7KUL

DNA modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')G

Summary for 7KUL

• Entry DOI: 10.2210/pdb7kul/pdb
• Descriptor: DNA/RNA (5'-R(*(LKC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*C)-D(P*G)-3'), DIGUANOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: rna, nonenzymatic rna extension, dna
• Biological source: synthetic construct
• Total number of polymer chains: 2
• Total formula weight: 10702.12

Authors

Fang, Z.,Giurgiu, C.,Szostak, J.W. (deposition date: 2020-11-25, release date: 2021-09-08, Last modification date: 2023-10-18)

Primary citation

Giurgiu, C.,Fang, Z.,Aitken, H.R.M.,Kim, S.C.,Pazienza, L.,Mittal, S.,Szostak, J.W.
Structure-Activity Relationships in Nonenzymatic Template-Directed RNA Synthesis.
Angew.Chem.Int.Ed.Engl., 60:22925-22932, 2021

PubMed Abstract: The template-directed synthesis of RNA played an important role in the transition from prebiotic chemistry to the beginnings of RNA based life, but the mechanism of RNA copying chemistry is incompletely understood. We measured the kinetics of template copying with a set of primers with modified 3'-nucleotides and determined the crystal structures of these modified nucleotides in the context of a primer/template/substrate-analog complex. pH-rate profiles and solvent isotope effects show that deprotonation of the primer 3'-hydroxyl occurs prior to the rate limiting step, the attack of the alkoxide on the activated phosphate of the incoming nucleotide. The analogs with a E ribose conformation show the fastest formation of 3'-5' phosphodiester bonds. Among those derivatives, the reaction rate is strongly correlated with the electronegativity of the 2'-substituent. We interpret our results in terms of differences in steric bulk and charge distribution in the ground vs. transition states.

PubMed: 34428345
DOI: 10.1002/anie.202109714

Experimental method

X-RAY DIFFRACTION (1.64 Å)