Adenylate oligomers

Figure 4- Circular dichoic spectra of adenylate oligomers at pH 4 5...

Figure 5 shows schematically the distributions of rotational strengths predicted by Equation 2 for adenylate oligomers as single-chain helices with eight residues per turn (a = 45°). To estimate the band splittings, we have used the fact that the nearest-neighbor theory predicts that the absorption band of the infinite, stacked-base helix will be shifted from the monomer band by an amount (2 V cos a)/h. Since this shift is experimentally known, V can be eliminated from Equation 1. 

The predicted features of the dichroic spectra are in good agreement with observations for the adenylate oligomers in neutral solution. Taking the simplest case, the dimer, we see that there should be two bands of opposite sign, spaced above and below the position of the monomer band their rotational strength should be given by... 

Figure 5. Schematic distributions of rotational strength as predicted by Equation 3 for first several adenylate oligomers...

Figure 6. Rotational strength of positive dichroic hand at 0°C. as a function of chain length N for adenylate oligomers...

Figure 8. Change in rotational strength of positive dichroic hand with temperature for some adenylate oligomers at pH 7.4 Chain length indicated by legend...

Table II. Thermodynamic Parameters for Thermal Denaturation of Adenylate Oligomers at Neutral pH (in 0.1M NaCl, 0.01 Mtris, pH 74).

Figure 11. Melting curves 1 for adenylate oligomers in acidic solution (pH 1. 5)...

Imidazolides of adenylic acid (ImpA) or uridylic acid (ImpU) are polycondensed to oligonucleotides by means of Zn2+ ions. 1673 The resulting phosphordiester bond was found to be of the 2, 5 type. In the reaction of nucleoside 5 -phosphoric acid methyl ester with ImpA in the presence of MgC, 2, 5 -dinucleotides are formed six to nine times more frequently than the corresponding 3, 5 compounds. 63 Polycondensations of ImpA in aqueous solution in the presence of various divalent metal ions lead to short oligo-adenylic acids (pA) (n = 1—5) mainly with 2, 5 -intemucleotide linkages. With Pb2+, for example, the total yield of oligomers was as high as 57%. 1683 1693... 

To eliminate some of the present ambiguity concerning these structures, we have examined the behavior of a number of oligomers and the polymer of adenylic acid, as well as the polymer of A6-hydroxyethyladenylic acid (poly HEA). We have been concerned with both the explanation of their optical properties in terms of proposed models and the thermodynamics of the melting process. It is hoped that the information so obtained will help to clarify the importance of order-disorder phenomena in biology and questions concerning the structure of such biologically important polynucleotides as RNA. 

We have chosen to investigate, primarily by circular dichroism measurements, a series of oligomers of adenylic acid (including the high polymer) as well as the closely related poly-A -hydroxyethyladenylic acid. The latter is of interest because the blocking of the nitrogen should prevent the formation of hydrogen-bonded double-strand helices under all conditions. 

The isolation of mRNA also became possible during the years of the decade. The discovery that a large proportion of mRNA species carried polymers of adenylate at their 3 -OH ends enabled the design of affinity chromatography supports such as oligo-dT cellulose and poly-U Sepharose which, because of their complementarity with the poly-A tails of the mRNA, could be employed to purify them from total RNA. These same poly-A tails made the purified mRNAs ideal substrates for reverse transcriptase. Oligomers of deoxythymidine (dT) could hydrogen bond to the poly-A and provide a primer for the initiation of transcription of a cDNA. 

Whanger, P. D., Phillips, A. T., Rabinowitz, K. W., Pipemo, J. R., Shada, J. D., and Wood, W. A., 1968, The mechanism of action of 5 -adenylic acid-activated threonine dehydrase. II. Protomer-oligomer interconversions and related properties, J. Biol. Chem. 243 167. 

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