Selective recognition of G-quadruplexes by a dimeric carbocyanine dye

RSC Advances ◽  
2016 ◽  
Vol 6 (90) ◽  
pp. 87400-87404 ◽  
Author(s):  
P. Chilka ◽  
P. R. Patlolla ◽  
B. Datta
Keyword(s):  
Selective Recognition ◽  
Dna Molecules ◽  
Double Stranded Dna ◽  
Mixed Sequence ◽  
Carbocyanine Dye ◽  
G Quadruplex

A novel dimeric carbocyanine dye is found to recognise G-quadruplex structures selectively compared to mixed sequence or double-stranded DNA molecules.

scholarly journals Selective recognition of human telomeric G-quadruplex with designed peptide via hydrogen bonding followed by base stacking interactions

RSC Advances ◽  
2019 ◽  
Vol 9 (69) ◽  
pp. 40255-40262 ◽  
Author(s):  
Shikhar Tyagi ◽  
Sarika Saxena ◽  
Nikita Kundu ◽  
Taniya Sharma ◽  
Amlan Chakraborty ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Synthetic Peptide ◽  
High Selectivity ◽  
Selective Recognition ◽  
Stacking Interactions ◽  
Base Stacking ◽  
Double Stranded Dna ◽  
G Quadruplex ◽  
Guanine Base

A new synthetic peptide is presented. A Glu residue binds through H-bonding to a guanine-base and a Trp residue intercalates with K+ resulting in stabilization of a human telomeric G-quadruplex with high selectivity over a complementary c-rich strand and double-stranded DNA.

Synchrony of Digestion of SV40 DNA by Exonuclease III Determined by EM

1975 ◽  
Vol 33 ◽  
pp. 674-675
Author(s):  
Ray Wu ◽  
G. Ruben ◽  
B. Siegel ◽  
P. Spielman ◽  
E. Jay
Keyword(s):  
Dark Field ◽  
Uranyl Acetate ◽  
Enzyme Digestion ◽  
Dna Molecules ◽  
Exonuclease Iii ◽  
Aluminum Films ◽  
Double Stranded Dna ◽  
Before And After ◽  
Exo Iii ◽  
Sv40 Dna

A method for determining long nucleotide sequences of double-stranded DNA is being developed. It involves (a) the synchronous digestion of the DNA from the 3' ends with EL coli exonuclease III (Exo III) followed by (b) resynthesis with labeled nucleotides and DNA polymerase. A crucial factor in the success of this method is the degree to which the enzyme digestion proceeds synchronously under proper conditions of incubation (step a). Dark field EM is used to obtain accurate measurements on the lengths and distribution of the DNA molecules before and after digestion with Exo III, while gel electrophoresis is used in parallel to obtain a mean length for these molecules. It is the measurements on a large enough sample of individual molecules by EM that provides the information on how synchronously the digestion proceeds. For length measurements, the DNA molecules were picked up on 20-30 Å thick carbon-aluminum films, using the aqueous Kleinschmidt technique and stained with 7.5 x 10-5M uranyl acetate in 90% ethanol for 3 minutes.

scholarly journals G4-Selective Ligand Induced Autophagy

2021 ◽  
Author(s):  
Piyali Majumder ◽  
Chinmayee Shukla ◽  
Bhaskar Datta
Keyword(s):  
Gene Regulation ◽  
Negative Regulator ◽  
Homeostatic Mechanism ◽  
Selective Ligand ◽  
Carbocyanine Dye ◽  
G Quadruplex ◽  
Selective Ligands ◽  
Functional Context ◽  
Stabilizing Ligands ◽  
Mtor Activity

G-quadruplex (G4) structures have emerged as singular therapeutic targets for cancer and neurodegeneration. Autophagy is a housekeeping cellular homeostatic mechanism and deregulation of autophagy is common in cancer and in neurodegenerative diseases. In this study, we identified the presence of 46 putative G4 sequences in the MTOR gene by use of QGRS mapper tool. We sought to connect these putative G4 sequences to a functional context by leveraging G4-targeting ligands. A G4-selective dimeric carbocyanine dye Bis-4,3 and the porphyrin TMPyP4 were used to affect the replication, transcription and translation of the MTOR gene. The ligand-induced induction of autophagic pathway via MTOR gene regulation was monitored upon treatment of HeLa and SHSY-5Y cells with G4-targeting ligands. The use of Bis-4,3 was compared with the known G4-stabilizing activity of TMPyP4. Our results show that treatment with G4-selective ligands downregulates mTOR activity and leads to the induction of excessive autophagy. This is first report on effect of G4-selective ligands on MTOR regulation and mTOR expression. mTOR being the key negative regulator of autophagy, the current work suggests potential of G4 stabilizing ligands towards induction of autophagy through the downregulation of mTOR.

Thiazole Orange-Modified Carbon Dots for Ratiometric Fluorescence Detection of G-Quadruplex and Double-Stranded DNA

2018 ◽  
Vol 10 (30) ◽  
pp. 25166-25173 ◽  
Author(s):  
Ming Jin ◽  
Xiangjun Liu ◽  
Xin Zhang ◽  
Linlin Wang ◽  
Tao Bing ◽  
...  
Keyword(s):  
Fluorescence Detection ◽  
Carbon Dots ◽  
Thiazole Orange ◽  
Ratiometric Fluorescence ◽  
Double Stranded Dna ◽  
G Quadruplex

scholarly journals Static Watson-Crick Context-Free Grammars

2019 ◽  
Vol 15 (10) ◽  
pp. 65 ◽  
Author(s):  
Wan Heng Fong ◽  
Aqilahfarhana Abdul Rahman ◽  
Nor Haniza Sarmin ◽  
Sherzod Turaev
Keyword(s):  
Dna Computing ◽  
Biological Properties ◽  
Dna Molecules ◽  
Context Free Grammar ◽  
Double Stranded Dna ◽  
New Variant ◽  
Sticker System ◽  
Relationship Of ◽  
Context Free ◽  
Context Free Grammars

Sticker systems and Watson-Crick automata are two modellings of DNA molecules in DNA computing. A sticker system is a computational model which is coded with single and double-stranded DNA molecules; while Watson-Crick automata is the automata counterpart of sticker system which represents the biological properties of DNA. Both of these models use the feature of Watson-Crick complementarity in DNA computing. Previously, the grammar counterpart of the Watson-Crick automata have been introduced, known as Watson-Crick grammars which are classified into three classes: Watson-Crick regular grammars, Watson-Crick linear grammars and Watson-Crick context-free grammars. In this research, a new variant of Watson-Crick grammar called a static Watson-Crick context-free grammar, which is a grammar counterpart of sticker systems that generates the double-stranded strings and uses rule as in context-free grammar, is introduced. The static Watson-Crick context-free grammar differs from a dynamic Watson-Crick context-free grammar in generating double-stranded strings, as well as for regular and linear grammars. The main result of the paper is to determine the generative powers of static Watson-Crick context-free grammars. Besides, the relationship of the families of languages generated by Chomsky grammars, sticker systems and Watson-Crick grammars are presented in terms of their hierarchy.

A Light‐up Logic Platform for Selective Recognition of Parallel G‐Quadruplex Structures via Disaggregation‐Induced Emission

2019 ◽  
Vol 132 (2) ◽  
pp. 906-912
Author(s):  
Marco Deiana ◽  
Karam Chand ◽  
Jan Jamroskovic ◽  
Ikenna Obi ◽  
Erik Chorell ◽  
...  
Keyword(s):  
Selective Recognition ◽  
G Quadruplex
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