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30 hits found for Trushar Patel

SASDNL2 – LincRNA-p21 Sense Alu Inverted Repeat

LincRNA-p21 AluSx1 Sense RNA experimental SAS data
DAMMIN model
Sample: LincRNA-p21 AluSx1 Sense RNA monomer, 100 kDa Homo sapiens RNA
Buffer: 50mM HEPES,150 mM NaCl, 15 mM MgCl2, 3% glycerol, pH: 7.4
Experiment: SAXS data collected at B21, Diamond Light Source on 2021 Jul 1
Biophysical characterisation of human LincRNA-p21 sense and antisense Alu inverted repeats. Nucleic Acids Res 50(10):5881-5898 (2022)
...Patel TR
RgGuinier 6.1 nm
Dmax 18.5 nm
VolumePorod 225 nm3

SASDNM2 – LincRNA-p21 Antisense Alu Inverted Repeat

LincRNA-p21 AluSx1 Antisense RNA experimental SAS data
DAMMIN model
Sample: LincRNA-p21 AluSx1 Antisense RNA monomer, 90 kDa Homo sapiens RNA
Buffer: 50mM HEPES,150 mM NaCl, 15 mM MgCl2, 3% glycerol, pH: 7.4
Experiment: SAXS data collected at B21, Diamond Light Source on 2021 Jul 1
Biophysical characterisation of human LincRNA-p21 sense and antisense Alu inverted repeats. Nucleic Acids Res 50(10):5881-5898 (2022)
...Patel TR
RgGuinier 5.9 nm
Dmax 18.1 nm
VolumePorod 375 nm3

SASDH93 – Braveheart Fragment 1

Braveheart Fragment 1 experimental SAS data
DAMMIN model
Sample: Braveheart Fragment 1 monomer, 116 kDa Homo sapiens RNA
Buffer: 50 mM HEPES-KOH, 100 mM KCl, 6 mM MgCl2, pH: 7.6
Experiment: SAXS data collected at B21, Diamond Light Source on 2018 Jun 23
Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution Nature Communications 11(1) (2020)
...Patel T, Sanbonmatsu K
RgGuinier 8.4 nm
Dmax 24.0 nm
VolumePorod 426 nm3

SASDHA3 – Braveheart Fragment 2

Braveheart Fragment 2 experimental SAS data
DAMMIN model
Sample: Braveheart Fragment 2 monomer, 112 kDa Homo sapiens RNA
Buffer: 50 mM HEPES-KOH, 100 mM KCl, 6 mM MgCl2, pH: 7.6
Experiment: SAXS data collected at B21, Diamond Light Source on 2018 Jun 23
Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution Nature Communications 11(1) (2020)
...Patel T, Sanbonmatsu K
RgGuinier 8.1 nm
Dmax 27.2 nm
VolumePorod 443 nm3

SASDHB3 – Braveheart Fragment 3

Braveheart Fragment 3 experimental SAS data
DAMMIN model
Sample: Braveheart Fragment 3 monomer, 111 kDa Homo sapiens RNA
Buffer: 50 mM HEPES-KOH, 100 mM KCl, 6 mM MgCl2, pH: 7.6
Experiment: SAXS data collected at B21, Diamond Light Source on 2018 Jun 23
Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution Nature Communications 11(1) (2020)
...Patel T, Sanbonmatsu K
RgGuinier 6.5 nm
Dmax 20.5 nm
VolumePorod 492 nm3

SASDHC3 – Braveheart in 0 mM MgCl2

Braveheart RNA experimental SAS data
DAMMIN model
Sample: Braveheart RNA monomer, 205 kDa Homo sapiens RNA
Buffer: 50 mM HEPES-KOH, 100 mM KCl, pH: 7.6
Experiment: SAXS data collected at B21, Diamond Light Source on 2018 Jun 23
Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution Nature Communications 11(1) (2020)
...Patel T, Sanbonmatsu K
RgGuinier 9.9 nm
Dmax 30.0 nm
VolumePorod 2150 nm3

SASDHD3 – Braveheart in 6 mM MgCl2

Braveheart RNA experimental SAS data
DAMMIN model
Sample: Braveheart RNA monomer, 205 kDa Homo sapiens RNA
Buffer: 50 mM HEPES-KOH, 100 mM KCl, 6 mM MgCl2, pH: 7.6
Experiment: SAXS data collected at B21, Diamond Light Source on 2018 Dec 16
Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution Nature Communications 11(1) (2020)
...Patel T, Sanbonmatsu K
RgGuinier 11.8 nm
Dmax 28.7 nm
VolumePorod 2380 nm3

SASDHE3 – Braveheart in 12 mM MgCl2

Braveheart RNA experimental SAS data
DAMMIN model
Sample: Braveheart RNA monomer, 205 kDa Homo sapiens RNA
Buffer: 50 mM HEPES-KOH, 100 mM KCl, 12 mM MgCl2, pH: 7.6
Experiment: SAXS data collected at B21, Diamond Light Source on 2018 Jul 20
Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution Nature Communications 11(1) (2020)
...Patel T, Sanbonmatsu K
RgGuinier 9.7 nm
Dmax 26.0 nm
VolumePorod 1370 nm3

SASDHF3 – Braveheart 5' module in 6 mM MgCl2

Braveheart 5' Module experimental SAS data
DAMMIN model
Sample: Braveheart 5' Module monomer, 32 kDa Homo sapiens RNA
Buffer: 50 mM HEPES-KOH, 100 mM KCl, 6 mM MgCl2, pH: 7.6
Experiment: SAXS data collected at B21, Diamond Light Source on 2018 Dec 16
Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution Nature Communications 11(1) (2020)
...Patel T, Sanbonmatsu K
RgGuinier 4.3 nm
Dmax 13.5 nm
VolumePorod 71 nm3

SASDHG3 – Braveheart 5' module in 12 mM MgCl2

Braveheart 5' Module experimental SAS data
DAMMIN model
Sample: Braveheart 5' Module monomer, 32 kDa Homo sapiens RNA
Buffer: 50 mM HEPES-KOH, 100 mM KCl, 12 mM MgCl2, pH: 7.6
Experiment: SAXS data collected at B21, Diamond Light Source on 2018 Dec 16
Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution Nature Communications 11(1) (2020)
...Patel T, Sanbonmatsu K
RgGuinier 4.8 nm
Dmax 15.0 nm
VolumePorod 99 nm3

SASDHH3 – Braveheart 3' module in 6 mM MgCl2

Braveheart 3' module experimental SAS data
DAMMIN model
Sample: Braveheart 3' module monomer, 72 kDa Homo sapiens RNA
Buffer: 50 mM HEPES-KOH, 100 mM KCl, 6 mM MgCl2, pH: 7.6
Experiment: SAXS data collected at B21, Diamond Light Source on 2018 Dec 16
Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution Nature Communications 11(1) (2020)
...Patel T, Sanbonmatsu K
RgGuinier 6.5 nm
Dmax 18.5 nm
VolumePorod 198 nm3

SASDHJ3 – Braveheart 3' module in 12 mM MgCl2

Braveheart 3' module experimental SAS data
DAMMIN model
Sample: Braveheart 3' module monomer, 72 kDa Homo sapiens RNA
Buffer: 50 mM HEPES-KOH, 100 mM KCl, 12 mM MgCl2, pH: 7.6
Experiment: SAXS data collected at B21, Diamond Light Source on 2018 Dec 16
Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution Nature Communications 11(1) (2020)
...Patel T, Sanbonmatsu K
RgGuinier 7.3 nm
Dmax 19.0 nm
VolumePorod 219 nm3

SASDHK3 – Braveheart RNA + Cellular nucleic acid-binding protein (CNBP)

Braveheart RNACellular nucleic acid-binding protein experimental SAS data
DAMMIN model
Sample: Braveheart RNA monomer, 205 kDa Homo sapiens RNA
Cellular nucleic acid-binding protein monomer, 22 kDa Homo sapiens protein
Buffer: 50 mM HEPES-KOH, 100 mM KCl, 6 mM MgCl2, pH: 7.6
Experiment: SAXS data collected at B21, Diamond Light Source on 2018 Jun 23
Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution Nature Communications 11(1) (2020)
...Patel T, Sanbonmatsu K
RgGuinier 9.8 nm
Dmax 30.2 nm
VolumePorod 1660 nm3

SASDHL3 – Braveheart Fragment 1 + Cellular nucleic acid-binding protein (CNBP)

Cellular nucleic acid-binding proteinBraveheart Fragment 1 experimental SAS data
DAMMIN model
Sample: Cellular nucleic acid-binding protein monomer, 22 kDa Homo sapiens protein
Braveheart Fragment 1 monomer, 116 kDa Homo sapiens RNA
Buffer: 50 mM HEPES-KOH, 100 mM KCl, 6 mM MgCl2, pH: 7.6
Experiment: SAXS data collected at B21, Diamond Light Source on 2018 Jun 23
Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution Nature Communications 11(1) (2020)
...Patel T, Sanbonmatsu K
RgGuinier 8.2 nm
Dmax 27.0 nm
VolumePorod 455 nm3

SASDG26 – Wild type 4-hydroxy-tetrahydrodipicolinate synthase

4-hydroxy-tetrahydrodipicolinate synthase experimental SAS data
DAMFILT model
Sample: 4-hydroxy-tetrahydrodipicolinate synthase tetramer, 131 kDa Campylobacter jejuni protein
Buffer: 20 mM Tris-HCl, 150 mM NaCl, pH: 8
Experiment: SAXS data collected at B21, Diamond Light Source on 2017 Aug 2
Asparagine-84, a regulatory allosteric site residue, helps maintain the quaternary structure of Campylobacter jejuni dihydrodipicolinate synthase. J Struct Biol :107409 (2019)
...Patel TR, Sanders DAR, Palmer DRJ
RgGuinier 3.4 nm
Dmax 9.0 nm
VolumePorod 188 nm3

SASDG36 – 4-hydroxy-tetrahydrodipicolinate synthase (N84D mutant)

4-hydroxy-tetrahydrodipicolinate synthase (N84D mutant) experimental SAS data
DAMFILT model
Sample: 4-hydroxy-tetrahydrodipicolinate synthase (N84D mutant) dimer, 65 kDa Campylobacter jejuni protein
Buffer: 20 mM Tris-HCl, 150 mM NaCl, pH: 8
Experiment: SAXS data collected at B21, Diamond Light Source on 2017 Aug 2
Asparagine-84, a regulatory allosteric site residue, helps maintain the quaternary structure of Campylobacter jejuni dihydrodipicolinate synthase. J Struct Biol :107409 (2019)
...Patel TR, Sanders DAR, Palmer DRJ
RgGuinier 3.1 nm
Dmax 9.5 nm
VolumePorod 108 nm3

SASDG46 – 4-hydroxy-tetrahydrodipicolinate synthase (N84A mutant)

4-hydroxy-tetrahydrodipicolinate synthase (N84A mutant) experimental SAS data
DAMFILT model
Sample: 4-hydroxy-tetrahydrodipicolinate synthase (N84A mutant) , 33 kDa Campylobacter jejuni protein
Buffer: 20 mM Tris-HCl, 150 mM NaCl, pH: 8
Experiment: SAXS data collected at B21, Diamond Light Source on 2017 Aug 2
Asparagine-84, a regulatory allosteric site residue, helps maintain the quaternary structure of Campylobacter jejuni dihydrodipicolinate synthase. J Struct Biol :107409 (2019)
...Patel TR, Sanders DAR, Palmer DRJ
RgGuinier 3.3 nm
Dmax 8.9 nm
VolumePorod 163 nm3

SASDGE6 – G-quadruplex DNA from Hepatitis B virus (wild type)

G-quadrupex experimental SAS data
DAMFILT model
Sample: G-quadrupex monomer, 6 kDa Hepatitis B virus DNA
Buffer: 20 mM HEPES, 100 mM KCl, 1 mM EDTA, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2018 Jan 15
G-quadruplex from HBV genome
Trushar Patel
RgGuinier 1.7 nm
Dmax 4.0 nm
VolumePorod 13 nm3

SASDGF6 – G-quadruplex DNA from Hepatitis B virus (mutant)

G-quadruplex mutant experimental SAS data
DAMFILT model
Sample: G-quadruplex mutant monomer, 6 kDa Hepatitis B virus DNA
Buffer: 20 mM HEPES, 100 mM KCl, 1 mM EDTA, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2018 Jan 15
G-quadruplex from HBV genome
Trushar Patel
RgGuinier 1.7 nm
Dmax 5.5 nm
VolumePorod 11 nm3

SASDQJ6 – Monkeypox viral synthetic DNA fragment (DNA sequence 1, MP1)

Monekypox DNA sequence 1 experimental SAS data
DAMMIN model
Sample: Monekypox DNA sequence 1 monomer, 6 kDa Monkeypox virus DNA
Buffer: 20 mM HEPES, 100 mM KCl, and 0.2 mM EDTA, pH: 7.4
Experiment: SAXS data collected at B21, Diamond Light Source on 2022 Sep 23
Mapping and characterization of G‐quadruplexes in monkeypox genomes Journal of Medical Virology 95(5) (2023)
...Patel T
RgGuinier 1.7 nm
Dmax 4.4 nm
VolumePorod 14 nm3

SASDQK6 – Monkeypox viral synthetic DNA fragment (DNA sequence 2, MP2)

Monekypox DNA sequence 1 experimental SAS data
DAMMIN model
Sample: Monekypox DNA sequence 1 monomer, 6 kDa Monkeypox virus DNA
Buffer: 20 mM HEPES, 100 mM KCl, and 0.2 mM EDTA, pH: 7.4
Experiment: SAXS data collected at B21, Diamond Light Source on 2022 Sep 23
Mapping and characterization of G‐quadruplexes in monkeypox genomes Journal of Medical Virology 95(5) (2023)
...Patel T
RgGuinier 1.6 nm
Dmax 4.5 nm
VolumePorod 11 nm3

SASDQL6 – Monkeypox viral synthetic DNA fragment (DNA sequence 1, MP1 mutant)

Monekypox DNA sequence 1 mutant experimental SAS data
DAMMIN model
Sample: Monekypox DNA sequence 1 mutant monomer, 6 kDa Monkeypox virus DNA
Buffer: 20 mM HEPES, 100 mM KCl, and 0.2 mM EDTA, pH: 7.4
Experiment: SAXS data collected at B21, Diamond Light Source on 2022 Sep 23
Mapping and characterization of G‐quadruplexes in monkeypox genomes Journal of Medical Virology 95(5) (2023)
...Patel T
RgGuinier 1.9 nm
Dmax 5.5 nm
VolumePorod 16 nm3

SASDQM6 – Monkeypox viral synthetic DNA fragment (DNA sequence 2, MP2 mutant)

Monekypox DNA sequence 2 mutant experimental SAS data
DAMMIN model
Sample: Monekypox DNA sequence 2 mutant monomer, 6 kDa Monkeypox virus DNA
Buffer: 20 mM HEPES, 100 mM KCl, and 0.2 mM EDTA, pH: 7.4
Experiment: SAXS data collected at B21, Diamond Light Source on 2022 Sep 23
Mapping and characterization of G‐quadruplexes in monkeypox genomes Journal of Medical Virology 95(5) (2023)
...Patel T
RgGuinier 1.9 nm
Dmax 6.0 nm
VolumePorod 8 nm3

SASDKP6 – G-quadruplex DNA from Hepatitis B virus, wild type (HBV G4 WT)

HBV G4 WT experimental SAS data
DAMMIN model
Sample: HBV G4 WT monomer, 7 kDa Hepatitis B virus DNA
Buffer: 20 mM HEPES, 100 mM KCl, 1 mM EDTA, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2019 Dec 15
HBV G-quad
Trushar Patel
RgGuinier 1.8 nm
Dmax 4.7 nm
VolumePorod 18 nm3

SASDKQ6 – G-quadruplex DNA from Hepatitis B virus, mutant (HBV G4 G1738A)

HBV G-quad G1738A experimental SAS data
DAMMIN model
Sample: HBV G-quad G1738A monomer, 7 kDa Hepatitis B virus DNA
Buffer: 20 mM HEPES, 100 mM KCl, 1 mM EDTA, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2019 Sep 14
HBV G-quad
Trushar Patel
RgGuinier 1.9 nm
Dmax 5.3 nm
VolumePorod 21 nm3

SASDKR6 – G-quadruplex DNA from Hepatitis B virus, mutant (HBV G4 G1748A)

HBV G4 G1748A experimental SAS data
DAMMIN model
Sample: HBV G4 G1748A monomer, 7 kDa Hepatitis B virus DNA
Buffer: 20 mM HEPES, 100 mM KCl, 1 mM EDTA, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2019 Sep 14
HBV G-quad
Trushar Patel
RgGuinier 2.0 nm
Dmax 6.0 nm
VolumePorod 21 nm3

SASDKS6 – G-quadruplex DNA from Hepatitis B virus, mutant (HBV G4 G1748A + G1748A)

HBV G4 G1748A + G1748A experimental SAS data
DAMMIN model
Sample: HBV G4 G1748A + G1748A monomer, 7 kDa Hepatitis B virus DNA
Buffer: 20 mM HEPES, 100 mM KCl, 1 mM EDTA, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2020 Feb 17
HBV G-quad
Trushar Patel
RgGuinier 2.0 nm
Dmax 6.0 nm
VolumePorod 23 nm3

SASDQL9 – Japanese encephalitis virus 5' TR RNA

Japanese encephaltitis 5' TR experimental SAS data
DAMMIN model
Sample: Japanese encephaltitis 5' TR monomer, 74 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)
...Patel TR
RgGuinier 7.0 nm
Dmax 22.4 nm
VolumePorod 356 nm3

SASDQM9 – Japanese encephalitis virus 3' UTR RNA

Japanese encephalitis virus 3' UTR experimental SAS data
DAMMIN model
Sample: Japanese encephalitis virus 3' UTR monomer, 186 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)
...Patel TR
RgGuinier 11.3 nm
Dmax 34.6 nm
VolumePorod 2900 nm3

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)
...Patel TR
RgGuinier 12.8 nm
Dmax 40.0 nm
VolumePorod 4550 nm3