scholarly journals High-resolution, hybrid optical trapping methods, and their application to nucleic acid processing proteins

Biopolymers ◽  
2016 ◽  
Vol 105 (10) ◽  
pp. 704-714 ◽  
Author(s):  
Yann R. Chemla
Author(s):  
D. P. Bazett-Jones ◽  
M. J. Hendzel

Structural analysis of combinations of nucleosomes and transcription factors on promoter and enhancer elements is necessary in order to understand the molecular mechanisms responsible for the regulation of transcription initiation. Such complexes are often not amenable to study by high resolution crystallographic techniques. We have been applying electron spectroscopic imaging (ESI) to specific problems in molecular biology related to transcription regulation. There are several advantages that this technique offers in studies of nucleoprotein complexes. First, an intermediate level of spatial resolution can be achieved because heavy atom contrast agents are not necessary. Second, mass and stoichiometric relationships of protein and nucleic acid can be estimated by phosphorus detection, an element in much higher proportions in nucleic acid than protein. Third, wrapping or bending of the DNA by the protein constituents can be observed by phosphorus mapping of the complexes. Even when ESI is used with high exposure of electrons to the specimen, important macromolecular information may be provided. For example, an image of the TATA binding protein (TBP) bound to DNA is shown in the Figure (top panel). It can be seen that the protein distorts the DNA away from itself and much of its mass sits off the DNA helix axis. Moreover, phosphorus and mass estimates demonstrate whether one or two TBP molecules interact with this particular promoter TATA sequence.


2020 ◽  
Author(s):  
Di Liu ◽  
Yaming Shao ◽  
Joseph A. Piccirilli ◽  
Yossi Weizmann

<p>Though advances in nanotechnology have enabled the construction of synthetic nucleic acid based nanoarchitectures with ever-increasing complexity for various applications, high-resolution structures are lacking due to the difficulty of obtaining good diffracting crystals. Here we report the design of RNA nanostructures based on homooligomerizable tiles from an RNA single-strand for X-ray determination. Three structures are solved to near-atomic resolution: a 2D parallelogram, an unexpectedly formed 3D nanobracelet, and a 3D nanocage. Structural details of their constituent motifs—such as kissing loops, branched kissing-loops and T-junctions—that resemble natural RNA motifs and resisted X-ray determination are revealed. This work unveils the largely unexplored potential of crystallography in gaining high-resolution feedback for nanostructure design and suggests a novel route to investigate RNA motif structures by configuring them into nanoarchitectures.</p>


1990 ◽  
Vol 535 ◽  
pp. 127-145 ◽  
Author(s):  
Donna M. Dion ◽  
Kevin O'Connor ◽  
Dorothy Phillips ◽  
George J. Vella ◽  
William Warren

Science ◽  
2020 ◽  
Vol 368 (6495) ◽  
pp. 1135-1140 ◽  
Author(s):  
Jason Qian ◽  
Zhi-xiang Lu ◽  
Christopher P. Mancuso ◽  
Han-Ying Jhuang ◽  
Rocío del Carmen Barajas-Ornelas ◽  
...  

Determining where an object has been is a fundamental challenge for human health, commerce, and food safety. Location-specific microbes in principle offer a cheap and sensitive way to determine object provenance. We created a synthetic, scalable microbial spore system that identifies object provenance in under 1 hour at meter-scale resolution and near single-spore sensitivity and can be safely introduced into and recovered from the environment. This system solves the key challenges in object provenance: persistence in the environment, scalability, rapid and facile decoding, and biocontainment. Our system is compatible with SHERLOCK, a Cas13a RNA-guided nucleic acid detection assay, facilitating its implementation in a wide range of applications.


2017 ◽  
Vol 45 (7) ◽  
pp. 3634-3642 ◽  
Author(s):  
C. Denise Okafor ◽  
Kathryn A. Lanier ◽  
Anton S. Petrov ◽  
Shreyas S. Athavale ◽  
Jessica C. Bowman ◽  
...  

2010 ◽  
Vol 35 (17) ◽  
pp. 2988 ◽  
Author(s):  
Wei Cheng ◽  
Ximiao Hou ◽  
Fangmao Ye

2018 ◽  
Author(s):  
Ahmed M. Malik ◽  
Roberto A. Miguez ◽  
Xingli Li ◽  
Ye-Shih Ho ◽  
Eva L. Feldman ◽  
...  

ABSTRACTAbnormalities in nucleic acid processing are associated with the development of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Mutations in Matrin 3 (MATR3), a poorly understood DNA- and RNA-binding protein, cause familial ALS/FTD, and MATR3 pathology is a feature of sporadic disease, suggesting that MATR3 dysfunction is integrally linked to ALS pathogenesis. Using a primary neuron model to assess MATR3-mediated toxicity, we noted that neurons were bidirectionally vulnerable to MATR3 levels, with pathogenic MATR3 mutants displaying enhanced toxicity. MATR3’s zinc finger domains partially modulated toxicity, but elimination of its RNA recognition motifs had no effect on neuronal survival, instead facilitating its self-assembly into liquid-like droplets. In contrast to other RNA-binding proteins associated with ALS, cytoplasmic MATR3 redistribution mitigated neurodegeneration, suggesting that nuclear MATR3 mediates toxicity. Our findings offer a foundation for understanding MATR3-related neurodegeneration and how nucleic acid binding functions, localization, and pathogenic mutations drive sporadic and familial disease.


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