Genomic DNA Extraction - PureLink
实验原理
The PureLink™ Genomic DNA Purification Kit is based on the selective binding of DNA to silica-based membrane in the presence of chaotropic salts.
The lysate is prepared from E. coli cells, yeast cells, mouse tails, and mammalian cells and tissues. The cells or tissues are digested with Proteinase K in the presence of EDTA to inhibit DNases. A detergent (SDS) is added during lysis to aid in denaturation of proteins and in solubilizing membrane proteins. The SDS also stimulates Proteinase K activity. The lysis step is performed at 55° C for E. coli , yeast, and tissues to accelerate the digestion procedure. Any residual RNA is removed by digestion with RNase prior to binding samples to the spin column.
The advantages of using PureLink™ Genomic DNA Purification Kit are:
- Rapid and efficient purification of genomic DNA from a variety of samples such as mammalian cells and tissue,mouse tails, E. coli , and yeast
- Designed to purify high-quality DNA in less than 15 minutes after sample preparation
- Simple lysis of cells and tissues with Proteinase K without the need for any mechanical lysis
- Minimal contamination from RNA
- Reliable performance of the purified DNA in PCR, restriction enzyme digestion, and Southern blotting
实验步骤
Preparing Lysates
Introduction
Instructions for preparing lysates from mammalian cells and tissues, mouse tail, bacteria, and yeast are described below.
To obtain high-quality genomic DNA, follow the guidelines recommended below. The PureLink™ Genomic DNA Purification Kit buffers contain guanidine isothiocyanate. Always wear a laboratory coat, disposable gloves, and eye protection when handling buffers.
Do not add bleach or acidic solutions directly to solutions containing guanidine isothiocyanate or sample preparation waste as it forms reactive compounds and toxic gases when mixed with bleach or acids.
Sample Amount
There are different protocols for preparing lysates depending on the starting material (sample). Based on your sample, choose an appropriate lysate preparation protocol from the table below.
The PureLink™ Genomic DNA Purification Kit is suitable for isolating DNA from a variety of samples using the recommended sample amount (see table below). If you wish to use less sample amount than the recommended amount listed in the table below, follow the appropriate protocol for the sample using the recommended volume of reagents except perform only one elution step or decrease the volume of elution buffer. Note: If you start with less amount of sample, the yield of DNA may also be lower.
If none of the sample preparation protocols match the type or size of your sample, then use the guidelines described below to develop your own protocol.
To obtain high yield of DNA and minimize DNA degradation, collect the sample and proceed immediately to sample preparation or freeze the sample in liquid nitrogen immediately after collection.
Follow the recommendations below to obtain the best results:
- Maintain a sterile environment when handling DNA to avoid any contamination from DNases
- Ensure that no DNases are introduced into the sterile solutions of the kit
- Make sure all equipment that comes in contact with DNA is sterile including pipette tips and microcentrifuge tubes
- Do not vortex the samples for more than 5-10 seconds at each vortexing step to avoid extensive shearing of DNA
- Be sure to mix well after addition of SDS and Binding Buffer (L3)
- To minimize DNA degradation, perform lysate preparation steps quickly, and avoid repeated freezing and thawing of DNA samples
Components supplied with the kit
Preparing Lysate from Mammalian Cells
Procedure to prepare lysate from mammalian cells is described below.
- Set a water bath or heat block at 70°C.
- For adherent cells (up to 5 x 106 cells), remove the growth medium from the culture plate and harvest cells by trypisinization or a method of choice. For suspension cells (up to 5 x 106 cells), harvest cells and centrifuge the cells at 250 x g for 5 minutes to pellet cells. Remove the growth medium.
- Resuspend the cells from Step 2 in 180 µl PBS.
- Optional: Add 20 µl RNase A (supplied with the kit) to the sample and incubate at room temperature for 2 minutes.
- Add 20 µl Proteinase K (supplied with the kit) to the sample and mix well by vortexing. Incubate at room temperature for 2 minutes.
- Add 10 µl 10% SDS (prepared from 20% SDS supplied with the kit) to the lysate and mix immediately by vortexing for 5 seconds to denature proteins. Add 200 µl Binding Buffer (L3) supplied with the kit to the lysate. Mix well by vortexing for 5 seconds. The SDS precipitates in the presence of guanidine isothiocyanate.
- Incubate at 70°C for 10 minutes to solubilize SDS and promote protein denaturation.
- Add 200 µl 96-100% ethanol to the lysate. Mix well by vortexing for 5 seconds.
- Proceed to Binding DNA
Preparing Mammalian Tissue Lysate
Procedure to prepare lysate from mammalian tissues is described below.
- Set 2 water baths or heat blocks at 55°C and 70°C, respectively.
- Place ~25 mg of minced mammalian tissue into a sterile microcentrifuge tube.
- Add 180 µl Lysis Buffer (L6) and 20 µl Proteinase K (supplied with the kit) to the tube. Ensure the tissue is completely immersed in Lysis Buffer (L6).
If you are using a hard mammalian tissue such as heart, you may also need to homogenize the tissue using a tissue homogenizer prior to the addition of Proteinase K. - Incubate at 55°C with occasional vortexing until lysis is complete (~3 hours).
- Optional: Add 20 µl RNase A (supplied in the kit) to lysate and incubate at room temperature for 2 minutes.
- Centrifuge the lysate at maximum speed for 5 minutes at room temperature to remove any particulate materials.
- Transfer the supernatant to a fresh microcentrifuge tube, add 10 µl 10% SDS (prepared from 20% SDS supplied with the kit) to the lysate and mix immediately by vortexing for 5 seconds to denature proteins. Add 200 µl Binding Buffer (L3) supplied with the kit to the lysate. Mix well by vortexing for 5 seconds. The SDS precipitates in the presence of guanidine isothiocyanate.
- Incubate at 70°C for 10 minutes to solubilize SDS and promote protein denaturation.
- Add 200 µl 96-100% ethanol to the lysate. Mix well by vortexing for 5 seconds.
- Proceed to Binding DNA.
Preparing Lysate from Mouse Tail
- Set 2 water baths or heat blocks at 55°C and 70°C, respectively.
- Cut the mouse tail in 0.5 cm pieces. Place one 0.5 cm piece into a sterile microcentrifuge tube and cut the tail piece into small pieces.
- Add 180 µl Lysis Buffer (L6) and 20 µl Proteinase K (supplied with the kit) to the tube and mix well. Ensure the pieces are completely immersed in buffer.
- Incubate at 55°C with occasional vortexing until lysis is complete (~6-8 hours). You can also perform the lysis overnight.
- Optional: Add 20 µl RNase A (supplied in the kit) to lysate and incubate at room temperature for 2-5 minutes.
- Centrifuge the lysate at maximum speed for 5 minutes at room temperature to remove any hair from the lysate.
- Transfer the supernatant to a fresh microcentrifuge tube, add 10 µl 10% SDS (prepared from 20% SDS supplied with the kit) to the lysate and mix immediately by vortexing for 5 seconds to denature proteins. Add 200 µl Binding Buffer (L3) supplied with the kit to the lysate. Mix well by vortexing for 5 seconds. The SDS precipitates in the presence of guanidine isothiocyanate.
- Incubate at 70°C for 10 minutes to solubilize SDS and promote protein denaturation.
- Add 200 µl 96-100% ethanol to the lysate. Mix well by vortexing for 5 seconds.
- Proceed to Binding DNA.
Procedure to prepare E. coli cell lysate is described below.
- Set 2 water baths or heat blocks at 55°C and 70°C, respectively.
- Harvest up to 2 x 109 E. coli cells by centrifugation. If you are using a frozen cell pellet, proceed to Step 3.
- Resuspend the cell pellet in 180 µl Lysis Buffer (L6) supplied with the kit. Add 20 µl Proteinase K solution (supplied with the kit) to lyse the cells. Mix well by vortexing for 5 seconds.
- Incubate the tube at 55°C for 15 minutes.
- Optional: Add 20 µl RNase A (supplied with the kit) to lysate and incubate at room temperature for 2 minutes.
- Add 10 µl 10% SDS (prepared from 20% SDS supplied with the kit) to the lysate and mix immediately by vortexing for 5 seconds to denature proteins. Add 200 µl Binding Buffer (L3) supplied with the kit to the lysate. Mix well by vortexing for 5 seconds. The SDS precipitates in the presence of guanidine isothiocyanate.
- Incubate at 70°C for 10 minutes to solubilize SDS and promote protein denaturation.
- Add 200 µl 96-100% ethanol to the lysate. Mix well by vortexing for 5 seconds.
- Proceed to Binding DNA.
Preparing Lysate from Yeast Cells
Procedure to prepare lysate from yeast cells is described below.
- Set 3 water baths or heat blocks at 37°C, 55°C, and 70°C, respectively.
- Prepare fresh 10 ml Zymolase Buffer (1 M sorbitol, 10 mM sodium EDTA, 14 mM ß-mercaptoethanol).
- Harvest up to 5 x 107 yeast cells by centrifugation. If you are using a frozen cell pellet, proceed to Step 4.
- Resuspend the cell pellet in 500 µl Zymolase Buffer prepared as described above. Add 15 units zymolase (lyticase) enzyme and incubate at 37° C for 1 hour to generate spheroplasts.
- Centrifuge at 3000 x g for 10 minutes at room temperature to pellet the spheroplasts.
- Resuspend the spheroplasts in 180 µl Lysis Buffer (L6) supplied with the kit. Add 20 µl Proteinase K (supplied with the kit). Mix well by vortexing for 5 seconds.
- Incubate the tube at 55°C for 45 minutes.
- Optional: Add 20 µl RNase A (supplied in the kit) to the lysate and incubate at room temperature for 2 minutes.
- Add 10 µl 10% SDS (prepared from 20% SDS supplied with the kit) to the lysate and mix immediately by vortexing for 5 seconds to denature proteins. Add 200 µl Binding Buffer (L3) supplied with the kit to the lysate. Mix well by vortexing for 5 seconds. The SDS precipitates in the presence of guanidine isothiocyanate.
- Incubate at 70°C for 10 minutes to solubilize SDS and promote protein denaturation.
- Add 200 µl 96-100% ethanol to the lysate. Mix well by vortexing for 5 seconds.
- Proceed to Binding DNA.
Guidelines for Lysate Protocol Development
- Lyse the sample using the Lysis Buffer (L6) and Proteinase K supplied with the kit or use specialized lysis buffer or protocols to perform lysis. You may need to optimize lysis conditions prior to DNA purification to obtain the best results for your specific sample.
- Mix the sample with Binding Buffer (L3) and 96-100% ethanol prior to loading the sample onto the column. Always maintain a ratio of 1:1:1 for Lysis Buffer:Binding Buffer:Ethanol to obtain optimal DNA binding.
A general protocol for lysate preparation can be as follows:
- For cells, harvest cells and resuspend cell pellet in 180 µl Lysis Buffer (L6) and 20 µl Proteinase K. Incubate at 55°C until lysis is complete.
For tissues, start with a small amount of minced tissue and add 180 µl Lysis Buffer (L6). Add 20 µl Proteinase K to the sample and mix well. Incubate at 55° C until lysis is complete.
Based on the results obtained using this lysis protocol, you may need to optimize the lysis protocol using different buffers or increasing the amount and time of Proteinase K digestion.
If you already have a lysate, proceed to Step 2. - Optional: Add 20 µl RNase A (supplied with the kit). Incubate at room temperature for 2 minutes.
- Centrifuge the lysate at maximum speed for 5 minutes at room temperature to remove any particulate material, if needed.
- Transfer the supernatant to a fresh microcentrifuge tube and add 10 µl 10% SDS (prepared from 20% SDS supplied with the kit) to the lysate. Add 200 µl Binding Buffer (L3) supplied with the kit to the lysate. Mix well by vortexing for 5 seconds. The SDS precipitates in the presence of guanidine isothiocyanate.
- Incubate at 70°C for 10 minutes to solubilize SDS and promote protein denaturation.
- Add 200 µl 96-100% ethanol to the lysate. Mix well by vortexing for 5 seconds.
- Lysates prepared as described above
- Sterile, DNase-free 1.5 ml microcentrifuge tubes for elution
- Microcentrifuge capable of centrifuging >10,000 x g
- Optional: sterile water, pH 7-8.5, if you are using water for elution
Components supplied with the kit
- Wash Buffers (W4) and (W5)
- Elution Buffer (E1)
- PureLink™ Spin Cartridge in Collection Tubes
- Wash Tubes
- Follow the recommendations below to obtain the best results:
- Perform all centrifugation steps at room temperature
- Perform a 1 minute incubation step with Elution Buffer (E1) or water
- Be sure to perform the recommended wash steps to obtain the best results
- Always use sterile water, pH 7-8.5, if you are using water for elution
1. Remove a PureLink™ Spin Cartridge in a Collection Tube from the package.
3. Centrifuge the cartridge at 12,000 x g for 30 seconds at room temperature.
- Add 500 µl Wash Buffer (W4) supplied in the kit to the cartridge.
- Centrifuge cartridge at room temperature at 12,000 x g for 30 seconds. Discard flow through from the Wash Tube and place cartridge into the Wash Tube.
- Repeat Steps 1-2, once. Discard the flow through.
- Add 500 µl Wash Buffer (W5) with ethanol to the cartridge.
- Centrifuge the cartridge at 12,000 x g for 30 seconds at room temperature. Discard the flow through from the Wash Tube and place the cartridge into the Wash Tube.
- Repeat Steps 4-5, once. Discard the flow through.
- Centrifuge the cartridge at maximum speed for 2 minutes at room temperature to remove any residual Wash Buffer (W5). Discard Wash Tube.
- Proceed to Eluting DNA.
- Place the spin cartridge in a sterile 1.5-ml microcentrifuge tube.
- Add 200 µl of Elution Buffer (E1) or sterile, distilled water (pH >7.0) to the cartridge.
- Incubate at room temperature for 1 minute. Centrifuge the cartridge at maximum speed for 1.5 minute at room temperature.
The tube contains purified DNA.
- To recover more DNA, perform a second elution step with 200 µl Elution Buffer (E1) or sterile, distilled water (pH >7.0) using another sterile 1.5 ml microcentrifuge tube.
- Centrifuge the column at maximum speed for 1.5 minute at room temperature.
The tube contains purified DNA. Remove and discard the cartridge.
- Store the purified DNA at -20° C or use DNA for the desired downstream application.
- For long-term storage, store the purified DNA in Elution Buffer (E1) at -20° C as DNA stored in water is subject to acid hydrolysis.
- To avoid repeated freezing and thawing of DNA, store the purified DNA at 4° C for immediate use or aliquot the DNA and store at -20° C for long-term storage.
Analyzing DNA Yield and Quality