Stephen P. Bell

Molecular mechanisms governing species-specific transcription of ribosomal RNA

An unusual property of ribosomal RNA transcription is the species specificity of promoter recognition. Unexpectedly, the sequence-specific RNA pol I transcription factors hUBF and xUBF, isolated from human and Xenopus cells, respectively, recognize the same DNA sequence elements. Despite this similarity in DNA binding activity, neither factor will functionally substitute for the other in reconstituted transcription assays, suggesting that the specificity of protein-DNA interactions cannot account for the species-specific activation of transcription by hUBF and xUBF. Interestingly, we find that hUBF and xUBF form distinctly different complexes with human SL1 at both the human and Xenopus promoters. Together these results strongly implicate specific protein-protein interactions between transcription factors as an important determinant of promoter selectivity and species specificity.

Abinitio SCF and CI studies of three states of NH2

Theoretical calculations have been made for the ? 2B1, ? 2A1,, ? 2B2 states of the NH2 radical using a double‐zeta and double‐zeta‐plus‐ polarization basis sets. With the most extensive basis set and configuration interaction the optimum geometry for the 2B1 state is r=1.029 A, ϑ=103.1°, while the experimental geometry is r=1.024 A, ϑ=103.3°. Similarly, the CI geometry for the 2A1 state is r=1.000 A, ϑ=143.4° while the experimental geometry is r=1.004±0.03 A, ϑ=144°±5°. The CI excitation energy between these states is Te=11 830 cm−1 compared with the origin of the ?–? transition of 11 122 cm−1 and the barrier to linearity in the 2A1 state by CI is 974 cm−1 compared with the experimental barrier of 777±100 cm−1. The ? 2B2 state is predicted to have the geometry r=1.162 A, ϑ=47.5° with an excitation energy from the ? 2B1 state of 38640 cm−1.

The effects of basis set and configuration interaction on the predicted geometries of AH2 molecules

The effects of basis set size and type on the theoretical optimum geometries calculated by ab initio SCF and CI methods is studied for the molecular species H2O 1A1, NH2 2B1, CH2 1A1, H2O+ 2B1, NH2 2A1, CH2 3B1, BH2 2A1, H2O+ 2A1, over the range from minimum to much extended basis sets. The difference in optimum geometry between SCF and CI calculations is also noted. Calculations made specially for this study have used double‐zeta and double‐zeta‐plus‐polarization Gaussian basis sets. The geometries predicted by these and many published calculations are plotted as points on diagrams of bond angle ϑ versus bond length r. It is observed that there are striking similarities between such diagrams for different species, and thus it is possible to use the diagrams in order to predict a molecular geometry with greater accuracy than by one method alone (except CI with a very extended basis). Such a prediction is made from calculations of the species NH−2 1A1.

Ab initio study of the 1 A 1, ã 3 A″ and à 1 A″ states of formaldehyde

Ab initio calculations of the 1 A 1 ground state and the a 3 A″ and A 1 A″ excited states of formaldehyde have been made in order to study optimum geometries, excitation energies and barriers to inversion in the non-planar excited states. Double-zeta and double-zeta-plus-polarization gaussian basis sets were used in the SCF calculations and CI calculations were made in at least one of these bases for each state. Good agreement is obtained with the ground state experimental structure but less than good agreement with the excited state structures. The barrier in the 3 A″ state is predicted well but, unlike experiment, the calculated barrier in the 1 A″ state is not significantly different from that in the 3 A″ state.