scholarly journals FRET‐MC : A fluorescence melting competition assay for studying G4 structures in vitro

Biopolymers ◽  
2020 ◽  
Author(s):  
Yu Luo ◽  
Anton Granzhan ◽  
Daniela Verga ◽  
Jean‐Louis Mergny
Keyword(s):  
Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 3039-3039
Author(s):  
Anthony Y. Tsai ◽  
Stephanie C. Filice ◽  
Elizabeth H. Javazon ◽  
Andrea T. Badillo ◽  
Alan W. Flake

Abstract Bone marrow derived mesenchymal stem cells (MSCs) have the capacity to differentiate into cells of the various mesodermal lineages. Efficiency of engraftment, however, remains a significant obstacle in MSC transplantation. P21 is a G1 checkpoint regulator and cyclin-dependent kinase inhibitor. In its absence, hematopoieitc stem cell (HSC) proliferation increases under normal homeostatic conditions. The aim of the study is to evaluate the effects of p21 deficiency on the proliferative capacity of MSCs. Therefore, MSCs from p21 KO and wildtype mice were maintained in culture in hypoxic and normoxic conditions. Cell counts and respective days in cultures were recorded from which population doubling (PD) times were calculated and compared. 1:1 Competition assays were performed between p21 KO MSCs transduced with DsRed and eGFP transduced WT MSCs as well as between DsRed transduced p21 KO MSCs and non-transduced WT MSCs. Osteogenic, chondrogenic, and adipogenic differentiation assays were performed on both cell populations using standard protocols. Sca-1, CD34, CD45, CD90, MHC Class I and II and other surface antigens were assessed using FACS analysis. In normoxic conditions, the p21 KO MSCs went through 25.68 population doublings in 60 days versus 25.43 population doublings in 103 days for the p21 WT MSCs. Under hypoxic conditions, the KO MSC population doubled 23.3 times in 58 days versus 14.78 times in 60 days for the WT MSCs. All population doubling times were taken from passage 10 cells. When the DsRed transduced KO MSCs (96.6-98.5% DsRed+) was placed in a 1:1 competition assay with eGFP transduced WT MSCs (99.3-99.9% eGFP+) or non-transduced WT MSCs (99.9–100% eGFP−), the normoxic results are as shown in Table 1. Similarly, the competition assay result between DsRed transduced KO MSCs (86.9–94.1% DsRed+) and eGFP transduced WT MSCs (99.7–100% eGFP+) or non-transduced WT MSCs (100% eGFP−) for the hypoxic condition are shown in Table 2. Both the p21 KO and wildtype MSCs populations were able to differentiate into ostenogenic, adipogenic, and chondrogenic lineages. No significant surface marker differences were observed between the 2 populations on FACS analysis. Our results clearly showed that p21 deficient MSCs have increased proliferative ability in vitro compared to normal MSCs. These findings have implications for expansion of MSC populations in vitro , and for the enhancement of competitive capacity of MSCs following in vivo administration. Table 1 - Normoxic Competition Assay KO MSC (DsRed) WT MSC (eGFP) KO MSC (DsRed) WT MSC (none) results analyzed by FACS Day 6 64.2±3.7% 34.5±4.3% 70.3±0.4% 19.7±0.6% Day 11 84.0±4.5% 13.6±4.6% 92.0±0.8% 6.4±0.7% Table 2 - Hypoxic Competition Assay KO MSC (DsRed) WT MSC (eGFP) KO MSC (DsRed) WT MSC (none) results analyzed by FACS Day 4 70.3±1.7% 30.0±1.7% 83.0±0.8% 18.6±0.9% Day 8 75.7±0.7% 25.8±0.7% 81.3±1.2% 20.6±1.2%


2018 ◽  
Vol 73 (6) ◽  
pp. 1604-1610 ◽  
Author(s):  
Sue C Nang ◽  
Faye C Morris ◽  
Michael J McDonald ◽  
Mei-Ling Han ◽  
Jiping Wang ◽  
...  

Abstract Objectives The discovery of mobile colistin resistance mcr-1, a plasmid-borne polymyxin resistance gene, highlights the potential for widespread resistance to the last-line polymyxins. In the present study, we investigated the impact of mcr-1 acquisition on polymyxin resistance and biological fitness in Klebsiella pneumoniae. Methods K. pneumoniae B5055 was used as the parental strain for the construction of strains carrying vector only (pBBR1MCS-5) and mcr-1 recombinant plasmids (pmcr-1). Plasmid stability was determined by serial passaging for 10 consecutive days in antibiotic-free LB broth, followed by patching on gentamicin-containing and antibiotic-free LB agar plates. Lipid A was analysed using LC–MS. The biological fitness was examined using an in vitro competition assay analysed with flow cytometry. The in vivo fitness cost of mcr-1 was evaluated in a neutropenic mouse thigh infection model. Results Increased polymyxin resistance was observed following acquisition of mcr-1 in K. pneumoniae B5055. The modification of lipid A with phosphoethanolamine following mcr-1 addition was demonstrated by lipid A profiling. The plasmid stability assay revealed the instability of the plasmid after acquiring mcr-1. Reduced in vitro biological fitness and in vivo growth were observed with the mcr-1-carrying K. pneumoniae strain. Conclusions Although mcr-1 confers a moderate level of polymyxin resistance, it is associated with a significant biological fitness cost in K. pneumoniae. This indicates that mcr-1-mediated resistance in K. pneumoniae could be attenuated by limiting the usage of polymyxins.


2020 ◽  
Vol 8 ◽  
Author(s):  
Ola El Atab ◽  
Rabih Darwiche ◽  
Nathanyal J. Truax ◽  
Roger Schneiter ◽  
Kenneth G. Hull ◽  
...  

During their infective stages, hookworms release excretory-secretory (E-S) products, small molecules, and proteins to help evade and suppress the host's immune system. Small molecules found in E-S products of mammalian hookworms include nematode derived metabolites like ascarosides, which are composed of the sugar ascarylose linked to a fatty acid side chain. The most abundant proteins found in hookworm E-S products are members of the protein family known as Ancylostoma secreted protein (ASP). In this study, two ascarosides and their fatty acid moieties were synthesized and tested for in vitro binding to Na-ASP-2 using both a ligand competition assay and microscale thermophoresis. The fatty acid moieties of both ascarosides tested and ascr#3, an ascaroside found in rat hookworm E-S products, bind to Na-ASP-2's palmitate binding cavity. These molecules were confirmed to bind to the palmitate but not the sterol binding sites. An ascaroside, oscr#10, which is not found in hookworm E-S products, does not bind to Na-ASP-2. More studies are required to determine the structural basis of ascarosides binding by Na-ASP-2 and to understand the physiological significance of these observations.


1989 ◽  
Vol 9 (6) ◽  
pp. 2315-2321
Author(s):  
Z C Lai ◽  
D J DeAngelo ◽  
M DiLiberto ◽  
G Childs

Normal development requires that individual genes be expressed in their correct temporal patterns, but the mechanisms regulating this process during early embryogenesis are poorly understood. We have studied the early and late sea urchin histone genes during embryogenesis to address the molecular mechanisms controlling temporal gene expression. By measuring the changes in expression of cloned H1-beta DNA constructs after microinjection into fertilized one-cell zygotes, we demonstrated that a highly conserved 30-base-pair segment of DNA between positions -288 and -317 (USE IV) is responsible for the transcriptional activation of this late histone gene at the late blastula stage. In this report, we demonstrate that an oligonucleotide corresponding to USE IV acts as an embryonic enhancer element capable of activating the simian virus 40 early promoter in a stage-specific manner. Using an in vivo competition assay and in vitro DNase I footprinting and mobility shift assays, we also identified a protein(s) that interacts with this enhancer. Results of the competition assay suggested that this factor acts to stimulate transcription of the H1-beta gene. The factor was found to be stored in mature eggs as well as in all embryonic stages examined. The mobility of the factor found in eggs, however, differed from that of the embryonic form, which suggested that posttranslational modification occurs after fertilization.


1986 ◽  
Vol 6 (2) ◽  
pp. 635-644 ◽  
Author(s):  
C L Greer

Splicing of tRNA precursors in Saccharomyces cerevisiae extracts proceeds in two steps; excision of the intervening sequence and ligation of the tRNA halves. The ability to resolve these two steps and the distinct physical properties of the endonuclease and ligase suggested that the splicing steps may not be concerted and that these two enzymes may act independently in vivo. A ligase competition assay was developed to examine whether the excision and ligation steps in tRNA splicing in vitro are concerted or independent. The ability of either yeast ligase or T4 ligase plus kinase to join the tRNA halves produced by endonuclease and the distinct structures of the reaction products provided the basis for the competition assay. In control reactions, joining of isolated tRNA halves formed by preincubation with endonuclease was measured. The ratio of yeast to T4 reaction products in these control assays reflected the ratio of the enzyme activities, as would be expected if each has equal access to the substrate. In splicing competition assays, endonuclease and pre-tRNA were added to ligase mixtures, and joining of the halves that were formed was measured. In these assays the products were predominantly those of the yeast ligase even when the T4 enzymes were present in excess. These results demonstrate preferential access of yeast ligase to the endonuclease products and provide evidence for the assembly of a functional tRNA splicing complex in vitro. This observation has important implications for the organization of the splicing components and of the gene expression pathway in vivo.


1988 ◽  
Vol 8 (4) ◽  
pp. 1809-1811 ◽  
Author(s):  
P Ghazal ◽  
H Lubon ◽  
L Hennighausen

The possibility of DNA-binding proteins interacting in vitro with the polymerase II transcriptional machinery was explored by using a competition assay with individual target sequences for enhancer-binding factors. Transcription factors binding to at least five specific enhancer sequences mediate the activity of the human cytomegalovirus immediate-early 1 gene in vitro. Furthermore, our data suggest that individual DNA-bound enhancer factors can interact with the promoter transcription complex.


1977 ◽  
Vol 146 (2) ◽  
pp. 600-605 ◽  
Author(s):  
J Forman

Spleen cells sensitized against trinitrophenyl (TNP)-modified stimulator cells displayed a cytotoxic effect against syngeneic TNP-modified but not dinitrophenyl (DNP)-modified target cells. The same finding was observed in the opposite direction; that is, effector cells sensitized against DNP-modified stimulator cells did not cross kill TNP-modified targets. The specificity of the anti-TNP effector cells was confirmed in a cold target competition assay. Presensitization in vivo with hapten-modified cells followed by rechallenge and testing in vitro did not alter the specificity of the response between the haptens. These data indicate that the receptor(s) on the cytotoxic T cell can distinguish between two closely related haptenic molecules.


1989 ◽  
Vol 9 (6) ◽  
pp. 2315-2321 ◽  
Author(s):  
Z C Lai ◽  
D J DeAngelo ◽  
M DiLiberto ◽  
G Childs

Normal development requires that individual genes be expressed in their correct temporal patterns, but the mechanisms regulating this process during early embryogenesis are poorly understood. We have studied the early and late sea urchin histone genes during embryogenesis to address the molecular mechanisms controlling temporal gene expression. By measuring the changes in expression of cloned H1-beta DNA constructs after microinjection into fertilized one-cell zygotes, we demonstrated that a highly conserved 30-base-pair segment of DNA between positions -288 and -317 (USE IV) is responsible for the transcriptional activation of this late histone gene at the late blastula stage. In this report, we demonstrate that an oligonucleotide corresponding to USE IV acts as an embryonic enhancer element capable of activating the simian virus 40 early promoter in a stage-specific manner. Using an in vivo competition assay and in vitro DNase I footprinting and mobility shift assays, we also identified a protein(s) that interacts with this enhancer. Results of the competition assay suggested that this factor acts to stimulate transcription of the H1-beta gene. The factor was found to be stored in mature eggs as well as in all embryonic stages examined. The mobility of the factor found in eggs, however, differed from that of the embryonic form, which suggested that posttranslational modification occurs after fertilization.


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