The radiolabeled liposomes bearing aminophenyl-alpha-D-mannopyranoside were maximally incorporated into the mouse brain after 48 hours, whereas in the spleen and liver, these radioactivities were maximum after 12 hours. The studies also showed that liposomes were most incorporated was glial cells rather than neuronal cell. The subcellular fractionation study indicates that mannose labeled liposomes are incorporated into lysosomes rich fraction both in liver and brain.
There are five mannosylated fluorescent control liposome products (m-Fluoroliposome®) for m-Clodrosome® (mannosylated clodronate liposomes). All five mannosylated fluorescent liposomes incorporate a lipophilic dye inside their membranes. They are insoluble in water; however, their fluorescence is easily detected when incorporated into membranes. DiI, DiO, DiD, DiR and DiA cover a wide range of excitation and emission wavelengths from 300s to 900s. DiI and DiO have fluorescence excitation and emission maxima separated by about 65 nm, facilitating two-color labeling. The emission spectrum of DiA is very broad, allowing it to be detected as green, orange, or even red fluorescence depending on the optical filter used. DiI, DiO, DiD and DiR belong to the dialkylcarbocyanines family of compounds. The spectral properties of the dialkylcarbocyanines are largely independent of the lengths of the alkyl chains, but are instead determined by the heteroatoms in the terminal ring systems and the length of the connecting bridge. They have extremely high extinction coefficients, moderate fluorescence quantum yields, and short excited state lifetimes in lipid environments (~1 ns). The fluorescence spectrum of each dye is shown below.
You can choose the m-Fluoroliposome® based on the type of the fluorescent equipment and filters that you use in your lab. Mannosylated clodronate liposomes cannot be made fluorescent simply due to the potential for inaccurate and/or uninterpretable data being generated by labelled m-Clodrosome®. For more information, please refer to the technical note section.


Formulation Information
Clodrosome® Liposomal Clodronate Suspension
Lipid Composition | Concentration (mg/ml) | Concentration (mM) | Molar Ratio Percentage |
---|---|---|---|
Total | 23 mg/ml | 35.1 mM | 100 |
L-alpha-Phosphatidylcholine | 18.8 | 24.3 | 70 |
Cholesterol | 4.2 | 10.9 | 30 |
Encapsulated Drug | Concentration |
---|---|
Clodronate ((Dichloro-phosphono-methyl)phosphonate), Disodium Salt | 18.4* mM |
* Depending on the type of the clodronate salt, itsconcentration (mg/ml) varies. If tetra hydrate salt is used, the concentration of the encapsulated drug will be ~7 mg/ml, and if a non-hydrated salt is used, the concentration will be ~5 mg/ml. |
Fluoroliposome®-DiI
Lipid Composition | Concentration (mg/ml) | Concentration (mM) | Molar Ratio Percentage |
---|---|---|---|
Total | 23 mg/ml | 35.1 mM | 100 |
L-alpha-Phosphatidylcholine | 18.8 | 24.3 | 70 |
Cholesterol | 4.2 | 10.9 | 30 |
Mannosylation | Concentration |
---|---|
4-Aminophenyl-alpha-D-mannopyranoside | 9.53 mol% |
Fluorescent Dye | Excitation/Emission (nm) | Concentration (mg/ml) | Concentration (mM) |
---|---|---|---|
1,1'-Dioctadecyl-3,3,3',3'-Tetramethylindocarbocyanine Perchlorate (DiI)![]() | 549/565 | 0.0625 | 0.065 |
Buffer and Liposome Size | Specification |
---|---|
Buffer | Phosphate Buffered Saline |
pH | 7.4 |
Liposome Size | 1.5-2 µm |
Technical Notes
- To reach bloodstream-accessible, mannose-receptor positive cells outside the liver, a significant number of liposomes will have to escape first-pass uptake by the liver and spleen, so that the target cells are exposed to a higher concentration of mannosylated liposomes from the blood. One strategy that has been used to ensure that liposomes escape the liver and spleen is known as reticuloendothelial system (RES) blockade in which animals are pre-dosed with a sufficient quantity of liposomes to temporarily saturate the phagocytic cells of the blood, liver and spleen, also known as the reticuloendothelial system (RES) or the mononuclear phagocyte system (MPS). This sufficient quantity is dependent upon the liposome type and composition as well as the species being dosed; the pre-dosed liposomes do not necessarily need to be the same type or composition as the therapeutic or diagnostic liposomes avoiding the RES. Soon after this pre-dose is cleared from the bloodstream (usually within a couple of hours), the liposomes of interest are dosed. Since the RES is involved in digesting the previous dose of liposomes, the subsequently dosed liposomes will remain in the circulation much longer thus be much more likely to bind to their target site outside the RES including those phagocytic cells which are accessible, but are not usually exposed to a higher concentration of liposomes.
- While RES blockade is usually thought of as saturating phagocytic cells, it has been shown that opsonin-binding by liposomes is a saturable phenomenon. Therefore, part of RES blockade may involve serum depletion of complement and other opsonins known to coat liposomes. In the current application, removal or reduction in the concentration of soluble mannose-receptors may further increase the probability of a mannosylated liposome being able to interact with mannose receptors on the target cell. Therefore, if the goal is to deplete a target subset of mannose-receptor + cells which may not normally be exposed to a substantial number of mannosylated liposomes, pre-dosing with mannosylated clodronate liposomes, in order to both saturate the blood, liver and spleen phagocytes and reduce the concentration of opsonins including soluble mannose receptors, should increase the number of subsequently dosed mannosylated clodronate liposomes available to this target subset hypothetically resulting in increased uptake and depletion by these targeted cells.
- The issue with fluorescent Clodrosome® has to do with the potential for inaccurate and/or uninterpretable data being generated by labelled Clodrosome®. When Clodrosome® induces macrophage apoptosis, the fluorescent lipid incorporated into the Clodrosome® that is disrupted and metabolized in the phagolysosome will be dispersed among the residual apoptotic bodies which are subsequently phagocytosed by other macrophages. Therefore, fluorescent lipid may be detected in phagocytic cells which never phagocytosed Clodrosome® especially when FACS or fluoroscopy are utilized to detect fluorescent cells (FACS) or fluorescence levels in a tissue homogenate (fluoroscopy). Another potential artifact arises from fluorescent lipid remaining in the extracellular “garbage”, which has not yet been cleared by other phagocytes, generating a high background fluorescence. However, experienced confocal microscopist may be able to differentiate between the punctate fluorescence resulting from fluorescent intact liposomes versus the more diffuse fluorescence characteristic of disrupted liposomes and some have successfully used fluorescent clodronate liposomes to visualize the cellular location of these liposomes by confocal microscopy in vivo [2]. A further complicating factor is that published data varies widely as to exactly when clodronate liposomes begin to induce apoptosis in macrophages. Mönkönnnen et al. show that macrophage death is measurable within the first hour after clodronate liposome treatment on RAW264 cells in vitro [3], while others have reported no signs of macrophage apoptosis until several hours after treatment in vivo. The variability in the data is likely due to different liposomal formulations of clodronate as well as the vastly different experimental conditions. Therefore, as with most biological studies, especially those involving liposomes, the amount of time between treating the animal or cells with clodronate liposomes and the onset of apoptosis will need to be established in each experimental model. If the nature of the research demands that Clodrosome® be tracked rather than the control, Encapsula can provide DiI-labelled Clodrosome® upon request, and assuming that the Clodrosome® distribution can definitively be assessed prior to the onset of apoptosis, clear and valid data on the biodistribution of fluorescent Clodrosome® should be obtainable. Still, for most purposes, Fluoroliposome® (fluorescent control liposomes) will provide the required data with far fewer potential artifacts.
- When monitoring monocyte uptake in vivo in normal animals, the circulating monocytes may “disappear” or show reduced counts within the first 2 h post-injection due to margination of the monocytes post-liposome phagocytosis. These cells will re-enter the circulation within a few hours. Sunderkötter et al. demonstrate this phenomenon and discuss the behavior in detail. Also consider that circulating monocytes have a lifetime of about 24 h so labeled monocytes will be continually leaving the circulation, even in normal animals, due to aging of the monocytes [4].
- When animals or cells are treated with Clodrosome®, phagocytic cells recognize the liposomes as invading foreign particles and proceed to remove the liposomes from the local tissue or serum via phagocytosis. The liposomes then release clodronate into the cytosol resulting in cell death. Unencapsulated clodronate cannot cross the cell membrane to initiate cell death.
- Encapsome® control liposomes are recognized and phagocytosed by the same mechanism as Clodrosome®. Since the control liposomes do not contain clodronate, the phagocytic cells are not killed. However, phagocytes do respond to the ingestion of the control liposomes by cytokine secretion, temporary suspension of phagocytic activity and other responses described in the literature.
- The product must be removed from the vial using sterile technique. Do not use if sterility is compromised. This is particularly important if a single vial is accessed multiple times over several weeks. The product should not be used more than 60 days after receipt, even if unopened.
- Liposomes may settle when left undisturbed for more than a few hours. Immediately prior to use, in order to ensure a homogeneous liposome suspension, slowly invert the vial several times until the suspension appears homogeneous by visual inspection. Vigorous or erratic shaking will not damage the liposomes but may induce foaming and bubble formation making it more difficult to accurately measure the desired dosage.
- If the personnel performing intravenous injections are not experienced in or familiar with, precautions for injecting larger volumes (~10% animal weight in ml), viscous liquids or particulate suspensions, consider having extra animals available in case serious injection-related adverse events occur. Dose control animals first to become familiar with large volume injections.
- Within hours after systemic administration of Clodrosome®, animals begin to lose important components of their immune system. Standard animal handling and housing protocols are not suitable for immunocompromised animals. Even when such precautions are taken, monitor the general health of each animal for opportunistic infections unrelated to the experimental protocol. There is no inherent toxicity to the product at the recommended dose levels.
- When dosing intravenously, use standard precautions for dosing larger volumes to animals including the following: a) warm product to room temperature prior to dosing; b) ensure that all air bubbles are removed from the syringe prior to dosing. Intravenous injection of air bubbles may result in air emboli which can kill or seriously injure animals; c) inject product at a slow, steady rate of no more than 1 ml/min; d) decrease infusion rate if animals display any atypical reactions such as unusual agitation.
- Infusion-related adverse reactions usually involve the animal gasping for air or other seizure-like movements. Animals often recover with no apparent permanent injury, but any potential effects on experimental results must be assessed by the researcher.
- Liposomes should be kept at 4°C and NEVER be frozen.
Dosage
Appearance
m-Clodrosome® is a white milky suspension, and m-Fluoroliposome®-DiI is a pink liquid suspension, both made of large micro size multilamellar liposomes. Due to their large size, some liposomes might settle to the bottom of the vial. If left sitting idle in the refrigerator, m-Fluoroliposome®-DiI will phase separate and form pellets in the bottom of the vial, leaving a clear solution on top. m-Clodrosome® might do the same only not as severely. Therefore, both should be gently shaken not to form bubbles but to form a homogeneous solution prior to use.
Educational Videos
Ordering/Shipping Information
- All liposome based formulations are shipped on blue ice at 4°C in insulated packages using overnight shipping or international express shipping.
- Liposomes should NEVER be frozen. Ice crystals that form in the lipid membrane can rupture the membrane, change the size of the liposomes and cause the encapsulated drug to leak out. Liposomes in liquid form should always be kept in the refrigerator.
- Clients who order from outside of the United States of America are responsible for their government import taxes and customs paperwork. Encapsula NanoSciences is NOT responsible for importation fees to countries outside of the United States of America.
- We strongly encourage the clients in Japan, Korea, Taiwan and China to order via a distributor. Tough customs clearance regulations in these countries will cause delay in custom clearance of these perishable formulations if ordered directly through us. Distributors can easily clear the packages from customs. To see the list of the distributors click here.
- Clients ordering from universities and research institutes in Australia should keep in mind that the liposome formulations are made from synthetic material and the formulations do not require a “permit to import quarantine material”. Liposomes are NOT biological products.
- If you would like your institute’s FedEx or DHL account to be charged for shipping, then please provide the account number at the time of ordering.
- Encapsula NanoSciences has no control over delays due to inclement weather or customs clearance delays. You will receive a FedEx or DHL tracking number once your order is confirmed. Contact FedEx or DHL in advance and make sure that the paperwork for customs is done on time. All subsequent shipping inquiries should be directed to Federal Express or DHL.
Storage and Shelf Life
Storage
m-Clodrosome® and m-Fluoroliposome® should always be stored at in the dark at 4°C, except when brought to room temperature for brief periods prior to animal dosing. DO NOT FREEZE. If the suspension is frozen, clodronate can be released from the liposomes thus limiting its effectiveness in depleting macrophages. ENS is not responsible for results generated by frozen product.
Shelf Life
m-Clodrosome® and m-Fluoroliposome® are made on daily basis. The batch that is shipped is manufactured on the same day. It is advised to use the products within 60 days of the manufacturing date.
References and background reading
1. Umezawa FA, Eto Y. Liposome targeting to mouse brain: mannose as a recognition marker. Biochemical and biophysical research communications. 1988 Jun 30;153(3):1038-44.
2. Polfliet MM, Goede PH, van Kesteren-Hendrikx EM, van Rooijen N, Dijkstra CD, van den Berg TK. A method for the selective depletion of perivascular and meningeal macrophages in the central nervous system. J. Neuroimmunol. 2001 Jun 1;116(2):188–95.
3. Mönkkönen J, Liukkonen J, Taskinen M, Heath TD, Urtti A. Studies on liposome formulations for intra-articular delivery of clodronate. Journal of Controlled Release. 1995 Aug;35(2–3):145–54.
4. Sunderkötter C, Nikolic T, Dillon MJ, van Rooijen N, Stehling M, Drevets DA, Leenen P. Subpopulations of Mouse Blood Monocytes Differ in Maturation Stage and Inflammatory Response. J Immunol. 2004 Apr 1;172(7):4410–7.
5. Nagai H, Kuwahira I, Schwenke DO, Tsuchimochi H, Nara A, Ogura S, Sonobe T, Inagaki T, Fujii Y, Yamaguchi R, Wingenfeld L. Pulmonary macrophages attenuate hypoxic pulmonary vasoconstriction via β3AR/iNOS pathway in rats exposed to chronic intermittent hypoxia. PLoS One. 2015 Jul 1;10(7):e0131923.
6. Zhu Y, Soderblom C, Krishnan V, Ashbaugh J, Bethea JR, Lee JK. Hematogenous macrophage depletion reduces the fibrotic scar and increases axonal growth after spinal cord injury. Neurobiology of disease. 2015 Feb 28;74:114-25.
7. Yun MH, Davaapil H, Brockes JP. Recurrent turnover of senescent cells during regeneration of a complex structure. Elife. 2015;4:e05505.
8. Arwert EN, Harney AS, Entenberg D, Wang Y, Sahai E, Pollard JW, Condeelis JS. A Unidirectional Transition from Migratory to Perivascular Macrophage Is Required for Tumor Cell Intravasation. Cell reports. 2018 May 1;23(5):1239-48.
9. Ito T, Ishigami M, Matsushita Y, Hirata M, Matsubara K, Ishikawa T, Hibi H, Ueda M, Hirooka Y, Goto H, Yamamoto A. Secreted Ectodomain of SIGLEC-9 and MCP-1 Synergistically Improve Acute Liver Failure in Rats by Altering Macrophage Polarity. Scientific reports. 2017 Mar 8;7:44043.
10. Miron VE, Boyd A, Zhao JW, Yuen TJ, Ruckh JM, Shadrach JL, van Wijngaarden P, Wagers AJ, Williams A, Franklin RJ. M2 microglia and macrophages drive oligodendrocyte differentiation during CNS remyelination. Nature neuroscience. 2013 Sep;16(9):1211.
11. Andreou K, Sarmiento Soto M, Allen D, Economopoulos V, de Bernardi A, Larkin J, Sibson NR. Anti-Inflammatory Microglia/Macrophages as a Potential Therapeutic Target in Brain Metastasis. Frontiers in oncology. 2017;7:251.
12. Alishekevitz D, Gingis-Velitski S, Kaidar-Person O, Gutter-Kapon L, Scherer SD, Raviv Z, Merquiol E, Ben-Nun Y, Miller V, Rachman-Tzemah C, Timaner M. Macrophage-induced lymphangiogenesis and metastasis following paclitaxel chemotherapy is regulated by VEGFR3. Cell reports. 2016 Oct 25;17(5):1344-56.
13. Oh SH, Kim HN, Park HJ, Shin JY, Bae EJ, Sunwoo MK, Lee SJ, Lee PH. Mesenchymal stem cells inhibit transmission of α-synuclein by modulating clathrin-mediated endocytosis in a Parkinsonian model. Cell reports. 2016 Feb 2;14(4):835-49.
14. Kano F, Matsubara K, Ueda M, Hibi H, Yamamoto A. Secreted Ectodomain of Sialic Acid‐Binding Ig‐Like Lectin‐9 and Monocyte Chemoattractant Protein‐1 Synergistically Regenerate Transected Rat Peripheral Nerves by Altering Macrophage Polarity. STEM CELLS. 2017 Mar 1;35(3):641-53.
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求采纳
3′-Full RACE Core Set Ver.2.0D314 20 次 1,800 元
5′-Full RACE Kit D315 RT反应10次 PCR反应50 次 3,980 元
RACE是基于PCR技术基础上由已知的一段cDNA片段,通过往两端延伸扩增从而获得完整的3'端和5'端的方法
RACE技术的原理和操作方法:http://wenku.baidu.com/link?url=J-9lPSGmRLQriSfXhOqcYYFvJx7ktGIRMgU6k9vDQIywtdJ8deNg7Qi5t4CgtjxuhWUBvQO6_qsULiqUIFckEZty75jYNw5yz6rNqiIKCwm
Clontech的非常好, 感觉. 效果不好可能是RNA问题, 或RTase的问题. 因为目前clontech的RTase是Takara的产品,而非原来clontech的产品,可单购。
步骤:1,RNA抽提(同RT)
2,逆转录,使用合成的oligo
3,p内参
4,使用根据已知序列设计的上游引物和提供下游引物做PCR,注意设计上游引物是退火温度与下游引物相差不大。
5,产物切胶回收,TA克隆测序
这个oligo和下游引物是我根据Takara和BD公司的manual自己设计的,经过我的使用效果很好。具体操作参照takara的3-racemanual。你先做3-race,了解熟悉下,成功后再做5-race。5-race要买试剂盒做,较为复杂!
请具体点,把联系方式和价位都说一下好吗?
cDNA完整序列的获得对基因结构、蛋白质表达、基因功能的研究至关重要。
完整的cDNA 序列可以通过文库的筛选和末端克隆技术获得。
末端克隆技术是20世纪80年代发展起来的。RACE(rapid-amplification of cDNA ends)是通过PCR进行cDNA末端快速克隆的技术。
RACE的优点
与筛库法相比较,有许多方面的优点
1)此方法是通过PCR技术实现的,无须建立cDNA文库,可以在很短的时间内获得有利用价值的信息。
2)节约了实验所花费的经费和时间。
3)只要引物设计正确,在初级产物的基础上可以获得大量的感兴趣基因的全长。
实验室现有的RACE试剂盒的简介
RACE是一种从一个相同的cDNA模板进行5‘和3‘末端快速克隆的方法。此方法会产生较少的错误条带。此过程中使用的酶混合物非常适合长链PCR。
使用此方法的要求是必须知道至少23-28个核苷酸序列信息,以此来设计5’末端和3‘末端RACE反应的基因特异性引物(GSPs)。
RACE引物的设计:
基因特异性引物(GSPs)应该是:
23-28nt
50-70%GC
Tm值≥65度,Tm值≥70度可以获得好的结果
需要实验者根据已有的基因序列设计5‘和3‘RACE反应的基因特异性引物(GSP1和GSP2).由于两个引物的存在,PCR的产物是特异性的。
反应中涉及到的一些事项
cDNA的合成起始于polyA RNA。如果使用其它的基因组DNA或总RNA,背景会很高。
RACE PCR的效率还取决于总的mRNA中目的mRNA的量和不同的引物有不同的退火和延伸温度。
在进行5‘和3’RACE PCR的时候应该使用热启动。
表4中给出了所有引物的相互关系。重叠引物的设计会对全长的产生有帮助。另外,重叠的引物可以为PCR反应提供一个对照。并不是绝对的要利用设计的引物产生重叠片段。
引物GSP中的GC含量要在50-70%之间。这样可以使用降落PCR。避免使用自身互补性的引物序列,否则会产生回折和
如果要用重叠片段来检测设计的引物,GSp1和GSp2之间至少是100-200碱基。只有这样才可以用扩增的产物来鉴定设计的引物是否正确。
降落PCR可以明显的增加RACE PCR产物的特异性。在最开始的循环中,退火温度高于AP1引物的Tm值,可以增加对特异性条带的扩增。随后的退火和延伸的温度降回到AP1的温度,可以进行随后的PCR循环。
形成分子内氢键。另外,避免使用与AP1互补的引物,尤其是在3‘末端。
验证基因特异性引物的对照:
单个引物的阴性对照:只用一个引物GSP来进行阴性对照。这样不应该产生任何的条带。如果可以看到明显的产物,应该改变循环的参数,或重新设计原始引物。
利用两个GSPS进行阳性对照:(只有两个GSP可以产生重叠的时候才可以采用此步。)为了确定RNA样品中目的基因确实表达,利用两个GSP和接头连接的cDNA来产生阳性对照。可以产生两个引物之间的重叠大小的片段。如果没有这个片段,应该重复cDNA的合成,或者从一个不同的组织或细胞来源进行cDNA的合成。
制备和抽提polyA RNA
不要使用DEPC处理过的水。
纯化完mRNA之后,利用琼脂糖凝胶电泳检测mRNA的质量。哺乳动物的mRNA样品是0.5-12kb的拖带,在其中有4.5和1.9kb的rRNA的条带。非哺乳动物的mRNA应略小。
具体的实验步骤
cDNA第一条链的合成:
我们建议进行cDNA合成的对照反应,这样可以对样品的cDNA的合成进行鉴定。加入各种试剂之后,在气浴中42度保温一个小时。
注意: 在水浴或酒精浴中保温回减少反应体积,从而降低第一链的合成效率。
将管放于冰上,以终止第一链的合成反应。
直接进行第二链的合成。
cDNA第二链的合成:
第二链合成的酶混合物中,含有聚合酶、RNaseH和连接酶。T4 DNA聚合酶的功能是补平dscDNA的末端。我们建议做阳性对照,试剂盒中提供人类骨骼肌的mRNA。
建议进行阳性对照,cDNA的质量取决于制备的polyA RNA的质量。非哺乳动物样品的mRNA大约在0.5-3kb之间。
通过电泳检测cDNA的产量,与对照进行对比,这样可以有利于在以后的步骤中对cDNA进行稀释。
接头的连接及连接产物的稀释
按照程序进行连接反应。
如果没有对比样品和对照的产量,利用Tricine-EDTA buffer制备接头连接的ds cDNA的1/50和1/250的稀释物,用两种稀释物进行以下的RACE PCR反应,直到鉴定出哪一种稀释可以得到好的效果。
RACE-PCR扩增
进行5’和3’的RACE-PCR扩增。
利用以下的程序进行降落PCR反应:
注意:
我们建议使用降落PCR反应,这就要求GSP的Tm值≥70度。
当循环结束时,利用1.2%琼脂糖凝胶电泳分析每一个管中的产物5μl,使用适当的分子量marker。
可以根据你的基因的特异性来设计最理想的循环参数。如果看不到带或者只有微弱的带,在68度多加5个循环。最佳的延伸时间取决于扩增条带的长度。如果片断的长度在2-5kb的时候,经常使用4min,0.2-2kb的时候将延伸时间减到2-3min,对于5-10kb的条带,延伸时间增加到10min。
RACE产物的验证:
应该对RACE的片段进行验证,以此来确定是否已经扩增了理想的产物。如果得到的是多条带或者研究的是多基因家族的成员,验证是非常有用的。
有3种验证RACE产物的方法:
(1)比较由GSP和NGSP获得RACE产物。
(2)Southern blot
(3)克隆并测序
我们建议最好测得RACE产物的部分序列。有的时候需要嵌套引物的存在。
比较由GSP和NGSP获得RACE产物
对于5‘末端的RACE产物,比较由AP1和GSP1扩增出来的产物和由AP1和NGSP1扩增出来的产物。
对于3‘末端的RACE产物,比较由AP1和GSP2扩增出来的产物和由AP1和NGSP2扩增出来的产物。这对于鉴定多条带是否是上一个PCR的特异性产物是非常有用的。
如果条带是正确的,在嵌套PCR反应中的条带应该是略微小一些。基本PCR和嵌套PCR产物的迁移率的不同取决于cDNA结构中GSP1和嵌套引物的位置。
RACE产物的克隆和测序:
可以利用胶回收试剂盒来回收RACE产物,此试剂盒适合回收2.5kb以下的RACE产物;对于长的片段,可以通过电洗脱获得好的结果。如果你选择使用其他的纯化方法,最后用Tricine-EDTA buffer 30μl重新悬浮DNA样品。
电泳5μl回收的样品来鉴定回收的质量。
将回收的PCR产物直接克隆到/A型的PCR克隆载体中。另外还可以利用接头和/或cDNA合成引物中的Not1、Srf1、Xma1、ECOR1等酶切位点,将产物克隆到常规载体中.
对于5‘端的RACE产物,我们建议挑取至少8-10个不同的克隆以获得5‘端的最大可能性的序列。(反转录并不总是进行到mRNA模板的5’末端,尤其是长模板。另外,T4 DNA聚合酶会移走5‘末端的0-20个碱基。)
一旦鉴定了含有插入片断的克隆,应该获得多的序列信息。理想的是,可以对整个开放读码框进行测序。包括5‘和3‘的非翻译区。
全长cDNA的获得
通过部分或全部测序鉴定了RACE产物后,可以通过两种选择获得全长的cDNA。
通过PCR的方法获得全长cDNA:
扩增长的cDNA需要较长的延伸时间,但是如果延伸的时间过长,可以产生拖带,所以要慎重的设计引物。
根据从5‘和3‘RACE产物获得序列信息设计5’和3‘GSP引物。这些引物应该来自cDNA的3’或者5‘的末端,应该是23-28nt长。不应该在引物的末端加上限制性位点,这样会导致高背景。在某些时候可以设计3’和5‘的嵌套引物。但是还是应该先利用一对引物进行PCR反应。
进行如下的热循环:
94度 30秒
25个循环 94度 5秒
72度 2-15分钟
延伸的时间应该等于预期的cDNA长度加上2分钟。例如:预期得到6kb的条带,用6+2=8分钟的延伸时间。
注意:如果没有条带或者条带弱,增加5个循环;或者优化PCR的条件。
在1.2%的琼脂糖凝胶上分析5μl的样品。通常情况下,可以见到一条单一带,如果这样,利用胶来纯化全长的cDNA。
制备1.2%的TAE buffer制备琼脂糖凝胶。不使用TBE buffer,TBE的胶很难制备全长的cDNA。
将剩下的45μl反应物点样,选用适当的marker。
利用长波紫外观察cDNA(≥300nm)切下全长的cDNA。注意:应该尽量减少紫外对cDNA的照射。
利用胶回收试剂盒回收cDNA。此试剂盒适合回收2.5kb以下的RACE产物;对于长的片段,可以通过电洗脱获得好的结果。如果你选择使用其他的纯化方法,最后用Tricine-EDTA buffer 30μl重新悬浮DNA样品。
将全长的cDNA克隆到T/A型的 PCR克隆载体中。