scholarly journals Hydration effects on the duplex stability of phosphoramidate DNA--RNA oligomers

1997 ◽  
Vol 25 (4) ◽  
pp. 830-835 ◽  
Author(s):  
D. Barsky ◽  
M. E. Colvin ◽  
G. Zon ◽  
S. M. Gryaznov
Keyword(s):  
Duplex Stability ◽  
Rna Oligomers

Postsynthetic Modification of Oligonucleotides with Imidazophenazine Dye and its Effect on Duplex Stability

2011 ◽  
Vol 30 (7-8) ◽  
pp. 585-596 ◽  
Author(s):  
Larysa Dubey ◽  
Olga Ryazanova ◽  
Victor Zozulya ◽  
Dmytro Fedoryak ◽  
Igor Dubey
Keyword(s):  
Postsynthetic Modification ◽  
Duplex Stability

Influence of Local Duplex Stability andN6-Methyladenine on Uracil Recognition by Mismatch-Specific Uracil-DNA Glycosylase (Mug)

2002 ◽  
Vol 15 (12) ◽  
pp. 1595-1601 ◽  
Author(s):  
Victoria Valinluck ◽  
Pingfang Liu ◽  
Artur Burdzy ◽  
Junichi Ryu ◽  
Lawrence C. Sowers
Keyword(s):  
Dna Glycosylase ◽  
Uracil Dna Glycosylase ◽  
Duplex Stability

scholarly journals Harnessing Chemical Energy for the Activation and Joining of Prebiotic Building Blocks

2019 ◽  
Author(s):  
Ziwei Liu ◽  
Long-Fei Wu ◽  
Jianfeng Xu ◽  
Claudia Bonfio ◽  
David Russell ◽  
...  
Keyword(s):  
Aqueous Solution ◽  
Carboxylic Acid ◽  
Peptide Nucleic Acid ◽  
Reactive Intermediates ◽  
Building Blocks ◽  
Acid System ◽  
Rna Oligomers ◽  
Prebiotic Activation ◽  
Simultaneous Activation ◽  
Acid Anhydrides

Simultaneous activation of carboxylates and phosphates provides multiple pathways for the generation of reactive intermediates, including mixed carboxylic acid-phosphoric acid anhydrides, for the synthesis of peptidyl-RNAs, peptides, RNA oligomers and primordial phospholipids. These results indicate that unified prebiotic activation chemistry could have enabled the joining of building blocks in aqueous solution from a common pool and enabled the progression of a system towards higher complexity foreshadowing the modern encapsulated peptide-nucleic acid system

scholarly journals Single Molecule Investigation of Ag+ Interactions with Single Cytosine-, Methylcytosine- and Hydroxymethylcytosine-Cytosine Mismatches in a Nanopore

2014 ◽  
Vol 4 (1) ◽  
Author(s):  
Yong Wang ◽  
Bin-Quan Luan ◽  
Zhiyu Yang ◽  
Xinyue Zhang ◽  
Brandon Ritzo ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Binding Site ◽  
Single Molecule ◽  
Metal Ion ◽  
Detection Method ◽  
Direct Detection ◽  
Alpha Hemolysin ◽  
Duplex Stability ◽  
Dynamics Simulations ◽  
Direct Detection Method

Abstract Both cytosine-Ag-cytosine interactions and cytosine modifications in a DNA duplex have attracted great interest for research. Cytosine (C) modifications such as methylcytosine (mC) and hydroxymethylcytosine (hmC) are associated with tumorigenesis. However, a method for directly discriminating C, mC and hmC bases without labeling, modification and amplification is still missing. Additionally, the nature of coordination of Ag+ with cytosine-cytosine (C-C) mismatches is not clearly understood. Utilizing the alpha-hemolysin nanopore, we show that in the presence of Ag+, duplex stability is most increased for the cytosine-cytosine (C-C) pair, followed by the cytosine-methylcytosine (C-mC) pair and the cytosine-hydroxymethylcytosine (C-hmC) pair, which has no observable Ag+ induced stabilization. Molecular dynamics simulations reveal that the hydrogen-bond-mediated paring of a C-C mismatch results in a binding site for Ag+. Cytosine modifications (such as mC and hmC) disrupted the hydrogen bond, resulting in disruption of the Ag+ binding site. Our experimental method provides a novel platform to study the metal ion-DNA interactions and could also serve as a direct detection method for nucleobase modifications.

Antisense Recognition of the HER-2 mRNA:  Effects of Phosphorothioate Substitution and Polyamines on DNA·RNA, RNA·RNA, and DNA·DNA Duplex Stability†

Biochemistry ◽  
2005 ◽  
Vol 44 (1) ◽  
pp. 303-312 ◽  
Author(s):  
Sripriya Venkiteswaran ◽  
Veena Vijayanathan ◽  
Akira Shirahata ◽  
Thresia Thomas ◽  
T. J. Thomas
Keyword(s):  
Duplex Stability ◽  
Her 2

Enhanced H-bonding and π-stacking in DNA: a potent duplex-stabilizing and mismatch sensing nucleobase analogue

2014 ◽  
Vol 5 (10) ◽  
pp. 3836-3844 ◽  
Author(s):  
Chenguang Lou ◽  
Andre Dallmann ◽  
Pietro Marafini ◽  
Rachel Gao ◽  
Tom Brown
Keyword(s):  
Electrostatic Attraction ◽  
Dna Duplex ◽  
Π Stacking ◽  
Duplex Stability

Combining enhanced π-stacking, H-bonding and electrostatic attraction in a single C-monomer greatly increases DNA duplex stability and massively destabilises mismatches.

A graphene oxide coated tapered microfiber acting as a super-sensor for rapid detection of SARS-CoV-2

Lab on a Chip ◽  
2021 ◽  
Author(s):  
Hao Jia ◽  
Ao Zhang ◽  
Yuquan Yang ◽  
Yaqi Cui ◽  
Jianrong Xu ◽  
...  
Keyword(s):  
Graphene Oxide ◽  
Rapid Detection ◽  
Innovative Approach ◽  
Sensor System ◽  
System P ◽  
Rna Oligomers ◽  
Optical Microfiber

COVID-19 is a new strain of highly contagious coronavirus. Now, an innovative approach to detect it by combining DNA/RNA oligomers as aptamers and a GO coated optical microfiber as a sensor system.

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