Selective deuteration of an RNA:RNA complex for structural analysis using small-angle scattering.

Munsayac A, Leite WC, Hopkins JB, Hall I, O'Neill HM, Keane SC
Structure (2025 Feb 6)

PMID: 39933513 doi: 10.1016/j.str.2025.01.017

Submitted to SASBDB: 2024 May 16 Published in SASBDB: 2025 Jan 15

SASDUS8 – HIV-1 DIS RNA with a CCCCCC apical loop (DIS-C) Sample: HIV-1 dimerization initiation site with a CCCCCC apical loop monomer, 9 kDa RNA Buffer: 50 mM potassium phosphate buffer, 1 mM MgCl2, 50 mM NaCl, pH: 7.5 Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2022 Feb 20 RgGuinier 1.5 nm Dmax 4.6 nm VolumePorod 11 nm3

SASDUT8 – HIV-1 DIS RNA with a GGGGGG apical loop, UCU bulge, and 16 bp helical extension (DIS-Gk) Sample: HIV-1 DIS with a GGGGGG apical loop, UCU bulge, and 16 bp helical extension monomer, 21 kDa RNA Buffer: 50 mM potassium phosphate buffer, 1 mM MgCl2, 50 mM NaCl, pH: 7.5 Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2022 Feb 20 RgGuinier 2.6 nm Dmax 10.5 nm VolumePorod 28 nm3

SASDUU8 – HIV-1 DIS-C:DIS-Gk RNA heterocomplex Sample: HIV-1 dimerization initiation site with a CCCCCC apical loop monomer, 9 kDa RNA HIV-1 DIS with a GGGGGG apical loop, UCU bulge, and 16 bp helical extension monomer, 21 kDa RNA Buffer: 50 mM potassium phosphate buffer, 1 mM MgCl2, 50 mM NaCl, pH: 7.5 Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2022 Feb 20 RgGuinier 3.5 nm Dmax 13.5 nm VolumePorod 40 nm3

SASDUV8 – HIV-1 ²H-DIS-C:¹H-DIS-Gk RNA heterocomplex (DIS-Gk contrast matched in 65% v/v D₂O - SANS data) Sample: HIV-1 dimerization initiation site with a CCCCCC apical loop monomer, 9 kDa RNA HIV-1 DIS with a GGGGGG apical loop, UCU bulge, and 16 bp helical extension monomer, 21 kDa RNA Buffer: 50 mM potassium phosphate buffer, 1 mM MgCl2, 50 mM NaCl, pH: 7.5 Experiment: SANS data collected at CG-3, High Flux Isotope Reactor on 2022 Oct 5 RgGuinier 1.6 nm Dmax 5.3 nm

SASDUW8 – HIV-1 ¹H-DIS-C:²H(42%)-DIS-Gk RNA heterocomplex (DIS-Gk contrast matched in 90% v/v D₂O - SANS data) Sample: HIV-1 dimerization initiation site with a CCCCCC apical loop monomer, 9 kDa RNA HIV-1 DIS with a GGGGGG apical loop, UCU bulge, and 16 bp helical extension monomer, 21 kDa RNA Buffer: 50 mM potassium phosphate buffer, 1 mM MgCl2, 50 mM NaCl, pH: 7.5 Experiment: SANS data collected at CG-3, High Flux Isotope Reactor on 2023 Sep 15 RgGuinier 1.4 nm Dmax 4.6 nm

SASDUX8 – HIV-1 ²H(42%)-DIS-C:¹H-DIS-Gk RNA heterocomplex (DIS-C contrast matched in 90% v/v D₂O - SANS data) Sample: HIV-1 dimerization initiation site with a CCCCCC apical loop monomer, 9 kDa RNA HIV-1 DIS with a GGGGGG apical loop, UCU bulge, and 16 bp helical extension monomer, 21 kDa RNA Buffer: 50 mM potassium phosphate buffer, 1 mM MgCl2, 50 mM NaCl, pH: 7.5 Experiment: SANS data collected at CG-3, High Flux Isotope Reactor on 2023 Sep 15 RgGuinier 2.9 nm Dmax 9.7 nm