Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	A unified Watson-Crick geometry drives transcription of six-letter expanded DNA alphabets by E. coli RNA polymerase.
Journal, issue, pages	Nat Commun, Vol. 14, Issue 1, Page 8219, Year 2023
Publish date	Dec 12, 2023
Authors	Juntaek Oh / Zelin Shan / Shuichi Hoshika / Jun Xu / Jenny Chong / Steven A Benner / Dmitry Lyumkis / Dong Wang /
PubMed Abstract	Artificially Expanded Genetic Information Systems (AEGIS) add independently replicable unnatural nucleotide pairs to the natural G:C and A:T/U pairs found in native DNA, joining the unnatural pairs ...Artificially Expanded Genetic Information Systems (AEGIS) add independently replicable unnatural nucleotide pairs to the natural G:C and A:T/U pairs found in native DNA, joining the unnatural pairs through alternative modes of hydrogen bonding. Whether and how AEGIS pairs are recognized and processed by multi-subunit cellular RNA polymerases (RNAPs) remains unknown. Here, we show that E. coli RNAP selectively recognizes unnatural nucleobases in a six-letter expanded genetic system. High-resolution cryo-EM structures of three RNAP elongation complexes containing template-substrate UBPs reveal the shared principles behind the recognition of AEGIS and natural base pairs. In these structures, RNAPs are captured in an active state, poised to perform the chemistry step. At this point, the unnatural base pair adopts a Watson-Crick geometry, and the trigger loop is folded into an active conformation, indicating that the mechanistic principles underlying recognition and incorporation of natural base pairs also apply to AEGIS unnatural base pairs. These data validate the design philosophy of AEGIS unnatural basepairs. Further, we provide structural evidence supporting a long-standing hypothesis that pair mismatch during transcription occurs via tautomerization. Together, our work highlights the importance of Watson-Crick complementarity underlying the design principles of AEGIS base pair recognition.
External links	Nat Commun / PubMed:38086811 / PubMed Central
Methods	EM (single particle)
Resolution	2.65 - 3.28 Å
Structure data	40862 8sy5 EMDB-40862, PDB-8sy5: E. coli DNA-directed RNA polymerase transcription elongation complex bound the unnatural dS-BTP base pair in the active site Method: EM (single particle) / Resolution: 2.7 Å 40863 8sy6 EMDB-40863, PDB-8sy6: E. coli DNA-directed RNA polymerase transcription elongation complex bound the unnatural dB-UTP base pair in the active site Method: EM (single particle) / Resolution: 3.28 Å 40864 8sy7 EMDB-40864, PDB-8sy7: E. coli DNA-directed RNA polymerase transcription elongation complex bound the unnatural dB-STP base pair in the active site Method: EM (single particle) / Resolution: 2.65 Å
Chemicals	ChemComp-ZN: Unknown entry ChemComp-MG: Unknown entry ChemComp-X0F: 2-oxo-2-hydroadenosine 5'-(tetrahydrogen triphosphate) ChemComp-HOH: WATER / Water ChemComp-DG: 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE / dGMPYM / Deoxyguanosine monophosphate ChemComp-UTP: URIDINE 5'-TRIPHOSPHATE / UTPYM / Uridine triphosphate ChemComp-X0O: [[(2~{R},3~{S},4~{R},5~{S})-5-(4-azanyl-1-methyl-2-oxidanylidene-pyrimidin-5-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
Source	escherichia coli (E. coli) synthetic construct (others)
Keywords	TRANSCRIPTION/DNA/RNA / complex / unnatural base pairs / synthetic biology / transcription / TRANSCRIPTION-DNA-RNA complex