scholarly journals Inside Cover: A Pyrimidopyrimidine Janus-AT Nucleoside with Improved Base-Pairing Properties to both A and T within a DNA Duplex: The Stabilizing Effect of a Second Endocyclic Ring Nitrogen (Chem. Eur. J. 6/2014)

2014 ◽  
Vol 20 (6) ◽  
pp. 1462-1462
Author(s):  
Eric Largy ◽  
Wenbo Liu ◽  
Abid Hasan ◽  
David M. Perrin
Keyword(s):  
Base Pairing ◽  
Dna Duplex ◽  
Stabilizing Effect ◽  
Ring Nitrogen

Studies on the thymine–mercury–thymine base pairing in parallel and anti-parallel DNA duplexes

2015 ◽  
Vol 39 (11) ◽  
pp. 8752-8762 ◽  
Author(s):  
Gaofeng Liu ◽  
Zhiwen Li ◽  
Junfei Zhu ◽  
Yang Liu ◽  
Ying Zhou ◽  
...  
Keyword(s):  
Dna Duplexes ◽  
Base Pairing ◽  
Dna Duplex ◽  
Base Pairs ◽  
Thermal Stabilities

Parallel and anti-parallel T–Hg–T base pairs have different thermal stabilities and conformational influences on DNA duplex structures.

scholarly journals Protonation, Tautomerism, and Base Pairing of the Antiviral Favipiravir (T-705)

2020 ◽  
Author(s):  
Gabriel da Silva
Keyword(s):  
Density Functional ◽  
Enol Form ◽  
Free Energies ◽  
Base Pairing ◽  
Base Pairs ◽  
Functional Theory ◽  
Important Solution ◽  
Ring Nitrogen ◽  
Acidic Conditions ◽  
Gas Phase Basicities

Favipiravir (T-705) is an antiviral medication used to treat influenza. T-705 is also currently being trialled as a repurposed COVID-19 treatment. To help accelerate these efforts, this study provides important solution-phase properties of T-705 determined via computational chemistry. Density functional theory (DFT) calculations combined with the SMD continuum solvation model demonstrate that T-705 prefers the aromatic enol form in solution over the ketone tautomer. Deprotonation constants for the conjugate acids of T-705 (pKas) are then evaluated, by combining the DFT/SMD calculations with accurate G4 gas-phase basicities. These calculations indicate that T-705 is a weak base that should not significantly protonate at physiological pH. The preferential site for protonation is at the ring nitrogen ortho to the alcohol functional group (pKa ~ 7.4), followed by protonation of the oxygen on the amide side-chain at more acidic conditions (pKa ~ -9.8). Significantly, protonation of the ring nitrogen produces an acid that can deprotonate to the enol form (pKa ~ -5.1), providing a pathway for their interconversion. Finally, base-pairing of the active ribose-bound form of T-705 to cytidine and uridine is also examined. These calculations indicate that both base pairs have large binding free energies of around 4 – 5 kcal/mol, supporting previous findings that T-705 can bind with both nucleobases, leading to mis-incorporation of these pairs into viral RNA.<br>

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

Can Copper(II) Mediate Hoogsteen Base-Pairing in a Left-Handed DNA Duplex? A Pulse EPR Study

ChemPhysChem ◽  
2009 ◽  
Vol 11 (3) ◽  
pp. 599-606 ◽  
Author(s):  
Maria Grazia Santangelo ◽  
Philipp M. Antoni ◽  
Bernhard Spingler ◽  
Gunnar Jeschke
Keyword(s):  
Base Pairing ◽  
Dna Duplex ◽  
Left Handed ◽  
Pulse Epr ◽  
Hoogsteen Base Pairing

Base-Pairing Behavior of a Carbocyclic Janus-AT Nucleoside Analogue Capable of Recognizing A and T within a DNA Duplex

ChemBioChem ◽  
2013 ◽  
Vol 14 (16) ◽  
pp. 2199-2208 ◽  
Author(s):  
Eric Largy ◽  
Wenbo Liu ◽  
Abid Hasan ◽  
David M. Perrin
Keyword(s):  
Nucleoside Analogue ◽  
Base Pairing ◽  
Dna Duplex ◽  
Pairing Behavior

Protonation, Tautomerism, and Base Pairing of the Antiviral Favipiravir (T-705)

2020 ◽  
Author(s):  
Gabriel da Silva
Keyword(s):  
Density Functional ◽  
Enol Form ◽  
Free Energies ◽  
Base Pairing ◽  
Base Pairs ◽  
Functional Theory ◽  
Important Solution ◽  
Ring Nitrogen ◽  
Acidic Conditions ◽  
Gas Phase Basicities

Favipiravir (T-705) is an antiviral medication used to treat influenza. T-705 is also currently being trialled as a repurposed COVID-19 treatment. To help accelerate these efforts, this study provides important solution-phase properties of T-705 determined via computational chemistry. Density functional theory (DFT) calculations combined with the SMD continuum solvation model demonstrate that T-705 prefers the aromatic enol form in solution over the ketone tautomer. Deprotonation constants for the conjugate acids of T-705 (pKas) are then evaluated, by combining the DFT/SMD calculations with accurate G4 gas-phase basicities. These calculations indicate that T-705 will preferentially protonate the ring nitrogen ortho to the alcohol functional group (pKa ~ 7.4), along with protonation of the oxygen on the amide side-chain at more acidic conditions (pKa ~ 9.8). No other protomers are expected to be important. Significantly, protonation of the ring nitrogen produces an acid that can deprotonate to the enol form (pKa ~ 5.1), providing a pathway for their facile interconversion. Finally, base-pairing of the active ribose-bound form of T-705 to cytidine and uridine is also examined. These calculations indicate that both base pairs have large binding free energies of around 7 – 8 kcal/mol, supporting previous findings that T-705 can bind with both nucleobases, leading to mis-incorporation of these pairs into viral RNA.<br>

scholarly journals The Excited-State Lifetimes in a G⋅C DNA Duplex are Nearly Independent of Helix Conformation and Base-Pairing Motif

ChemPhysChem ◽  
2009 ◽  
Vol 10 (9-10) ◽  
pp. 1421-1425 ◽  
Author(s):  
Kimberly de La Harpe ◽  
Carlos E. Crespo-Hernández ◽  
Bern Kohler
Keyword(s):  
Excited State ◽  
Base Pairing ◽  
Dna Duplex ◽  
Helix Conformation ◽  
Excited State Lifetimes
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