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Full-Text Articles in Physical Sciences and Mathematics
On The Mechanism Of Rna Phosphodiester Backbone Cleavage In The Absence Of Solvent, Christian Riml, Heidelinde Glasner, M T. Rodgers, Ronald Micura, Kathrin Breuker
On The Mechanism Of Rna Phosphodiester Backbone Cleavage In The Absence Of Solvent, Christian Riml, Heidelinde Glasner, M T. Rodgers, Ronald Micura, Kathrin Breuker
Chemistry Faculty Research Publications
Ribonucleic acid (RNA) modifications play an important role in the regulation of gene expression and the development of RNA-based therapeutics, but their identification, localization and relative quantitation by conventional biochemical methods can be quite challenging. As a promising alternative, mass spectrometry (MS) based approaches that involve RNA dissociation in ‘top-down’ strategies are currently being developed. For this purpose, it is essential to understand the dissociation mechanisms of unmodified and posttranscriptionally or synthetically modified RNA. Here, we have studied the effect of select nucleobase, ribose and backbone modifications on phosphodiester bond cleavage in collisionally activated dissociation (CAD) of positively and negatively …
Hypothesis Driven Single Nucleotide Polymorphism Search (Hydn-Snp-S), Rebecca J. Swett, Angela Elias, Jeffrey A. Miller, Gregory E. Dyson, G. AndréS Cisneros
Hypothesis Driven Single Nucleotide Polymorphism Search (Hydn-Snp-S), Rebecca J. Swett, Angela Elias, Jeffrey A. Miller, Gregory E. Dyson, G. AndréS Cisneros
Chemistry Faculty Research Publications
The advent of complete-genome genotyping across phenotype cohorts has provided a rich source of information for bioinformaticians. However the search for SNPs from this data is generally performed on a study-by-study case without any specific hypothesis of the location for SNPs that are predictive for the phenotype. We have designed a method whereby very large SNP lists (several gigabytes in size), combining several genotyping studies at once, can be sorted and traced back to their ultimate consequence in protein structure. Given a working hypothesis, researchers are able to easily search whole genome genotyping data for SNPs that link genetic locations …
Carcinogenic Adducts Induce Distinct Dna Polymerase Binding Orientations, Kyle B. Vrtis, Radoslaw P. Markiewicz, Louis J. Romano, David Rueda
Carcinogenic Adducts Induce Distinct Dna Polymerase Binding Orientations, Kyle B. Vrtis, Radoslaw P. Markiewicz, Louis J. Romano, David Rueda
Chemistry Faculty Research Publications
DNA polymerases must accurately replicate DNA to maintain genome integrity. Carcinogenic adducts, such as 2-aminofluorene (AF) and N-acetyl-2-aminofluorene (AAF), covalently bind DNA bases and promote mutagenesis near the adduct site. The mechanism by which carcinogenic adducts inhibit DNA synthesis and cause mutagenesis remains unclear. Here, we measure interactions between a DNA polymerase and carcinogenic DNA adducts in real-time by single-molecule fluorescence. We find the degree to which an adduct affects polymerase binding to the DNA depends on the adduct location with respect to the primer terminus, the adduct structure and the nucleotides present in the solution. Not only do the …
Transparent Conducting Films Of Cdse(Zns) Core(Shell) Quantum Dot Xerogels, Lasantha Korala, Li Li, Stephanie L. Brock
Transparent Conducting Films Of Cdse(Zns) Core(Shell) Quantum Dot Xerogels, Lasantha Korala, Li Li, Stephanie L. Brock
Chemistry Faculty Research Publications
A method of fabricating sol–gel quantum dot (QD) films is demonstrated, and their optical, structural and electrical properties are evaluated. The CdSe(ZnS) xerogel films remain quantum confined, yet are highly conductive (10−3 S cm−1). This approach provides a pathway for the exploitation of QD gels in optoelectronic applications.
Robust Quantization Of A Molecular Motor Motion In A Stochastic Environment, Vladimir Y. Chernyak, Nikolai A. Sinitsyn
Robust Quantization Of A Molecular Motor Motion In A Stochastic Environment, Vladimir Y. Chernyak, Nikolai A. Sinitsyn
Chemistry Faculty Research Publications
We explore quantization of the response of a molecular motor to periodic modulation of control parameters. We formulate the pumping-quantization theorem (PQT) that identifies the conditions for robust integer quantized behavior of a periodically driven molecular machine. Implication of PQT on experiments with catenane molecules are discussed. ACKNOWLEDGMENTS We are grateful to M. Chertkov, J. R. Klein, and J. Horowitz for useful discussions. This material is based upon work supported by NSF under Grant Nos. CHE-0808910 and ECCS-0925618.