scholarly journals Alternative Secondary Structures in the Phage G4 Origin of the Complementary DNA Strand Synthesis: Effects of NaCl Concentration on the Bleomycin-DNA Interaction

1992 ◽  
Vol 56 (3) ◽  
pp. 394-398 ◽  
Author(s):  
Kazumitsu Ueda ◽  
Hiroshi Hiasa ◽  
So Takebe ◽  
Hiroshi Sakai ◽  
Tohru Komano
Keyword(s):  
Secondary Structures ◽  
Dna Interaction ◽  
Complementary Dna ◽  
Nacl Concentration ◽  
Dna Strand

Role of the potential secondary structures in phage g4 origin of complementary dna strand synthesis

Gene ◽  
1988 ◽  
Vol 71 (2) ◽  
pp. 323-330 ◽  
Author(s):  
Sakai Hiroshi ◽  
Hiasa Hiroshi ◽  
Iwamoto Keiji ◽  
Horimoto Taizo ◽  
Komano Tohru ◽  
...  
Keyword(s):  
Secondary Structures ◽  
Complementary Dna ◽  
Dna Strand

Distinct functional contributions of three potential secondary structures in the phage G4 origin of complementary DNA strand synthesis

Gene ◽  
1989 ◽  
Vol 84 (1) ◽  
pp. 17-22 ◽  
Author(s):  
Hiroshi Hiasa ◽  
Katsunori Tanaka ◽  
Hiroshi Sakai ◽  
Kanako Yoshida ◽  
Yoichi Honda ◽  
...  
Keyword(s):  
Secondary Structures ◽  
Complementary Dna ◽  
Dna Strand

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.

scholarly journals Covalently Functionalized DNA Duplexes and Quadruplexes as Hybrid Catalysts in an Enantioselective Friedel–Crafts Reaction

Molecules ◽  
2020 ◽  
Vol 25 (14) ◽  
pp. 3121
Author(s):  
Surjendu Dey ◽  
Andres Jäschke
Keyword(s):  
Secondary Structures ◽  
Catalytic Performance ◽  
Dna Duplexes ◽  
Quadruplex Dna ◽  
Hybrid Catalysts ◽  
Modified Dna ◽  
G Quadruplex ◽  
Dna Secondary Structures ◽  
Dna Strand

The precise site-specific positioning of metal–ligand complexes on various DNA structures through covalent linkages has gained importance in the development of hybrid catalysts for aqueous-phase homogeneous catalysis. Covalently modified double-stranded and G-quadruplex DNA-based hybrid catalysts have been investigated separately. To understand the role of different DNA secondary structures in enantioselective Friedel–Crafts alkylation, a well-known G-quadruplex-forming sequence was covalently modified at different positions. The catalytic performance of this modified DNA strand was studied in the presence and absence of a complementary DNA sequence, resulting in the formation of two different secondary structures, namely duplex and G-quadruplex. Indeed, the secondary structures had a tremendous effect on both the yield and stereoselectivity of the catalyzed reaction. In addition, the position of the modification, the topology of the DNA, the nature of the ligand, and the length of the linker between ligand and DNA were found to modulate the catalytic performance of the hybrid catalysts. Using the optimal linker length, the quadruplexes formed the (−)-enantiomer with up to 65% ee, while the duplex yielded the (+)-enantiomer with up to 62% ee. This study unveils a new and simple way to control the stereochemical outcome of a Friedel–Crafts reaction.

scholarly journals Crystal Structure of Chiral γPNA with Complementary DNA Strand: Insights into the Stability and Specificity of Recognition and Conformational Preorganization

2010 ◽  
Vol 132 (31) ◽  
pp. 10717-10727 ◽  
Author(s):  
Joanne I. Yeh ◽  
Boris Shivachev ◽  
Srinivas Rapireddy ◽  
Matthew J. Crawford ◽  
Roberto R. Gil ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Complementary Dna ◽  
Dna Strand ◽  
The Stability
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