Browse by MACROMOLECULE type: nucleic acid

SASDQN9 – Japanese encephalitis virus 5' TR and 3' UTR RNA complex

Japanese encephalitis virus 5' TR and 3' UTR complex experimental SAS data
MONSA model
Sample: Japanese encephalitis virus 5' TR and 3' UTR complex monomer, 260 kDa Japanese encephalitis virus RNA
Buffer: 10 mM Bis-tris, 100 mM NaCl, 15 mM KCl 15 mM MgCl2, 10% glycerol, pH: 5
Experiment: SAXS data collected at B21, Diamond Light Source on 2022 May 22
Investigating RNA-RNA interactions through computational and biophysical analysis. Nucleic Acids Res (2023)
Mrozowich T, Park SM, Waldl M, Henrickson A, Tersteeg S, Nelson CR, De Klerk A, Demeler B, Hofacker IL, Wolfinger MT, Patel TR
RgGuinier 12.8 nm
Dmax 40.0 nm
VolumePorod 4550 nm3

SASDQ69 – 28 base pair DNA substrate (used in experiments with 7-deazapurine in DNA proteins)

Custom 28 base pair double stranded DNA experimental SAS data
GROMACS model
Sample: Custom 28 base pair double stranded DNA monomer, 17 kDa Synthetic, purchased from … DNA
Buffer: 100 mM KCl, 50 mM Tris pH 7.0, 1 mM DTT, pH: 7
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2021 Dec 22
7-Deazaguanines in DNA: functional and structural elucidation of a DNA modification system. Nucleic Acids Res (2023)
Gedara SH, Wood E, Gustafson A, Liang C, Hung SH, Savage J, Phan P, Luthra A, de Crécy-Lagard V, Dedon P, Swairjo MA, Iwata-Reuyl D
RgGuinier 2.6 nm
Dmax 10.2 nm
VolumePorod 24 nm3

SASDPB5 – SAXS curve of RNA Xist A-repeats (Liu buffer)

Xist A-repeat lncRNA experimental SAS data
Xist A-repeat lncRNA Kratky plot
Sample: Xist A-repeat lncRNA monomer, 148 kDa Homo sapiens RNA
Buffer: 25 mM K-HEPES, 0.1 mM Na-EDTA, 150 mM KCl, 15 mM MgCl2, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Jun 20
Cotranscriptional folding of the lncRNA Xist A-repeats indicates a modular structure
Alisha Jones
RgGuinier 12.1 nm
Dmax 45.0 nm

SASDPC5 – SAXS curve of RNA Xist A-repeats (Smola buffer)

Xist A-repeat lncRNA experimental SAS data
Xist A-repeat lncRNA Kratky plot
Sample: Xist A-repeat lncRNA monomer, 148 kDa Homo sapiens RNA
Buffer: 100 mM HEPES, 100 mM NaCl, 10 mM MgCl2, pH: 8
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Jun 20
Cotranscriptional folding of the lncRNA Xist A-repeats indicates a modular structure
Alisha Jones
RgGuinier 9.8 nm
Dmax 40.0 nm
VolumePorod 657 nm3

SASDPD5 – SAXS curve of RNA Xist A-repeats (Maenner buffer)

Xist A-repeat lncRNA experimental SAS data
Xist A-repeat lncRNA Kratky plot
Sample: Xist A-repeat lncRNA monomer, 148 kDa Homo sapiens RNA
Buffer: 20 mM HEPES-KOH, 100 mM KCl, 0.2 mM EDTA, 0.5 mM DTT, 0.5 mM PMSF, 20% glycerol, 3.25 mM MgCl2, pH: 7.9
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Jun 20
Cotranscriptional folding of the lncRNA Xist A-repeats indicates a modular structure
Alisha Jones
RgGuinier 8.9 nm
Dmax 35.0 nm
VolumePorod 414 nm3

SASDPE5 – SAXS curve of RNA Xist A-repeats (Duszczyk buffer)

Xist A-repeat lncRNA experimental SAS data
Xist A-repeat lncRNA Kratky plot
Sample: Xist A-repeat lncRNA monomer, 148 kDa Homo sapiens RNA
Buffer: 10 mM NaH2PO4/Na2HPO4, 100 mM NaCl, 0.02 mM EDTA, 0.02% azide, pH: 6
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Jun 20
Cotranscriptional folding of the lncRNA Xist A-repeats indicates a modular structure
Alisha Jones
RgGuinier 7.6 nm
Dmax 30.0 nm
VolumePorod 370 nm3

SASDPF5 – SAXS curve of RNA Xist A-repeats (14mer)

Xist A-repeat lncRNA 14 mer experimental SAS data
Xist A-repeat lncRNA 14 mer Kratky plot
Sample: Xist A-repeat lncRNA 14 mer monomer, 5 kDa RNA
Buffer: 50 mM HEPES, 150 mM NaCl, 2 mM MgCl2, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Jun 20
Cotranscriptional folding of the lncRNA Xist A-repeats indicates a modular structure
Alisha Jones
RgGuinier 2.1 nm
Dmax 8.5 nm
VolumePorod 13 nm3

SASDPG5 – SAXS curve of RNA Xist A-repeats (26mer)

Xist A-repeat lncRNA 24 mer experimental SAS data
Xist A-repeat lncRNA 24 mer Kratky plot
Sample: Xist A-repeat lncRNA 24 mer dimer, 16 kDa RNA
Buffer: 50 mM HEPES, 150 mM NaCl, 2 mM MgCl2, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Jun 20
Cotranscriptional folding of the lncRNA Xist A-repeats indicates a modular structure
Alisha Jones
RgGuinier 3.1 nm
Dmax 14.5 nm
VolumePorod 28 nm3

SASDPH5 – SAXS curve of RNA Xist A-repeats (1 repeat)

Xist A-repeat lncRNA 1 repeat experimental SAS data
Xist A-repeat lncRNA 1 repeat Kratky plot
Sample: Xist A-repeat lncRNA 1 repeat dimer, 41 kDa RNA
Buffer: 50 mM HEPES, 150 mM NaCl, 2 mM MgCl2, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Jun 20
Cotranscriptional folding of the lncRNA Xist A-repeats indicates a modular structure
Alisha Jones
RgGuinier 3.9 nm
Dmax 16.0 nm
VolumePorod 42 nm3

SASDPJ5 – SAXS curve of RNA Xist A-repeats (2 repeats)

Xist A-repeat lncRNA 2 repeats experimental SAS data
Xist A-repeat lncRNA 2 repeats Kratky plot
Sample: Xist A-repeat lncRNA 2 repeats monomer, 34 kDa RNA
Buffer: 50 mM HEPES, 150 mM NaCl, 2 mM MgCl2, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Jun 20
Cotranscriptional folding of the lncRNA Xist A-repeats indicates a modular structure
Alisha Jones
RgGuinier 5.0 nm
Dmax 23.0 nm
VolumePorod 87 nm3