SANS with Magnetic Contrast

1. SANS with Magnetic Contrast neutron magnetic moment Neutrons are scattered by inhomogeneities in the scattering length density of a material Chemical contrast matrix “particle” And, by inhomogeneities in the magnetization (magnetic moment per unit volume) of a material Magnetic contrast

2. SANS with Magnetic Contrast I(Q┴) ┴ Inhomogeneities in magnitude and direction of M produce scattering, e.g. domain walls Q I(Q) Sample with randomly oriented Magnetic domains Magnetic contrast

3. I(Q ) Q ┴ SANS with Magnetic Contrast By aligning magnetic domains with an applied magnetic field, domain wall scattering is eliminated I(Q) Sample with randomly oriented Magnetic domains Magnetic contrast

4. Magnetic contrast Nuclear contrast matrix “particle” SANS with Magnetic Contrast (unpolarized neutrons) I(Q┴) I(Q) similar terms for each species Magnetic scattering comes From only!

5. Using SANS to Correlate Radiation Dose with Microstructural Changes in Reactor Pressure Vessel Steels G. R. Odette, G. Lucas, et al. (U. California at Santa Barbara) Reactor Vessel Measurements aimed at determining what factors and mechanisms cause reactor vessels to embrittle SANS is particularly useful because of its sensitivity to both chemical and magnetic inhomogeneities

6. Unirradiated sample Irradiated sample H H Typical SANS Patterns for Reactor Pressure Vessel Steels Irradiated sample Irradiated sample = 11 for pure Cu = 1.5 for voids

7. Hc2 H (kG) Hc1 T (K) Type II Superconductor Mixed state Normal state normal conductor mixed state Complete flux penetration Meissner state Complete magnetic flux exclusion

8. SANS 2D detector Diffraction from fluxoid lattices Neutron diffraction reveals: • fluxoid size, shape and interface thickness • fluxoid lattice symmetry • fluxoid interactions • details of phase tranisitions • strength of pinning centers Sample in mixed state with magnetic field along beam direction n

9. Vortex Matter in Superconductor Nb T=4.6 K 3.05 kG Hc2 H (kG) Hc1 2.15 kG T (K) 3.75 kG 4.6 K 4.1 K 4.4 K 1.1 kG Real space depiction of vortex lattice X. S. Ling and S.-R. Park (Brown University) S.-M Choi, D. Dender and J. Lynn, (NCNR/NIST)

10. Characterization of Protein/RNA Complexes: Contrast Variation Deborah Kuzmanovic, Catherine O’ Connell, NIST Biotech. Div. Susan Krueger, NIST NCNR Charles Wick, Aberdeen Proving Ground MS2 Bacteriophage

11. Small Angle Scattering from Macromolecules in Solution Reciprocal Space Real Space Form Factor, Scattering Length Density, in V Solvent of Infinite Extent (Not Observed!) Scattering Length Density, in V Macromolecule in Solvent = + s (0) -

12. SANS Data Analysis Radius of Gyration (Rg) Guinier Approx. Higher Angles: • Model specific • Calculate I(Q) for model and compare to data Low Angles: QRg ~ 1 I(0)/c = constant x Mw • Not model specific • Simple shape models from Rg, Mw and V

13. Distance Distribution Function Debye-Porod Correlation Function 4P(r)  number of distances within the molecule Dmax maximum distance within the molecule P(0) = 0 P(2rDmax) = 0

14. Standard Assays for Diseases Promoter Standard RNA Coat Protein Packaging Vector Transcription Translation 1 Standard RNA Assembly 90 Dimers One Particle of Armored RNATM • Commercially available model recombinant non- infectious virus can be used as a RNA carrier • Any gene (RNA) for a disease of interest can be incorporated for use in clinical assays.

15. Samples for SANS Measurements • WT MS2 phage (3500bp) • Wild-type • Found in nature • Infectious (to bacteria only) • Empty capsid (0bp) Recombinant RNA samples: • Lambda phage (1000bp) • HCV (500bp) IS there one RNA per capsid?

16. Capsid and WT MS2 Protein Capsid and WT MS2 protein structures look similar when measured in 65% D2O solvent, where I(Q)RNA ~ 0.

17. Contrast Variation of MS2 Complexes Deuterated Lipid Head Group CD2 Deuterated RNA Deuterated Protein Water RNA Core RNA DNA Protein Protein Shell Lipid Head Group CH2 Contrast ()

18. Knowns: 1, 2: contrast for components 1 and 2 contrast: d1, d2: mass density for components 1 and 2 n: Mw-independent number density (IVDS) Structure and Mw Determination Scattered intensity and Mw from protein and RNA components can be determined separately by making measurements at several contrasts. I(q) = 12 I1(q) + 1 2I12(q) + 22 I2(q)

19. Structure and Mw of WT MS2 Phage SANS+IVDS Results Protein Mw= 2.5(±0.3) x106 RNA Mw= 1.0(±0.2) x106 Total Mw= 3.5(±0.5) x106 RNA in core packs tightly within a radius of ~ 80Å.

20. Structure of MS2 Complexes Wild-type MS2 HCV Armored RNATM 0% and 10% D2O: RNA scattering is strongest 100% D2O: RNA scattering is weaker 85% D2O: RNA scattering is weakest

21. Wild-type MS2 HCV Armored RNATM Structure of MS2 Complexes Protein shell is less well-defined in HCV particles. RNA is not as tightly packed in HCV particles.

22. Conclusions • Empty capsid and WT MS2 protein shell have similar structures. • Protein shell is thicker and less well-defined in HCV and  particles. • RNA is WT MS2 is tightly packed within a radius of ~80Å. • RNA is not as tightly packed in HCV and  particles. • Mw measurements confirmed the known amounts of protein and RNA in WT MS2. • Freshly prepared HCV and  particles likely contain more than one RNA per capsid.