scholarly journals Synthesis and biophysical analysis of modified thymine-containing DNA oligonucleotides

2017 ◽  
Vol 53 (8) ◽  
pp. 1389-1392 ◽  
Author(s):  
F. Kawasaki ◽  
P. Murat ◽  
Z. Li ◽  
T. Santner ◽  
S. Balasubramanian
Keyword(s):  
Biophysical Characterization ◽  
Dna Oligonucleotides ◽  
Biophysical Analysis

We report the synthesis of a 5-formyl-2′-deoxyuridine (5fU) phosphoramidite, and the preparation and biophysical characterization of oligonucleotides comprising all known, naturally observed eukaryotic thymidine modifications.

scholarly journals Characterization of an Amino-Terminal Dimerization Domain from Retroviral Restriction Factor Fv1

2006 ◽  
Vol 80 (16) ◽  
pp. 8225-8235 ◽  
Author(s):  
Kate N. Bishop ◽  
Gulnahar B. Mortuza ◽  
Steven Howell ◽  
Melvyn W. Yap ◽  
Jonathan P. Stoye ◽  
...  
Keyword(s):  
Leukemia Virus ◽  
Limited Proteolysis ◽  
Dimerization Domain ◽  
Biophysical Characterization ◽  
Amino Terminal ◽  
Terminal Domain ◽  
Biophysical Analysis ◽  
Baculovirus System ◽  
Resistance To Infection

ABSTRACT The Fv1 protein is an endogenous factor in mice that confers resistance to infection by certain classes of murine leukemia virus, a phenomenon referred to as restriction. The mechanism of restriction is not understood, and the low endogenous level of Fv1 in cells has prevented any biochemical or biophysical analysis of the protein. We have now purified recombinant Fv1n protein from a baculovirus system and demonstrate that Fv1 exists in a multimeric form. Furthermore, we have mapped the position of two domains within the protein using limited proteolysis. Biophysical characterization of the N-terminal domain reveals that it comprises a highly helical and extended dimeric structure. Based on these biochemical and biophysical data, we propose a model for the arrangement of domains in Fv1 and suggest that dimerization of the N-terminal domain is necessary for Fv1 function to allow the protein to interact with multiple capsid protomers in retroviral cores.

Archaeal RNA polymerase: the influence of the protruding stalk in crystal packing and preliminary biophysical analysis of the Rpo13 subunit

2011 ◽  
Vol 39 (1) ◽  
pp. 25-30 ◽  
Author(s):  
Magdalena Wojtas ◽  
Bibiana Peralta ◽  
Marina Ondiviela ◽  
Maria Mogni ◽  
Stephen D. Bell ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Laser Light ◽  
Crystal Packing ◽  
Biophysical Characterization ◽  
Crystal Forms ◽  
Space Groups ◽  
Biophysical Analysis ◽  
Sulfolobus Shibatae ◽  
Archaeal Transcription

We review recent results on the complete structure of the archaeal RNAP (RNA polymerase) enzyme of Sulfolobus shibatae. We compare the three crystal forms in which this RNAP packs (space groups P212121, P21212 and P21) and provide a preliminary biophysical characterization of the newly identified 13-subunit Rpo13. The availability of different crystal forms for this RNAP allows the analysis of the packing degeneracy and the intermolecular interactions that determine this degeneracy. We observe the pivotal role played by the protruding stalk composed of subunits Rpo4 and Rpo7 in the lattice contacts. Aided by MALLS (multi-angle laser light scattering), we have initiated the biophysical characterization of the recombinantly expressed and purified subunit Rpo13, a necessary step towards the understanding of Rpo13's role in archaeal transcription.

Purification and Biophysical Characterization of an 11S Globulin from Wrightia tinctoria Exhibiting Hemagglutinating Activity

2013 ◽  
Vol 20 (5) ◽  
pp. 499-509 ◽  
Author(s):  
Pramod Kumar ◽  
Dipak N. Patil ◽  
Anshul Chaudhary ◽  
Shailly Tomar ◽  
Dinesh Yernool ◽  
...  
Keyword(s):  
Hemagglutinating Activity ◽  
Biophysical Characterization ◽  
11S Globulin ◽  
Wrightia Tinctoria

Biophysical Characterization of Glycodendrimers As Nano-carriers for HIV Peptides

2013 ◽  
Vol 20 (31) ◽  
pp. 3935-3943 ◽  
Author(s):  
M. Ionov ◽  
K. Ciepluch ◽  
B. Moreno ◽  
D. Appelhans ◽  
J. Sanchez-Nieves ◽  
...  
Keyword(s):  
Biophysical Characterization

scholarly journals Remote Sensing Methods for the Biophysical Characterization of Protected Areas Globally: Challenges and Opportunities

2021 ◽  
Vol 10 (6) ◽  
pp. 384
Author(s):  
Javier Martínez-López ◽  
Bastian Bertzky ◽  
Simon Willcock ◽  
Marine Robuchon ◽  
María Almagro ◽  
...  
Keyword(s):  
Remote Sensing ◽  
Protected Areas ◽  
Large Scale ◽  
Anthropogenic Activities ◽  
Global Scale ◽  
Area Network ◽  
Biophysical Characterization ◽  
Challenges And Opportunities ◽  
Scale Characterization

Protected areas (PAs) are a key strategy to reverse global biodiversity declines, but they are under increasing pressure from anthropogenic activities and concomitant effects. Thus, the heterogeneous landscapes within PAs, containing a number of different habitats and ecosystem types, are in various degrees of disturbance. Characterizing habitats and ecosystems within the global protected area network requires large-scale monitoring over long time scales. This study reviews methods for the biophysical characterization of terrestrial PAs at a global scale by means of remote sensing (RS) and provides further recommendations. To this end, we first discuss the importance of taking into account the structural and functional attributes, as well as integrating a broad spectrum of variables, to account for the different ecosystem and habitat types within PAs, considering examples at local and regional scales. We then discuss potential variables, challenges and limitations of existing global environmental stratifications, as well as the biophysical characterization of PAs, and finally offer some recommendations. Computational and interoperability issues are also discussed, as well as the potential of cloud-based platforms linked to earth observations to support large-scale characterization of PAs. Using RS to characterize PAs globally is a crucial approach to help ensure sustainable development, but it requires further work before such studies are able to inform large-scale conservation actions. This study proposes 14 recommendations in order to improve existing initiatives to biophysically characterize PAs at a global scale.

scholarly journals Fluorescence Fluctuation Spectroscopy enables quantification of potassium channel subunit dynamics and stoichiometry

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Giulia Tedeschi ◽  
Lorenzo Scipioni ◽  
Maria Papanikolaou ◽  
Geoffrey W. Abbott ◽  
Michelle A. Digman
Keyword(s):  
Plasma Membrane ◽  
Protein Diffusion ◽  
Ion Diffusion ◽  
Fluorescence Fluctuation Spectroscopy ◽  
Biophysical Characterization ◽  
Kv Channels ◽  
Subunit Stoichiometry ◽  
Spatio Temporal ◽  
Voltage Sensing Domain

AbstractVoltage-gated potassium (Kv) channels are a family of membrane proteins that facilitate K+ ion diffusion across the plasma membrane, regulating both resting and action potentials. Kv channels comprise four pore-forming α subunits, each with a voltage sensing domain, and they are regulated by interaction with β subunits such as those belonging to the KCNE family. Here we conducted a comprehensive biophysical characterization of stoichiometry and protein diffusion across the plasma membrane of the epithelial KCNQ1-KCNE2 complex, combining total internal reflection fluorescence (TIRF) microscopy and a series of complementary Fluorescence Fluctuation Spectroscopy (FFS) techniques. Using this approach, we found that KCNQ1-KCNE2 has a predominant 4:4 stoichiometry, while non-bound KCNE2 subunits are mostly present as dimers in the plasma membrane. At the same time, we identified unique spatio-temporal diffusion modalities and nano-environment organization for each channel subunit. These findings improve our understanding of KCNQ1-KCNE2 channel function and suggest strategies for elucidating the subunit stoichiometry and forces directing localization and diffusion of ion channel complexes in general.

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