Tris-borate-EDTA buffer

Stellwagen, NC, Apparent Pore Size of Polyacrylamide Gels Comparison of Gels Cast and Run in Tris-acetate-EDTA and Tris-borate-EDTA Buffers, Electrophoresis 19, 1542, 1998. Stellwagen, NC Gelfi, C Righetti, PG, The Free Solution Mobility of DNA, Biopolymers 42, 687, 1997. 

Fig. 17.11. Bottom CGE separation of components of poly U (sigma) in 25% pluronic F127. Top Note the resolution of two contaminants between each of the oligonucleotides from about 15 to 27 nucleotides long in this expanded section of the bottom electropherogram. Electrophoresis was performed in 25% pluronic F127 in tris-borate-EDTA buffer (90 mM tris, 90 mM boric acid, 2 mM Na EDTA, pH 8.3.) (25°C, 500 V cm-1, effective column length 30 cm). Reprinted with permission from Ref. [82],...

It is often convenient to make up buffer solutions at ten times normal strength (10 x) which can then be diluted accordingly. For example lOxTBE is ten times normal strength Tris-borate-EDTA buffer, x 1TBE is a ten-fold dilution with distilled water. 

To assay for the presence of supercoiled, circular mtDNA several approaches can be taken. The simplest method is to run a small part of the entire sample (1/20 of the total), either undigested or digested with a restriction enzyme, on a 0.8% (w/v) agarose gel in 1X TBE (Tris-borate-EDTA buffer) and to visualize the DNA by staining the gel with ethidium bromide. If the DNA is undigested by a... 

Fig. 7. Image of the agarose gel to 2% in which the corresponding bands of control of bromophenol blue and xylenecyanol dyes (1) and DNA/monomaleimido-Nanogold 1.4 nm conjugate (l) are observed. Conditions 80V, electrophoresis time 20 min, using x0.5 Tris-borate-EDTA buffer as running buffer.

Sodium tartrate Succinic acid Succinic anhydride Tetrasodium pyrophosphate Trisodium citrate buffer, gel electrophoresis Tris-borate-EDTA buffer, high pressure equip. 

Fig. 8.12. Urea gradient electrophoresis of (A) native and reduced carboxymethylated bovine RNase A (0.05 M Tris-acetate buffer, pH 4.0) (B) bovine serum albumin (Tris-borate EDTA buffer, pH 8.6). The linear gradient of 0-8 M urea was superimposed on the inverse linear gradient of 15-11% acrylamide (courtesy of Creighton, 1979a).

Tris-borate-EDTA (TBE) buffer (lOx solution) 0.89 M TRIZMA base, 0.89 M H3BO3,20 mM EDTA. Per liter 108 g TRIZMA base, 55 g boric acid, 40 ml 0.5 M ethylenedi-aminetetraacetate (EDTA) solution. 

Standard research-grade agarose is usually sufficient, but special agaroses may be used for specific applications (e.g. high-resolution gels). The electrophoresis buffer is usually prepared and stored as a 10 x concentrated stock. The most commonly used buffer is Tris-borate-EDTA (TBE), or alternatively, one may use Tris-acetate-EDTA (TAE) buffer ... 

Tris-borate (TBE) buffer 5.4 g/liter Tris base, 2.75 g/liter boric acid, 1 mAf EDTA, pH 8.0... 

Tris/Borate/EDTA (TBE) Buffer (0.5 x, working solution)... 

X Tris/borate/EDTA, pH 8.3 DNase-free, RNase-free, and protease-free buffer. 

Running Tris-Borate-EDTA (TBE) buffer (lx) 45 nM Tris-Borate, 1 mM Na EDTA pH 8.2. Store at room temperature. 

Details of DNA electrophoresis methods are given in Table 9.3. The most widely used buffers in gel electrophoresis of nucleic acids are Tris/acetate/EDTA (TAE) and Tris/borate/EDTA (TBE). TBE has the best buffering capacity but the use of TAE tends to result in somewhat sharper bands. For some purposes, such as DNA extraction with glassmilk, TBE should be avoided unless sorbitol is... 

As a standard electrophoresis running buffer for polyacrylamide gels, 1.0-0.5% Tris-borate-EDTA (TBE) is used. To run electrophoresis, use low voltage ranging over 1-8 V/cm to prevent denaturation of small DNA fragments due to high temperature. 

Electrophoresis running buffer Tris-borate-EDTA, Tris-... 

Tris-borate-EDTA (TBE buffer) has more buffering capacity than TAE and provides a better resolution for the separation of small nucleic acid fragments (0.1-3.0kb). A 5x stock TBE solution has the following components ... 

TBC-NF. See Tri butyl citrate TBDMSIM. Seet-Butyidimethylsilyl imidazole TBDPE. See Tetrabromodipentaerythritol TBE TBE Buffer. See Tris-borate-EDTA TBEP TBEP. See Tributoxyethyl phosphate TBGE TBGE. See t-Butyl glycidyl ether... 

High-viscosity gels (e.g., the high-Mw LPA) require either in situ polymerization or very high pressure to replace them in the capillary. In contrast, many of the low-viscosity polymer solutions do not require polymerization by the user. It is necessary only to dissolve a known amount of the polymer in basic buffers, such as tris-borate-EDTA (TBE) or 3-[[tris(hydroxymethyl)methyl]amino] propane-sulfonic acid (TAPS) (pH 8-9), or isoelectric buffers, such as His or Lys. Because the low conductivity of the isoelectric buffers minimizes Joule heating, high electric fields can be used for rapid separation. For oligonucleo-... 

Tris-borate-EDTA (TBE) buffer (5x) 445 mM Tris, 445 mM borate, 10 mM EDTA, prepared with RNase-ffee H2O. 

X TBE (Tris, borate, EDTA) electrophoresis buffer 445 mM Tris base (54.0 g). 445 mM boric acid (27.5 g), and 10 mM EDTA (3.72 g Na2EDTA2H20), adjust to 1 litre with distilled water... 

C. Reagents for gel electrophoresis (Acrylamide/BIS [19 1], urea, ammonium persulfate, M MA .A -tetramethylethylene diamine [TEMED], lOX Tris-Borate-EDTA [TBE] buffer [pH 8.3], bromphenol blue) and the cation-exchange resin AG 50W-X12 hydrogen form (100-200 mesh). 

Photopolymerizable formulations of gels from acrylamide and bis-acrylamide powder were prepared by combining monomer, crosslinker, and 7.2 g urea (a denaturant additive commonly used in DNA electrophoresis) in deionized water to make a total volume 16 mL. A 4 mL volume of lOx Tris-Borate-EDTA (TBE) electrophoresis buffer (Extended Range TBE Buffer Bio-Rad Laboratories, Hercules, CA) was then added to bring the total volume to 20 mL (6 M final urea concentration). Immediately before each experiment, 3 pL of a freshly prepared (10% w/v) aqueous ammonium persulfate (APS) solution was added, along with 2.5 pL of a (0.4% w/v) aqueous riboflavin solution, to serve as a photoinitiator... 

List of Abbreviations PCR, polymerase chain reaction RT-PCR, reverse transcription polymerase chain reaction DNA, deoxyribonucleic acid RNA, ribonucleic acid RNase, ribonuclease mRNA, messenger RNA GABAa, y-aminobutyric acid type A cRNA, copy RNA dNTPs, deoxy nucleoside triphosphates MMLV, Mouse Moloney murine leukemia vims RT, reverse transcriptase bp, base pair Tm, melting temperature DEPC, diethylpyrocarbonate OD, optical density mL, milliliter SA-PMPs, streptavidin paramagnetic particles dT, deoxy thymidine DTT, dithiothreitol DNase, deoxyribonuclease RNasin, ribonuclease inhibitor UV, ultraviolet TBE, Tris-borate, 1 mM EDTA EDTA, ethylenediaminetetraacetic acid Buffer RET, guanidium thiocyanate lysis buffer PBS, phosphate buffered saline NT2, Ntera 2 neural progenitor cells... 

The species to be compared are loaded in 6% Ficoll (w/v) onto an 8% or 10% polyacrylamide gel with 29 1 monomer bisacrylamide. We generally use 90 mM Tris—borate (pH 8.3) buffer containing either EDTA or added metal salts. Electrophoresis is typically performed for 1—2 days at 5 V/cm at room temperature. When salts are included in the electrophoresis buffer, this must be recirculated between the cathodic and anodic reservoirs at a rate of 1 L/h. This may require a little modification of commercial gel electrophoresis apparatus. Our RNA species generally include at least one strand that is radioactively [5/-32P] -labeled. When the electrophoresis is complete the gel is dried onto Whatman 3MM paper and exposed to storage phosphor plates at 4 °C followed by phosphorimaging to provide a gel image. 

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