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Full-Text Articles in Medicine and Health Sciences
Nanorings To Probe Mechanical Stress Of Single-Stranded Dna Mediated By The Dna Duplex, Karen Zagorski, Tommy Stormberg, Mohtadin Hashemi, Anatoly B. Kolomeisky, Yuri L. Lyubchenko
Nanorings To Probe Mechanical Stress Of Single-Stranded Dna Mediated By The Dna Duplex, Karen Zagorski, Tommy Stormberg, Mohtadin Hashemi, Anatoly B. Kolomeisky, Yuri L. Lyubchenko
Journal Articles: Pharmaceutical Sciences
The interplay between the mechanical properties of double-stranded and single-stranded DNA is a phenomenon that contributes to various genetic processes in which both types of DNA structures coexist. Highly stiff DNA duplexes can stretch single-stranded DNA (ssDNA) segments between the duplexes in a topologically constrained domain. To evaluate such an effect, we designed short DNA nanorings in which a DNA duplex with 160 bp is connected by a 30 nt single-stranded DNA segment. The stretching effect of the duplex in such a DNA construct can lead to the elongation of ssDNA, and this effect can be measured directly using atomic …
Samhd1 Is A Single-Stranded Nucleic Acid Binding Protein With No Active Site-Associated Nuclease Activity., Kyle J. Seamon, Zhiqiang Sun, Luda S. Shlyakhtenko, Yuri L. Lyubchenko, James T. Stivers
Samhd1 Is A Single-Stranded Nucleic Acid Binding Protein With No Active Site-Associated Nuclease Activity., Kyle J. Seamon, Zhiqiang Sun, Luda S. Shlyakhtenko, Yuri L. Lyubchenko, James T. Stivers
Journal Articles: Pharmaceutical Sciences
The HIV-1 restriction factor SAMHD1 is a tetrameric enzyme activated by guanine nucleotides with dNTP triphosphate hydrolase activity (dNTPase). In addition to this established activity, there have been a series of conflicting reports as to whether the enzyme also possesses single-stranded DNA and/or RNA 3'-5' exonuclease activity. SAMHD1 was purified using three chromatography steps, over which the DNase activity was largely separated from the dNTPase activity, but the RNase activity persisted. Surprisingly, we found that catalytic and nucleotide activator site mutants of SAMHD1 with no dNTPase activity retained the exonuclease activities. Thus, the exonuclease activity cannot be associated with any …
Bridged Filaments Of Histone-Like Nucleoid Structuring Protein Pause Rna Polymerase And Aid Termination In Bacteria., Matthew V. Kotlajich, Daniel R. Hron, Beth A. Boudreau, Zhiqiang Sun, Yuri L. Lyubchenko, Robert Landick
Bridged Filaments Of Histone-Like Nucleoid Structuring Protein Pause Rna Polymerase And Aid Termination In Bacteria., Matthew V. Kotlajich, Daniel R. Hron, Beth A. Boudreau, Zhiqiang Sun, Yuri L. Lyubchenko, Robert Landick
Journal Articles: Pharmaceutical Sciences
Bacterial H-NS forms nucleoprotein filaments that spread on DNA and bridge distant DNA sites. H-NS filaments co-localize with sites of Rho-dependent termination in Escherichia coli, but their direct effects on transcriptional pausing and termination are untested. In this study, we report that bridged H-NS filaments strongly increase pausing by E. coli RNA polymerase at a subset of pause sites with high potential for backtracking. Bridged but not linear H-NS filaments promoted Rho-dependent termination by increasing pause dwell times and the kinetic window for Rho action. By observing single H-NS filaments and elongating RNA polymerase molecules using atomic force microscopy, we …