Replication of bacteriophage ribonucleic acid: some properties of native and denatured replicative intermediate

Separation of replicative intermediate from single-stranded ribonucleic acid by sedimentation at low ionic strength

By sedimentation in 2.5 x 10(-4)m sodium ethylenediaminetetraacetate at 25 C, replicative intermediate could be separated from single-stranded ribonucleic acid, both viral and ribosomal. All of the label in the replicative intermediate after a brief pulse of titrated uridine was resistant to ribonuclease.

Replication of bacteriophage ribonucleic acid: analysis of the ultrastructure of the replicative form and the replicative intermediate of bacteriophage R17

A detailed qualitative and quantitative comparison was made of the ultrastructure of single-stranded ribonucleic acid (RNA) from bacteriophage R17 and double-stranded replicative form (RF) and replicative intermediate (RI) from cells infected with this bacteriophage. The nucleic acids were prepared for electron microscopy by the protein monolayer spreading technique of Kleinschmidt. Single-stranded RNA aggregated during spreading in the absence of urea, whereas RF and RI did not. On the other hand, RF and RI appeared to be susceptible to shear during spreading, whereas R17 RNA was not. From the maximal length of RF, a base translation of 3.14 A was calculated. This value favors a 10-fold helix model of double-stranded RNA. The same base translation was found for R17 RNA, indicating a stacked base structure for single-stranded RNA spread in the presence of urea. RI is a branched structure and the branches are removed by ribonuclease treatment. The branches are believed to be nascent single-stranded viral RNA. The contour length of the branch was equal to the contour length of the main chain up to the branch point, as predicted from theoretical analysis of the replication of viral RNA. The structure of RF and the main chain of RI was also analyzed by plotting the log (end-to-end distance squared) versus log (contour length). This demonstrated structures intermediate in stiffness between a random coil and a rigid rod.

Denaturation and renaturation of viral ribonucleic acd. II. Characterization of the products resulting from annealing R17 ribonucleic acid with denatured replicative form or with denatured replicative intermediate

The ribonucleic acid (RNA) product resulting from annealing R17 RNA with denatured replicative form or replicative intermediate could be divided into two distinct types of RNA by precipitation in 1.5 m NaCl. The RNA found in the salt supernatant fluid was resistant to digestion by ribonuclease, had a sedimentation coefficient of 15S, and displayed a sharp thermal transition. The RNA in the salt supernatant fluid appeared to be identical to replicative form. The RNA found in the salt precipitate was resistant to digestion by ribonuclease, but possessed both single- and double-stranded characteristics. The RNA sedimented as a broad band in a sucrose gradient, with a sedimentation coefficient of 15S, and displayed a melting transition characteristic of a mixture of single- and double-stranded RNA. Mild ribonuclease digestion of the salt-precipitable RNA produced a ribonuclease-resistant material with sedimentation properties identical to the RNA found in the salt supernatant fluid.

Denaturation and renaturation of viral ribonucleic acid. I. Annealing R17 ribonucleic acid with denatured replicative form or with denatured replicative intermediate

Purified replicative form (RF) and replicative intermediate (RI) prepared from Escherichia coli infected with R17 were denatured in 0.15 m NaCl, 0.015 m sodium citrate containing 65% dimethylsulfoxide. Denaturation of RF or RI was demonstrated spectrophotometrically, chromatographically, and by sedimentation analysis. Denatured RF or RI was annealed by carefully decreasing the temperature from 62 to 20 C. Annealing was accompanied by a decreased absorbance at 260 mmu. The decrease in absorbance during annealing appeared to be dependent upon the rate of cooling and the concentration of ribonucleic acid (RNA). Denatured RF or RI was annealed with R17 RNA which was labeled with (3)H-uridine. The annealed product was 73 to 82% resistant to 0.1 mug/ml of ribonuclease. Annealing R17 RNA with either denatured RF or RI resulted in the formation of a ribonuclease-resistant product with a sedimentation profile resembling that of native RI. Melting the annealed products in 85.7% dimethyl sulfoxide produced 27S single-stranded R17 RNA and a heterogeneous population of more slowly sedimenting RNA.