WOOLFORD.THOMPSON@BIONET-20.ARPA (06/02/88)
From: JOHN R. THOMPSON <WOOLFORD.THOMPSON@BIONET-20.ARPA> I recall that a particular salt (the name of which escapes me) is advantageous to add to hybridizations involving oligomers. It seems this salt minimizes GC bias and makes the Tm strictly dependent on length thereby decreasing false signals from sequences with one or two mismatches. Can anyone give me a pointer to this? Thanks, JRT -------
BRUTLAG@BIONET-20.ARPA (06/05/88)
From: Doug Brutlag <brutlag@BIONET-20.ARPA> John, I think that the salts that you are talking about for performing hybridization are the tetraalkylamonium salts. They are found to decrease the difference in Tm between AT and GC bases and to allow very specific hybridization of probes to complex genomic DNAs. Here are some references: AN 88013408. 8801. AU DiLella-A-G. Woo-S-L. TI Hybridization of genomic DNA to oligonucleotide probes in the presence of tetramethylammonium chloride. SO Methods-Enzymol. 1987. 152. P 447-51. AN 85166176. 8500. AU Wood-W-I. Gitschier-J. Lasky-L-A. Lawn-R-M. IN Department of Molecular Biology, Genentech, Inc., South San Francisco, Ca 94080. TI Base composition-independent hybridization in tetramethylammonium chloride: a method for oligonucleotide screening of highly complex gene libraries. SO Proc-Natl-Acad-Sci-USA. 1985 Mar. 82(6). P 1585-8. AN 81232835. 8100. AU Wetmur-J-G. Ruyechan-W-T. Douthart-R-J. IN Department of Microbiology, Mount Sinai School of Medicine of the City University of New York. TI Denaturation and renaturation of Penicillium chrysogenum mycophage double-stranded ribonucleic acid in tetraalkylammonium salt solutions. SO Biochemistry. 1981 May 26. 20(11). P 2999-3002. AN 77222297. 7700. AU Orosz-J-M. Wetmur-J-G. TI DNA melting temperatures and renaturation rates in concentrated alkylammonium salt solutions. SO Biopolymers. 1977 Jun. 16(6). P 1183-99. AN 76149669. 7600. AU Voskoboinik-A-D. Monaselidze-D-R. Mgeladze-G-N. Chanchalashvili-Z-I. Lazurkin-IuS. Frank-kamenetskii-I-M. TI [Study of DNA melting in the region of the inversion of relative stability of AT and GC pairs]. TT Issledovanie plavleniia DNK v oblasti inversii otnositel'noi stabil'nosti AT- i GC-PAR. SO Mol-Biol (Mosk). 1975 Sep-Oct. 9(5). P 783-90. Hope this is what you were looking for. Doug Brutlag -------