Journal: Nature Communications

Article Title: Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction

doi: 10.1038/s41467-020-19371-y

Figure Lengend Snippet: a Overlay of the dynamic ensembles of the TAR bulge. b RNA backbone torsion angles exhibiting different and similar distributions between Anton-MD-NMR and FARFAR-NMR are colored red and green, respectively (“Methods”). c 2D density maps of δ versus γ comparing Anton-MD-NMR and FARFAR-NMR ensembles ( N = 2000) for bulge residues as well as A22 and U40. The bin width is 20°. d Structure of the ribose moiety in C3′- endo and C2′- endo conformations. e Population of C2′- endo pucker at bulge residues as well as A22 and U40 in the FARFAR-library ( N = 10,000, red open), FARFAR-NMR ( N = 20 × 100 = 2000, red fill), Anton-MD library ( N = 10,000, blue open) and Anton-MD-NMR ( N = 20 × 100 = 2000, blue fill). Experimental estimates of the C2′- endo population based on 13 C chemical shifts are indicated above the bars (“Methods”). f The population of conformers in the ensemble as a function of the number of C2′- endo bulge residues for FARFAR-NMR (red, N = 20 × 100 = 2000) and Anton-MD-NMR (blue, N = 20 × 100 = 2000).

Article Snippet: TAR, TAR-Nm-U23, and TAR-Nm-C24 RNA samples were synthesized using a MerMade 6 Oligo Synthesizer (BioAutomation) via solid-phase synthesis using standard phosphoramidite chemistry and deprotection protocols.

Techniques:

Journal: Nature Communications

Article Title: Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction

doi: 10.1038/s41467-020-19371-y

Figure Lengend Snippet: a Overlay of conformers showing motions in bulge residues for linear (| β h | < 45°), intermediate bend (45° < | β h | < 70°) and kinked (| β h | > 70°) inter-helical conformations in the FARFAR-NMR and Anton-MD-NMR ensembles. b , c The fractional populations of conformers with the number of b extra-helical and c C2′- endo residues (color-coded) in the bulge residues (U23, C24, and U25) as a function of bending angle in the FARFAR-NMR (“F”) and Anton-MD-NMR (“A”) ensembles ( N = 20). d Comparison of one coaxially stacked FARFAR-NMR conformer with the crystal structure of Ca 2+ -bound TAR (PDBID: 397D) . e Nm shifts sugar-pucker equilibrium towards C3′- endo . f Overlay of 2D [ 13 C, 1 H] HSQC NMR spectra of the aromatic spins for TAR-Nm-C24 without Mg 2+ (blue) with blue arrows indicate unstacking, TAR without Mg 2+ (cyan) and TAR with 3 mM Mg 2+ (red) with red arrows indicating increased coaxial stacking.

Article Snippet: TAR, TAR-Nm-U23, and TAR-Nm-C24 RNA samples were synthesized using a MerMade 6 Oligo Synthesizer (BioAutomation) via solid-phase synthesis using standard phosphoramidite chemistry and deprotection protocols.

Techniques:

Journal: Nature Communications

Article Title: Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction

doi: 10.1038/s41467-020-19371-y

Figure Lengend Snippet: a Overlay of conformers showing motions in bulge residues for linear (| β h | < 45°), intermediate bend (45° < | β h | < 70°) and kinked (| β h | > 70°) inter-helical conformations in the FARFAR-NMR and Anton-MD-NMR ensembles. b , c The fractional populations of conformers with the number of b extra-helical and c C2′- endo residues (color-coded) in the bulge residues (U23, C24, and U25) as a function of bending angle in the FARFAR-NMR (“F”) and Anton-MD-NMR (“A”) ensembles ( N = 20). d Comparison of one coaxially stacked FARFAR-NMR conformer with the crystal structure of Ca 2+ -bound TAR (PDBID: 397D) . e Nm shifts sugar-pucker equilibrium towards C3′- endo . f Overlay of 2D [ 13 C, 1 H] HSQC NMR spectra of the aromatic spins for TAR-Nm-C24 without Mg 2+ (blue) with blue arrows indicate unstacking, TAR without Mg 2+ (cyan) and TAR with 3 mM Mg 2+ (red) with red arrows indicating increased coaxial stacking.

Article Snippet: TAR, TAR-Nm-U23, and TAR-Nm-C24 RNA samples were synthesized using a MerMade 6 Oligo Synthesizer (BioAutomation) via solid-phase synthesis using standard phosphoramidite chemistry and deprotection protocols.

Techniques: