6DVK

Computationally designed mini tetraloop-tetraloop receptor by the RNAMake program - construct 6 (miniTTR 6)

6DVK の概要

• エントリーDOI: 10.2210/pdb6dvk/pdb
• 分子名称: RNA (95-MER), MAGNESIUM ION, COBALT (II) ION, ... (4 entities in total)
• 機能のキーワード: automated rna structure design, tetra-loop tetra-loop receptor, rna motif, rna
• 由来する生物種: synthetic construct
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 30934.46

構造登録者

Eiler, D.R.,Yesselman, J.D.,Costantino, D.A.,Das, R.,Kieft, J.S. (登録日: 2018-06-24, 公開日: 2019-06-26, 最終更新日: 2024-03-13)

主引用文献

Yesselman, J.D.,Eiler, D.,Carlson, E.D.,Gotrik, M.R.,d'Aquino, A.E.,Ooms, A.N.,Kladwang, W.,Carlson, P.D.,Shi, X.,Costantino, D.A.,Herschlag, D.,Lucks, J.B.,Jewett, M.C.,Kieft, J.S.,Das, R.
Computational design of three-dimensional RNA structure and function.
Nat Nanotechnol, 14:866-873, 2019

PubMed Abstract: RNA nanotechnology seeks to create nanoscale machines by repurposing natural RNA modules. The field is slowed by the current need for human intuition during three-dimensional structural design. Here, we demonstrate that three distinct problems in RNA nanotechnology can be reduced to a pathfinding problem and automatically solved through an algorithm called RNAMake. First, RNAMake discovers highly stable single-chain solutions to the classic problem of aligning a tetraloop and its sequence-distal receptor, with experimental validation from chemical mapping, gel electrophoresis, solution X-ray scattering and crystallography with 2.55 Å resolution. Second, RNAMake automatically generates structured tethers that integrate 16S and 23S ribosomal RNAs into single-chain ribosomal RNAs that remain uncleaved by ribonucleases and assemble onto messenger RNA. Third, RNAMake enables the automated stabilization of small-molecule binding RNAs, with designed tertiary contacts that improve the binding affinity of the ATP aptamer and improve the fluorescence and stability of the Spinach RNA in cell extracts and in living Escherichia coli cells.

PubMed: 31427748
DOI: 10.1038/s41565-019-0517-8

実験手法

X-RAY DIFFRACTION (2.55 Å)