Priming of superhelical SV40 DNA by Escherichia coli RNA polymerase for in vitro DNA synthesis.

When closed circular SV40 DNA containing 58 negative superhelical turns is used as a template for RNA synthesis with Escherichia coli RNA polymerase, a fraction of the RNA product remains complexed with the DNA. The RNA in the complex is resistant to ribonuclease in high salt, and the Tm indicates that it is hydrogen bonded to the DNA. The mole ratio of RNA to DNA nucleotides in the complex ranges from 0.01 to 0.08; the RNA ranges in length from 80 to 600 nucleotides. The formation of the complex is dependent on the circular DNA being topologically underwound since no complex is formed when closed circular DNA containing zero superhelical turns is used as the template. The DNA-RNA complex can serve as a primer-template combination for in vitro DNA synthesis by E. coli DNA polymerase I. After synthesis with (alpha-32P)-labeled deoxyribonucleoside triphosphates followed by alkaline hydrolysis, the isolation of 32P-labeled ribonucleotides is evidence for a covalent linkage between the RNA and the DNA synthesized. During the in vitro DNA synthesis, the template is nicked at a low rate, and the nicked molecules support extensive DNA synthesis. This observation indicates that only limited synthesis can occur on unnicked molecules possibly owing to the topological constraints against unwinding of the helix. Possible models for in vivo priming of double-stranded DNA by E. coli RNA polymerase are discussed.     

In vitro transcription of Drosophila ribosomal genes using Drosophila RNA polymerases

Drosophila RNA polymerases I &; II were used to transcribe a recombinant bacterial plasmid containing one copy of Drosophila ribosomal DNA. Both supercoiled and relaxed, closed circular plasmids were used. With Mg⁺² as the divalent cation, enzyme I is much more active on both forms of the plasmid; the relaxed form in particular supports almost no RNA synthesis by enzyme II. When Mn⁺² is present, differences in template efficiencies are minimal. The differences observed in the absence of Mn⁺² seem to depend only on different preferences for the physical state of the template and not on recognition of specific promotor sequences, since enzyme I shows no strand selection when transcribing these plasmids.     

Comparative study of calf thymus and wheat germ RNA polymerase II: stability of initiation complexes and elongation rates.

Pure wheat germ RNA polymerase II but not calf thymus RNA polymerase II forms relatively stable binary complexes (half life time of 30 minutes at 0°C) with superhelical SV 40 DNA. On the contrary, the addition of a specific dinucleotide and a single ribotriphosphate permits the formation of highly stable complexes between both enzymes and SV 40 DNA. The elongation of RNA chains with preinitiated wheat germ enzyme only is stimulated by sarkosyl. These observations suggest that the wheat germ enzyme, as compared to that isolated from calf thymus, may contain a protein factor, a more native structure or both that permit efficient initiation and elongation of RNA chains on double stranded DNA.