Modified OligoDNA Having Two Consecutive Silylated-pyrene Moieties in Minor Groove Exhibiting an Excimer Fluorescent Signal upon Binding to Fully Complementary DNA Strand

2010 ◽  
Vol 39 (12) ◽  
pp. 1254-1255 ◽  
Author(s):  
Mika Mogi ◽  
Md. Gias Uddin ◽  
Mayumi Ichimura ◽  
Tomohisa Moriguchi ◽  
Kazuo Shinozuka
Keyword(s):  
Minor Groove ◽  
Complementary Dna ◽  
Fluorescent Signal ◽  
Dna Strand

Synthesis and Properties of Molecular Beacon DNA Probe Bearing Novel Silylated Pyrene Derivative

2011 ◽  
Vol 497 ◽  
pp. 47-50 ◽  
Author(s):  
M. Gias Uddin ◽  
Tomohisa Moriguchi ◽  
Mayumi Ichimura ◽  
Kazuo Shinozuka
Keyword(s):  
Molecular Beacon ◽  
Dna Probe ◽  
Stem Segment ◽  
Excimer Emission ◽  
Stem Loop ◽  
Complementary Dna ◽  
Single Base ◽  
Fluorescent Signal ◽  
Modified Dna ◽  
Dna Strand

A novel stem-loop structured fluorescent oligoDNA probe (molecular beacon probe) bearing a silylated pyrene derivative at C-5 position of deoxyuridine has been synthesized. The fluorescently labeled modified nucleoside has been incorporated into two consecutive positions in the stem segment of the DNA using an automated DNA synthesizer. The resulting modified DNA exhibited an excimer fluorescent signal upon binding to the fully matched complementary DNA strand. The excimer emission was, however, effectively quenched while it stays alone or it hybridizes to a single base mismatched complementary target.

scholarly journals Modular protein-oligonucleotide signal exchange

2020 ◽  
Vol 48 (12) ◽  
pp. 6431-6444
Author(s):  
Deepak K Agrawal ◽  
Rebecca Schulman
Keyword(s):  
Specific Protein ◽  
Vascular Endothelial ◽  
Complementary Dna ◽  
Exchange Processes ◽  
Dna Strand Displacement ◽  
Specific Proteins ◽  
Dna Strand ◽  
Endothelial Growth Factor ◽  
Signal Exchange

Abstract While many methods are available to measure the concentrations of proteins in solution, the development of a method to quantitatively report both increases and decreases in different protein concentrations in real-time using changes in the concentrations of other molecules, such as DNA outputs, has remained a challenge. Here, we present a biomolecular reaction process that reports the concentration of an input protein in situ as the concentration of an output DNA oligonucleotide strand. This method uses DNA oligonucleotide aptamers that bind either to a specific protein selectively or to a complementary DNA oligonucleotide reversibly using toehold-mediated DNA strand-displacement. It is possible to choose the sequence of output strand almost independent of the sensing protein. Using this strategy, we implemented four different exchange processes to report the concentrations of clinically relevant human α-thrombin and vascular endothelial growth factor using changes in concentrations of DNA oligonucleotide outputs. These exchange processes can operate in tandem such that the same or different output signals can indicate changes in concentration of distinct or identical input proteins. The simplicity of our approach suggests a pathway to build devices that can direct diverse output responses in response to changes in concentrations of specific proteins.

Cloning and molecular analysis of promoter-like sequences isolated from the chromosomal DNA ofLactobacillus acidophilusATCC 4356

1997 ◽  
Vol 43 (1) ◽  
pp. 61-69 ◽  
Author(s):  
G. Djordjevic ◽  
B. Bojovic ◽  
N. Miladinov ◽  
L. Topisirovic
Keyword(s):  
Lactococcus Lactis ◽  
Molecular Analysis ◽  
Lactobacillus Acidophilus ◽  
Promoter Activity ◽  
Lactobacillus Reuteri ◽  
Bacterial Species ◽  
Chromosomal Dna ◽  
Complementary Dna ◽  
E Coli ◽  
Dna Strand

Promoter-like sequences from the chromosomal DNA of thermophilic strain Lactobacillus acidophilus ATCC 4356 were cloned. Analysis of the three DNA fragments showing promoter activity, designated P3, P6, and P15, were performed in Lactobacillus reuteri, Lactococcus lactis, and E. coli. The reporter cat-86 gene was expressed in all three bacterial species under control of the fragments P3 and P6. Fragment P15 showed promoter activity only in Lactobacillus reuteri and E. coli but not in Lactococcus lactis. The three host-specific transcriptional start points (TSPs) were used when transcription of the cat-86 gene was controlled by fragment P3 in Lactobacillus reuteri, E. coli, and Lactococcus lactis. Similarly, fragment P15 initiated transcription of the cat-86 gene at two distinctive sites in Lactobacillus reuteri and E. coli. Only within fragment P6, a common TSP was used in Lactobacillus reuteri and E. coli, but different from that used in Lactococcus lactis. Each TSP was preceded by the putative −35 and −10 hexamers. Computer analysis of the fragment P3 sequence revealed the existence of divergent promoterlike sequence (P3rev) located on the complementary DNA strand. Fragments P6 and P15 were also functional in Lactobacillus acidophilus ATCC 4356 from which chromosomal DNA they were originally cloned.Key words: Lactobacillus acidophilus, promoter-like sequences, regulation.

scholarly journals Reliable microspotting methodology for peptide-nucleic acid layers with high hybridization efficiency on gold SPR imaging chips

2015 ◽  
Vol 7 (15) ◽  
pp. 6077-6082 ◽  
Author(s):  
L. Simon ◽  
G. Lautner ◽  
R. E. Gyurcsányi
Keyword(s):  
Nucleic Acid ◽  
Peptide Nucleic Acid ◽  
Gold Surfaces ◽  
Complementary Dna ◽  
Spr Imaging ◽  
Hybridization Efficiency ◽  
Dna Strand

Microspotting of HS-PNA strands prehybridized with a complementary DNA strand onto gold surfaces results in PNA layers with excellent hybridization efficiency.

scholarly journals Control of Aptamer Function Using Radiofrequency Magnetic Field

2011 ◽  
Vol 2011 ◽  
pp. 1-6 ◽  
Author(s):  
Kenichi Taira ◽  
Koichi Abe ◽  
Takayuki Ishibasi ◽  
Katsuaki Sato ◽  
Kazunori Ikebukuro
Keyword(s):  
Magnetic Field ◽  
Control System ◽  
Gold Nanoparticle ◽  
Inhibitory Activity ◽  
Protein Function ◽  
Local Heating ◽  
Activity Assay ◽  
Complementary Dna ◽  
Dna Strand ◽  
Control Protein

Remote control of aptamer function has allowed us to control protein function in space and time. Here, we propose a novel control system for aptamer function by radiofrequency magnetic field- (RFMF-) induced local heating of a gold nanoparticle conjugated with an aptamer. In this study, we used a 31-mer thrombin-binding aptamer (TBA), which can inhibit thrombin activity, as a model aptamer. We evaluated the RFMF control of the inhibitory activity of a gold nanoparticle-conjugated TBA. To evaluate the effect of RFMF on enzymatic activity, we utilized a complementary DNA strand that maintains the broken structure during the activity assay. We observed a decrease in the inhibitory activity of TBA after RFMF irradiation. It indicates that RFMF is capable of controlling the TBA structure. Because RFMF allows noninvasive control of aptamer function, this strategy is expected to be novel way of controlling aptamer drug activity.

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