May 13, 2024
Protocol for DNA Extraction from Cowpea
Forked from Protocol for DNA Extraction from Tepary Bean
- 1Boyce Thompson Institute
Protocol Citation: Aparna Srinivasan, Magdalena M Julkowska 2024. Protocol for DNA Extraction from Cowpea. protocols.io https://dx.doi.org/10.17504/protocols.io.81wgbyddqvpk/v1
Manuscript citation:
Semagn K. Leaf tissue sampling and DNA extraction protocols. Methods Mol Biol. 2014;1115:53-67. doi: 10.1007/978-1-62703-767-9_3. PMID: 24415469.
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: August 24, 2022
Last Modified: May 13, 2024
Protocol Integer ID: 69133
Keywords: DNA Extraction, CTAB, Tepary bean
Abstract
Protocol to extract high quality DNA from Cowpea leaves using modified CTAB method.
Materials
Buffer and Chemicals Required
1. CTAB Buffer pH.8
- CTAB- 20 g/L
- Tris- 12.11 g/L
- EDTA- 7.44 g/L
- NaCl - 81.89 g/L
2. RNAse A (10mg/ml)- Dissolve in TNE buffer
- Tris-cl - 10mM
- Nacl - 15 mM
- EDTA - 1 mM
- Reconstitution as per Sigma Aldrich Roche Document (Product code: 10109142001)
RNase A can be dissolved at a concentration of 1 to 10 mg/ml in 10 mM Tris-HCl, pH 7.5, 15 mM NaCl, heated to
100 °C for 15 minutes to inactivate contaminating DNases and cooled slowly to room temperature and dispend
into aliquots. Roche recommends subsequent storage at -15 to -25 °C.
3. Proteinase K (20mg/ml) : Dissolve in TE buffer
4. Phenol:Chloroform kit - Stored at 4 °C
5. Isopropanol (room temperature)
6. 3M Sodium Acetate
7. 70 % Ethanol (Ice-cold)
8. TE Buffer pH.8
- Tris- 10mM
- EDTA- 1mM
9. Agarose
10. Ethidium Bromide
11.Size Marker: 1 kb DNA ladder
Instrument
1. Centrifuge
2. Hot Water Bath
3. Spectrophotometer- Nanodrop
4. Gel Documentation system
Collection of leaf sample
Collection of leaf sample
Collect 1 fully expanded leaf from Cowpea plants in a 50ml centrifuge tube containing five sterile glass beads (5mm diameter) and freeze immediately in liquid nitrogen.
Grind tissue using vortex, ensuring tissue remains frozen. Transfer ~.5 mL of ground tissue to a new 2 mL eppendorf tube containing two 2mm glass beads.
Further beat the tissue by placing in the bead beater for 1 minute in one direction, then 1 minute in the opposite direction.
DNA Extraction
DNA Extraction
Before beginning:
Heat water bath to 65 °C and place CTAB buffer in 65 °C water bath for 20 minutes
Heat incubator to 37 °C
Place 70% ethanol in 4 °C
Make sure RNAse (10mg/mL) is already made and treated
Make sure proteinase K (20mg/mL) is made
*Note on CTAB buffer: Because of high phenol content in the leaf tissue, it may be helpful to add 1% PVP to the CTAB buffer
Add 600 μl of pre-warmed CTAB buffer and 12 ul of proteinase K (20 mg/ml), invert the tubes gently to mix together and incubate the tubes in water bath at 65 °C for 30 min.
Invert the tubes once in every 10 min to homogenize the tissue and buffer.
CTAB buffer added to sample- clear green solution
After 30 min, remove the tubes from water bath and centrifuge at 14000 rpm for 15 min to ensure lysate is cleared.
Transfer cleared lysate of 500 μl to a new 1.5 ml tube. Add 10 ul of RNase (10 mg/ml) and keep at 37 °C for 30 min.
Add equal volume of Chloroform, and vortex well.
Tepary sample with Phenol:Chloroform mixed with sample
Note: for cowpea we use only chloroform, but it looks the same after vortexing
Centrifuge at 14000 rpm for 15 min. Transfer the upper aqueous layer to a new 1.5 ml Ep tube (~350-400 uL)
Transfer upper aqueous layer to a new tube
Do not touch below layers while transferring the aqueous phase.
Repeat the Phenol: Chloroform alcohol step if the aqueous phase is not clear.
Add equal volume of isopropanol, and mix very gently, keep for few minutes to precipitate nucleic acid.
Note: It may take up to 30 minutes of incubation at room temperature to observe precipitate nucleic acid
White strands noticed after adding isopropanol
Centrifuge at 14000 rpm for 10 min.
Pellet can be seen at the bottom.
Discard the supernatant.
Add 300 μl of 3M Sodium Acetate and 500 μl 70 % ethanol and centrifuge at 14000 rpm for 5 min.
Discard the supernatant.
Add 200 μl 70 % Ethanol and centrifuge at 14000 rpm for 5 min.
Discard the supernatant.
Air-dry the pellet, dissolve the pellet in 50 μl TE Buffer.
Place at 4°C overnight, then measure concentration and purity on a Nanodrop
DNA is run on a 0.8% Agarose gel to check whether it is degraded or having RNA contamination.
If RNA is present, treat the samples with RNAse A and precipitate again from phenol:chloroform step 4.
Nucleic acid concentration is measured in Nanodrop, and Ratio of A260/A230 with 1.8-2.0 indicates purity of DNA.
In case the values are <1.8, it indicates contamination such as carbohydrate or phenol.
0.8 % Agarose Gel picture
Store DNA sample at -80 °C until use.