scholarly journals Sedimentation Velocity Ultracentrifugation Analysis for Hydrodynamic Characterization of G-Quadruplex Structures

Author(s):  
Nichola C. Garbett ◽  
Chongkham S. Mekmaysy ◽  
Jonathan B. Chaires
2021 ◽  
Author(s):  
Anirban Ghosh ◽  
Eric Largy ◽  
Valérie Gabelica

Abstract G-quadruplex DNA structures have become attractive drug targets, and native mass spectrometry can provide detailed characterization of drug binding stoichiometry and affinity, potentially at high throughput. However, the G-quadruplex DNA polymorphism poses problems for interpreting ligand screening assays. In order to establish standardized MS-based screening assays, we studied 28 sequences with documented NMR structures in (usually ∼100 mM) potassium, and report here their circular dichroism (CD), melting temperature (Tm), NMR spectra and electrospray mass spectra in 1 mM KCl/100 mM trimethylammonium acetate. Based on these results, we make a short-list of sequences that adopt the same structure in the MS assay as reported by NMR, and provide recommendations on using them for MS-based assays. We also built an R-based open-source application to build and consult a database, wherein further sequences can be incorporated in the future. The application handles automatically most of the data processing, and allows generating custom figures and reports. The database is included in the g4dbr package (https://github.com/EricLarG4/g4dbr) and can be explored online (https://ericlarg4.github.io/G4_database.html).


Biochemistry ◽  
2015 ◽  
Vol 54 (49) ◽  
pp. 7168-7177 ◽  
Author(s):  
Yasuhiko Yamamoto ◽  
Masashi Kinoshita ◽  
Yuya Katahira ◽  
Haruna Shimizu ◽  
Yue Di ◽  
...  

2014 ◽  
Vol 86 (15) ◽  
pp. 7688-7695 ◽  
Author(s):  
Borries Demeler ◽  
Tich-Lam Nguyen ◽  
Gary E. Gorbet ◽  
Virgil Schirf ◽  
Emre H. Brookes ◽  
...  

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Orsolya Réka Molnár ◽  
András Végh ◽  
Judit Somkuti ◽  
László Smeller

AbstractSpecific guanine rich nucleic acid sequences can form non-canonical structures, like the four stranded G-quadruplex (GQ). We studied the GQ-forming sequence (named HepB) found in the genome of the hepatitis B virus. Fluorescence-, infrared- and CD-spectroscopy were used. HepB shows a hybrid form in presence of K+, but Na+, Li+, and Rb+ induce parallel structure. Higher concentrations of metal ions increase the unfolding temperature, which was explained by a short thermodynamic calculation. Temperature stability of the GQ structure was determined for all these ions. Na+ has stronger stabilizing effect on HepB than K+, which is highly unusual. The transition temperatures were 56.6, 53.8, 58.5 and 54.4 °C for Na+, K+, Li+, and Rb+ respectively. Binding constants for Na+ and K+ were 10.2 mM and 7.1 mM respectively. Study of three ligands designed in cancer research for GQ targeting (TMPyP4, BRACO19 and PhenDC3) showed unequivocally their binding to HepB. Binding was proven by the increased stability of the bound form. The stabilization was higher than 20 °C for TMPyP4 and PhenDC3, while it was considerably lower for BRACO19. These results might have medical importance in the fight against the hepatitis B virus.


1973 ◽  
Vol 19 (7) ◽  
pp. 831-836 ◽  
Author(s):  
Martin Kessel ◽  
Robert MacColl ◽  
Donald S. Berns ◽  
Mercedes R. Edwards

The particulate material (intact and dissociated phycobilisomes), adjacent to the thylakoids of Plectonema boryanum and Calothrix parietina, was examined in thin sections and in freshly prepared C-phycocyanin extracts. For the latter a method was developed using spheroplasts of log-phase cells. When examined by sedimentation velocity centrifugation, the sedimentation coefficients of the rapidly extracted C-phycocyanin were found to be 18 S and 5 S. Also, a 10-S boundary was observed with P. boryanum. When C. parietina was grown under red light the 18-S aggregates increased to 20 S. The 18 S particles, in electron micrographs of negatively stained preparations, displayed eight subunits surrounding a central one. The possibility that some subunits fall out of the plane of view is contemplated in proposing a dodecamer arrangement for such particles. The 20-S particles were also examined by electron microscopy. However, the precise number of monomer units associated with either the 18-S or 20-S particles has not yet been ascertained. Thin sections of intact algal cells are presented to demonstrate the presence of phycobilisomes along the outer faces of the thylakoid membranes.


PLoS ONE ◽  
2015 ◽  
Vol 10 (12) ◽  
pp. e0144510 ◽  
Author(s):  
Emmanuel O. Ariyo ◽  
Evan P. Booy ◽  
Trushar R. Patel ◽  
Edis Dzananovic ◽  
Ewan K. McRae ◽  
...  

1995 ◽  
Vol 28 (4) ◽  
pp. 325-332 ◽  
Author(s):  
A. Seifert ◽  
L. Heinevetter ◽  
H. Cölfen ◽  
S.E. Harding

1976 ◽  
Vol 143 (5) ◽  
pp. 1220-1238 ◽  
Author(s):  
J M Fidler ◽  
M C Howard ◽  
K Shortman

The characteristics of antibody-forming cell (AFC) progenitors lacking previous contact with specific antigen (virgin AFC progenitors) has been studied using sedimentation velocity and buoyant density separation for the investigation of physically distinct B-cell subpopulations. Functional characterization of isolated subsets was made using a quantitative adoptive immune assay for the IgM AFC progenitors responding to the antigen 4-hydroxy-3-iodo-5-nitrophenylacetic acid conjugated polymerized bacterial flagellin. Extensive heterogeneity is present among B lymphocytes, only some subpopulations of which exhibit AFC progenitor function. In the spleen of adult conventional CBA mice, atypically fast sedimenting cells of low buoyant density are active, while typical small B lymphocytes do not appear to be progenitors of IgM AFC. Spleen of adult specific pathogen-free (SPF), germfree, and athymic nude mice give similar results, although a minor population of typical slowly sedimenting dense cells are active in the latter two sources. Adult conventional bone marrow cells are as physically and functionally heterogeneous as splenic B cells, and although a significant proportion of AFC progenitor activity is found among dense, slowly sedimenting cells, most of the activity is among low density, faster sedimenting cells. In contrast to this situation in adult animals, where most of the unprimed AFC progenitors are large, atypical B cells, the spleens of neonatal mice provide a site where virgin AFC progenitors with the physical properties of typical small B lymphocytes are found. While being present in conventional and SPF neonatal spleens, these virgin cells are predominant in 7-day-old germfree mouse spleen. These findings suggest that the newborn virgin B cell is a typical small lymphocyte. However, few cells of this type are found in the adult animal. The unprimed AFC-progenitor population in the adult consists of large, fast sedimenting, low buoyant density, adherent cells, the physical properties of which are characteristic of activated B lymphocytes. It is suggested that these atypical cells are derived from the small newborn virgin B cell by the nonspecific effects of environmental antigenic stimuli.


Sign in / Sign up

Export Citation Format

Share Document