Poly tract location

DNA Bending Assume that a poly(A) tract five base pairs long produces a 20° bend in a DNA strand. Calculate the total (net) bend produced in a DNA if the center base pairs (the third of five) of two successive (dA)5 tracts are located (a) 10 base pairs apart (b) 15 base pairs apart. Assume 10 base pairs per turn in the DNA double helix. 

RNase A can use one-dimensional diffusion along a poly(dA) tract to accelerate the location of a uridine substrate. Use of this mechanism depends on the concentration of NaCl, as expected if the enzyme were binding to the nucleic acid by nonspecific interactions with phosphoryl groups. Binding of the enzymic active site to adenosine residues is 20-fold weaker than to uridine residues, which could enhance the ability of the enzyme to slide along the poly(dA) tract. 

Alkaline hydrolysates of mRNA from vaccinia virus (Kates, 1970) and mouse sarcoma 180 cells (Mendecki et al, 1972) show that the poly (A) tracts, 100-200 nucleotides in length, are located at the 3 -ter-minal end of the RNA molecules. Analysis of the reaction products of highly purified exoribonuclease specific for 3 -OH termini also indicates that most (and possibly all) of the poly (A) sequences are at the 3 -terminal end of the mRNA s (Molloy et al, 1972). This is supported by the fact that the time course of poly( A) labeling in polysomes indicates that this sequence is assembled after the rest of the RNA molecule has been completed (Mendecki et al, 1972). Poly (A) synthesis is sensitive to actinomycin D but to an extent less than that of the rest of the RNA molecule which further argues that the poly (A) segment is added after transcription is completed (Darnell et al, 1971b Mendecki et al, 1972). 

PEREZ-BERCOIT, R. and GARDEE, M. The genomic ERA of Mengo virus. I. Location of the poly(C) tract. Virology (1977) ... 

In general, these poly(A) tracts have been isolated by complete digestion of the viral ENAs with both T and pancreatic RNases. The 3 terminal location is suggested by (a) end-labelling of the tenninal adenosine residue with H-borohydride (57) or 5s-isoniazid (50) ( ) the absence of any G or pyrimidine residues in highly-purified preparations of the poly(A) tract (50). 

The only extensive studies which have been carried out on the nucleotide sequences of picornavims RNAs concern those sequences adjacent to the J - te miinal poly(A) tract (65-67). In view of their location, it might be expected that these sequences could be involved in specific interactions with the viral replicases, or else act in some other way as control elements. 

ROWLANDS, D.J., HARRIS, T.J.R. and BROWN, F. A more precise location of the poly(c) tract in foot-and-mouth disease virus RNA. J. Virol. (1978), 26, 335-343. 

We have very little idea about the stoichiometry of the two major polysomal mRNP proteins, or their location on the mRNA, apart from the fact that the 8,000 dalton protein seems to be associated with the poly A tract at the 5 end (59) The function of the proteins is even more obscure. In cell-free translation assays the activity of polysomal mRNP is no greater than that of deproteinised mRNA (20). This result is open to the qualification that in crude cell-free systems the added deproteinised mRNA mi t pick up proteins from the cell-free extract and thereby be effectively converted into polysomal mRNP particles, but since the same result is obtained in highly fractionated systems (11) this reservation can probably be discounted. The major polysomal mRNP proteins are distinct from all seven recognised initiation factors (ll), and initiation complex formation is found to require the same set of seven factors regardless of whether polysomal mRNP or deproteinised mRNA is used (11). In short, there is no evidence that these proteins play a role in mRNA translation. 

Perez-Bercoff, R., and Gander, M., 1977, The genomic RNA of mengovirus. I Location of the poly(C) tract. Virology 80 426. 

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