Chemicals Commonly Used in Biochemistry and Molecular Biology and Their Properties

Authored by: Roger L. Lundblad

Biochemistry and Molecular Biology Compendium

Print publication date:  June  2007
Online publication date:  June  2007

Print ISBN: 9781420043471
eBook ISBN: 9781420043488
Adobe ISBN:

10.1201/9781420043488.ch3

 

Abstract

Tunnicliff, G. and Smith, J.A., Competitive inhibition of gamma-aminobutyric acid receptor binding by N-hydroxyethylpiperazine-N′-2-ethanesulfonic acid and related buffers, J. Neurochem. 36, 1122–1126, 1981; Chappel, D.J., N-[(carbamoylmethyl) amino] ethanesulfonic acid improves phenotyping of α-1-antitrypsin by isoelectric focusing on agarose gel, Clin. Chem. 31, 1384–1386, 1985; Liu, Q., Li, X., and Sommer, S.S., pk-matched running buffers for gel electrophoresis, Anal. Biochem. 270, 112–122, 1999; Taha, M., Buffers for the physiological pH range: acidic dissociation constants of zwitterionic compounds in various hydroorganic media, Ann. Chim. 95, 105–109, 2005.

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Chemicals Commonly Used in Biochemistry and Molecular Biology and Their Properties

 

Tunnicliff, G. and Smith, J.A., Competitive inhibition of gamma-aminobutyric acid receptor binding by N-hydroxyethylpiperazine-N′-2-ethanesulfonic acid and related buffers, J. Neurochem. 36, 1122–1126, 1981; Chappel, D.J., N-[(carbamoylmethyl) amino] ethanesulfonic acid improves phenotyping of α-1-antitrypsin by isoelectric focusing on agarose gel, Clin. Chem. 31, 1384–1386, 1985; Liu, Q., Li, X., and Sommer, S.S., pk-matched running buffers for gel electrophoresis, Anal. Biochem. 270, 112–122, 1999; Taha, M., Buffers for the physiological pH range: acidic dissociation constants of zwitterionic compounds in various hydroorganic media, Ann. Chim. 95, 105–109, 2005.

 

Burton, R.M. and Stadtman, E.R., The oxidation of acetaldehyde to acetyl coenzyme A, J. Biol. Chem. 202, 873–890, 1953; Gruber, M. and Wesselius, J.C., Nature of the inhibition of yeast carboxylase by acetaldehyde, Biochim. Biophys. Acta 57, 171–173, 1962; Holzer, H., da Fonseca-Wollheim, F., Kohlhaw, G., and Woenckhaus, C.W., Active forms of acetaldehyde, pyruvate, and glycolic aldehyde, Ann. N.Y. Acad. Sci. 98, 453–465, 1962; Brooks, P.J. and Theruvathu, J.A., DNA adducts from acetaldehyde: implications for alcohol-related carcinogenesis, Alcohol 35, 187–193, 2005; Tyulina, O.V., Prokopieva, V.D., Boldyrev, A.A., and Johnson, P., Erthyrocyte and plasma protein modification in alcoholism: a possible role of acetaldehyde, Biochim. Biophys. Acta 1762, 558–563, 2006; Pluskota-Karwatka, D., Pawlowicz, A.J., and Kronberg, L., Formation of malonaldehyde-acetaldehyde conjugate adducts in calf thymus DNA, Chem. Res. Toxicol. 19, 921–926, 2006.

 

Banfield, A.G., Age changes in the acetic acid-soluble collagen in human skin, Arch. Pathol. 68, 680–684, 1959; Steven, F.S. and Tristram, G.R., The denaturation of acetic acid-soluble calf-skin collagen. Changes in optical rotation, viscosity, and susceptibility towards enzymes during serial denaturation in solutions of urea, Biochem. J. 85, 207–210, 1962; Neumark, T. and Marot, I., The formation of acetic-acid soluble collagen under polarization and electron microscrope, Acta Histochem. 23, 71–79, 1966; Valfleteren, J.R., Sequential two-dimensional and acetic acid/urea/Triton X-100 gel electrophoresis of proteins, Anal. Biochem. 177, 388–391, 1989; Smith, B.J., Acetic acid-urea polyacrylamide gel electrophoresis of proteins, Methods Mol.Biol. 32, 39–47, 1994; Banfield, W.G., MacKay, C.M., and Brindley, D.C., Quantitative changes in acetic acid-extractable collagen of hamster skin related to anatomical site and age, Gerontologia 12, 231–236, 1996; Lian, J.B., Morris, S., Faris, B. et al., The effects of acetic acid and pepsin on the crosslinkages and ultrastructure of corneal collagen, Biochim. Biophys. Acta. 328, 193–204, 1973; Canto, M.I., Chromoendoscopy and magnifying endoscopy for Barrett’s esophagus, Clin.Gastroenterol.Hepatol. 3 (7 Suppl. 1), S12–S15, 2005; Sionkowska, A., Flash photolysis and pulse radiolysis studies on collagen Type I in acetic acid solution, J. Photochem. Photobiol. B 84, 38–45, 2006.

 

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Calcium Chloride

CaCl2; Various Hydrates

110.98

Anhydrous form as drying agent for organic solvents, variety of manufacturing uses; meat quality enhancement; therapeutic use in electrolyte replacement and bone cements; source of calcium ions for biological assays.

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Chloroform

Trichloromethane

177.38

Used for extraction of lipids, usually in combination with methanol.

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Mitchell, P., Crystallization of Congo red, Nature 165, 772–773, 1950; Helander, S., The distribution of Congo red in the tissues, Acta. Med. Scand. 138, 188–190, 1950; Hahn, N.J., The Congo red reaction in bacteria and its usefulness in the identification of rhizobia, Can. J. Microbiol. 12, 725–733, 1966; R.W. Horobin and J.A. Kiernan, Eds., Conn’s Biological Stains, 10th ed., Bios Scientific Publishers, Oxford, UK, 2002; Inouye, H. and Kirschner, D.A., Alzheimer’s beta-amyloid: insights into fibril formation and structure from Congo red binding, Subcell. Biochem. 38, 203–224, 2005; Inestrosa, N.C., Alvarez, A., Dinamarca, M.C. et al., Acetylcholinesterase-amyloid-beta-protein interaction: effect of Congo red and the role of the Wnt pathway, Curr. Alzheimer Res. 2, 301–306, 2005; Wu, X., Sun, S., Guo, C. et al., Resonance light scattering technique for the determination of proteins with Congo red and Triton X-100, Luminescence 21, 56–61, 2006; Halimi, M., Dayan-Amouyal, Y., Kariv-Inbal, Z. et al., Prion urine comprises a glycosaminoglycan-light chain IgG complex that can be stained by Congo red, J. Virol. Methods 133, 205–210, 2006; Bely, M. and Makovitzky, J., Sensitivity and specificity of Congo red staining according to Romhanyi. Comparison with Puchtler’s or Bennhold’s methods, Acta Histochem. 108, 175–180, 2006; McLaughlin, R.W., De Stigter, J.K., Sikkink, L.A. et al., The effects of sodium sulfate, glycosaminoglycans, and Congo red on the structure, stability, and amyloid formation of an immunoglobulin light-chain protein, Protein Sci. 15, 1710–1722, 2006; Cheung, S.T., Maheshwari, M.B., and Tan, C.Y., A comparative study of two Congo red stains for the detection of primary cutaneous amyloidosis, J. Am. Acad. Dermatol. 55, 363–364, 2006.

 

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Vesterberg, O., Hansen, L., and Sjosten, A., Staining of proteins after isoelectric focusing in gels by a new procedure, Biochim. Biophys. Acta 491, 160–166, 1977; Micko, S. and Schlaepfer, W.W., Metachromasy of peripheral nerve collagen on polyacrylamide gels stained with Coomassie Brilliant Blue R-250, Anal. Biochem. 88, 566–572, 1978; Osset, M., Pinol, M., Fallon, M.J. et al., Interference of the carbohydrate moiety in Coomassie Brilliant Blue R-250 protein staining, Electrophoresis 10, 271–273, 1989; Pryor, J.L., Xu, W., and Hamilton, D.W., Immunodetection after complete destaining of Coomassie blue-stained proteins on immobilon-PVDF, Anal. Biochem. 202, 100–104, 1992; Metkar, S.S., Mahajan, S.K., and Sainis, J.K., Modified procedure for nonspecific protein staining on nitrocellulose paper using Coomassie Brilliant Blue R-250, Anal. Biochem. 227, 389–391, 1995; Kundu, S.K., Robey, W.G., Nabors, P. et al., Purification of commercial Coomassie Brilliant Blue R-250 and characterization of the chromogenic fractions, Anal. Biochem. 235, 134–140, 1996; Choi, J.K., Yoon, S.H., Hong, H.Y. et al., A modified Coomassie blue staining of proteins in polyacrylamide gels with Bismark brown R, Anal. Biochem. 236, 82–84, 1996; Moritz, R.L., Eddes, J.S., Reid, G.E., and Simpson, R.J., S-pyridylethylation of intact polyacrylamide gels and in situ digestion of electrophoretically separated proteins: a rapid mass spectrometric method for identifying cysteine-containing peptides, Electrophoresis 17, 907–917, 1996; Choi, J.K. and Yoo, G.S., Fast protein staining in sodium dodecyl sulfate polyacrylamide gel using counter ion-dyes, Coomassie Brilliant Blue R-250, and neutral red, Arch. Pharm. Res. 25, 704–708, 2002; Bonar, E., Dubin, A., Bierczynska-Krzysik, A. et al., Identification of major cellular proteins synthesized in response to interleukin-1 and interleukin-6 in human hepatoma HepG2 cells, Cytokine 33, 111–117, 2006.

 

Tonge, R., Shaw, J., Middleton, B. et al., Validation and development of fluorescence two-dimensional differential gel electrophoresis proteomics technology, Proteomics 1, 377–396, 2001; Chan, H.L., Gharbi, S., Gaffney, P.R. et al., Proteomic analysis of redox- and ErbB2-dependent changes in mammary luminal epithelial cells using cysteine- and lysine-labeling two-dimensional difference gel electrophoresis, Proteomics 5, 2908–2926, 2005; Misek, D.E., Kuick, R., Wang, H. et al., A wide range of protein isoforms in serum and plasma uncovered by a quantitative intact protein analysis system, Proteomics 5, 3343–3352, 2005; Doutette, P., Navet, R., Gerkens, P. et al., Steatosis-induced proteomic changes in liver mitochondria evidenced by two-dimensional differential in-gel electrophoresis, J. Proteome Res. 4, 2024–2031, 2005.

 

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Gobom, J., Schuerenberg, M., Mueller, M. et al., α-cyano-4-hydroxycinnamic acid affinity sample preparation. A protocol for MALDI-MS peptide analysis in proteomics, Anal. Chem. 73, 434–438, 2001; Zhu, X. and Papayannopoulos, I.A., Improvement in the detection of low concentration protein digests on a MALDI TOF/TOF workstation by reducing α-cyano-4-hydroxycinnamic acid adduct ions, J. Biomol. Tech. 14, 298–307, 2003; Neubert, H., Halket, J.M., Fernandez Ocana, M., and Patel, R.K., MALDI post-source decay and LIFT-TOF/TOF investigation of α-cyano-4-hydroxycinnamic acid cluster interferences, J. Am. Soc. Mass Spectrom. 15, 336–343, 2004; Kobayashi, T., Kawai, H., Suzuki, T. et al., Improved sensitivity for insulin in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry by premixing α-cyano-4-hydroxycinnamic acid with transferrin, Rapid Commun. Mass Spectrom. 18, 1156–1160, 2004; Pshenichnyuk, S.A. and Asfandiarov, N.L., The role of free electrons in MALDI: electron capture by molecules of α-cyano-4-hydroxycinnamic acid, Eur. J. Mass Spectrom. 10, 477–486, 2004; Bogan, M.J., Bakhoum, S.F., and Agnes, G.R., Promotion of α-cyano-4-hydroxycinnamic acid and peptide cocrystallization within levitated droplets with net charge, J. Am. Soc. Mass Spectrom. 16, 254–262, 2005. As enzyme inhibitor: Clarke, P.D., Clift, D.L., Dooledeniya, M. et al., Effects of α-cyano-4-hydroxycinnamic acid on fatigue and recovery of isolated mouse muscle, J. Muscle Res. Cell Motil. 16, 611–617, 1995; Del Prete, E., Lutz, T.A., and Scharrer, E., Inhibition of glucose oxidation by α-cyano-4-hydroxycinnamic acid stimulates feeding in rats, Physiol. Behav. 80, 489–498, 2004; Briski, K.P. and Patil, G.D., Induction of Fox immunoreactivity labeling in rat forebrain metabolic loci by caudal fourth ventricular infusion of the monocarboxylate transporter inhibitor, α-cyano-4-hydroxycinnamic acid, Neuroendocrinology 82, 49–57, 2005.

 

Ghenbot, G., Emge, T., and Day, R.A., Identification of the sites of modification of bovi carbonic anhydrase II (BCA II) by the salt bridge reagent cyanogen, C2N2, Biochim. Biophys. Acta 1161, 59–65, 1993; Karagozler, A.A., Ghenbot, G., and Day, R.A., Cyanogen as a selective probe for carbonic anhydrase hydrolase, Biopolymers 33, 687–692, 1993; Winters, M.S. and Day, R.A., Identification of amino acid residues participating in intermolecular salt bridges between self-associating proteins, Anal. Biochem. 309, 48–59, 2002; Winters, M.S. and Day, R.A., Detecting protein–protein interactions in the intact cell of Bacillus subtilis(ATCC 6633), J. Bacteriol. 185, 4268–4275, 2003.

 

Hofmann, T., The purification and properties of fragments of trypsinogen obtained by cyanogen bromide cleavage, Biochemistry 3, 356–364, 1964; Chu, R.C. and Yasunobu, K.T., The reaction of cyanogen bromide and N-bromosuccinimide with some cytochromes C, Biochim. Biophys. Acta 89, 148–149, 1964; Inglis, A.S. and Edman, P., Mechanism of cyanogen bromide reaction with methionine in peptides and proteins. I. Formation of imidate and methyl thiocyanate, Anal. Biochem. 37, 73–80, 1970; Kagedal, L. and Akerstrom, S., Binding of covalent proteins to polysaccharides by cyanogen bromide and organic cyanates. I. Preparation of soluble glycine-, insulin- and ampicillin-dextran, Acta Chem. Scand. 25, 1855–1899, 1971; Sipe, J.D. and Schaefer, F.V., Preparation of solid-phase immunosorbents by coupling human serum proteins to cyanogen bromide–activated agarose, Appl. Microbiol. 25, 880–884, 1973; March, S.C., Parikh, I., and Cuatrecasas, P., A simplified method for cyanogen bromide activation of agarose for affinity chromatography, Anal. Biochem. 60, 149–152, 1974; Boulware, D.W., Goldsworthy, P.D., Nardella, F.A., and Mannik, M., Cyanogen bromide cleaves Fc fragments of pooled human IgG at both methionine and tryptophan residues, Mol. Immunol. 22, 1317–1322, 1985; Jaggi, K.S. and Gangal, S.V., Monitoring of active groups of cyanogen bromide-activated paper discs used as allergosorbent, Int. Arch. Allergy Appl. Immunol. 89, 311–313, 1989; Villa, S., De Fazio, G., and Canosi, U., Cyanogen bromide cleavage at methionine residues of polypeptides containing disulfide bonds, Anal. Biochem. 177, 161–164, 1989; Luo, K.X., Hurley, T.R., and Sefton, B.M., Cyanogen bromide cleavage and proteolytic peptide mapping of proteins immobilized to membranes, Methods Enzymol. 201, 149–152, 1991; Jennissen, H.P., Cyanogen bromide and tresyl chloride chemistry revisited: the special reactivity of agarose as a chromatographic and biomaterial support for immobilizing novel chemical groups, J. Mol. Recognit. 8, 116–124, 1995; Kaiser, R. and Metzka, L., Enhancement of cyanogen bromide cleavage yields for methionyl-serine and methionyl-threonine peptide bonds, Anal. Biochem. 266, 1–8, 1999; Kraft, P., Mills, J., and Dratz, E., Mass spectrometric analysis of cyanogen bromide fragments of integral membrane proteins at the picomole level: application to rhodopsin, Anal. Biochem. 292, 76–86, 2001; Kuhn, K., Thompson, A., Prinz, T. et al., Isolation of N-terminal protein sequence tags from cyanogen bromide-cleaved proteins as a novel approach to investigate hydrophobic proteins, J. Proteome Res. 2, 598–609, 2003; Macmillan, D. and Arham, L., Cyanogen bromide cleavage generates fragments suitable for expressed protein and glycoprotein ligation, J. Am. Chem. Soc. 126, 9530–9531, 2004; Lei, H., Minear, R.A., and Marinas, B.J., Cyanogen bromide formation from the reactions of monobromamine and dibromamine with cyanide ions, Environ. Sci. Technol. 40, 2559–2564, 2006.

 

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Dansyl Chloride

5-(dimethylamino)-1-naphthalenesulfonyl Chloride

269.8

Fluorescent label for proteins; amino acid analysis.

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Deoxycholic Acid

Desoxycholic Acid

392.57

Detergent, nanoparticles.

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Deuterium Oxide

“Heavy Water”

20.03

Structural studies in proteins, enzyme kinetics; in vivo studies of metabolic flux.

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Hydrazine

N2H4

32.05

Reducing agent; modification of aldehydes and carbohydrates; hydrazinolysis used for release of carbohydrates from protein; derivatives such as dinitrophenylhydrazine used for analysis of carbonyl groups in oxidized proteins; detection of acetyl and formyl groups in proteins.

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p-Nitrophenol

4-nitrophenol

139.11

Popular signal from indicator enzymes such as alkaline phosphatase.

 

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Picric Acid

2,4,6-trinitrophenol

229.1

Analytical reagent.

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Sodium Borohydride

NaBH4

37.83

Reducing agent for Schiff bases; reduction of aldehydes; other chemical reductions.

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Sodium Chloride

Salt; NaCl

58.44

Ionic strength; physiological saline.

Sodium Cholate

430.55

Detergent.

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Sodium Cyanoborohydride

NaBH3 (CN)

62.84

Reducing agent; considered more selective than NaBH4.

Rosen, G.M., Use of sodium cyanoborohydride in the preparation of biologically active nitroxides, J. Med. Chem. 17, 358–360, 1974; Chauffe, L. and Friedman, M., Factors affecting cyanoborohydride reduction of aromatic Schiff’s bases in proteins, Adv. Exp. Med. Biol. 86A, 415–424, 1977; Baues, R.J. and Gray, G.R., Lectin purification on affinity columns containing reductively aminated disaccharides, J. Biol. Chem. 252, 57–60, 1977; Jentoft, N. and Dearborn, D.G., Labeling of proteins by reductive methylation using sodium cyanoborohydride, J. Biol. Chem. 254, 4359–4365, 1979; Jentoft, N., and Dearborn, D.G., Protein labeling by reductive methylation with sodium cyanoborohydride: effect of cyanide and metal ions on the reaction, Anal. Biochem. 106, 186–190, 1980; Bunn, H.F. and Higgins, P.T., Reaction of monosaccharides with proteins: possible evolutionary significance, Science 213, 222–224, 1981; Geoghegan, K.F., Cabacungan, J.C., Dixon, H.B., and Feeney, R.E., Alternative reducing agents for reductive methylation of amino groups in proteins, Int. J. Pept. Protein Res. 17, 345–352, 1981; Habeeb, A.F., Comparative studies on radiolabeling of lysozyme by iodination and reductive methylation, J. Immunol. Methods 65, 27–39, 1983; Prakash, C. and Vijay, I.K., A new fluorescent tag for labeling of saccharides, Anal. Biochem. 128, 41–46, 1983; Acharya, A.S. and Sussman, L.G., The reversibility of the ketoamine linkages of aldoses with proteins, J. Biol. Chem. 259, 4372–4378, 1984; Climent, I., Tsai, L., and Levine, R.L., Derivatization of gamma-glutamyl semialdehyde residues in oxidized proteins by fluorescamine, Anal. Biochem. 182, 226–232, 1989; Hartmann, C. and Klinman, J.P., Reductive trapping of substrate to methylamine oxidase from Arthrobacter P1, FEBS Lett. 261, 441–444, 1990; Meunier, F. and Wilkinson, K.J., Nonperturbing fluorescent labeling of polysaccharides, Biomacromolecules 3, 858–864, 2002; Webb, M.E., Stephens, E., Smith, A.G., and Abell, C., Rapid screening by MALDITOF mass spectrometry to probe binding specificity at enzyme active sites, Chem. Commun. 19, 2416–2417, 2003; Sando, S., Matsui, K., Niinomi, Y. et al., Facile preparation of DNA-tagged carbohydrates, Bioorg. Med. Chem. Lett. 13, 2633–2636, 2003; Peelen, D. and Smith, L.M., Immobilization of anine-modified oligonucleotides on aldehyde-terminated alkanethiol monolayers on gold, Langmuir 21, 266–271, 2005; Mirzaei, H. and Regnier, F., Enrichment of carbonylated peptides using Girard P reagent and strong cation exchange chromatography, Anal. Chem. 78, 770–778, 2006.

Sodium Deoxycholate

Desoxycholic Acid, Sodium Salt

414.55

Detergent; potential therapeutic use with adipose tissue.

Bril, C., van der Horst, D.J., Poort, S.R., and Thomas, J.B., Fractionation of spinach chloroplasts with sodium deoxycholate, Biochim. Biophys. Acta 172, 345–348, 1969; Smart, J.E. and Bonner, J., Selective dissociation of histones from chromatin by sodium deoxycholate, J. Mol. Biol. 58, 651–659, 1971; Part, M., Tarone, G., and Comoglio, P.M., Antigenic and immunogenic properties of membrane proteins solubilized by sodium desoxycholate, papain digestion, or high ionic strength, Immunochemistry 12, 9–17, 1975; Johansson, K.E. and Wbolewski, H., Crossed immunoelectrophoresis, in the presence of tween 20 or sodium deoxycholate, or purified membrane proteins from Acholeplasma laidlawii, J. Bacteriol. 136, 324–330, 1978; Lehnert, T. and Berlet, H.H., Selective inactivation of lactate dehydrogenase of rat tissues by sodium deoxycholate, Biochem. J. 177, 813–818, 1979; Suzuki, N., Kawashima, S., Deguchi, K., and Ueta, N., Low-density lipoproteins form human ascites plasma. Characterization and degradation by sodium deoxycholate, J. Biochem. 87, 1253–1256, 1980; Robern, H., The application of sodium deoxycholate and Sephacryl S-200 for the delipidation and separation of high-density lipoprotein, Experientia 38, 437–439, 1982; Nedivi, E. and Schramm, M., The beta-adrenergic receptor survives solubilization in deoxycholate while forming a stable association with the agonist, J. Biol. Chem. 259, 5803–5808, 1984; McKernan, R.M., Castro, S., Poat, J.A., and Wong, E.H., Solubilization of the N-methyl-D-aspartate receptor channel complex from rat and porcine brain, J. Neurochem. 52, 777–785, 1989; Carter, H.R. Wallace, M.A., and Fain, J.N., Activation of phospholipase C in rabbit brain membranes by carbachol in the presence of GTP gamma S: effects of biological detergents, Biochim. Biophys. Acta 1054, 129–134, 1990; Shivanna, B.D. and Rowe, E.S., Preservation of the native structure and function of Ca2+-ATPase from sarcoplasmic reticulum: solubilization and reconstitution by new short-chain phospholipid detergent 1,2-diheptanoyl-sn-phosphatidylcholine, Biochem. J. 325, 533–542, 1997; Arnold, U. and Ulbrich-Hofmann, R., Quantitative protein precipitation from guandine hydrochloride-containing solutions by sodium deoxycholate/trichloroacetic acid, Anal. Biochem. 271, 197–199, 1999; Haque, M.E., Das, A.R., and Moulik, S.P., Mixed micelles for sodium deoxycholate and polyoxyethylene sobitan monooleate (Tween 80), J. Colloid Interface Sci. 217, 1–7, 1999; Srivastava, O.P. and Srivastava, K., Characterization of a sodium deoxycholate-activable proteinase activity associated with betaA3/A1-crystallin of human lenses, Biochim. Biophys. Acta 1434, 331–346, 1999; Rotunda, A.M., Suzuki, H., Moy, R.L., and Kolodney, M.S., Detergent effects of sodium deoxycholate are a major feature of an injectable phosphatidylcholine formulation used for localized fat dissolution, Dermatol. Surg. 30, 1001–1008, 2004; Asmann, Y.W., Dong, M., and Miller, L.J., Functional characterization and purification of the secretin receptor expressed in baculovirus-infected insect cells, Regul. Pept. 123, 217–223, 2004; Ranganathan, R., Tcacenco, C.M., Rosseto, R., and Hajdu, J., Characterization of the kinetics of phospholipase C activity toward mixed micelles of sodium deoxycholate and dimyristoylphophatidylcholine, Biophys. Chem. 122, 79–89, 2006.

 

Shapiro, A.L., Vinuela, E., and Maizel, J.V., Jr., Molecular weight estimation of polypeptide chains by electrophoresis in SDS-polyacrylamide gels, Biochem. Biophys. Res. Commun. 28, 815–820, 1967; Shapiro, A.L., and Maizel, J.V., Jr., Molecular weight estimation of polypeptides by SDS-polyacrylamide gel electrophoresis: further data concerning resolving power and general considerations, Anal. Biochem. 29, 505–514, 1969; Weber, K. and Osborn, M., The reliability of molecular weight determinations of dodecyl sulfate-polyacryalmide gel electrophoresis, J. Biol. Chem. 244, 4406–4412, 1969; Weber, K. and Kuter, D.J., Reversible denaturation of enzymes by sodium dodecyl sulfate, J. Biol. Chem. 246, 4504–4509, 1971; de Haen, C., Molecular weight standards for calibration of gel filtration and sodium dodecyl sulfatepolyacrylamide gel electrophoresis: ferritin and apoferritin, Anal. Biochem. 166, 235–245, 1987; Smith, B.J., SDS polyacrylamide gel electrophoresis of proteins, Methods Mol. Biol. 32, 23–34, 1994; Guttman, A., Capillary sodium dodecyl sulfate-gel electrophoresis of proteins, Electrophoresis 17, 1333–1341, 1996; Bischoff, K.M., Shi, L., and Kennelly, P.J., The detection of enzyme activity following sodium dodecyl sulfate-polyacryalamide gel electrophoresis, Anal. Biochem. 260, 1–17, 1998; Maizel, J.V., SDS polyacrylamide gel electrophoresis, Trends Biochem. Sci. 35, 590–592, 2000; Robinson, J.M. and Vandre, D.D, Antigen retrieval in cells and tissues: enhancement with sodium dodecyl sulfate, Histochem. Cell Biol. 116, 119–130, 2001; Todorov, P.D., Kralchevsky, P.A., Denkov, N.D. et al., Kinetics of solublization of n-decane and benzene by micellar solutions of sodium dodecyl sulfate, J. Colloid Interface Sci. 245, 371–382, 2002; Zhdanov, S.A., Starov, V.M., Sobolev, V.D., and Velarde, M.G., Spreading of aqueous SDS solutions over nitrocellulose membranes, J. Colloid Interface Sci. 264, 481–489, 2003; Santos, S.F., Zanette, D., Fischer, H., and Itri, R., A systematic study of bovine serum albumin (BSA) and sodium dodecyl sulfate (SDS) interactions by surface tension and small angle X-ray scattering, J. Colloid Interface Sci. 262, 400–408, 2003; Biswas, A. and Das, K.P., SDS-induced structural changes in alpha-crystallin and its effect on refolding, Protein J. 23, 529–538, 2004; Jing, P., Kaneta, T., and Imasaka, T., On-line concentration of a protein using denaturation by sodium dodecyl sulfate, Anal. Sci. 21, 37–42, 2005; Choi, N.S., Hahm, J.H., Maeng, P.J., and Kim, S.H., Comparative study of enzyme activity and stability of bovine and human plasmins in electrophoretic reagents, β-mercaptoethanol, DTT, SDS, Triton X-100, and urea, J. Biochem. Mol. Biol. 38, 177–181, 2005; Miles, A.P. and Saul, A., Quantifying recombinant proteins and their degradation products using SDS-PAGE and scanning laser densitometry, Methods Mol. Biol. 308, 349–356, 2005; Thongngam, M. and McClements, D.J., Influence of pH, ionic strength, and temperature on self-association and interactions of sodium dodecyl sulfate in the absence and presence of chitosan, Langmuir 21, 79–86, 2005; Romani, A.P., Gehlen, M.H., and Itri, R., Surfactant-polymer aggregates formed by sodium dodecyl sulfate, poly(N-vinyl-2-pyrrolidone), and poly(ethylene glycol), Langmuir 21, 1271–1233, 2005; Gudiksen, K.L., Gitlin, I., and Whitesides, G.M., Differentiation of proteins based on characteristic patterns of association and denaturation in solutions of SDS, Proc. Natl. Acad. Sci. USA 103, 7968–7972, 2006; Freitas, A.A., Paulo, L., Macanita, A.L, and Quina, F.H., Acid-base equilibria and dynamics in sodium dodecyl sulfate micelles: geminate recombination and effect of charge stabilization, Langmuir 22, 7986–7893, 2006.

Sodium Metabisulfite

Sodium Bisulfite

190.1

Mild reducing agent; converts unmethylated cytosine residues to uracil residues (DNA methylation).

Miller, R.F., Small, G., and Norris, L.C., Studies on the effect of sodium bisulfite on the stability of vitamin E, J. Nutr. 55, 81–95, 1955; Hayatsu, H., Wataya, Y., Kai, K., and Iida, S., Reaction of sodium bisulfite with uracil, cytosine, and their derivatives, Biochemistry 9, 2858–2865, 1970; Seno, T., Conversion of Escherichia coli tRNATrp to glutamine-accepting tRNA by chemical modification with sodium bisulfite, FEBS Lett. 51, 325–329, 1975; Tasheva, B. and Dessev, G., Artifacts in sodium dodecyl sulfate-polyacrylamide gel electrophoresis due to 2-mercaptoethanol, Anal. Biochem. 129, 98–102, 1983; Draper, D.E., Attachment of reporter groups to specific, selected cytidine residues in RNA using a bisulfite-catalyzed transamination reaction, Nucleic Acids Res. 12, 989–1002, 1984; Oakeley, E.J., DNA methylation analysis: a review of current methodologies, Pharmacol. Ther. 84, 389–400, 1999; Geisler, J.P., Manahan, K.J., and Geisler, H.E., Evaluation of DNA methylation in the human genome: why examine it and what method to use, Eur. J. Gynaecol. Oncol. 25, 19–24, 2004; Thomassin, H., Kress, C., and Grange, T., MethylQuant: a sensitive method for quantifying methylation of specific cytosines within the genome, Nucleic Acids Res. 32, e168, 2004; Derks, S., Lentjes, M.H., Mellebrekers, D.M. et al., Methylation-specific PCR unraveled, Cell. Oncol. 26, 291–299, 2004; Galm, O. and Herman, J.G., Methylation-specific polymerase chain reaction, Methods Mol. Biol. 113, 279–291, 2005; Ogino, S., Kawasaki, T., Brahmandam, M. et al., Precision and performance characteristics of bisulfite conversion and real-time PCR (MethylLight) for quantitative DNA methylation analysis, J. Mol. Diagn. 8, 209–217, 2006; Yang, I., Park, I.Y., Jang, S.M. et al., Rapid quantitation of DNA methylation through dNMP analysis following bisulfite PCR, Nucleic Acids Res. 34, e61, 2006; Wischnewski, F., Pantel, K., and Schwazenbach, H., Promoter demethylation and histone acetylation mediate gene expression of MAGE-A1, -A2, -A3, and -A12 in human cancer cells, Mol. Cancer Res. 4, 339–349, 2006; Zhou, Y., Lum, J.M., Yeo, G.H. et al., Simplified molecular diagnosis of fragile X syndrome by fluorescent methylation-specific PCR and GeneScan analysis, Clin. Chem. 52, 1492–1500, 2006.

 

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Sucrose

342.30

Osmolyte; density gradient centrifugation.

Cann, J.R., Coombs, R.O., Howlett, G.J. et al., Effects of molecular crowding on protein self-association: a potential source of error in sedimentation coefficients obtained by zonal ultracentrifugation in a sucrose gradient, Biochemistry 33, 10185–10190, 1994; Camacho-Vanegas, O., Lorein, F., and Amaldi, F., Flat absorbance background for sucrose gradients, Anal. Biochem. 228, 172–173, 1995; Ben-Zeev, O. and Doolittle, M.H., Determining lipase subunit structure by sucrose gradient centrifugation, Methods Mol. Biol. 109, 257–266, 1999; Lustig, A., Engel, A., Tsiotis, G. et al., Molecular weight determination of membrane proteins by sedimentation equilibrium at the sucrose of nycodenz-adjusted density of the hydrated detergent micelle, Biochim. Biophys. Acta 1464, 199–206, 2000; Kim, Y.S., Jones, L.A., Dong, A. et al., Effects of sucrose on conformational equilibria and fluctuations within the native-state ensemble of proteins, Protein Sci. 12, 1252–1261, 2003; Srinivas, K.A., Chandresekar, G., Srivastava, R., and Puvanakrishna, R., A novel protocol for the subcellular fractionation of C3A hepatoma cells using sucrose-density gradient centrifugation, J. Biochem. Biophys. Methods 60, 23–27, 2004; Richter, W., Determining the subunit structure of phosphodiesterase using gel filtration and sucrose-density gradient centrifugation, Methods Mol. Biol. 307, 167–180, 2005; Cioni, P., Bramanti, E., and Strambini, G.B., Effects of sucrose on the internal dynamics of azurin, Biophys. J. 88, 4213–4222, 2005; Desplats, P., Folco, E. and Salerno, G.L., Sucrose may play an additional role to that of an osmolyte in Synechocystis sp. PCC 6803 salt-shocked cells, Plant Physiol. Biochem. 43, 133–138, 2005; Chen, L., Ferreira, J.A., Costa, S.M. et al., Compaction of ribosomal protein S6 by sucrose occurs only under native conditions, Biochemistry 21, 2189–2199, 2006.

 

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Walseth, T.F., Graff, G., Moos, M.C., Jr., and Goldberg, N.D., Separation of 5′-ribonucleoside monophosphates by ion-pair reverse-phase high-performance liquid chromatography, Anal. Biochem. 107, 240–245, 1980; Ozkul, A. and Oztunc, A., Determination of naprotiline hydrochloride in tables by ion-pair extraction using bromthymol blue, Pharmzie 55, 321–322, 2000; Cecchi, T., Extended thermodynamic approach to ion interaction chromatography. Influence of the chain length of the solute ion; a chromatographic method for the determination of ion-pairing constants, J. Sep. Sci 28, 549–554, 2005; Pistos, C., Tsantili-Kakoulidou, A., and Koupparis, M., Investigation of the retention/pH profile of zwitterionic fluoroquinolones in reversed-phase and ion-interaction high-performance liquid chromatography, J. Pharm. Biomed. Anal. 39, 438–443, 2005; Choi, M.M., Douglas, A.D., and Murray, R.W., Ion-pair chromatographic separation of water-soluble gold monolayer-protected clusters, Anal. Chem. 78, 2779–2785, 2006; Saradhi, U.V., Prarbhakar, S., Reddy, T.J., and Vairamani, M., Ion-pair solid-phase extraction and gas chromatography mass spectrometric determination of acidic hydrolysis products of chemical warfare agents from aqueous samples, J. Chromatog. A, 1129, 9–13, 2006.

 

Leuty, S.J., Rapid dehydration of plant tissues for paraffin embedding; tetrahydrofuran vs. t-butanol, Stain Technol. 44, 103–104, 1969; Tandler, C.J. and Fiszer de Plazas, S., The use of tetrahydrofuran for delipidation and water solubilization of brain proteolipid proteins, Life Sci. 17, 1407–1410, 1975; Dressman, J.B., Himmelstein, K.J., and Higuchi, T., Diffusion of phenol in the presence of a complexing agent, tetrahydrofuran, J. Pharm. Sci. 72, 12–17, 1983; Diaz, R.S., Regueiro, P., Monreal, J., and Tandler, C.J., Selective extraction, solubilization, and reversed-phase high-performance liquid chromatography separation of the main proteins from myelin using tetrahydrofuran/water mixtures, J. Neurosci. Res. 29, 114–120, 1991; Santa, T., Koga, D., and Imai, K., Reversed-phase high-performance liquid chromatography of fullerenes with tetrahydrofuran-water as a mobile phase and sensitive ultraviolet or electrochemical detection, Biomed. Chromatogr. 9, 110–111, 1995; Lee, J., Kang, J.H., Lee, S.Y. et al., Protein kinase C ligands based on tetrahydrofuran templates containing a new set of phorbol ester pharmacophores, J. Med. Chem. 42, 4129–4139, 1999; Edwards, A.A., Ichihara, O., Murfin, S. et al., Tetrahydrofuran-based amino acids as library scaffolds, J. Comb. Chem. 6, 230–238, 2004; Baron, C.P., Refsgaard, H.H., Skibsted, L.H., and Andersen, M.L., Oxidation of bovine serum albumin initiated by the Fenton reaction — effect of EDTA, tert-butylhydroperoxide, and tetrahydrofuran, Free Radic. Res. 40, 409–417, 2006; Bowron, D.T., Finney, J.L., and Soper, A.K., The structure of liquid tetrahydrofuran, J. Am. Chem. Soc. 128, 5119–5126, 2006; Hermida, S.A., Possari, E.P., Souza, D.B. et al., 2′-deoxyguanosine, 2′-deoxycytidine, and 2′-deoxyadenosine adducts resulting from the reaction of tetrahydrofuran with DNA bases, Chem. Res. Toxicol. 19, 927–936, 2006; Li, A.C., Li, Y., Guirguis, M.S., Advantages of using tetrahydrofuran-water as mobile phases in the quantitation of cyclosporine A in monkey and rat plasma by liquid chromatography-tandem mass spectrometry, J. Pharm. Biomed. Anal. 43, 277–284, 2007.

 

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Rogers, D.R., Screening for amyloid with the thioflavin T fluorescent method, Am. J. Clin. Pathol. 44, 59–61, 1965; Saeed, S.M. and Fine, G., Thioflavin T for amyloid, Am. J. Clin. Pathol. 47, 588–593, 1967; Levine, H., III, Stopped-flow kinetics reveal multiple phase of thioflavin T binding to Alzheimer beta (1–40) amyloid fibrils, Arch. Biochem. Biophys. 342, 306–316, 1997; De Ferrari, G.V., Mallender, W.D., Inestrosa, N.C., and Rosenberry, T.L., Thioflavin T is a fluorescent probe of the acetylcholinesterase peripheral site that reveals conformational interactions between the peripheral and acylation sites, J. Biol. Chem. 276, 23282–23287, 2001; Ban, T., Hamada, D., Hasegawa, K. et al., Direct observation of amyloid fibril growth monitored by thioflavin T fluorescence, J. Biol. Chem. 278, 16462–16465, 2003; Krebs, M.R., Bromley, E.H., and Donald, A.M., The binding of thioflavin T to amyloid fibrils: localization and implications, J. Struct. Biol. 149, 30–37, 2005; Khurana, R., Coleman, C., Ionescu-Zanetti, C. et al., Mechanisms of thioflavin T binding to amyloid fibrils, J. Struct. Biol. 151, 229–238, 2005; Darhal, N., Garnier-Suillerot, A., and Salerno, M., Mechanism of thioflavin T accumulation inside cells overexpressing P-glycoprotein or multidrug resistance-associated protein: role of lipophilicity and positive charge, Biochem. Biophys. Res. Commun. 343, 623–629, 2006; Eisert, R., Felau, L., and Brown, L.R., Methods for enhancing the accuracy and reproducibility of Congo red and thioflavin T assays, Anal. Biochem. 353, 144–146, 2006.

Thionyl Chloride

Sulfurous Oxychloride

118.97

Preparation of acyl chlorides.

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Sokolovsky, M., Riordan, J.F., and Vallee, B.L., Tetranitromethane. A reagent for the nitration of tyrosyl residues in proteins, Biochemistry 5, 3582–3589, 1966; Nishikimi, M. and Yagi, K., Reaction of reduced flavins with tetranitromethane, Biochem. Biophys. Res. Commun. 45, 1042–1048, 1971; Kunkel, G.R., Mehrabian, M., and Martinson, H.G., Contact-site crosslinking agents, Mol. Cell. Biochem. 34, 3–13, 1981; Rial, E. and Nicholls, D.G., Chemical modification of the brown-fatmitochondrial uncoupling protein with tetranitromethane and N-ethylmaleimide. A cysteine residue is implicated in the nucleotide regulation of anion permeability, Eur. J. Biochem. 161, 689–694, 1986; Prozorovski, V., Krook, M., Atrian, S. et al., Identification of reactive tyrosine residues in cysteine-reactive dehydrogenases. Differences between liver sorbitol, liver alcohol, and Drosophila alcohol dehydrogenase, FEBS Lett. 304, 46–50, 1992; Gadda, G., Banerjee, A., and Fitzpatrick, P.F., Identification of an essential tyrosine residue in nitroalkane oxidase by modification with tetranitromethane, Biochemistry 39, 1162–1168, 2000; Hodges, G.R. and Ingold, K.U., Superoxide, amine buffers, and tetranitro-methane: a novel free radical chain reaction, Free Radic. Res. 33, 547–550, 2000; Capeillere-Blandin, C., Gausson, V., DescampsLatscha, B., and Witko-Sarsat, V., Biochemical and spectrophotometric significance of advanced oxidation protein products, Biochim. Biophys. Acta 1689, 91–102, 2004; Lundblad, R.L., Chemical Reagents for Protein Modification, CRC Press, Boca Raton, FL, 2004; Negrerie, M., Martin, J.L., and Nghiem, H.O., Functionality of nitrated acetylcholine receptor: the two-step formation of nitrotyrosines reveals their differential role in effectors binding, FEBS Lett. 579, 2643–2647, 2005; Carven, G.J. and Stern, L.J., Probing the ligand-induced conformational change in HLA-DR1 by selective chemical modification and mass spectrometry mapping, Biochemistry 44, 13625–13637, 2005.

Trehalose

α-D-glucopyranoglucopyranosyl-1,1-α-Dglucopyranoside; Mycose

342.3

A nonreducing sugar that is found in a variety of organisms where it is thought to protect against stress such as dehydration; there is considerable interest in the use of trehalose as a stabilizer in biopharmaceutical proteins.

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Trifluoroacetic Acid

114.0

Ion-pair reagent; HLPC; peptide synthesis.

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Gray, W.R., Disulfide structures of highly bridged peptides: a new strategy for analysis, Protein Sci. 2, 1732–1748, 1993; Gray, W.R., Echistatin disulfide bridges: selective reduction and linkage assignment, Protein Sci. 2, 1749–1755, 1993; Han, J.C. and Han, G.Y., A procedure for quantitative determination of Tris(2-carboxyethyl)phosphine, an odorless reducing agent more stable and effective than dithiothreitol, Anal. Biochem. 220, 5–10, 1994; Wu, J., Gage, D.A., and Watson, J.T., A strategy to locate cysteine residues in proteins by specific chemical cleavage followed by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry, Anal. Biochem. 235, 161–174, 1996; Han, J., Yen. S., Han, G., and Han, F., Quantitation of hydrogen peroxide using Tris(2-carboxyethyl) phosphine, Anal. Biochem. 234, 107–109, 1996; Han, J., Clark, C., Han, G. et al., Preparation of 2-nitro-5-thiobenzoic acid using immobilized Tris(2-carboxyethyl) phosphine, Anal. Biochem. 268, 404–407, 1999; Anderson, M.T., Trudell, J.R., Voehringer, D.W. et al., An improved monobromobimane assay for glutathione utilizing Tris-(2-carboxyethyl)phosphine as the reductant, Anal. Biochem. 272, 107–109, 1999; Shafer, D.E., Inman, J.K. and Lees, A. Reaction of Tris(2-carboxyethyl)phosphine (TCEP) with maleimide and alpha-haloacyl groups: anomalous elution of TCEP by gel filtration, Anal. Biochem. 282, 161–164, 2000; Rhee, S.S. and Burke, D.H., Tris(2-carboxyethyl)phosphine stabilization of RNA: comparison with dithiothreitol for use with nucleic acid and thiophosphoryl chemistry, Anal. Biochem. 325, 137–143, 2004; Legros, C., Celerier, M.L., and Guette, C., An unusual cleavage reaction of a peptide observed during dithiothreitol and Tris(2-carboxyethyl)phosphine reduction: application to sequencing of HpTx2 spider toxin using nanospray tandem mass spectrometry, Rapid Commun. Mass Spectrom. 19, 1317–1323, 2004; Xu, G., Kiselar, J., He, Q., and Chance, M.R., Secondary reactions and strategies to improve quantitative protein footprinting, Anal. Chem. 77, 3029–3037, 2005; Valcu, C.M. and Schlink, K., Reduction of proteins during sample preparation and two-dimensional gel electrophoresis of woody plant samples, Proteomics 6, 1599–1605, 2006; Scales, C.W., Convertine, A.J., and McCormick, C.L., Fluorescent labeling of RAFT-generated poly(N-isopropylacrylamide) via a facile maleimide-thiol coupling reaction, Biomacromolecules 7, 1389–1392, 2006.

Urea

Carbamide

60.1

Chaotropic agent.

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