DSSR-PyMOL cartoon-block schematics: PDB entry 7kee

PDB-id

7kee; DSSR-derived features in text and JSON formats

Class

transcription-DNA-RNA

Method

X-ray (3.45 Å)

Summary

RNA polymerase ii elongation complex with unnatural base dtpt3, rnamtp bound to e-site

Reference

Oh J, Shin J, Unarta IC, Wang W, Feldman AW, Karadeema RJ, Xu L, Xu J, Chong J, Krishnamurthy R, Huang X, Romesberg FE, Wang D (2021): "Transcriptional processing of an unnatural base pair by eukaryotic RNA polymerase II." Nat.Chem.Biol., 17, 906-914. doi: 10.1038/s41589-021-00817-3.

Abstract

The development of unnatural base pairs (UBPs) has greatly increased the information storage capacity of DNA, allowing for transcription of unnatural RNA by the heterologously expressed T7 RNA polymerase (RNAP) in Escherichia coli. However, little is known about how UBPs are transcribed by cellular RNA polymerases. Here, we investigated how synthetic unnatural nucleotides, NaM and TPT3, are recognized by eukaryotic RNA polymerase II (Pol II) and found that Pol II is able to selectively recognize UBPs with high fidelity when dTPT3 is in the template strand and rNaMTP acts as the nucleotide substrate. Our structural analysis and molecular dynamics simulation provide structural insights into transcriptional processing of UBPs in a stepwise manner. Intriguingly, we identified a novel 3'-RNA binding site after rNaM addition, termed the swing state. These results may pave the way for future studies in the design of transcription and translation strategies in higher organisms with expanded genetic codes.