E. coli RNA Polymerase Reads 8-Letter DNA, Cryo-EM Maps 4 Structures at 2.42–2.75 Å
Updated
Updated · Nature.com · Sep 2
E. coli RNA Polymerase Reads 8-Letter DNA, Cryo-EM Maps 4 Structures at 2.42–2.75 Å
3 articles · Updated · Nature.com · Sep 2
Summary
Four cryo-EM structures show E. coli RNA polymerase accommodating the synthetic P:Z and P:Z* base pairs in near-native pre-catalytic states, establishing that an eight-letter alphabet can be transcribed by a cellular multi-subunit enzyme.
Kinetic and transcription assays found cognate synthetic pairs were incorporated efficiently and selectively, with P:Z running only about twofold slower than a natural G:C pair and elongation continuing past the synthetic site without detectable pausing.
A redesigned base, Z*, cut the main fidelity problem—G:Z mispairing—by replacing Z’s nitro group with a carboxamide that raises its pKa above 10 and suppresses deprotonation-driven errors.
The structures also identified a water-mediated nitro-group interaction that appears to favor trigger-loop closure and faster incorporation in the dZ:PTP complex, suggesting synthetic base chemistry can tune RNA polymerase conformational dynamics.
The work extends earlier six-letter and T7 polymerase results to a cellular transcription machine, laying groundwork for eight-letter RNAs and eventually expanded coding or aptamer systems.