The enzymatic synthesis of polyribonucleotides using 5'-adenylylmethylenediphosphonate: a phosphonic acid analog of adenosine triphosphate

The mechanism of pyrophosphorolysis of RNA by RNA polymerase. Endowment of RNA polymerase with artificial exonuclease activity

DNA-directed RNA polymerase from Escherichia coli can break down RNA by catalysing the reverse of the reaction: NTP + (RNA)n = (RNA)n+1 + PPi where n indicates the number of nucleotide residues in the RNA molecule, to yield nucleoside triphosphates. This reaction requires the ternary complex of the polymerase with template DNA and the RNA that it has synthesized. It is now shown that methylenebis(arsonic acid) [CH2(AsO3H2)2], arsonomethylphosphonic acid (H2O3As-CH2-PO3H2) and arsonoacetic acid (H2O3As-CH2-CO2H) can replace pyrophosphate in this reaction. When they do so, the low-Mr products of the reaction prove to be nucleoside 5'-phosphates, so that the arsenical compounds endow the polymerase with an artificial exonuclease activity, an effect previously found by Rozovskaya, Chenchik, Tarusova, Bibilashvili & Khomutov [(1981) Mol. Biol. (Moscow) 15, 636-652] for phosphonoacetic acid (H2O3P-CH2-CO2H). This is explained by instability of the analogues of nucleoside triphosphates believed to be the initial products. Specificity of recognition of pyrophosphate is discussed in terms of the sites, beta and gamma, for the -PO3H2 groups of pyrophosphate that will yield P-beta and P-gamma of the nascent nucleoside triphosphate. Site gamma can accept -AsO3H2 in place of -PO3H2, but less well; site beta can accept both, and also -CO2H. We suggest that partial transfer of an Mg2+ ion from the attacking pyrophosphate to the phosphate of the internucleotide bond of the RNA may increase the nucleophilic reactivity of the pyrophosphate and the electrophilicity of the diester, so that the reaction is assisted.

31P nuclear magnetic resonance of phosphonic acid analogues of adenosine nucleotides as functions of pH and magnesium ion concentration

The 31P NMR proton-decoupled spectra of alpha, beta-methylene-ATP [Ap(CH2)pp], beta, gamma-methylene-ATP [App(CH2)p], and alpha, beta-methylene-ADP [Ap(CH2)p] were measured as functions of pH and Mg2+ concentration. Each ATP analogue yielded three resonances: two doublets and one doublet-of-a-doublet. Assignments of resonances were based upon spin-coupling multiplets, their coupling constant magnitudes (24-27 Hz for -P-O-P- and 4-10 Hz for -P-CH2-P-), and the magnitude of the chemical shift movement during proton titration or its direction of movement. All phosphonyl resonances are substantially downfield compared to phosphoryl resonances. The chemical shifts of terminal phosphonyl units moved upfield with increasing pH or rising Mg2+ concentration. The chemical shifts of phosphonyl and phosphoryl anhydride plus ester units usually either moved downfield during proton titration and addition of Mg2+ or remained constant. Accurate pKa' values were readily determined from chemical shift movements as a function of pH: 3.05 +/- 0.04 and 8.80 +/- 0.05 for App(CH2)p, 7.34 +/- 0.06 for Ap(CH2)pp, and 8.29 +/- 0.02 for Ap(CH2)p. Addition of Mg2+ or Tris produced an acidic shift of the alkaline pKa' values. Addition of Mg2+ at pH 7.0 to the nucleotides caused large movements in the chemical shifts of their terminal two phosphorus atoms.

Effect of ATP analogs of DNA synthesis in isolated nuclei

Optimal synthesis of DNA in Ehrlich ascites cell nuclei is shown to be dependent upon the presence of both ATP and ADP. ATP can be replaced only by dATP. An ATP regenerating system is less effective than ATP alone or ATP in combination with ADP. ATP does not stimulate DNA synthesis primarily by maintenance of deoxyribonucleotide triphosphate levels. When the inhibition of DNA synthesis by high ATP levels is taken into account, the ATP analogs adenosine 5'-(alpha,beta-methylene)triphosphate, adenosine 5'-(beta, gamma-methylene)-triphosphate, and adenosine 5'-(beta, gamma-imino)triphosphate can neither substitute for ATP nor inhibit the ATP stimulation of DNA synthesis. Adenosine 5'-(3-thio)triphosphate, however, is a competitive inhibitor of DNA synthesis.

Imidodiphosphate and Pyrophosphate: Possible Biological Significance of Similar Structures

The structure of sodium imidodiphosphate has been determined by single crystal x-ray diffraction. The P-N-P bond angle (127.2 degrees) and P-N bond distance (1.68 angstroms) are remarkably similar to newly refined values for the P-O-P bond angle (128.6 degrees) and the bridging P-O bond distance (1.63 angstroms) of sodium pyrophosphate. This close similarity may explain why P-N-P linkages in algal "polyphosphates" escaped detection until recently and why adenosine triphosphate analogs with this linkage mimic adenosine triphosphate so closely.