Donor activation in the T4 RNA ligase reaction

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Abstract
T4 RNA ligase catalyzes the adenylation of donor oligonucleotide substrates. These activated intermediates react with an acceptor oligonucleotide which results in phosphodiester bond formation and the concomitant release of AMP. Adenylation of the 4 common nucleoside 3'',5''-bisphosphates as catalyzed by T4 RNA ligase in the absence of an acceptor oligonucleotide was examined. The extents of product formation indicate that pCp is the best substrate in the reaction and pGp is the poorest. Kinetic parameters for the joining reaction between the preadenylated nucleoside 3'',5''-bisphosphates, A(5'')pp(5'')Cp or A-(5'')pp(5'')Gp, and a good acceptor substrate (ApApA) or a poor acceptor substrate (UpUpU) were determined. The apparent Km values for both preadenylated donors in the joining reaction are similar, and the reaction velocity is much faster than observed in the overall joining reaction. The nonnucleotide adenylated substrate P1-(5''-adenosyl) P2-(o-nitrobenzyl) diphosphate also exhibits a similar apparent Km but reacts with a velocity 80-fold slower than the adenylated nucleoside 3'',5''-bisphosphates. By use of preadenylated donors, oligonucleotide substrates can be elongated more efficiently than occurs with the nucleoside 3'',5''-bisphosphates.