Template Conformation Research Articles

The stability of abortively cycling T7 RNA polymerase complexes depends upon template conformation.

We have developed a promoter competition assay to determine whether T7 RNA polymerase dissociates from its template during abortive cycling. We find that the stability of the initiation complex (IC) depends upon the conformation of the promoter, and that the degree to which the template is unwound contributes importantly to the stability of the IC. On linear DNA or a relaxed plasmid template, the stability of the IC is very low (t1/2 < 1 min). However, on a supercoiled template, the IC has a stability that is comparable to that of a paused elongation complex (t1/2 = 14 min). At a synthetic promoter that is single stranded in the initiation region (from -5 and downstream), the polymerase forms a highly stable complex (t1/2 > 30 min) even in the absence of RNA synthesis. These findings are important to our understanding of the transition from the IC to an EC.

A genetic algorithm based molecular modeling technique for RNA stem-loop structures.

A new modeling technique for arriving at the three dimensional (3-D) structure of an RNA stem-loop has been developed based on a conformational search by a genetic algorithm and the following refinement by energy minimization. The genetic algorithm simultaneously optimizes a population of conformations in the predefined conformational space and generates 3-D models of RNA. The fitness function to be optimized by the algorithm has been defined to reflect the satisfaction of known conformational constraints. In addition to a term for distance constraints, the fitness function contains a term to constrain each local conformation near to a prepared template conformation. The technique has been applied to the two loops of tRNA, the anticodon loop and the T-loop, and has found good models with small root mean square deviations from the crystal structure. Slightly different models have also been found for the anticodon loop. The analysis of a collection of alternative models obtained has revealed statistical features of local variations at each base position.

The influence of an alternate template conformation on elongating phage T7 RNA polymerase

We investigated the effect of left-handed Z-DNA on transcription by bacteriophage T7 RNA polymerase in vitro and, surprisingly, found that the enzyme can efficiently utilize a template containing a stretch of left-handed DNA close to the promoter. Analysis of transcription products revealed that only a small fraction of elongating polymerases abort transcription either at the promoter proximal or at the distal B-to-Z junction and, even less frequently, within the stretch of left-handed DNA. Our results indicate that, unlike E. coli RNA polymerase, T7 RNA polymerase can utilize a template with a CG stretch in an alternate conformation. In contrast, polymerases are completely blocked at the promoter proximal junction by a monoclonal antibody directed against Z-DNA. This blockage remains stable over a remarkable time, even when negative supercoiling is released by linearization of the template. Together with our recent finding of transcription-induced formation of Z-DNA (3), our data provide an example for a possible auto-regulatory mechanism that employs a change in DNA conformation.

Replication-dependent transactivation of the polyomavirus late promoter

When a plasmid containing the wild-type polyomavirus intergenic regulatory region fused to the bacterial cat gene was introduced into mouse NIH 3T3 cells along with a plasmid coding for the early viral proteins (T antigens), chloramphenicol transacetylase enzyme activity and mRNA levels were increased about 10-fold over levels observed in the absence of early proteins. To investigate this transactivation phenomenon further, 11 specific deletion mutant derivatives of the wild-type parent plasmid were constructed and studied. One mutant (NAL) with a minimal level of chloramphenicol transacetylase expression in the absence of T antigens was capable of being transactivated more than 40-fold. A number of other mutants, however, had little capacity for transactivation. Each of these mutants had in common a defect in large T-antigen-mediated DNA replication. Interestingly, one of the transactivation-defective mutants showed a basal late promoter activity fivefold higher than that of wild type and replicated in mouse cells in the absence of large T antigen. Subsequently, a small deletion abolishing viral DNA replication was introduced into those mutants capable of transactivation. The effect of the second deletion was to eliminate both replication and transactivation. Finally, wild-type and mutant constructs were transfected into Fisher rat F-111 cells in the presence or absence of early proteins. No transactivation or replication was ever observed in these cells. We concluded from these studies that the observed transactivation of the polyomavirus late promoter by one or more of the viral early proteins was due to either higher template concentration resulting from DNA replication or replication-associated changes in template conformation.

Changes in endonuclease activity during growth and regression of the Shionogi mammary carcinoma

Autodigestion of nuclei isolated from the androgen-dependent Shionogi mouse mammary carcinoma revealed the presence of endogenous endonuclease activity which was stimulated by Ca 2+ and Mg 2+ and generated a repeating pattern of DNA fragments with an average monomeric size of 179 base pairs. The nuclear concentration of endonuclease activity declined rapidly after castration to a level 45% of that measured in tumours from non-castrated hosts. Most of the endonuclease activity (80%) could be extracted in a soluble form after sonication of the nuclei and subsequent centrifugation. The reduced concentration of endonuclease activity in regressing tumours following castration was not due to changes in chromatin template conformation and could be restored to normal levels within 1 day of androgen treatment. Examination of DNA synthetic activity and the concentration of nuclear androgen receptors during tumour regression indicated that the decrease in endonuclease activity paralleled the declining rate of DNA synthesis but was preceded by a loss of nuclear androgen receptors. Together these results suggest that the endonuclease activity of the Shionogi carcinoma is more likely involved with androgen-stimulated cell proliferation rather than with the autophagic mechanism responsible for tumour regression and cell death.

Origins of life: Conformational energy calculations on primitive tRNA nestling an amino acid

We report conformational energy calculations on our proposal of a molecular interaction theory for the origin of the nucleic acid-directed, adaptor-mediated synthesis of proteins that links the phenomena of chemical and biological evolution. A particular conformation of a pentanucleotide turns out to be a double-sided template for a primitive decoding system. It is able to neatly nestle an amino acid via hydrogen bonds, and this complex is found to be an energetically favourable conformation. The total potential energy of the complex is calculated using semi-empirical potential energy functions. A local-minimum conformation is obtained and its features are reported. The template conformation of the pentanucleotide is found to have an energy value far lower than a regular helical conformation. When the amino acid is nestled in the cleft of the template-conformation through specific hydrogen bonds, the energy is further lowered. A D-amino acid nestled into the PIT (Primitive tRNA) is found to be less stable than its L counterpart, as revealed by energy calculations.