Optimization of the hybridization-based method for purification of thermostable tRNAs in the presence of tetraalkylammonium salts

Nucleic Acids Research

Volumn 38, Issue 6, 2009, Pages

  Yokogawa, Takashi ^a   Kitamura, Yusuke ^a   Nakamura, Daigo ^a   Ohno, Satoshi ^a   Nishikawa, Kazuya ^a  

^a GIFU UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; TETRAMETHYLAMMONIUM CHLORIDE; TETRYLAMMONIUM CHLORIDE; TRANSFER RNA; BUFFER; METHIONINE TRANSFER RNA; MONOVALENT CATION; OLIGODEOXYRIBONUCLEOTIDE; PHENYLALANINE TRANSFER RNA; QUATERNARY AMMONIUM DERIVATIVE; TETRAMETHYLAMMONIUM; TETRYLAMMONIUM;

ARTICLE; CONTROLLED STUDY; DNA RNA HYBRIDIZATION; GENE TARGETING; NONHUMAN; NUCLEIC ACID IMMOBILIZATION; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROTEIN TERTIARY STRUCTURE; RNA PURIFICATION; RNA SEQUENCE; RNA STABILITY; THERMOPHILE; THERMOSTABILITY; CHEMISTRY; CONFORMATION; DNA DENATURATION; ESCHERICHIA COLI; GENETICS; ISOLATION AND PURIFICATION; METHODOLOGY; NUCLEIC ACID HYBRIDIZATION; TEMPERATURE;

TETRA;

BUFFERS; CATIONS, MONOVALENT; ESCHERICHIA COLI; NUCLEIC ACID CONFORMATION; NUCLEIC ACID DENATURATION; NUCLEIC ACID HYBRIDIZATION; OLIGODEOXYRIBONUCLEOTIDES; QUATERNARY AMMONIUM COMPOUNDS; RNA STABILITY; RNA, TRANSFER; RNA, TRANSFER, MET; RNA, TRANSFER, PHE; TEMPERATURE; TETRAETHYLAMMONIUM;

EID: 77951276163     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp1182     Document Type: Article

References (26)

1. In Söll,D. and RajBhandary,U.L. (eds) (1995), tRNA: Structure, Biosynthesis, and Function. ASM Press, Washington, DC.
2. Sampson,J.R. and Uhlenbeck,O.C. (1988) Biochemical and physical characterization of an unmodified yeast phenylalanine transfer RNA transcribed in vitro. Proc. Natl Acad. Sci. USA, 85, 1033-1037.
3. Giegé,R., Sissler,M. and Florentz,C. (1998) Universal rules and idiosyncratic features in tRNA identity. Nucleic Acids Res., 26, 5017-5035.
4. Agris,P.F., Vendeix,F.A. and Graham,W.D. (2007) tRNA's wobble decoding of the genome: 40 years of modification. J. Mol. Biol., 366, 1-13.
5. Phe lacking the 'conserved' GG and T psi CG sequences as inferred by enzymatic and chemical probing. Nucleic Acids Res., 22, 347-353.
6. Tsurui,H., Kumazawa,Y., Sanokawa,R., Watanabe,Y., Kuroda,T., Wada,A., Watanabe,K. and Shirai,T. (1994) Batchwise purification of specific tRNAs by a solid-phase DNA probe. Anal. Biochem., 221, 166-172.
7. Tomita,K., Ueda,T. and Watanabe,K. (1999) The presence of pseudouridine in the anticodon alters the genetic code: a possible mechanism for assignment of the AAA lysine codon as asparagine in echinoderm mitochondria. Nucleic Acids Res., 27, 1683-1689.
8. Tomita,K., Ueda,T., Ishiwa,S., Crain,P.F., McCloskey,J.A. and Watanabe,K. (1999) Codon reading patterns in Drosophila melanogaster mitochondria based on their tRNA sequences: a unique wobble rule in animal mitochondria. Nucleic Acids Res., 27, 4291-4297.
9. Suzuki,T., Suzuki,T., Wada,T., Saigo,K. and Watanabe,K. (2002) Taurine as a constituent of mitochondrial tRNAs: new insights into the functions of taurine and human mitochondrial diseases. EMBO J., 21, 6581-6589.
10. Kaneko,T., Suzuki,T., Kapushoc,S.T., Rubio,M.A., Ghazvini,J., Watanabe,K., Simpson,L. and Suzuki,T. (2003) Wobble modification differences and subcellular localization of tRNAs in Leishmania tarentolae: implication for tRNA sorting mechanism. EMBO J., 22, 657-667.
11. Kirino,Y., Yasukawa,T., Ohta,S., Akira,S., Ishihara,K., Watanabe,K. and Suzuki,T. (2004) Codon-specific translational defect caused by a wobble modification deficiency in mutant tRNA from a human mitochondrial disease. Proc. Natl Acad. Sci. USA, 101, 15070-15075.
12. Suzuki,T. and Suzuki,T. (2007) Chaplet column chromatography: isolation of a large set of individual RNAs in a single step. Methods Enzymol., 425, 231-239.
13. Yokogawa,T., Kumazawa,Y., Miura,K. and Watanabe,K. (1989) Purification and characterization of two serine isoacceptor tRNAs from bovine mitochondria by using a hybridization assay method. Nucleic Acids Res., 17, 2623-2638.
14. Miyauchi,K., Ohara,T. and Suzuki,T. (2007) Automated parallel isolation of multiple species of non-coding RNAs by the reciprocal circulating chromatography method. Nucleic Acids Res., 35, e24.
15. Melchior,W.B. and Von Hippel,P.H. (1973) Alteration of the relative stability of dA-dT and dG-dC base pairs in DNA. Proc. Natl Acad. Sci. USA, 70, 298-302.
16. Golaś,T., Miller,M. and Shugar,D. (1980) The effects of tetraalkylammonium salts on helix-coil transition parameters in natural and synthetic ribo-and deoxyribo-polynucleotides. Chem. Biol. Interact., 30, 209-222.
17. Zubay,G. (1962) The isolation and fractionation of soluble ribonucleic acid. J. Mol. Biol., 4, 347-356.
18. Holley,R.W. (1963) Large-scale preparation of yeast "soluble" ribonucleic acid. Biochem. Biophys. Res. Commun., 10, 186-188.
19. Wimmer,E., Maxwell,I.H. and Tener,G.M. (1968) A simple method for isolating highly purified yeast phenylalanine transfer ribonucleic acid. Biochemistry, 7, 2623-2628.
20. Ohno,S., Yokogawa,T. and Nishikawa,K. (2001) Changing the amino acid specificity of yeast tyrosyl-tRNA synthetase by genetic engineering. J. Biochem., 130, 417-423.
21. Kumazawa,Y., Yokogawa,T., Tsurui,H., Miura,K. and Watanabe,K. (1992) Effect of the higher-order structure of tRNAs on the stability of hybrids with oligodeoxyribonucleotides: separation of tRNA by an efficient solution hybridization. Nucleic Acids Res., 20, 2223-2232.
22. Hasegawa,T. and Yokogawa,T. (2000) Escherichia coli proline tRNA: structure and recognition sites for prolyl-tRNA synthetase. Nucleic Acids Symp. Ser., 44, 7-8.
23. 2-guanine)-dimethyltransferase (Trm1) catalyzes transfer of methyl groups not only to guanine 26 but also to guanine 27 in tRNA. J. Biol. Chem., 284, 20467-20478.
24. Watanabe,K., Oshima,T., Iijima,K., Yamaizumi,Z. and Nishimura,S. (1980) Purification and thermal stability of several amino acid-specific tRNAs from an extreme thermophile, Thermus thermophilus HB8. J. Biochem., 87, 1-13.
25. Kumazawa,Y., Yokogawa,T., Hasegawa,E., Miura,K. and Watanabe,K. (1989) The aminoacylation of structurally variant phenylalanine tRNAs from mitochondria and various nonmitochondrial sources by bovine mitochondrial phenylalanyl-tRNA synthetase. J. Biol. Chem., 264, 13005-13011.
26. Jacobs,K.A., Rudersdorf,R., Neill,S.D., Dougherty,J.P., Brown,E.L. and Fritsch,E.F. (1988) The thermal stability of oligonucleotide duplexes is sequence independent in tetraalkylammonium salt solutions: application to identifying recombinant DNA clones. Nucleic Acids Res., 16, 4637-4650.