EZgeneTM EndoFree Plasmid ezFlow Maxiprep kit (BG0056) Handbook For research use only. Not intended for diagnostic testing. www.abgent.com Table of Contents Introduction…………………………………………………………. 2 Important Notes………………….………………………………….. 2 Storage and Stability………………………………………………... 3 Kit Contents………………………………………………...………. 4 Safety Information………………………………………………….. 5 Before Starting……………………………………………….……... 5 EndoFree Plasmid ezFlow Maxiprep Spin Protocol………………... 6 快速型无内毒素质粒大提………………………………………… 9 Purification of Low-Copy-Number Plasmid and Cosmid…………... 11 Trouble Shooting Guide..................................................…….…….. 12 1 Introduction Key to the plasmid purification kit is our proprietary DNA binding system that allows the high efficient binding of DNA to our ezBindTM matrix while proteins and other impurities are removed by wash buffer. Nucleic acids are easily eluted with sterile water or Elution Buffer. Unlike other kits in the markets, our patented plasmid purification kit has no chaotropic salts in the buffer.The purified DNA is guanidine/anion exchange resin residues free. The EZgene™ endofree system uses a specially formulated buffer that extracts the endotoxin from the bacterial lysate. The endotoxin level is less than 0.1 EU (Endotoxin) per µg of plasmid DNA. This kit is designed for fast and efficient purification of plasmid DNA from 150 to 400 mL of E. coli culture.The maxi column has a DNA binding capacity of 1200 µg. The purified endofree DNA is ready for downstream applications such as transfection of endotoxin-sensitive cell lines, primary cultured cells or microinjection. Two endotoxin removal procedures are provided. Protocol A removes endotoxin during the purification of plasmid DNA and Protocol B removes endotoxin after the purification of plasmid DNA. Important Notes Plasmid Copy numbers numbers:: The yield of plasmid DNA depends on the origin of the replication and the size of the plasmid. The protocols are optimized for high copy number plasmid purification. For low copy number plasmids, both the culture volume and the buffer volume need to be scaled up 2 to 3 times. Reference Table 1 for the commonly used plasmids, Table 1 Commomly used plasmids 5 Expected Yield (µg per 200 mL) 12 P15A 10-12 25-40 pSuperCos pMB1 10-20 30-50 pBR322 pMB1 15-20 35-50 pGEMR Muted pMB1 300-400 350-450 pBluescriptR ColE1 300-500 450-600 PUC Muted pMB1 500-700 700-1,000 Plasmid Origin pSC101 pSC101 PACYC Copy Numbers 2 Host Strains: Strains:The strains used for propagating plasmid have significant influence on yield. Host strains such as Top 10 and DH5a yield high-quality plasmid DNA. endA+ strains such as JM101, JM110, HB101, TG1 and their derivatives, normally have low plasmid yield due to either endogenous endonucleases or high carbohydrates released during lysis. We recommend transform plasmid to an endAstrain if the yield is not satisfactory. Please reference Table 2 for the endA information. Table2 endA strains of E. Coli. EndA- Strains of E. Coli DH5α DH1 DH21 JM106 JM109 SK2267 SRB TOP10 DH10B JM103 JM107 SK1590 MM294 Stbl2™ BJ5182 DH20 JM105 JM108 SK1592 Select96™ Stbl4™ XLO XL1Blue XL10Gold EndA+ Strains of E. Coli C600 HB101 JM110 TG1 JM101 JM83 All NM strains RR1 ABLE® C TB1 ABLE® TKB1 HMS174 CJ236 KW251 DH12S LE392 ™ ES1301 M1061 All Y strains K P2392 PR700 Q358 BL21(DE3) BL21(DE3) pLysS BMH 71-18 Optimal Cell Mass (OD600 x mL of Culture): Culture):This procedure is designed for isolating plasmid grown in standard LB medium (Luria Bertani) for 12 -16 hours to a density of OD600 2.0 to 3.0. If rich medium such as TB or 2xYT are used, make sure the cell density doesn’t exceed 3.0 (OD600). A high ratio of biomass over lysis buffers result in low DNA yield and purity. The maxi column has an optimal biomass of 450-550. For example, if the OD600 is 2.5, the optimal culture volume should be 200 mL. Culture Volume Volume:: Use a flask or tube with a volume at 4 times the culture medium to secure optimal condition for bacteria growth. Don’t exceed the maximum culture volume suggested in the protocol. Incomplete lysis due to over amount of bacterial culture results in lower yield and less purity. Storage and Stability Buffer A1 should be stored at 4°C once RNase A is added and Buffer ER should be stored at 4°C. All other materials can be stored at room temperature (22-25°C). The Guaranteed shelf life is 12 months from the date of purchase. 3 Kit Contents alog # Cat Catalog BG0055 BG0056 Preps 10 25 ezBindTM Columns 10 25 Buffer A1 110 mL 270 mL Buffer ER 5.5 mL 14 mL Buffer B1 110 mL 270 mL Buffer D1 11 mL 28 mL Buffer N3 40 mL 80 mL Buffer RET 200 mL 2×250 mL DNA Wash Buffer* 54 mL 2×54 mL 11 mg (550 μL) 27 mg (1.35 mL) 60 mL 135 mL 1 1 RNase A (20 mg/mL) Endofree Elution Buffer User Manual *Add 216 mL (BG0055) or 2×216 mL (BG0056) 96-100% ethanol to each DNA Wash Buffer bottle before use. Safety Information • • Buffer N3 contains acidic acid, wear gloves and protective eyewear when handling. Buffer N3and RET contains chaotropic salts, which may form reactive compounds when combines with bleach. Do not add bleach or acidic solutions directly to the preparation waste. 4 Before Starting Alternative endotoxin removal procedures are provided. Protocol A removes endotoxin during the purification of plasmid DNA and Protocol B removes endotoxin after the purification of plasmid DNA. Prepare all components and get all necessary materials ready by examining this instruction booklet and become familiar with each step. Important � RNase A: It is stable for more than half a year when stored at room temperature.Spin down the RNase A vial briefly. Add the RNase A solution to Buffer A1 and mix well before use. Store at 4°C. � Buffer ER should be stored at 4°C. � .It is critical to warm up the Buffer B1 precipitates below room temperature temperature.It buffer at 50 50°°C to dissolve the precipitates before use. � Buffer N3 may form precipitates below 10 10°°C, warm up at 37 37°°C to dissolve the precipitates before use use.. � Keep the cap tightly closed for Buffer B1 after use. � Make sure the availability of centrifuge, especially, after mixing the lysate with ethanol, the sample needs to be processed immediately either by centrifugation. � In case the collection tube doesn’t fit in high-speed centrifuge rotor, use benchtop centrifuge and spin at 2,500 x g with double centrifugation time. For example, centrifuge at 2,500 x g for 10 min instead of 5,000 x g for 5 min. � � Carry out all centrifugations at room temperature. For certain reasons,Buffer KB are not involved in this kit from now on Materials supplied by users � 100% ethanol � High speed centrifuge or vacuum manifold. � 30 mL high speed centrifuge tubes and 50 mL tubes. 5 EZgeneTMEndoFree Plasmid ezFlow Max Maxiiprep Spin Protocol Note:The Maxi column has a plasmid DNA capacity of more than 1.0 mg. To yield more plasmid DNA, please use more bacterial culture. The following information is suitable for high copy plasmid and the OD600 of culture is between 2.0-3.0. If the OD600 is lower than 2.0, that will reduce the yield of the plasmid DNA. Please use more culture accordingly. Table for the corresponding culture volume and solution volume Culture Volume Buffer A1/RNase Buffer ER Buffer B1 Buffer D1 Buffer N3 Buffer RET 100% ethanol DNA Wash Buffer Endofree Elution Buffer < 200 mL 300 mL 400 mL 500 mL Ratio 10 mL 15 mL 20 mL 25 mL 1V 0.5 mL 9 mL 1 mL 3 mL 0.7-1.0 V of Supernatant 10 mL 0.75 mL 13.5 mL 1.5 mL 4.5 mL 0.7-1.0 V of Supernatant 15 mL 1.0 mL 18 mL 2 mL 6 mL 0.7-1.0 V of Supernatant 20 mL 1.25 mL 22.5 mL 2.5 mL 7.5 mL 0.7-1.0 V of Supernatant 25 mL 0.05 V 0.9 V 0.1 V 0.3 V 0.7-1.0 V of Supernatant 1V 10 mL 10 mL 10 mL 10 mL 10 mL 1.5-2.0 mL 1.5-2.0 mL 1.5-2.0 mL 1.5-2.0 mL 1.5-2.0 mL Note: The volume of solution is supplied for 200 mL culture (OD600 between 2.0-3.0) Please contact Abgent if you need more solutions. • 150- 200 mL LB containing appropriate antibiotic with 100 µL fresh Inoculate150starter culture. Grow at 37°C for 14-16 h with vigorous shaking. Note Note:The best way to prepare a starter culture: Inoculate a single colony from a freshly grown selective plate into 1 mL LB medium containing the appropriate antibiotic and grow at 37°C for 6-8 h with vigorous shaking (~250 rpm). Note: Do not use a starter culture that has been stored at 4°C. Note: Do not grow starter culture directly from glycerol stock. Note: Note:Do not use more than 200 mL culture or cell mass greater than 550.The buffer volumes need to be scaled up if processing over 200 mL of culture. 2. Harvest the bacterial by centrifugation at 5,000 x g for 10 minutes at room temperature. Pour off the supernatant and blot the inverted tube on paper towels to remove residual medium completely. 6 Buffer A1 (Add RNase A to Buffer A1 beforeuse) and completely 3. Add 10 mL mLB resuspend bacterial pellet by vortexing or pipetting (Complete resuspension is Bu ffer ER into the suspended critical for optimal yields). yields).Then add 0.5 mL mLBu Buffer bacterial culture. Mix well by inverting 5-10 times. Note Note: if room temperature is below 25°C, warm up the mix solution after adding Buffer ER at 45°C for 5 min. Buffer B1 4. Add 9 mL mLB B1, mix gently but thoroughly by inverting 5-10 times. If necessary, continue inverting the tube until the solution becomes slightly clear. Incubate at room temperature for 5 minutes to obtain a slightly clear lysate. Buffer D1 Then add 1mL 1mLBuffer D1, mix gently and incubating for another 5 minutes. I. Buffer N3 Add 3 mL mLB N3, mix immediately by sharp hand shaking for 5-10 times. Transfer the sample to a high speed centrifuge tube and centrifuge at 12,000 x g for 10 min at room temperature. Note: It is critical to mix the solution well. If the mixture still appearsconglobated, brownish or viscous, more mix is required to completely neutralize the solution. Note: Syringe filter (Supplied in BG0057 or purchase separately from Abgent) could be used to filtrate the lysate if high-speed centrifuge is not available. II. Transfer clear lysate to a clean 50 mL conical tube and add0.7-1.0 0.7-1.0 20 mL mLclear 14 to 20m Lof Buffer RET to 20 mLof volume of Buffer RET (For example,14 20mL clear lysate) lysate),and 10 mL 100% ethanol ethanol.Mix well by sharp hand shaking for 5 times. The mixture of the solution needs to be centrifuged through the DNA column immediately. Note: Increase the volume of Buffer RET could reduce endotoxin level in the plasmid while the DNA yield will be affected by the Buffer RET. Different volume of Buffer RET should bechosen according to the downstream application. 1. Immediately apply 20 mL of the solution into a DNA column with the collection tube. Centrifuge at 5,000 x g for 2 min at room temperature. Remove the column from the tube and discard the flow-through liquid. Process the remaining solution solution,, discard the flow-through liquid and put the column back to the collection tube. Note: If the 50 mL collection tube doesn’t match the rotor (for example, the lid of rotor cannot close), the column with the collection can be centrifuged at a benchtop centrifuge at > 2,500g for 5 min. DNA Wash Buffer 2. Add 10 mL mLDNA Bufferinto the column, centrifuge at 2,500 x g for 1 7 min. Remove the column from the tube and discard the flow through. Reinsert the column into the collection tube. Repeat step 8. 100% ethanol into the column, centrifuge at 2,500 x g for 1 min. 3. Add 3 mL mL100% Remove the column from the tube and discard the flow through. Reinsert the column into the collection tub. 4. Centrifuge the column at 5,000 x g, with the lid open, open,for 10 min to remove the ethanol residues. Incubate at 65oC for 10 min will help to remove the ethonal and increase the elution efficiency. Note: Ethanol residues in the column will affect the elution of DNA. If the speed is less than5,000 x g, centrifuge the column for 20 min and dry in the air to completely remove the ethanol. 5. Endofree Transfer the column to a clean 50 mL tube and add 1.5-2.0 mL mLEndofree Elution Buffer Bufferto the center of the column and incubate for 1 minute at room temperature. Elute the DNA by centrifugation at >5,000 x g for 5 minutes. 6. Reload the eluant into the center of the column and incubate for 1 minute. Elute the DNA by centrifugation at>5,000 x g for 5 minutes. Note: Note:The DNA is ready for downstream applications such as cloning/subcloning, RFLP, Library screening, in vitro translation, sequencing, transfection, and microinjection . Note: Two elutions will increase DNA yield. 7. Optional: Instead of step 12, for maximum the DNA yield, please add 4.0-5.0 Endofree Elution Buffer mL mLEndofree Bufferto the center of the column and incubate for 5 minutes at room temperature. Elute the DNA by centrifugation at >5,000 x g for 5 minutes. Reload the eluant twice to elute the plasmid DNA absorbed on the membrane. This will give rise to maximum DNA yield. Note: For DNA concentration, add 0.1 volume 3M Potassium Acetate or Sodium acetate (pH 5.2) and 0.7 volume isopropanol. Centrifuge at top speed for 10 min. Discard supernatant. Wash the DNA with 1 mL 70% ethanol, centrifuge for 5 min, carefully decant. Air-dry the pellet for 20 minutes in a tissue culture hood. Resuspend the DNA in Endofree Elution Buffer. L)= OD260 nm x 50 x dilution factor. DNA concentration (µg/m g/mL 8 快速型去内毒素质粒大提试剂盒 详细资料请参阅英文资料 • 实验前准备 RNase A:室温下可稳定保存半年,使用前将提供的所有RNase A瞬时离心后加入Buffer A1, 使用后将 Buffer A1/RNase A置于4oC保存。 Buffer ER:保存于4oC。 Buffer B1:在低于室温时可能会沉淀,请于50oC左右水浴加热至沉淀完全溶解,溶液澄清,使用后保 证Buffer B1瓶盖旋紧。 Buffer N3:低于10oC会沉淀,请于37 oC左右水浴加热至沉淀完全溶解,溶液澄清。 准备100%的乙醇。 在室温下(22-25oC)进行所有离心操作。 • 注意事项 质粒拷贝数: 纯化中低拷贝的质粒时,请使用 2 倍体积的菌液,2 倍体积的 Buffer A1, ER, B1, D1, N3, RET,相同体积的 DNA Wash Buffer 和 Endofree Elution Buffer。 转化菌:若为-70oC 甘油冻存的菌,请先涂布平板培养后,再重新挑选新的单个菌落进行培养。 切勿直接取冻存在 4oC 的菌进行培养。 柱结合能力:1 mg-1.5 mg 对富含内源核酸酶的宿主菌( endA+)如HB101, JM101, TG1等,需去内源核酸酶,请使用BG0069。 • 操作步骤 注:本试剂盒中柱子结合能力大于 1 mg,若实验中质粒得率较低,可以加大菌液用量。下表列出了处 理不同菌液应使用的溶液的量。下表的数据适用于 OD600 在 2.0-3.0 的高拷贝菌液。如果是低拷贝质粒 或者 OD 600<2.0,将会影响质粒的得率,请相应的增加菌液用量。 注:本试剂盒中提供的溶液量及操作步骤是根据 OD600 在 2.0-3.0 的高拷贝质粒的 200mL 菌液提供,如 需更多溶液,请联系 Abgent 公司。 Culture Volume Buffer A1/RNase Buffer ER Buffer B1 Buffer D1 Buffer N3 Buffer RET 100% ethanol DNA Wash Buffer Endofree Elution Buffer < 200 mL 300 mL 400 mL 500 mL Ratio 10 mL 15 mL 20 mL 25 mL 1V 0.5 mL 9 mL 1 mL 3 mL 0.7-1.0 V of Supernatant 10 mL 0.75 mL 13.5 mL 1.5 mL 4.5 mL 0.7-1.0 V of Supernatant 15 mL 1.0 mL 18 mL 2 mL 6 mL 0.7-1.0 V of Supernatant 20 mL 1.25 mL 22.5 mL 2.5 mL 7.5 mL 0.7-1.0 V of Supernatant 25 mL 0.05 V 0.9 V 0.1 V 0.3 V 0.7-1.0 V of Supernatant 1V 10 mL 10 mL 10 mL 10 mL 1.5-2.0 mL 1.5-2.0 mL 1.5-2.0 mL 1.5-2.0 mL 9 10 mL 1.5-2.0 mL 150-200 mL 1. 取100 µL新鲜的菌液接种到150-200 mL的LB培养基(含适量抗生素),37oC震荡培养14-16小时。 2. 室温下5,000 x g离心10分钟,收集菌体,并尽可能的吸去上清。 注:残留的液体培养基容易导致菌液裂解不充分,离心后沉淀较松,不能有效吸取上清。 注:本说明书中的操作程序适用于标准LB (Luria Bertani) 培养基培养12-16 小时后,OD600(细菌密度) 在2.0-3.0之间的菌液。若采用的是富集培养基,例如TB 或2×YT,请注意保证OD 600不超过3.0。 10 mL Buffer A1 3. 加入10 mLBuffer A1(确保已加入RNase A),用移液器或涡流震荡确保细菌沉淀重新悬浮。 再向悬 0.5 mL Buffer ER 浮的菌液中加入0.5 mL的Buffer ER,反转5-10次,混合均匀。 注:不完全悬浮易导致菌体裂解不完全,从而使产量降低。 注:如果室温低于25°C,混合液在加入Buffer ER混匀后,置于45°C温育5min。 Buffer B1 4. 加入99 mL mLBuffer B1,轻轻地反转5-10 次以混合均匀,若有必要,请反复反转使溶液变为清澈无菌 团,在室温放置5 分钟。再加入11 mL Buffer D1 D1,轻轻地反转5-10 次以混合均匀,室温温育5分钟。 注:若溶液未清亮澄清,则表明菌体裂解不充分,应加大Buffer B1的用量或减少菌体量。 5. 加入33 mL Buffer N3 N3,用手甩3-5次使溶液充分混匀,此时出现白色絮状沉淀。将离心管转至高速离 心机,在室温下12,000 x g离心10分钟。 注:低温下RNase不工作,易有RNA污染。如果离心机转子较冷,将离心管在室温下温育 10分钟后 再离心。若无告速离心机,可用Syringe filter替代(在BG0057)中提供,也可单独购买)。 20 mL 6. 转移上清液20 mL(不超过20mL) 至新的50mL离心管中(若上清中仍有白色沉淀,可再次离心),加入 7-1.0 Buffer RET 20 mL 14-20 mL Buffer RET)及10 10 mL 100% ethonal 0. 0.7-1.0 7-1.0倍体积的Buffer RET(即每20 mL裂解液加入14-20 mL的100% ethonal, 用手用力甩5次以混匀,溶液需马上离心过DNA柱。 注:使用1倍体积的Buffer RET(<1 EU/μg),但是会稍微降低质粒的得率。请根据不同的实验需求选 择Buffer RET的使用体积。 20 mL 7. 立即转移20 mL裂解液/收集管至带收集管的DNA柱中,室温下5,000 x g离心2分钟,倒掉收集管中 的废液,将离心柱重新放回到收集管中。将剩余溶液转移至DNA柱中,室温下5,000 x g离心2分 钟,倒掉收集管中的废液,将离心柱重新放回到收集管中。重复直至所有的溶液通过DNA柱。 注:如果50 mL的收集管与离心机转子不符,可在台式离心机> 2,500 x g 离心5分钟。 10 mL DNA Wash Buffer 8. 向离心柱中加入10 mLDNA Buffer,室温下2,500 x g离心1分钟,倒掉收集管中的废液,将离 心柱重新放回到收集管中。重复步骤“88”。 100% ethonal 9. 向离心柱中加入33 mL mL100% ethonal,室温下2,500 x g离心1分钟,倒掉收集管中的废液,将离心柱 重新放回到收集管中。 10 10. 将离心柱放回高速离心机中,室温下5,000 x g开盖离心10分钟。离心后,将离心柱在65度烘箱中放 Endofree Elution Buffer 的洗脱效率。 置10分钟有助于彻底去除乙醇,提高Endofree 注:此步骤中开盖离心将会更有效的去除残留的乙醇,乙醇是否去除干净将会影响最后的洗脱效 率。若转速低于5,000 x g,需离心20分钟,并可放在空气中晾干。 1.5 Endofree Elution 11. 将离心柱转至一个新的50 mL离心管中,向DNA柱膜的正中加入1 .5--2.0 mL 的Endofree Buffer Buffer,室温放置1分钟,>5,000 x g离心5分钟,以洗脱质粒DNA。 12. 将50mL离心管中的洗脱液上柱再放置洗脱1分钟,>5,000 x g离心5分钟。两次洗脱将提高得率。 注:提取到的无内毒质粒DNA可用于转染内毒素敏感性细胞株,原代细胞及微注射。 13. 可 选: 不 用操 作第 12步 ,为 提高 DNA 的 得率 ,请 向柱 中央 加入 4.0-5.0 mL 的 Endofree Elution Buffer Buffer,温育5分钟,在>5,000 x g离心5分钟。再将洗脱液重新上柱重复洗脱两次。这将有利于洗脱 柱上吸附的所有的质粒DNA。 0.1 3M pH5.2 0.7 注:得到的DNA需要浓缩,请加入0.1 0.1倍体积的3M 3M的醋酸钠(pH5.2 pH5.2)和0.7 0.7倍体积的异丙醇,室温 1mL 70% 下高速离心10分钟,底部可见白色的DNA沉淀,弃去上清,加入1mL 1mL70% 70%乙醇,高速离心5分钟, Endofree Elution Buffer 弃去上清,空气干燥20分钟,加入Endofree Buffer重新溶解质粒DNA。 Purification of Low-Copy-Number Plasmid and Cosmid The yield of low copy number plasmid is normally around 0.1 – 1 µg /mL of overnight culture. For isolating low copy number or medium copy number plasmid DNA, use the following guideline: 1. Culture volume: Use 2x volume of the high copy number culture. Use up to 400 mL for the maxiprep. 2. ,Buffer ER, Buffer D1, Use 2x volume of the Buffer A1, Buffer B1 B1,Buffer Buffer N3 N3,, Buffer RET RETand 100% ethanol ethanol. Additional buffers can be purchased from Abgent. 3. ash Buffer and Endofree Elution Buffer Use same volume of DNAW DNAWash Buffer. 11 Trouble Shooting Guide Problems Possible Reasons Suggested Improvements Low Yield Poor Cell lysis. � Resuspend pellet thoroughly by votexing and pipetting prior adding Buffer B1. � Make fresh Buffer B1 if the cap had not been closed tightly. (Buffer B1: 0.2N NaOH and 1%SDS). Low Yield Bacterial culture overgrown or not fresh. Grow bacterial 12-16 hours. Spin down cultures and store the pellet at -20°C. if the culture is not purified the same day. Do not store culture at 4°C over night. Low Yield Low copy-number plasmid. No DNA Plasmid lost in Host E.coli Increase culturevolume and the volume of Buffer according to instruction on page 8. Prepare fresh culture. Genomic DNA contamination Over-time incubation Do not vortex or mix aggressively after adding Buffer after adding buffer B1. Do not B1. incubate more than 5 minutes after adding Buffer B1. RNA contamination RNase A not added to Buffer A1. Plasmid DNA floats out of wells while running in agarose gel, DNA doesn’t freeze or smell of ethanol Ethanol traces not Make sure that no ethanol residual completely removed remaining in the silicon membrane from column. beforeeluting the plasmid DNA. Recentrifuge again if necessary. 12 Add RNase A to Buffer A1. USA Abgent,Inc. Toll Free (888)735-7227 Or (858)875-1900 [email protected] CHINA Abgent Suzhou +86 512 69369088 [email protected] EUROPE Abgent Europe +44(0) 1235 854042 [email protected] For other countries www.abgent.com
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