Wickstrom, Eric and Behlen, Linda S. and Reuben, Michael A. and Ainpour, Parviz R. (1981) Molecular rulers for measuring RNA structure: sites of crosslinking in chlorambucilyl-phenylalanyl-tRNA^(Phe) (yeast) and chlorambucilyl-pentadecaprolyl-phenylalanyl-tRNA^(Phe) (yeast) intramolecularly crosslinked in aqueous solution. Proceedings of the National Academy of Sciences of the United States of America, 78 (4). pp. 2082-2085. ISSN 0027-8424 http://resolver.caltech.edu/CaltechAUTHORS:20120717-132948081
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Intramolecular crosslinking of yeast phenylalanine tRNA in aqueous solution with rigid, variable-length crosslinking reagents, which we call "molecular rulers," has given results in reasonable agreement with the crystal structure. Chlorambucilyl-[^(3)H]phenylalanyl-tRNA^(Phe) crosslinked intramolecularly at G-71 and A-73, whereas chlorambucilyl-pentadecaprolyl-[^(3)H]phenylalanyl-tRNA^(Phe) crosslinked at G-20 and Y-37. The pentadecaprolyl reagent was predicted to be 62 Å long, including chlorambucil and phenylalanine; the sites that it reached are 60 Å distant from the 3' OH (in the case of G-20) or 80 Å distant (in the case of Y-37) in the crystal structure of tRNA^(Phe). The close agreement between the length of the reagent and the distance of G-20 from the 3' OH in the crystal structure illustrates the rigidity of the tRNA^(Phe) molecule in the dihydrouridine loop region at the corner of the molecule. The apparent ability of the 62-Å-long reagent to crosslink to a site, Y-37, that is 80 Å distant from the 3' OH in the crystal structure appears to illustrate the flexibility of both the 3' A-C-C-A terminus and the anticodon stem and loop, with respect to the tRNA molecule. These observations demonstrate the utility of oligoproline-based crosslinking reagents as rigid, variable-length molecular rulers for biological macromolecules in solution.
|Additional Information:||© 1981 by the National Academy of Sciences. Communicated by Melvin Calvin, December 15, 1980. We wish to thank Drs. Debra Peattie and Olke Uhlenbeck for helpful discussions of gel sequence determinations and end labeling and Drs. Alexander Rich and Gary Quigley for the exact crystal structure distances between the 3' OH and our crosslinking sites. This work was supported by grants from the National Science Foundation (PCM 79-23471) and the National Institutes of Health (GM 24128). The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in accordance with 18 U. S. C. §1734 solely to indicate this fact.|
|Subject Keywords:||tRNA solution structure; alkylation; gel sequence-determinations|
|Usage Policy:||No commercial reproduction, distribution, display or performance rights in this work are provided.|
|Deposited By:||Jason Perez|
|Deposited On:||17 Jul 2012 21:17|
|Last Modified:||17 Jul 2012 21:17|
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