Sodium acetate buffer
Table Of Contents
Introduction
Various authors (Gomori, 1955; Pearse 1980) are cited as a source for buffer composition, although it should be said that probably the first author specifying this buffer was Walpole (1914). However, the composition of the cited buffers is really similar. Thanks to the pH variability and composition of available compounds, it is sometimes the first choice for many reactions.
The sodium acetate buffer could be replaced with various other buffers (depending on application) as mentioned below.
- For use in animal physiology / medical use, replacement by sodium bicarbonate buffer is sometimes possible (Neavyn et al., 2013).
- In enzymology, it could be replaced by citrate, which has a similar range of pH but lowers buffering capacity.
- In nucleic acid precipitation protocols by sodium chloride (preferred in detergents),
- Ammonium acetate (in high dNTPs, without kinases),
- Potassium acetate (for cell-free translation, avoid SDS),
- Lithium chloride (useful in RNA, avoid in translation) (Genelink).
- When using acetate for protein crystallization, it has as wide application as ammonium sulfate but it was found to be less effective than sodium malonate (Mcpherson, 2001).
Applications
- This buffer is used in several enzymes using protocols enabling them to work in mildly acidic pH.
- Other important protocols utilizing sodium acetate buffer are purification and precipitation of nucleic acids, protein crystallization, and staining of gels after protein gel electrophoresis.
Composition
| Reagent | Molecular weight | 1X molarity | Add for 500ml of 1X | Add for 1L of 1X |
|---|---|---|---|---|
| Sodium acetate | 82.03 (anhydrous) | 100 mM | 4.1 g | 8.2 g |
| Sodium acetate | 136.08 (trihydrate) | 100 mM | 6.8 g | 13.6 g |
| Acetic acid (glacial) | 60.05 | 100 mM | 3.0 g (2.9 ml) | 6.0 g (5.8 ml) |
Table 1. For enzymology or chromatography.
| Reagent | Molecular weight | 1X molarity | 10X molarity | Add for 100 ml of 10X | Add for 1L of 10X |
|---|---|---|---|---|---|
| Sodium acetate | 82.03 (anhydrous) | 300 mM | 3 M | 26.6 g | 246 g |
| Sodium acetate | 136.08 (trihydrate) | 300 mM | 3 M | 40.8 g | 408 g |
Table 2. For precipitation.
| Reagent | Molecular weight | 1X molarity | 10X molarity | Add for 100 ml of 10X | Add for 1L of 10X |
|---|---|---|---|---|---|
| Sodium acetate | 82.03 (anhydrous) | 400 mM | 4 M | 32.8 g | 328 g |
| Sodium acetate | 136.08 (trihydrate) | 400 mM | 4 M | 54.4 g | 544 g |
Table 3. For staining.
| Reagent | Molecular weight | 1X molarity | Add for 100 ml of 1X | Add for 1 l of 1X |
|---|---|---|---|---|
| Acetic acid (glacial) | 60.05 | 75 mM | 0.435 g (0.45 ml) | 4.35 g (4.5 ml) |
| Ethanol | 46.07 | -0.3 | 30 ml | 300 ml |
| Glutaraldehyde (25%) | 100.12 | 50 mM (0.5%) | 2 ml | 20 ml |
| Sodium thiosulfate | 158.11 | 6.3 mM (0.1%) | 0.1 g | 1 g |
Table 4. Non-factorable compounds.
pH
- For enzymology and chromatography: In the range from 3.6 to 5.6.
- For precipitation of nucleic acids: 3 M stock with pH from 5.2 to 5.5. pH is adjusted by glacial acetic acid / NaOH.
- For protein crystallization: Various pH used based on the need of protein. Some reported pHs are 4.0-4.9 for x-ray crystallography (Dessau and Modis, 2011) and 7.2 (Mcpherson, 2001). pH is adjusted by glacial acetic acid / NaOH.
- For gel silver staining: 0.4 M solution with pH 6.0 (Heukeshoven and Dernick, 1988).
Preparation
1. For enzymology and chromatography, 1 L of the final solution:
Firstly, prepare the stock solution of sodium acetate:
Add about ¾ of the final volume of distilled water to a glass beaker.
Prepare the exact amounts of sodium acetate (either anhydrous or trihydrate) using balance and put it into the water to dissolve. A magnetic stirrer can be used to speed up the process.
After the acetate is dissolved, add distilled water to the final volume.
Secondly, prepare the stock of acetic acid with similar steps:
Add about ¾ of the final volume of distilled water to the glass beaker.
Prepare the exact amounts of acetic acid (glacial) volumetrically (or gravimetrically) and put it into the water to mix well.
Add distilled water to the final volume.
Autoclave the solutions.
In the next step, mix specific amounts of sodium acetate solution and acetic acid solution according to the table below to obtain the buffer of the required pH.
2. For precipitation and staining
Firstly, prepare stock (10x) of sodium acetate:
Add about ¾ of the final volume of distilled water to a glass beaker.
Prepare the exact amounts of sodium acetate (anhydrous or trihydrate) using balance and put it into the water to dissolve. A magnetic stirrer can be used to speed up the process.
After the sodium acetate is dissolved, adjust the pH with acetic acid (glacial) or NaOH.
Add distilled water to the final volume.
(It is sometimes recommended to let the solution stay for a day and recheck the pH / adjust again).
Autoclave this solution/filter it.
If you are willing to use this buffer for precipitation, you just end with preparation here, and you can dilute your stock solution 10x when needed. Still, for staining, the solution contains additional compounds, which will be added in the next step.
In the last step, prepare the solution for staining use (1L):
Mix ethanol (300 ml) with sodium acetate stock (100 ml) solution and add distilled water to the final volume. (Recheck the pH; It should be 6,0; adjust with glacial acid)
Add the exact volume of glutaraldehyde (Toxic!) and the exact amount of sodium thiosulfate. Let it dissolve and mix well.
Storage
It can be stored at room temperature or at 4° C (better for less concentrated solutions to avoid precipitation). If you added thiosulfate, store it only for a few days.
Points to be noted
- Glutaraldehyde is a toxic compound, similar to other aldehydes. Wear gloves and glasses. Omit skin or mucosa contact.
- Glacial acid is a highly concentrated acetic acid; thus, you should treat it as carefully as with strong acids. Omit any skin or eye contact.
Reference
- Acetate Buffer (pH 3.6 to 5.6) Preparation and Recipe | AAT Bioquest.
- Dessau, M. A., & Modis, Y. (2011). Protein crystallization for X-ray crystallography. JoVE (Journal of Visualized Experiments), (47), e2285.
- Gomori, G. (1955). [16] Preparation of buffers for use in enzyme studies.
- Heukeshoven, J., & Dernick, R. (1988). Improved silver staining procedure for fast staining in PhastSystem Development Unit. I. Staining of sodium dodecyl sulfate gels. Electrophoresis, 9(1), 28-32.
- DNA & RNA Precipitation Solutions.
- Mcpherson, A. (2001). A comparison of salts for the crystallization of macromolecules. Protein Science, 10(2), 418-422.
- Neavyn, M. J., Boyer, E. W., Bird, S. B., & Babu, K. M. (2013). Sodium acetate as a replacement for sodium bicarbonate in medical toxicology: a review. Journal of Medical Toxicology, 9(3), 250-254.
- Pearse, A. G. E. (1980). Histochemistry, Vol. 1–2: Theoretical and applied. Churchill Livingstone, Edimburgh, London.
- Snyder, L. R., Kirkland, J. J., & Glajch, J. L. (2012). Practical HPLC method development. John Wiley & Sons.
- Sodium acetate buffer solution for molecular biology (Sigma-Aldrich).
- Walpole, G. S. (1914). CCXXXIII.—Hydrogen potentials of mixtures of acetic acid and sodium acetate. Journal of the Chemical Society, Transactions, 105, 2501-2521.