Life as we know it depends on turning on and off the proper genes at the correct time. This process of gene expression starts when an RNA message is copied from DNA. Scientists have long known that an enzyme called RNA polymerase II plays the central role in this delicate transcription process. But the exact mechanism by which RNA polymerase II selects specific nucleotides and catalyzes the reaction that incorporates them into a growing RNA strand has not been well understood.

In a new study published in the December 1, 2006 issue of Cell, the 2006 Chemistry Nobel Prize Laureate, Roger Kornberg, and his research group at Stanford University performed x-ray studies at SSRL Beam Lines 11-1 and 9-2 and at the Advanced Light Source at Berkeley to investigate the molecular structure of this enzyme in action. The study revealed that a structural element of the enzyme called the trigger loop is involved in both nucleotide recognition and catalysis.

To ensure the accuracy of the transcription process, RNA polymerase II must distinguish between ribonucleotides (nucleotides that make up RNA) and deoxyribonucleotides (nucleotides that make up DNA) in the cell. It also must distinguish between different types of ribonucleotides and add to the RNA strand the one that is complimentary to the deoxyribonucleotide in the DNA template. When such a "correct" ribonucleotide is present, it fits together with an extensive network consisting of the trigger loop, a structural element known as the bridge helix, and other nearby polymerase residues, which all fit together like pieces of a puzzle. Additionally, when a correct ribonucleotide is present, the interactions between these puzzle pieces cause the trigger loop to then swing into position beneath the nucleotide and seal off the active site. This move puts the ribonucleotide into the right position to be added to the growing RNA strand, and the interaction between the side chain of trigger loop and nucleotide phosphate thus acts as a trigger for the catalytic reaction. The trigger loop's role in both selection and catalysis therefore ensures the accuracy of the transcription process, without which cells would have inefficient transcription and become unhealthy or die. This finding promises to inform future efforts to manipulate the transcription process for therapeutic and other purposes.

To learn more about this research see the full scientific highlight at:
http://www-ssrl.slac.stanford.edu/research/highlights_archive/pol-II.html

Wang, D., Bushnell, D.A., Westover, K.D., Kaplan, C.D., and Kornberg, R.D. (2006) Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis. Cell 127, 941-954.