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BUFFERS
Introduction to Buffers......................................1
Importance of Buffers.........................................1
pH..............................................................1
pK a ..............................................................1
Buffers and Buffering Range..........................2
Choosing Buffers...........................................2
Biological Buffers.............................................2
General Considerations.................................3
Practical Considerations................................3
Electrophoresis Buffers......................................4
General Considerations.................................4
Nucleic Acid Electrophoresis.........................4
Protein Electrophoresis..................................4
Molecular Biology Buffers..................................5
Membrane Transfer.......................................5
Enzymatic Reactions.....................................5
Nucleic Acid & Protein Purification....................5
Ultra Pure Buffers.............................................6
Buffers for Blotting............................................6
Zwitterionic Buffers............................................7
1
Introduction to Buffers (Part 2)
Biological Buffers
Table 1. Common Biological
Buffers and their Associated
pKa Values
BUFFER pKa at 25C
2
Biological Buffers
The determination that the precursor com-
pounds required for the synthesis of some
General Considerations:
zwitterionic buffers were carcinogenic led
to the synthesis of hydroxyl derivatives of
the buffers by Ferguson et al. (1980).
Many biological systems generate and
These compounds were found to be com-
consume hydrogen ions as by-products
patible to a number of biological systems
of their cellular reactions, yet respond
while expressing better chemical stability
dramatically to small changes in environ-
and improved solubility over the earlier
mental pH. To maintain a physiologically
Good’s buffers. The most useful hydroxyl
relevant pH (pH = 6.0-8.5) under such
buffers are listed in Table 3 with their
dynamic conditions, in vitro biological sys-
associated pKa values. Ferguson et al.
tems must be stabilized by the incorpora-
(1980) found that many chemical proper-
tion of buffers that undergo reversible
ties of the new zwitterionic buffers were
protonation. Many early buffers were not
advantageous to biological systems.
suitable for biological applications be-
cause the pH of the solutions depended
upon the concentration of the ionic com- Practical Considerations:
ponents and the temperature of the solu-
tion. Moreover, the pKa values of many of
these buffers were outside physiological Because many zwit-
pH ranges. For illustration, many early terionic compounds Biological Buffers Code Size
biological buffers and their associated exhibit effects upon Boric Acid 0588 500 g
pKa values are summarized in Table 1. biological systems 1 kg
In 1966, Good et al. described 12 buffers which are unrelated 2.5 kg
which were useful for most common bio- to their pH stabiliza- Citric Acid, Trisodium Dihydrate 0101 1 kg
logical applications, having pKa values tion properties, fac- 2.5 kg
between 6.1 and 8.4. Most of these buff- tors other than pKa Formic Acid 0961 Call
ers were zwitterionic, capable of possess- need to be consid-
Glycine 0167 1 kg
ing both positive and negative charges. ered when choosing
5 kg
The nature of the original Good’s buffers a biological buffer. It
is recommended Imidazole 0527 10 g
made them particularly suitable for bio-
logical applications because their buffer- that biological inves- 50 g
ing capacity was independent of tempera- tigations employ a 100 g
ture and concentration. They were very wide range of buff- Phosphoric Acid 0239 Call
soluble in water but poorly soluble in ers or pH conditions Succinic Acid, Disodium Salt, Anhydrous E288 Call
organic solvents. This property made it to verify that the ob- Succinic Acid, Disodium Salt, Hexahydrate 0477 Call
difficult for the buffers to traverse cellular servations are not Succinic Acid, Free Acid 0165 500 g
membranes or accumulate within bio- distorted by the 2.5 kg
logical systems. The reduced ion effects choice of buffer. Be- Tris Acetate 0189 100 g
observed with these buffers allowed the fore eukaryotic cells
Tris Hydrochloride 0234 500 g
preparation of solutions from concentrated are used in experi-
1 kg
stocks with minimal pH effects from the ments, the survival of
dilution of buffer components. A list of the cells should be
these zwitterionic buffers and their pKa tested over a seven-day period at both low
values are summarized in Table 2. and high density seeding. At low densi- Table 3. Hydroxyl Zwitterionic Buffers and
ties, cells will be extremely sensitive to Associated pKa Values & Useful pH Ranges
Table 2. Zwitterionic Buffers and their
low levels of toxicity which may occur in BUFFER pKa at 25C Useful pH Range
certain buffers. Growth and viability of the
Associated pKa Values and Useful pH Ranges MOPSO 6.88 6.20-8.60
cells at higher densities (or after 4-5 days
BUFFER pKa at 25C Useful pH Range growth from a less concentrated cell popu-
DIPSO 7.60 7.00-8.20
HEPPSO 7.80 7.10-8.50
MES 6.15 5.50-6.50 lation) will demonstrate the ability of the POPSO 7.80 7.20-8.50
Bis-Tris 6.50 5.80-7.30 buffer to support cell metabolism at higher AMPSO 9.00 8.30-9.70
PIPES, Na Salt 6.80 6.10-7.50 cell densities and maintain pH at increased CAPSO 9.60 8.90-10.30
ACES 6.88 6.00-7.50 metabolite concentration. This is an im-
MOPS 7.20 6.50-7.90 portant characteristic of a maintenance
TES 7.40 6.80-8.20
HEPES, Na Salt 7.55
buffer for cells being used for weekly sub-
6.80-8.20
HEPPS 8.00 7.30-8.70 culturing.
Tricine 8.15 7.80-8.80
Bicine 8.35 7.60-9.00
CHES 9.50 8.60-10.00
CAPS 10.40 9.70-11.10
3
Electrophoresis Buffers
of the DNA bands in sequencing gels. and ionic components in buffers, native
General Considerations: gel electrophoresis of proteins requires a
Gel electrophoresis of RNA presents
buffer choice based upon the pI of the
some unique problems that are not ob-
protein. For this reason, there is no single
served with DNA
Effective separation of nucleic acids and samples. The pro-
proteins by agarose or polyacrylamide gel pensity of RNA to Electrophoresis Buffers Code Size
electrophoresis depends upon the effec- form intramolecular TAE Buffer, 25X Liquid Concentrate 0796 1.6 L
tive maintenance of pH within the matrix. secondary structures TAE Buffer, Powder 0912 40 L
Therefore, buffers are an integral part of requires that the mol- TAE Buffer, 25X Ready-PackTM 0912 2 pk
any electrophoresis technique. In addi- ecules be thoroughly TBE Buffer, Powder* 0478 40 L
tion to their role in the maintenance of pH, denatured before TBE Buffer, 10X Ready-PackTM 0478 2 pk
buffers provide ions which are needed for application to the gel
TBE Buffer, 10X Liquid Concentrate 0658 4L
electrophoretic migration. and maintained in a
TBE Buffer, 5X Liquid Concentrate J885 1L
reduced condition
4L
throughout electro-
Nucleic Acid Electrophoresis: phoretic separation. TBE Buffer, 10X Ready-PackTM J490 2 pk
Denaturation may be EZ TBE BufferTM, 50X Concentrate J752 10x10 ml
(Each 10 ml Tablet Prepares 500 ml 1X TBE)
performed in 60-
Electrophoretic separation of DNA is domi- EZ TBE BufferTM, 50X Concentrate J755 10x20 ml
85% formamide so- (Each 20 ml Tablet Prepares 1 Liter 1X TBE)
nated by the Tris-based buffers. Tris- lution at 65C, but 0251 40 L
TG Buffer, Powder
Acetate EDTA (TAE; 0.04 M Tris-Acetate, buffering is required
TG Buffer, 10X Ready-PackTM 0251 2 pk
0.001M EDTA, pH = 8.0) is less expensive, or the RNA will de-
but not as stable as Tris-Borate-EDTA. TG Buffer, 10X Liquid Concentrate 0307 4L
grade. Often, 0.5X
TAE gives better resolution of DNA bands TBE is used to buffer TG-SDS Buffer, Powder 0147 40 L
in short electrophoretic separations and RNA samples during TG-SDS Buffer, 10X Ready-PackTM 0147 2 pk
is often used when subsequent DNA iso- denaturation. TG-SDS Buffer, 10X Liquid Concentrate 0783 4L
lation from the matrix is desired. Tris- TG-SDS Buffer, 5X Liquid Concentrate E696 500 ml
RNA electrophoresis
requires the use of TT Buffer, 10X Ready-PackTM E461 1 pk
agarose gels con- TT Buffer, 10X Liquid Concentrate E471 1L
taining a denaturing TT-SDS Buffer, 10X Ready-PackTM E457 1 pk
agent such as form- TT-SDS Buffer, 10X Liquid Concentrate E449 1L
aldehyde or glyoxal NOTE: 1 Ready-Pack prepares 1 L of the respective buffer concentrate.
for maximum reso- *TBE Buffer (0478) is prepared using EDTA, Free Acid (0322). All other TBE Buffers are prepared using EDTA,
Disodium Dihydrate (0105).
lution of bands. Buff- buffer system for native gel electrophore-
ers are required to maintain a steady pH sis of proteins.
because the denaturing agents decom-
SDS is an anionic detergent that is added
pose during electrophoresis and alter the
to samples to denature the proteins and
pH of the gel. RNA is unstable in slightly
produce a uniform negative charge on the
alkaline solution, so lower pH ranges are
molecules prior to denaturing protein gel
required in RNA gels. Thus, Tris-based
electrophoresis. Treatment with SDS al-
buffers (pKa = 8.3) are unsuitable for RNA
Borate-EDTA (TBE; 0.089M Tris Base, lows proteins to migrate through the elec-
electrophoresis. MOPS buffer has a pKa =
0.089M Boric Acid, 0.002M EDTA, pH = tric field according to their approximate
7.2 and is the buffer of choice for denatur-
8.3) is used for polyacrylamide gel elec- mass. Because the rate of protein migra-
ing gel electrophoresis of RNA. MOPS is
trophoresis of smaller molecular weight tion depends upon interactions with ionic
available in a free acid and sodium salt
DNA (MW < 2000) and slab agarose gel components of the buffer, even small
form and works exceptionally well at con-
electrophoresis of larger DNA where high changes in the pH of a buffer may alter the
centrations of 20mM.
resolution is not essential. association of SDS with the protein and
influence the molecular weight calcula-
DNA sequencing requires the addition of
urea to polyacrylamide gels to maintain tions as judged by denaturing gel electro-
Protein Electrophoresis: phoresis. The addition of SDS (0.1% w/v)
the single stranded, denatured state of
to Tris-Glycine (0.025M Tris Base; and
DNA required for reproducible resolution
of the individual DNA bands. TBE has 0.25M Glycine, pH = 8.3) or Tris-Tricine
Unlike nucleic acids, proteins exhibit both (0.1M Tris Base, and 0.1M Tricine) pro-
been the traditional buffer system for DNA anionic and cationic characteristics which duces an excellent buffering system for
sequencing projects though the borate are highly dependent upon the pH of the
component of the buffer is known to inter- denaturing protein gels.
medium for their biochemical activity.
act with glycerol which may be present in Small changes in the pH of a buffer can
DNA samples after treatment with DNA affect both the structure and the net charge
polymerase or restriction enzymes. This of a protein molecule. Because of the
interaction of borate with glycerol can dynamic relationship between a protein
cause distortion in the spacing and shape
4
Molecular Biology Buffers
in the transfer buffer. Without buffers, the graphic desalting, extraction or dialysis
Membrane Transfer: directional migration of macromolecules are recommended to minimize the ionic
and the reproducible transfer of larger crossover between buffers and maximize
molecules would be haphazard, at best. enzymatic activity.
The separation of proteins or nucleic ac- Recommended buffers for most common
ids by gel electrophoresis and subse- blotting techniques are shown in Table 4.
Nucleic Acid and Protein
quent transfer of macromolecules to ni-
Isolation/Purification:
trocellulose or nylon membranes allows
scientists to study molecular interactions Enzymatic Reactions:
between defined subsets of molecules. Many of the common specialty solutions
Many characteristics of buffers that are which are used for the isolation and purifi-
important for gel electrophoresis are also Many biochemical reactions that are used cation of nucleic acids are readily avail-
important during direct blotting or transfer in molecular biology require specialized able. These solutions include RNase-
techniques, especially since the advent of buffers and salt optima. The general free sodium acetate for the precipitation of
electrophoretic transfer protocols. The rules of choosing buffers (see Introduc- non-degraded RNA, NaOH-SDS solution
binding of macromolecules to mem- tion) apply when a new experimental tech- for the alkaline lysis method of plasmid
branes is charge-dependent and relies nique is being developed. Often, zwitteri- purification from bacterial cells, sodium
upon the maintenance of a consistent pH onic buffers are not required and many of chloride and potassium acetate for the
the common biologi- precipitation of purified DNA, and nu-
cal buffers listed in clease-free water for purification and bio-
Molecular Biology Buffers & Reagents Code Size Table 1 may be em- chemical work with all nucleic acids. So-
20% Glucose E545 100 ml ployed. An under- lutions used in protein purification and
20% Sucrose E543 100 ml standing of the pH isolation are also available, including gly-
Ammonium Acetate, 10M J515 100 ml optima for a specific cine for use in protein gel electrophoresis
250 ml enzyme and knowl- and 10X TG-SDS Liquid for protein blot-
edge of the ionic prod- ting.
Calcium Chloride, 1M Sterile E506 100 ml
ucts of the reaction
500 ml
should be consid-
Complete Cell Lysis Solution E203 5 ml
ered when choosing
EDTA, 0.5M pH 8.0 E177 Call the buffer. Multiple
GTE (TE-Glucose) E524 100 ml buffers should be
500 ml tested to verify that
Magnesium Chloride, 1M Sterile E525 100 ml the results are not an
500 ml artifact of the buffer
Magnesium Sulfate, 1M Sterile E541 100 ml system. When buff-
NaOH/SDS Lysis Solution J611 500 ml ers change between
protocols, chromato-
Potassium Acetate Solution E130 500 ml
Potassium Acetate, 1M J616 250 ml
SM Buffer J614 500 ml
Sodium Acetate, 2M, pH 4.2 E502 100 ml
Sodium Acetate, 3M, pH 5.2 E521 100 ml
Sodium Acetate, 3M, pH 7.0 J618 100 ml
Table 4. Buffers for Common Blotting Techniques
Sodium Chloride, 5M E529 100 ml
Technique Recommended Buffer(s)a
500 ml
STET Buffer J613 500 ml Proteins
E112 100 ml Transfer to Membranes Tris-Glycine or Tris-Tricine (pg. 18.64)
TE Buffer
Immunoblotting Phosphate Buffered Saline (PBS) (pg. 18.70)
500 ml Nucleic Acids
TEN (STE) J384 Call Transfer to Membranes Sodium Chloride-Sodium Citrate (pg. 9.38)
TM Buffer J615 500 ml Southern Blotting Sodium Chloride-Sodium Citrate (pg. 9.34)
Northern Blotting Sodium Chloride-Sodium Citrate (pg. 7.46)
TNT Buffer J612 500 ml
Tris Base 0826 500 g a
Additional solutions and buffers may be required to prepare membranes for blotting, to block nonspecific
binding sites or to remove unbound macromolecules. These solutions may vary with the membrane type and
1 kg manufacturer. The manufacturer’s recommended buffers should be used for such ancillary procedures. Cited
protocols are described in Sambrook, Fritsch and Maniatis (1989); page #’s are in parentheses after each
Tris, 0.1M pH 7.4 E553 100 ml buffer.
500 ml
Tris, 1M pH 8.0 E199 100 ml
500 ml
Water, Nuclease-Free E476 500 ml
5
Ultra Pure Buffers
For molecular and biochemical protocols,
General Considerations: buffers should be free of proteinases,
nucleases, and macromolecules, low in
free metals, and devoid of other macro-
molecules that can interfere with the direct
All cellular and molecular protocols which
analysis of the experimental data.
depend upon buffers should use high
quality reagents. For
most biological or
biochemical applica- Ultra Pure Buffer Components Code Size
tions, buffers should
EDTA, Disodium Salt 0105 500 g
not absorb light be-
1 kg
tween the wave-
lengths of 240 and 2.5 kg
700 nm. EDTA, Free Acid 0322 500 g
1 kg
For biological appli-
Tris Base 0497 500 g
cations, especially
1 kg
eukaryotic tissue cul-
ture, they should be 5 kg
free of endotoxin and
mycoplasma, low in free metal ions, and REFERENCES:
Good, N.E., et al. Biochemistry 5:467 (1966).
preferably contain an indicator dye to moni- Ferguson, W.J., et al. Anal. Biochem. 104:300 (1980).
tor pH changes visually. Sambrook, J., Fritsch, E.F. and Maniatis, T., Molecular Cloning: A Laboratory Manual, 2nd edition, Cold Spring Harbor Press (1989).
6
Zwitterionic Buffers
General Considerations:
7
TM
BUFFERS
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