scholarly journals RIG-I Recognition of RNA Targets: The Influence of Terminal Base Pair Sequence and Overhangs on Affinity and Signaling

Cell Reports ◽  
2019 ◽  
Vol 29 (12) ◽  
pp. 3807-3815.e3
Author(s):  
Xiaoming Ren ◽  
Melissa M. Linehan ◽  
Akiko Iwasaki ◽  
Anna Marie Pyle
Keyword(s):  
Base Pair ◽  
Rna Targets ◽  
Pair Sequence

scholarly journals Genetic analysis of the human thymidine kinase gene promoter.

1986 ◽  
Vol 6 (8) ◽  
pp. 2903-2909 ◽  
Author(s):  
J A Kreidberg ◽  
T J Kelly
Keyword(s):  
Thymidine Kinase ◽  
Base Pair ◽  
Promoter Region ◽  
Genomic Sequence ◽  
Gene Promoter ◽  
Thymidine Kinase Gene ◽  
Rich Region ◽  
Kinase Gene ◽  
Inverted Orientation ◽  
Pair Sequence

The promoter of the human thymidine kinase gene was defined by DNA sequence and genetic analyses. Mutant plasmids with deletions extending into the promoter region from both the 5' and 3' directions were constructed. The mutants were tested in a gene transfer system for the ability to transform TK- cells to the TK+ phenotype. This analysis delimited the functional promoter to within an 83-base-pair region upstream of the mRNA cap site. This region contains sequences common to other eucaryotic promoters including G X C-rich hexanucleotides, a CAAT box, and an A X T-rich region. The CAAT box is in an inverted orientation and is part of a 9-base-pair sequence repeated twice in the promoter region. Comparison of the genomic sequence with the cDNA sequence defined the first exon of the thymidine kinase gene.

Genetic analysis of the human thymidine kinase gene promoter

1986 ◽  
Vol 6 (8) ◽  
pp. 2903-2909
Author(s):  
J A Kreidberg ◽  
T J Kelly
Keyword(s):  
Thymidine Kinase ◽  
Base Pair ◽  
Promoter Region ◽  
Genomic Sequence ◽  
Gene Promoter ◽  
Thymidine Kinase Gene ◽  
Rich Region ◽  
Kinase Gene ◽  
Inverted Orientation ◽  
Pair Sequence

The promoter of the human thymidine kinase gene was defined by DNA sequence and genetic analyses. Mutant plasmids with deletions extending into the promoter region from both the 5' and 3' directions were constructed. The mutants were tested in a gene transfer system for the ability to transform TK- cells to the TK+ phenotype. This analysis delimited the functional promoter to within an 83-base-pair region upstream of the mRNA cap site. This region contains sequences common to other eucaryotic promoters including G X C-rich hexanucleotides, a CAAT box, and an A X T-rich region. The CAAT box is in an inverted orientation and is part of a 9-base-pair sequence repeated twice in the promoter region. Comparison of the genomic sequence with the cDNA sequence defined the first exon of the thymidine kinase gene.

Regulation of the Discoidin I gamma gene in Dictyostelium discoideum: identification of individual promoter elements mediating induction of transcription and repression by cyclic AMP

1990 ◽  
Vol 10 (8) ◽  
pp. 4080-4088
Author(s):  
F Vauti ◽  
P Morandini ◽  
J Blusch ◽  
A Sachse ◽  
W Nellen
Keyword(s):  
Gene Expression ◽  
Cyclic Amp ◽  
Dictyostelium Discoideum ◽  
Base Pair ◽  
Regulation Of Gene Expression ◽  
Promoter Elements ◽  
Down Regulation ◽  
Heterologous Promoter ◽  
Sequence Element ◽  
Pair Sequence

We dissected the promoter of the developmentally induced and cyclic AMP-repressed discoidin I gamma gene and identified a sequence element essential for developmental induction. Transfer of the element to an inactive heterologous promoter demonstrated that this sequence is sufficient to confer expression in axenically growing cells and to induce gene activity in development after growth on bacteria. A 16-base-pair sequence within this element was shown to be sufficient for induction in the discoidin promoter context and was used to reactivate different truncated promoter constructs. This led to the localization of an element necessary for down regulation of gene expression by extracellular cyclic AMP.

scholarly journals Regulation of the Discoidin I gamma gene in Dictyostelium discoideum: identification of individual promoter elements mediating induction of transcription and repression by cyclic AMP.

1990 ◽  
Vol 10 (8) ◽  
pp. 4080-4088 ◽  
Author(s):  
F Vauti ◽  
P Morandini ◽  
J Blusch ◽  
A Sachse ◽  
W Nellen
Keyword(s):  
Gene Expression ◽  
Cyclic Amp ◽  
Dictyostelium Discoideum ◽  
Base Pair ◽  
Regulation Of Gene Expression ◽  
Promoter Elements ◽  
Down Regulation ◽  
Heterologous Promoter ◽  
Sequence Element ◽  
Pair Sequence

We dissected the promoter of the developmentally induced and cyclic AMP-repressed discoidin I gamma gene and identified a sequence element essential for developmental induction. Transfer of the element to an inactive heterologous promoter demonstrated that this sequence is sufficient to confer expression in axenically growing cells and to induce gene activity in development after growth on bacteria. A 16-base-pair sequence within this element was shown to be sufficient for induction in the discoidin promoter context and was used to reactivate different truncated promoter constructs. This led to the localization of an element necessary for down regulation of gene expression by extracellular cyclic AMP.

Resolving the Sequence-Dependent Stiffness of DNA Using Cyclization Experiments and a Computational Rod Model

2007 ◽  
Author(s):  
Sachin Goyal ◽  
Noel C. Perkins ◽  
Jens-Christian Meiners
Keyword(s):  
Gene Expression ◽  
Experimental Data ◽  
Material Properties ◽  
Base Pair ◽  
Biological Processes ◽  
Significant Challenge ◽  
Sequence Dependent ◽  
Rod Model ◽  
Structural Deformations ◽  
Pair Sequence

Structural deformations of DNA play a central role in many biological processes including gene expression. The structural deformations are sensitive to the material properties of the molecule and these, in turn, vary along the molecule’s length according to its base-pair sequence. Example ‘sequence-dependent’ material properties include the stress-free curvature and the stiffness for bending and torsion. Separating and quantifying these sequence-dependent properties from experimental data remains a significant challenge as they often work in unison in nature. In this paper, we offer a method for resolving and quantifying the sequence-dependent stiffness of DNA from cyclization (loop closure) experiments using a computational rod model of the molecule.

scholarly journals Detection and identification of dengue virus isolates from Brazil by a simplified reverse transcription - polymerase chain reaction (RT-PCR) method

1997 ◽  
Vol 39 (2) ◽  
pp. 79-84
Author(s):  
Luiz Tadeu Moraes FIGUEIREDO ◽  
Weber Chelli BATISTA ◽  
Akira IGARASHI
Keyword(s):  
Dengue Virus ◽  
Reverse Transcription ◽  
Base Pair ◽  
Uv Light ◽  
Virus Titer ◽  
Yellow Fever Vaccine ◽  
Rt Pcr ◽  
Pair Sequence ◽  
Consensus Primers

We show here a simplified RT-PCR for identification of dengue virus types 1 and 2. Five dengue virus strains, isolated from Brazilian patients, and yellow fever vaccine 17DD as a negative control, were used in this study. C6/36 cells were infected and supernatants were collected after 7 days. The RT-PCR, done in a single reaction vessel, was carried out following a 1/10 dilution of virus in distilled water or in a detergent mixture containing Nonidet P40. The 50 µl assay reaction mixture included 50 pmol of specific primers amplifying a 482 base pair sequence for dengue type 1 and 210 base pair sequence for dengue type 2. In other assays, we used dengue virus consensus primers having maximum sequence similarity to the four serotypes, amplifying a 511 base pair sequence. The reaction mixture also contained 0.1 mM of the four deoxynucleoside triphosphates, 7.5 U of reverse transcriptase, 1U of thermostable Taq DNA polymerase. The mixture was incubated for 5 minutes at 37ºC for reverse transcription followed by 30 cycles of two-step PCR amplification (92ºC for 60 seconds, 53ºC for 60 seconds) with slow temperature increment. The PCR products were subjected to 1.7% agarose gel electrophoresis and visualized by UV light after staining with ethidium bromide solution. Low virus titer around 10 3, 6 TCID50/ml was detected by RT-PCR for dengue type 1. Specific DNA amplification was observed with all the Brazilian dengue strains by using dengue virus consensus primers. As compared to other RT-PCRs, this assay is less laborious, done in a shorter time, and has reduced risk of contamination

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