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- Microfluidic LC Device with Orthogonal Sample Extraction for On-Chip MALDI-MS DetectionLazar, Iuliana M.; Kabulski, Jarod L. (The Royal Society of Chemistry, 2013-03-20)A microfluidic device that enables on-chip matrix assisted laser desorption ionization-mass spectrometry (MALDI-MS) detection for liquid chromatography (LC) separations is described. The device comprises an array of functional elements to carry out LC separations, integrates a novel microchip-MS interface to facilitate the orthogonal transposition of the microfluidic LC channel into an array of reservoirs, and enables sensitive MALDI-MS detection directly from the chip. Essentially, the device provides a snapshot MALDI-MS map of the content of the separation channel present on the chip. The detection of proteins with biomarker potential from MCF10A breast epithelial cell extracts, and detection limits in the low fmol range, are demonstrated. In addition, the design of the novel LC-MALDI-MS chip entices the promotion of a new concept for performing sample separations within the limited time-frame that accompanies the dead-volume of a separation channel.
- Self-Assembly of Chiral TubulesCheng, Shengfeng; Stevens, Mark J. (The Royal Society of Chemistry, 2013-11-26)The efficient and controlled assembly of complex structures from macromolecular building blocks is a critical open question in both biological systems and nanoscience. Using molecular dynamics simulations we study the self-assembly of tubular structures from model macromolecular monomers with multiple binding sites on their surfaces [Cheng et al., Soft Matter, 2012, 8, 5666_5678]. In this work we add chirality to the model monomer and a lock-and-key interaction. The self-assembly of free monomers into tubules yields a pitch value that often does not match the chirality of the monomer (including achiral monomers). We show that this mismatch occurs because of a twist deformation that brings the lateral interaction sites into alignment when the tubule pitch differs from the monomer chirality. The energy cost for this deformation is small as the energy distributions substantially overlap for small differences in the pitch and chirality. In order to control the tubule pitch by preventing the twist deformation, the interaction between the vertical surfaces must be increased without resulting in kinetically trapped structures. For this purpose, we employ lock-and-key interactions and obtain good control of the self-assembled tubule pitch. These results explain some fundamental features of microtubules. The vertical interaction strength is larger than the lateral in microtubules because this yields a controlled assembly of tubules with the proper pitch. We also generally find that the control of the assembly into tubules is difficult, which explains the wide range of pitch values and protofilament numbers observed in microtubule assembly.
- Targeting folded RNA: A branched peptide boronic acid that binds to large surface area of HIV-1 RRE RNAZhang, Wenyu; Bryson, David I.; Crumpton, Jason B.; Wynn, Jessica E.; Santos, Webster L. (The Royal Society of Chemistry, 2013-08-02)On-bead high-throughput screening of a medium-sized (1000_2000 Da) branched peptideboronic acid (BPBA) library consisting of 46 656 unique sequences against HIV-1 RRE RNA generated peptides with binding affinities in the low micromolar range. In particular, BPBA1 had a Kd of 1.4 _M with RRE IIB, preference for RNA over DNA (27 fold), and selectivity of up to >75 fold against a panel of RRE IIB variants. Structure_activity studies suggest that the boronic acid moiety and ͐branching in peptides are key structural features for efficient binding and selectivity for the folded RNA target. BPBA1 was efficiently taken up by HeLa and A2780 cells. RNA-footprinting studies revealed that the BPBA1 binding site encompasses a large surface area that spans both the upper stem as well as the internal loop regions of RRE IIB.
- Theoretical Study of the Ozonolysis of C60: Primary Ozonide Formation, Dissociation, and Multiple Ozone AdditionsChapleski, Robert C. Jr.; Morris, John R.; Troya, Diego (The Royal Society of Chemistry, 2014-01-28)We present an investigation of the reaction of ozone with C60 fullerene using electronic structure methods. Motivated by recent experiments of ozone exposure to a C60 film, we have characterized stationary points in the potential energy surface for the reactions of O3 with C60 that include both the formation of primary ozonide and subsequent dissociation reactions of this intermediate that lead to C_C bond cleavage. We have also investigated the addition of multiple O3 molecules to the C60 cage to explore potential reaction pathways under the high ozone flux conditions used in recent experiments. The lowest-energy product of the reaction of a single ozone molecule with C60 that results in C_C bond breakage corresponds to an open-cage C60O3 structure that contains ester and ketone moieties at the seam. This open-cage product is of much lower energy than the C60O + O2 products identified in prior work, and it is consistent with IR experimental spectra. Subsequent reaction of the open-cage C60O3 product with a second ozone molecule opens a low-energy reaction pathway that results in cage degradation via the loss of a CO2 molecule. Our calculations also reveal that, while full ozonation of all bonds between hexagons in C60 is unlikely even under high ozone concentration, the addition of a few ozone molecules to the C60 cage is favorable at room temperature.