X-ray structural analysis of in-situ polynucleotide surface adsorption and metal-phosphonate multilayer film self-assembly

The X-ray Standing Wave (XSW) analytical technique was adapted to measure nano-scale structures in the 0.5--50 nm length range using large d-spacing layered synthetic microstructure (LSM) X-ray mirrors. This allowed for the first ever use of multiple orders of Bragg reflection in long-period XSW analysis. XSW analysis was combined with X-ray reflectivity (XRR) and X-ray fluorescence (XRF) to analyze layer-by-layer assembly of metal-phosphonate multilayer films as a test case and to measure for the first time the in-situ process of adsorption of polynucleotides and counterions to charged planar surfaces. The surface chemistry was built on the outermost silica surfaces of 19--22 nm d-spacing Si/Mo LSMs. XSW experiments were conducted by simultaneously collecting X-ray reflectivity and X-ray fluorescence data in continuous theta-2theta scans from the total external reflection (TER) region through four or five orders of Bragg reflection.; Multilayer metal phosphonate thin films were prepared via a layer-by-layer assembly process using the metallic ions Zr4+, Y3+, Hf4+, and phosphonate molecules 1,12-dodecanediylbis(phosphonic acid) (DDBPA), porphyrin bis(phosphonic acid) (PBPA) and porphyrin square bis(phosphonic acid) (PSBPA). An initial study of PBPA and PSBPA using Y, Hf and Zr led to the optimized design of DDBPA and PSBPA films using Zr and Hf only prepared in 1, 2, 3, 4, 6, and 8 layer series on both Si(001) substrates for XRR and on 18.6 nm period Si/Mo LSMs for XSW.; Positively and negatively charged surfaces were prepared for the in-situ study of the adsorption of Zn2+ and Hg-poly(U). Hydroxyl-terminated surfaces were used to examine the adsorption of Hg-poly(U) to like charged surfaces using Zn2+ counterion-mediated adsorption. The measurements were performed in a liquid-solid interface (LSI) cell using aqueous solutions of Hg-poly(U) and ZnCl2. Using 50 muM ZnCl 2 alone, adsorption of Zn2+ was observed to the hydroxyl terminated surface. When 25 muM Hg-poly(U) and 50 muM ZnCl2 were used, a time-dependent adsorption was observed with no initial absorption of either Zn or Hg-poly(U) followed by Zn adsorption and then Hg-poly(U) adsorption.