The influence of symmetric internal loops on the flexibility of RNA

Journal of Molecular Biology
M Zacharias, P J Hagerman

Abstract

Internal loops are structural elements, often highly conserved, that are found in many RNA molecules of biological importance. They consist of short stretches of sequence in which the bases in one strand are not able to form canonical pairs with bases in the other strand, and are bounded on either side by helical RNA. In an effort to examine the influence of internal loops on the relative angular orientations of the flanking helices, we have quantified the apparent bend angles for symmetric internal loops of the form A(n)-A(n) and U(n)-U(n) (n=2, 4, and 6), located at the center of 150 to 154 bp RNA molecules, using the method of transient electric birefringence. This hydrodynamic method exploits the extreme sensitivity of the rate of rotational reorientation of the RNA molecules to the presence and magnitude of internal bends and/or points of increased flexibility. The birefringence decay behavior of the loop-containing RNA molecules was found to be much less strongly influenced by the presence of symmetric internal loops than by bulges of the same sequence and size. This general observation is mirrored by the electrophoretic behavior of the loop-containing molecules, which are much less strongly retarded on polyacrylamide gel...Continue Reading

Citations

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