Browse by MACROMOLECULE type: nucleic acid

SASDPK5 – SAXS curve of RNA Xist A-repeats (3 repeats)

Xist A-repeat lncRNA 3 repeats experimental SAS data
Xist A-repeat lncRNA 3 repeats Kratky plot
Sample: Xist A-repeat lncRNA 3 repeats monomer, 48 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 6.3 nm
Dmax 22.0 nm
VolumePorod 97 nm3

SASDPL5 – SAXS curve of RNA Xist A-repeats (4 repeats)

Xist A-repeat lncRNA 4 repeats experimental SAS data
Xist A-repeat lncRNA 4 repeats Kratky plot
Sample: Xist A-repeat lncRNA 4 repeats monomer, 62 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 7.2 nm
Dmax 34.0 nm

SASDPM5 – SAXS curve of RNA Xist A-repeats (5 repeats)

Xist A-repeat lncRNA 5 repeats experimental SAS data
Xist A-repeat lncRNA 5 repeats Kratky plot
Sample: Xist A-repeat lncRNA 5 repeats monomer, 81 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 7.7 nm
Dmax 30.0 nm
VolumePorod 186 nm3

SASDPN5 – SAXS curve of RNA Xist A-repeats (6 repeats)

Xist A-repeat lncRNA 6 repeats experimental SAS data
Xist A-repeat lncRNA 6 repeats Kratky plot
Sample: Xist A-repeat lncRNA 6 repeats monomer, 96 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 12.9 nm
Dmax 38.0 nm

SASDPP5 – SAXS curve of RNA Xist A-repeats (8 repeats)

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: 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 11.2 nm
Dmax 50.0 nm

SASDP74 – AT-rich DNA

AT-rich dsDNA experimental SAS data
DAMMIN model
Sample: AT-rich dsDNA monomer, 7 kDa DNA
Buffer: 20 mM Tris-HCl, pH 7.5, 200 mM NaCl, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2020 Feb 6
Structure of SALL4 zinc finger domain reveals link between AT-rich DNA binding and Okihiro syndrome. Life Sci Alliance 6(3) (2023)
Watson JA, Pantier R, Jayachandran U, Chhatbar K, Alexander-Howden B, Kruusvee V, Prendecki M, Bird A, Cook AG
RgGuinier 1.7 nm
Dmax 4.6 nm
VolumePorod 12 nm3

SASDPZ8 – Gli-233 - ssDNA aptamer specific to glioma brain tumor cells

Gli-233 - ssDNA aptamer to glioma brain tumor cells experimental SAS data
GROMACS model
Sample: Gli-233 - ssDNA aptamer to glioma brain tumor cells monomer, 10 kDa Artificially synthesized DNA
Buffer: Dulbecco phosphate-buffered saline (DPBS, with Ca and Mg), pH: 7.4
Experiment: SAXS data collected at BM29, ESRF on 2018 Jun 17
Development of DNA Aptamers for Visualization of Glial Brain Tumors and Detection of Circulating Tumor Cells Molecular Therapy - Nucleic Acids (2023)
Kichkailo A, Narodov A, Komarova M, Zamay T, Zamay G, Kolovskaya O, Erakhtin E, Glazyrin Y, Veprintsev D, Moryachkov R, Zabluda V, Shchugoreva I, Artyushenko P, Mironov V, Morozov D, Khorzhevskii V, Gorbushin A, Koshmanova A, Nikolaeva E, Grinev I, Voronkovskii I, Grek D, Belugin K, Volzhentsev A, Badmaev O, Luzan N, Lukyanenko K, Peters G, Lapin I, Kirichenko A, Konarev P, Morozov E, Mironov G, Gargaun A, Muharemagic D, Zamay S, Kochkina E, Dymova M, Smolyarova T, Sokolov A, Modestov A, Tokarev N, Shepelevich N, Ozerskaya A, Chanchikova N, Krat A, Zukov R, Bakhtina V, Shnyakin P, Shesternya P, Svetlichnyi V, Petrova M, Artyukhov I, Tomilin F, Berezovski M
RgGuinier 1.9 nm
Dmax 6.8 nm
VolumePorod 13 nm3

SASDP29 – Gli-55 - ssDNA aptamer specific to glioma brain tumor cells

Gli-55 - ssDNA aptamer specific to glioma brain tumor cells experimental SAS data
DAMMIN model
Sample: Gli-55 - ssDNA aptamer specific to glioma brain tumor cells monomer, 19 kDa Artificially synthesized DNA
Buffer: Dulbecco phosphate-buffered saline (DPBS), pH: 7.4
Experiment: SAXS data collected at EMBL P12, PETRA III on 2018 Oct 30
Development of DNA Aptamers for Visualization of Glial Brain Tumors and Detection of Circulating Tumor Cells Molecular Therapy - Nucleic Acids (2023)
Kichkailo A, Narodov A, Komarova M, Zamay T, Zamay G, Kolovskaya O, Erakhtin E, Glazyrin Y, Veprintsev D, Moryachkov R, Zabluda V, Shchugoreva I, Artyushenko P, Mironov V, Morozov D, Khorzhevskii V, Gorbushin A, Koshmanova A, Nikolaeva E, Grinev I, Voronkovskii I, Grek D, Belugin K, Volzhentsev A, Badmaev O, Luzan N, Lukyanenko K, Peters G, Lapin I, Kirichenko A, Konarev P, Morozov E, Mironov G, Gargaun A, Muharemagic D, Zamay S, Kochkina E, Dymova M, Smolyarova T, Sokolov A, Modestov A, Tokarev N, Shepelevich N, Ozerskaya A, Chanchikova N, Krat A, Zukov R, Bakhtina V, Shnyakin P, Shesternya P, Svetlichnyi V, Petrova M, Artyukhov I, Tomilin F, Berezovski M
RgGuinier 2.8 nm
Dmax 11.5 nm
VolumePorod 34 nm3

SASDRY7 – Gli-55 - ssDNA aptamer to glioma brain tumor cells

Gli-55 - ssDNA aptamer to glioma brain tumor cells experimental SAS data
DAMMIF model
Sample: Gli-55 - ssDNA aptamer to glioma brain tumor cells monomer, 19 kDa synthetic construct DNA
Buffer: Dulbecco phosphate-buffered saline (DPBS), pH: 7.4
Experiment: SAXS data collected at EMBL P12, PETRA III on 2018 Oct 30
Development of DNA Aptamers for Visualization of Glial Brain Tumors and Detection of Circulating Tumor Cells Molecular Therapy - Nucleic Acids (2023)
Kichkailo A, Narodov A, Komarova M, Zamay T, Zamay G, Kolovskaya O, Erakhtin E, Glazyrin Y, Veprintsev D, Moryachkov R, Zabluda V, Shchugoreva I, Artyushenko P, Mironov V, Morozov D, Khorzhevskii V, Gorbushin A, Koshmanova A, Nikolaeva E, Grinev I, Voronkovskii I, Grek D, Belugin K, Volzhentsev A, Badmaev O, Luzan N, Lukyanenko K, Peters G, Lapin I, Kirichenko A, Konarev P, Morozov E, Mironov G, Gargaun A, Muharemagic D, Zamay S, Kochkina E, Dymova M, Smolyarova T, Sokolov A, Modestov A, Tokarev N, Shepelevich N, Ozerskaya A, Chanchikova N, Krat A, Zukov R, Bakhtina V, Shnyakin P, Shesternya P, Svetlichnyi V, Petrova M, Artyukhov I, Tomilin F, Berezovski M
RgGuinier 2.8 nm
Dmax 11.5 nm
VolumePorod 35 nm3

SASDPJ3 – IMP-1 saRNA encoding NSP1-4 of VEEV and the spike glycoprotein of SARS-CoV-2

IMP-1 saRNA experimental SAS data
IMP-1 saRNA Kratky plot
Sample: IMP-1 saRNA monomer, 3720 kDa RNA
Buffer: 5 mM Sodium Citrate, pH: 6.4
Experiment: SAXS data collected at B21, Diamond Light Source on 2021 Apr 27
Biophysical characterisation of the structure of a SARS-CoV-2 self-amplifying—RNA (saRNA) vaccine Biology Methods and Protocols (2023)
Myatt D, Wharram L, Graham C, Liddell J, Branton H, Pizzey C, Cowieson N, Rambo R, Shattock R
RgGuinier 23.8 nm
Dmax 85.9 nm
VolumePorod 6265 nm3