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Longhini A.P.,University of Maryland University College | Leblanc R.M.,University of Maryland University College | Becette O.,University of Maryland University College | Salguero C.,Harvard University | And 6 more authors.
Nucleic Acids Research | Year: 2015

Stable isotope labeling is central to NMR studies of nucleic acids. Development of methods that incorporate labels at specific atomic positions within each nucleotide promises to expand the size range of RNAs that can be studied by NMR. Using recombinantly expressed enzymes and chemically synthesized ribose and nucleobase, we have developed an inexpensive, rapid chemo-enzymatic method to label ATP and GTP site specifically and in high yields of up to 90%. We incorporated these nucleotides into RNAs with sizes ranging from 27 to 59 nucleotides using in vitro transcription: A-Site (27 nt), the iron responsive elements (29 nt), a fluoride riboswitch from Bacillus anthracis (48 nt), and a frame-shifting element from a human corona virus (59 nt). Finally, we showcase the improvement in spectral quality arising from reduced crowding and narrowed linewidths, and accurate analysis of NMR relaxation dispersion (CPMG) and TROSY-based CEST experiments to measure μs-ms time scale motions, and an improved NOESY strategy for resonance assignment. Applications of this selective labeling technology promises to reduce difficulties associated with chemical shift overlap and rapid signal decay that have made it challenging to study the structure and dynamics of large RNAs beyond the 50 nt median size found in the PDB. © 2016 The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Brown J.D.,University of Maryland Baltimore County | Summers M.F.,University of Maryland Baltimore County | Johnson B.A.,University of Maryland Baltimore County | Johnson B.A.,One Moon Scientific Inc. | Johnson B.A.,Advanced Science Research Center
Journal of Biomolecular NMR | Year: 2015

The Biological Magnetic Resonance Data Bank (BMRB) contains NMR chemical shift depositions for over 200 RNAs and RNA-containing complexes. We have analyzed the 1H NMR and 13C chemical shifts reported for non-exchangeable protons of 187 of these RNAs. Software was developed that downloads BMRB datasets and corresponding PDB structure files, and then generates residue-specific attributes based on the calculated secondary structure. Attributes represent properties present in each sequential stretch of five adjacent residues and include variables such as nucleotide type, base-pair presence and type, and tetraloop types. Attributes and 1H and 13C NMR chemical shifts of the central nucleotide are then used as input to train a predictive model using support vector regression. These models can then be used to predict shifts for new sequences. The new software tools, available as stand-alone scripts or integrated into the NMR visualization and analysis program NMRViewJ, should facilitate NMR assignment and/or validation of RNA 1H and 13C chemical shifts. In addition, our findings enabled the re-calibration a ring-current shift model using published NMR chemical shifts and high-resolution X-ray structural data as guides. © 2015 Springer Science+Business Media Dordrecht.

Deshko Y.,City College of New York | Krusin-Elbaum L.,City College of New York | Menon V.,City College of New York | Khanikaev A.,Queens College, City University of New York | Trevino J.,Advanced Science Research Center
Optics Express | Year: 2016

We investigate the propagation of surface plasmon polaritons (SPPs) in thin films of topological insulators. Cases of single films and multilayered stacks are analyzed. The materials considered are second generation three dimensional topological insulators Bi2Se3, Bi2Te3, and Sb2Te3. Dispersion relations and propagation lengths of SPPs are estimated numerically, taking into account the variation of bulk dielectric functions of topological insulators, as well as substrate, using the Drude-Lorentz model. The key factors affecting propagation length are identified and experimental modifications for tuning the dispersion relations are proposed. The apparent discrepancy between the experimental data and previously considered theory is resolved. © 2016 Optical Society of America.

A team of international scientists led by researchers of the CUNY Advanced Science Research Center (ASRC) and the Politecnico of Milan in Italy has demonstrated a novel approach for designing fully reconfigurable magnetic nanopatterns whose properties and functionality can be programmed and reprogrammed on-demand. The method—published in Nature Nanotechnology and led by Elisa Riedo, professor of Physics with the ASRC's Nanoscience Initiative, and Riccardo Bertacco, a professor with the Politecnico of Milan—is based on thermal scanning probe lithography and uses a hot nano-tip to perform a highly localized field heating and cooling in antiferromagnetic and ferromagnetic thin films. The hot tip is then used to align the spins in the material in any desired direction with nanoscale resolution. "The proposed technique is straightforward and combines the full reversibility and stability of exchange bias, as the same pattern can be written and reset many times, with the resolution and versatility of scanning probe lithography," said Riedo. "In particular, this work demonstrates how thermal scanning probe lithography is gaining momentum as a key nanofabrication method for the next generation of nanodevices, from biomedical sensing to sprintronics." This approach offers researchers the opportunity to control magnetism at the nanoscale as never before. The authors used this method to fabricate channels where spin waves can propagate. Spin waves are a propagating re-ordering of the magnetization in a material. A new generation of computing and sensing devices can be fabricated based on the propagation of spin waves instead of the more conventional electric current. ​Bertacco noted these findings will allow for the development of novel metamaterials with finely-tuned magnetic properties, as well as a reconfigurable computing device architectures. "Equally promising is the creation of structures with high response to external magnetic fields, as they can be used as sensors in new architectures of spintronic devices," he said. "The potential target market for these devices is extremely large—especially with the advent of the age of the 'Internet of things'—in which every object has a growing need for integrated sensors and computational capacity." Edoardo Albisetti, postdoctoral research associate at the Politecnico of Milan and the paper's first author, said the new magnetic nanostructure patterning method gives researchers an increased amount of control. "So far, the patterning of magnetic nanostructures has been mainly achieved through irreversible structural or chemical modifications," Albisetti said. "On the contrary, by using this new thermal assisted magnetic scanning probe lithography (tam-SPL) method, the magnetic nanopatterns are fully reconfigurable and obtained without modifying the film chemistry and topography." The ability to draw new meta-magnetic materials opens the way for the development of innovative devices for information processing based on logic cells as well as on the propagation and manipulation of spin waves in magnonic structures.

Gagne D.,University of Quebec | Gagne D.,Advanced Science Research Center | French R.L.,University of Illinois at Chicago | French R.L.,Washington University in St. Louis | And 7 more authors.
Structure | Year: 2015

Summary The role of internal dynamics in enzyme function is highly debated. Specifically, how small changes in structure far away from the reaction site alter protein dynamics and overall enzyme mechanisms is of wide interest in protein engineering. Using RNase A as a model, we demonstrate that elimination of a single methyl group located >10 Å away from the reaction site significantly alters conformational integrity and binding properties of the enzyme. This A109G mutation does not perturb structure or thermodynamic stability, both in the apo and ligand-bound states. However, significant enhancement in conformational dynamics was observed for the bound variant, as probed over nano- to millisecond timescales, resulting in major ligand repositioning. These results illustrate the large effects caused by small changes in structure on long-range conformational dynamics and ligand specificities within proteins, further supporting the importance of preserving wild-type dynamics in enzyme systems that rely on flexibility for function. © 2015 Elsevier Ltd.

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