Browse by MODEL: Ab initio only

SASDXD3 – Dengue Virus 2 (DENV2) 3' UTR

DENV2 3' untranslated region experimental SAS data
DAMMIN model
Sample: DENV2 3' untranslated region monomer, 160 kDa RNA
Buffer: 10 mM Bis-Tris, 100 mM NaCl, 5 mM MgCl2, 15 mM KCl, 5% glycerol, pH: 6
Experiment: SAXS data collected at B21, Diamond Light Source on 2023 Sep 10
Structural Dynamics of Dengue Virus UTRs and Their Cyclization. Biophys J (2025)
Robinson ZE, Pereira HS, D'Souza MH, Patel TR
RgGuinier 6.0 nm
Dmax 18.7 nm
VolumePorod 155 nm3

SASDXE3 – Dengue Virus 2 (DENV2) complex 5'-3'

DENV2 complex 5'-3' experimental SAS data
DAMMIN model
Sample: DENV2 complex 5'-3' monomer, 217 kDa RNA
Buffer: 10 mM Bis-Tris, 100 mM NaCl, 5 mM MgCl2, 15 mM KCl, 5% glycerol, pH: 6
Experiment: SAXS data collected at B21, Diamond Light Source on 2023 Sep 10
Structural Dynamics of Dengue Virus UTRs and Their Cyclization. Biophys J (2025)
Robinson ZE, Pereira HS, D'Souza MH, Patel TR
RgGuinier 7.5 nm
Dmax 22.0 nm
VolumePorod 320 nm3

SASDXT3 – Dengue Virus 2 (DENV2) RNA, 5' Untranslated region

DENV2 RNA, 5' Untranslated region experimental SAS data
DAMMIN model
Sample: DENV2 RNA, 5' Untranslated region monomer, 57 kDa RNA
Buffer: 10 mM Bis-Tris, 100 mM NaCl, 5 mM MgCl2, 15 mM KCl, 5% glycerol, pH: 6
Experiment: SAXS data collected at B21, Diamond Light Source on 2023 Sep 8
Structural Dynamics of Dengue Virus UTRs and Their Cyclization. Biophys J (2025)
Robinson ZE, Pereira HS, D'Souza MH, Patel TR
RgGuinier 3.7 nm
Dmax 11.5 nm
VolumePorod 66 nm3

SASDS39 – G4 dumbbell RNA - 3' UTR of Dengue virus

G4 dumbbell RNA - 3' untranslated region (3' UTR) Dengue virus experimental SAS data
DAMMIN model
Sample: G4 dumbbell RNA - 3' untranslated region (3' UTR) Dengue virus monomer, 31 kDa dengue virus type … RNA
Buffer: 20 mM HEPES, 100 mM KCl, 0.01 mM EDTA, pH: 7
Experiment: SAXS data collected at B21, Diamond Light Source on 2022 Sep 9
Unravelling structural dynamics of Dengue virus 3' UTR and its impact on viral life cycle
Trushar Patel
RgGuinier 3.0 nm
Dmax 9.0 nm
VolumePorod 47 nm3

SASDS49 – Dumbbell RNA - 3' UTR of Dengue virus

Dumbbell RNA - 3' untranslated region (3' UTR) Dengue virus experimental SAS data
DAMMIN model
Sample: Dumbbell RNA - 3' untranslated region (3' UTR) Dengue virus monomer, 31 kDa dengue virus type … RNA
Buffer: 20 mM HEPES, 100 mM NaCl, 5 mM MgCl2, pH: 7
Experiment: SAXS data collected at B21, Diamond Light Source on 2022 Sep 9
Unravelling structural dynamics of Dengue virus 3' UTR and its impact on viral life cycle
Trushar Patel
RgGuinier 3.6 nm
Dmax 11.7 nm
VolumePorod 44 nm3

SASDS59 – G4 dumbbell RNA mutant - 3' UTR of Dengue virus

G4 dumbbell Mut - 3' untranslated region (3' UTR) Dengue virus experimental SAS data
DAMMIN model
Sample: G4 dumbbell Mut - 3' untranslated region (3' UTR) Dengue virus dimer, 61 kDa dengue virus type … RNA
Buffer: 20 mM HEPES, 100 mM KCl, 0.01 mM EDTA, pH: 7
Experiment: SAXS data collected at B21, Diamond Light Source on 2023 Jun 30
Unravelling structural dynamics of Dengue virus 3' UTR and its impact on viral life cycle
Trushar Patel
RgGuinier 5.0 nm
Dmax 14.8 nm
VolumePorod 92 nm3

SASDT72 – GAGE6 60bp dsDNA oligonucleotide

GAGE6 60bp dsDNA oligo experimental SAS data
DAMMIN model
Sample: GAGE6 60bp dsDNA oligo monomer, 37 kDa Homo sapiens DNA
Buffer: 150 mM KCl, 20 mM HEPES, 5% glycerol, 5 mM MgCl2, 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2023 Mar 14
Probing the statistics of sequence-dependent DNA conformations in solution using SAXS
Heidar Koning
RgGuinier 4.7 nm
Dmax 20.7 nm
VolumePorod 101 nm3

SASDRK9 – single self-amplifying RNA

self-amplifying RNA experimental SAS data
DAMMIF model
Sample: Self-amplifying RNA monomer, 3030 kDa RNA
Buffer: MBG buffer: 5% w/v D-Glucose, 10mM MES (2-(N-morpholino)ethanesulfonic acid) in double distillated sterile/RNAse free water, pH: 6.1
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 Nov 10
Compact polyethylenimine-complexed mRNA vaccines Nature Nanotechnology (2025)
Moreno Herrero J, Stahl T, Erbar S, Maxeiner K, Schlegel A, Bacic T, Schumacher J, Cavalcanti L, Schroer M, Svergun D, Sahin U, Haas H
RgGuinier 90.5 nm
Dmax 200.0 nm

SASDRL9 – single self-amplifying RNA + 50 mM NaCl

self-amplifying RNA experimental SAS data
DAMMIF model
Sample: Self-amplifying RNA monomer, 3030 kDa RNA
Buffer: MBG buffer: 5% w/v D-Glucose, 10mM MES (2-(N-morpholino)ethanesulfonic acid) in double distillated sterile/RNAse free water, pH: 6.1
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Mar 10
Compact polyethylenimine-complexed mRNA vaccines Nature Nanotechnology (2025)
Moreno Herrero J, Stahl T, Erbar S, Maxeiner K, Schlegel A, Bacic T, Schumacher J, Cavalcanti L, Schroer M, Svergun D, Sahin U, Haas H
RgGuinier 30.7 nm
Dmax 107.4 nm
VolumePorod 112000 nm3

SASDRM9 – Polyethylenimine-compacted single self-amplifying RNA for prophylactic and therapeutic application, specifically for vaccination

self-amplifying RNAlinear polyethylenimine experimental SAS data
DAMMIF model
Sample: Self-amplifying RNA monomer, 3030 kDa RNA
Linear polyethylenimine monomer, 25 kDa none (polymer)
Buffer: MBG buffer: 5% w/v D-Glucose, 10mM MES (2-(N-morpholino)ethanesulfonic acid) in double distillated sterile/RNAse free water, pH: 6.1
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 Nov 10
Compact polyethylenimine-complexed mRNA vaccines Nature Nanotechnology (2025)
Moreno Herrero J, Stahl T, Erbar S, Maxeiner K, Schlegel A, Bacic T, Schumacher J, Cavalcanti L, Schroer M, Svergun D, Sahin U, Haas H
RgGuinier 12.0 nm
Dmax 40.0 nm
VolumePorod 9100 nm3