Small Angle Scattering Biological Data Bank SASBDB

Browse by MACROMOLECULE type: nucleic acid

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 molecules as quintessential vaccines
Martin Schroer

R_g^Guinier	90.5	nm
D_max	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 molecules as quintessential vaccines
Martin Schroer

R_g^Guinier	30.7	nm
D_max	107.4	nm
Volume^Porod	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 molecules as quintessential vaccines
Martin Schroer

R_g^Guinier	12.0	nm
D_max	40.0	nm
Volume^Porod	9100	nm³

SASDNX6 – ASO1 DNA in the absence of target RNA

LNA-DNA-LNA experimental SAS data

LNA-DNA-LNA Kratky plot

Sample:	LNA-DNA-LNA monomer, 4 kDa DNA
Buffer:	phosphate buffered saline, pH: 7.4
Experiment:	SAXS data collected at B21, Diamond Light Source on 2021 Oct 21

Application of enhanced biophysical strategies to determine ASO/target RNA binding affinity and kinetics
Michael Lerche

R_g^Guinier	1.3	nm
D_max	4.0	nm
Volume^Porod	4	nm³

SASDNY6 – ASO2 DNA in the absence of target RNA

MOE PS gapmers 3-8-3 experimental SAS data

DAMMIF model

Sample:	MOE PS gapmers 3-8-3 monomer, 4 kDa DNA
Buffer:	phosphate buffered saline, pH: 7.4
Experiment:	SAXS data collected at B21, Diamond Light Source on 2021 Oct 21

Application of enhanced biophysical strategies to determine ASO/target RNA binding affinity and kinetics
Michael Lerche

R_g^Guinier	1.4	nm
D_max	4.3	nm
Volume^Porod	5	nm³

SASDNZ6 – ASO3 RNA in the absence of target RNA

oME ASO experimental SAS data

oME ASO Kratky plot

Sample:	OME ASO monomer, 4 kDa RNA
Buffer:	phosphate buffered saline, pH: 7.4
Experiment:	SAXS data collected at B21, Diamond Light Source on 2021 Oct 21

Application of enhanced biophysical strategies to determine ASO/target RNA binding affinity and kinetics
Michael Lerche

R_g^Guinier	1.4	nm
D_max	4.0	nm
Volume^Porod	7	nm³

SASDN27 – ASO1 DNA in the presence target RNA

LNA-DNA-LNAPSCK9, 24mer ASO binding site experimental SAS data

LNA-DNA-LNA PSCK9, 24mer ASO binding site Kratky plot

Sample:	LNA-DNA-LNA monomer, 4 kDa DNA PSCK9, 24mer ASO binding site monomer, 8 kDa RNA
Buffer:	phosphate buffered saline, pH: 7.4
Experiment:	SAXS data collected at B21, Diamond Light Source on 2021 Oct 21

Application of enhanced biophysical strategies to determine ASO/target RNA binding affinity and kinetics
Michael Lerche

R_g^Guinier	1.9	nm
D_max	6.2	nm
Volume^Porod	15	nm³

SASDN37 – ASO2 DNA in the presence of target RNA

MOE PS gapmers 3-8-3PSCK9, 24mer ASO binding site experimental SAS data

DAMMIF model

Sample:	MOE PS gapmers 3-8-3 monomer, 4 kDa DNA PSCK9, 24mer ASO binding site monomer, 8 kDa RNA
Buffer:	phosphate buffered saline, pH: 7.4
Experiment:	SAXS data collected at B21, Diamond Light Source on 2021 Oct 21

Application of enhanced biophysical strategies to determine ASO/target RNA binding affinity and kinetics
Michael Lerche

R_g^Guinier	2.1	nm
D_max	6.4	nm
Volume^Porod	16	nm³

SASDN47 – ASO3 RNA in the presence of target RNA

oME ASOPSCK9, 24mer ASO binding site experimental SAS data

oME ASO PSCK9, 24mer ASO binding site Kratky plot

Sample:	OME ASO monomer, 4 kDa RNA PSCK9, 24mer ASO binding site monomer, 8 kDa RNA
Buffer:	phosphate buffered saline, pH: 7.4
Experiment:	SAXS data collected at B21, Diamond Light Source on 2021 Oct 21

Application of enhanced biophysical strategies to determine ASO/target RNA binding affinity and kinetics
Michael Lerche

R_g^Guinier	1.9	nm
D_max	6.2	nm
Volume^Porod	16	nm³

SASDSP8 – RNA Device 43 in ligand-free state (apo-D43)

RNA Device 43 in ligand-free state experimental SAS data

OTHER model

Sample:	RNA Device 43 in ligand-free state monomer, 40 kDa synthetic construct RNA
Buffer:	10 mM Bis-Tris, 100 mM KCl, and 1 mM MgCl2, pH: 6.8
Experiment:	SAXS data collected at 16-ID (LiX), National Synchrotron Light Source II (NSLS-II) on 2023 Jul 25

Structural investigation of an RNA device that regulates PD-1 expression in mammalian cells. Nucleic Acids Res 53(5) (2025)
Stagno JR, Deme JC, Dwivedi V, Lee YT, Lee HK, Yu P, Chen SY, Fan L, Degenhardt MFS, Chari R, Young HA, Lea SM, Wang YX

R_g^Guinier	3.4	nm
D_max	12.2	nm
Volume^Porod	58	nm³

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