Double-Coding Nucleic Acids: Introduction of a Nucleobase Sequence in the Major Groove of the DNA Duplex Using Double-Headed Nucleotides

2014 ◽  
Vol 79 (17) ◽  
pp. 8020-8030 ◽  
Author(s):  
Pawan Kumar ◽  
Antoni Figueras Sorinas ◽  
Lise J. Nielsen ◽  
Maria Slot ◽  
Kirstine Skytte ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Major Groove ◽  
Dna Duplex

Pyrenemethyl ara-Uridine-2′-carbamate: A Strong Interstrand Excimer in the Major Groove of a DNA Duplex

ChemBioChem ◽  
2003 ◽  
Vol 4 (9) ◽  
pp. 841-847 ◽  
Author(s):  
Natalia N. Dioubankova ◽  
Andrei D. Malakhov ◽  
Dmitry A. Stetsenko ◽  
Michael J. Gait ◽  
Pavel E. Volynsky ◽  
...  
Keyword(s):  
Major Groove ◽  
Dna Duplex

scholarly journals Design of the Crosslinking Reactions for Nucleic Acids-Binding Protein and Evaluation of the Reactivity

2020 ◽  
Vol 10 (21) ◽  
pp. 7709
Author(s):  
Kenta Odaira ◽  
Ken Yamada ◽  
Shogo Ishiyama ◽  
Hidenori Okamura ◽  
Fumi Nagatsugi
Keyword(s):  
Nucleic Acids ◽  
Binding Protein ◽  
Molecular Study ◽  
Pyrimidine Derivative ◽  
Major Groove ◽  
Covalent Bonds ◽  
Biological Studies ◽  
Selective Chemical ◽  
Crosslinking Reactions ◽  
Vinyl Group

Selective chemical reactions of biomolecules are some of the important tools for investigations by biological studies. We have developed the selective crosslinking reactions to form covalent bonds to DNA or RNA using crosslinking oligonucleotides (CFO) bearing reactive bases. In this study, we designed the cross-linkable 4-amino-6-oxo-2-vinyltriazine derivative with an acyclic linker (acyAOVT) to react with the nucleic acids-binding protein based on our previous results. We hypothesized that the acyAOVT base would form a stable base pair with guanine by three hydrogen bonds at the positions of the vinyl group in the duplex DNA major groove, and the vinyl group can react with the nucleophilic species in the proximity, for example, the cysteine or lysine residue in the nucleic acids-binding protein. The synthesized oligonucleotides bearing the acyAOVT derivative showed a higher reactivity than that of the corresponding pyrimidine derivative without one nitrogen. The duplex containing acyAOVT-guanine (G) formed complexes with Hha1 DNMT even in the presence of 2-mercaptoethanol. We expect that our system will provide a useful tool for the molecular study of nucleic acids-binding proteins.

Investigation of changes in the arrangement of water molecules and salt ions surrounding different atoms of the DNA molecule during the melting process: a molecular dynamics simulation study

2015 ◽  
Vol 93 (3) ◽  
pp. 348-361 ◽  
Author(s):  
C. Izanloo
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Double Helix ◽  
Melting Process ◽  
Minor Groove ◽  
Dynamics Simulation ◽  
Transition Curve ◽  
Water Molecules ◽  
Major Groove ◽  
Dna Duplex

A molecular dynamics simulation was performed on a B-DNA duplex (CGCGAATTGCGC) at different temperatures. The DNA was immerged in a saltwater medium with 1 mol/L NaCl concentration. The arrangements of water molecules and cations around the different atoms of DNA on the melting pathway were investigated. Almost for all atoms of the DNA by double helix → single-stranded transition, the water molecules released from the DNA duplex and cations were close to single-stranded DNA, but this behavior was not clearly seen at melting temperatures. Therefore, release of water molecules and cations approaching the DNA by the increase of temperature does not have any effect on the sharpness of the transition curve. Most of the water molecules and cations were found to be around the negatively charged phosphate oxygen atoms. The number of water molecules released from the first shell hydration upon melting in the minor groove was higher than in the major groove, and intrusion of cations into the minor groove after melting was higher than into the major groove. The hydrations of imino protons were different from each other and were dependent on DNA bases.

scholarly journals The study of complexation between dicationic surfactants and the DNA duplex using structural and spectroscopic methods

RSC Advances ◽  
2017 ◽  
Vol 7 (42) ◽  
pp. 26006-26018 ◽  
Author(s):  
W. Andrzejewska ◽  
M. Wilkowska ◽  
M. Chrabąszczewska ◽  
M. Kozak
Keyword(s):  
Nucleic Acids ◽  
Plasmid Dna ◽  
Living Cells ◽  
Spectroscopic Methods ◽  
Dna Duplex ◽  
Dna Oligomers ◽  
Different Types ◽  
Dicationic Surfactants ◽  
Viral Transfection

Dicationic (also known as gemini or dimeric) bis-alkylimidazolium surfactants belong to a group of non-viral transfection systems proposed for the successful introduction of different types of nucleic acids (i.e., siRNA, DNA oligomers, and plasmid DNA) into living cells.

Magnesium effect on premelting transitions in nucleic acids: DNA duplex and RNA hairpin models

2011 ◽  
Vol 993 (1-3) ◽  
pp. 324-327 ◽  
Author(s):  
Pavla Ottová ◽  
Shirly Josefina Espinoza-Herrera ◽  
Josef Štěpánek
Keyword(s):  
Nucleic Acids ◽  
Dna Duplex ◽  
Rna Hairpin

Separation of Nucleic Acids Using Single- and Multimodal Chromatography

2018 ◽  
Vol 20 (1) ◽  
pp. 49-55 ◽  
Author(s):  
Tiago Matos ◽  
Leif Bülow
Keyword(s):  
Nucleic Acids ◽  
Chemical Properties ◽  
Single Mode ◽  
Major Groove ◽  
Base Pairs ◽  
Chromatographic Separations ◽  
Multimodal Chromatography ◽  
Phosphate Backbone ◽  
Target Molecules ◽  
Polymerase Chain

The needs for purified nucleic acids for preparative and analytical applications have increased constantly, demanding for the development of new and more efficient methods for their recovery and isolation. DNA molecules harbour some intrinsic chemical properties that render them suitable for chromatographic separations. These include a negatively charged phosphate backbone as well as a hydrophobic character originating mainly from the major groove of DNA which exposes the base pairs on the surface of the molecule. In addition, single stranded DNA often allows for a free exposure of the hydrophobic aromatic bases. In this review, multimodal chromatography (MMC) has been evaluated as an alternative tool for complex separations of nucleic acids. MMC embraces more than one kind of interaction between the chromatographic ligand and the target molecules. These resins have often proved superior to conventional single-mode chromatographic materials for DNA isolation, including, e.g., the purification of plasmid DNA from crude cell lysates and for the preparation of DNA fragments before or after a polymerase chain reaction (PCR).

2′-O ,4′-C -Methylene-Bridged Nucleic Acids Stabilize Metal-Mediated Base Pairing in a DNA Duplex

ChemBioChem ◽  
2018 ◽  
Vol 19 (22) ◽  
pp. 2372-2379 ◽  
Author(s):  
Osamu Nakagawa ◽  
Akane Fujii ◽  
Yuki Kishimoto ◽  
Yusuke Nakatsuji ◽  
Natsumi Nozaki ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Base Pairing ◽  
Dna Duplex

scholarly journals Front Cover: 2′-O ,4′-C -Methylene-Bridged Nucleic Acids Stabilize Metal-Mediated Base Pairing in a DNA Duplex (ChemBioChem 22/2018)

ChemBioChem ◽  
2018 ◽  
Vol 19 (22) ◽  
pp. 2321-2321
Author(s):  
Osamu Nakagawa ◽  
Akane Fujii ◽  
Yuki Kishimoto ◽  
Yusuke Nakatsuji ◽  
Natsumi Nozaki ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Base Pairing ◽  
Dna Duplex ◽  
Front Cover
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