Effects of the biological backbone on DNA–protein stacking interactions

Cassandra D. M. Churchill, Lex Navarro-Whyte, Lesley R. Rutledge and Stacey D. Wetmore

Phys. Chem. Chem. Phys., 2009, 11, 10657
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Effects of the biological backbone on stacking interactions at DNA–protein interfaces: the interplay between the backbone⋯π and π⋯π components

Cassandra D. M. Churchill, Lesley R. Rutledge and Stacey D. Wetmore

Phys. Chem. Chem. Phys., 2010, 12, 14515
DOI: 10.1039/c0cp00550a

Universal base analogues and their applications in DNA sequencing technology

Feng Liang, Ying-Zhu Liu and Peiming Zhang

RSC Adv., 2013, 3, 14910
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Reference MP2/CBS and CCSD(T) quantum-chemical calculations on stacked adenine dimers. Comparison with DFT-D, MP2.5, SCS(MI)-MP2, M06-2X, CBS(SCS-D) and force field descriptions

Claudio A. Morgado, Petr Jurečka, Daniel Svozil, Pavel Hobza and Jiří Šponer

Phys. Chem. Chem. Phys., 2010, 12, 3522
DOI: 10.1039/b924461a

yDNA versus yyDNA pyrimidines: computational analysis of the effects of unidirectional ring expansion on the preferred sugar–base orientation, hydrogen-bonding interactions and stacking abilities

Purshotam Sharma, Linda A. Lait and Stacey D. Wetmore

Phys. Chem. Chem. Phys., 2013, 15, 2435
DOI: 10.1039/c2cp43910g

A computational proposal for the experimentally observed discriminatory behavior of hypoxanthine, a weak universal nucleobase

Lesley R. Rutledge and Stacey D. Wetmore

Phys. Chem. Chem. Phys., 2012, 14, 2743
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Nature and magnitude of aromatic stacking of nucleic acid bases

Jiří Šponer, Kevin E. Riley and Pavel Hobza

Phys. Chem. Chem. Phys., 2008, 10, 2595
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How do hydrophobic nucleobases differ from natural DNA nucleobases? Comparison of structural features and duplex properties from QM calculations and MD simulations

Indu Negi, Preetleen Kathuria, Purshotam Sharma and Stacey D. Wetmore

Phys. Chem. Chem. Phys., 2017, 19, 16365
DOI: 10.1039/C7CP02576A

Three polymorphs of hypoxanthine obtained by evaporation from three distinct solvents

Haoxin Hu, Shizhao Ren, Feiting Gan, Rongrong Xue and Fenghua Chen

CrystEngComm, 2025
DOI: 10.1039/D5CE00155B

How does modification of adenine by hydroxyl radical influence the stability and the nature of stacking interactions in adenine-cytosine complex?

Żaneta Czyżnikowska

J Mol Model, 2009, 15, 615
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A QM/QTAIM microstructural analysis of the tautomerisationviathe DPT of the hypoxanthine·adenine nucleobase pair

Ol'ha O. Brovarets’, Roman O. Zhurakivsky and Dmytro M. Hovorun

Molecular Physics, 2014, 112, 2005
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yDNA versus xDNA Pyrimidine Nucleobases: Computational Evidence for Dependence of Duplex Stability on Spacer Location

Linda A. Lait, Lesley R. Rutledge, Andrea L. Millen and Stacey D. Wetmore

J. Phys. Chem. B, 2008, 112, 12526
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The physico-chemical “anatomy” of the tautomerization through the DPT of the biologically important pairs of hypoxanthine with DNA bases: QM and QTAIM perspectives

Ol’ha O. Brovarets’, Roman O. Zhurakivsky and Dmytro M. Hovorun

J Mol Model, 2013, 19, 4119
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Intrinsic Rashba coupling due to hydrogen bonding in DNA

S. Varela, B. Montañes, F. López, B. Berche, B. Guillot, V. Mujica and E. Medina

The Journal of Chemical Physics, 2019, 151
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How Do Size-Expanded DNA Nucleobases Enhance Duplex Stability? Computational Analysis of the Hydrogen-Bonding and Stacking Ability of xDNA Bases

Tom L. McConnell and Stacey D. Wetmore

J. Phys. Chem. B, 2007, 111, 2999
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Theoretical study of inosine tetrad and octamer interacting with alkali metal ions

Fancui Meng and Xian Zhao

Journal of Molecular Structure: THEOCHEM, 2008, 869, 94
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Self-assembly of macrocyclic oligofurans to create novel organic nanotubes through π–π stacking: a computational study

Hamid Reza Masoodi, Sotoodeh Bagheri and Masoud Rohani Moghadam

Molecular Simulation, 2024, 50, 207
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Comparison of Intrinsic Stacking Energies of Ten Unique Dinucleotide Steps in A-RNA and B-DNA Duplexes. Can We Determine Correct Order of Stability by Quantum-Chemical Calculations?

Daniel Svozil, Pavel Hobza and Jiří Šponer

J. Phys. Chem. B, 2010, 114, 1191
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Effect of Watson−Crick and Hoogsteen Base Pairing on the Conformational Stability of C8-Phenoxyl-2′-deoxyguanosine Adducts

Andrea L. Millen, Cassandra D. M. Churchill, Richard A. Manderville and Stacey D. Wetmore

J. Phys. Chem. B, 2010, 114, 12995
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Inosine and its methyl derivatives: Occurrence, biogenesis, and function in RNA

Nivedita Dutta, Indrajit Deb, Joanna Sarzynska and Ansuman Lahiri

Progress in Biophysics and Molecular Biology, 2022, 169-170, 21
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Molecular modeling study of binding site selectivity of TQMP to G-quadruplex DNA

Li Aixiao, Maurel François, Barbault Florent, Delamar Michel, Wang Baoshan, Zhou Xiang and Wang Ping

European Journal of Medicinal Chemistry, 2010, 45, 983
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Insight on the interaction of polychlorobiphenyl with nucleic acid–base

Soraya Abtouche, Thibaut Very, Antonio Monari, Meziane Brahimi and Xavier Assfeld

J Mol Model, 2013, 19, 581
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Investigation of the π–π stacking interactions without direct electrostatic effects of substituents: the aromatic∥aromatic and aromatic∥anti-aromatic complexes

Ali Ebrahimi, Pouya Karimi, Farideh Badichi Akher, Roya Behazin and Najmeh Mostafavi

Molecular Physics, 2014, 112, 1047
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Comparison of the molecular influences of NO-induced lesions in DNA strands on the reactivity of polynucleotide kinases, DNA ligases and DNA polymerases

A. Doi, S. P. Pack and K. Makino

Journal of Biochemistry, 2010, 147, 697
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Stability of DNA Duplexes Containing Hypoxanthine (Inosine): Gas versus Solution Phase and Biological Implications

Xuejun Sun and Jeehiun K. Lee

J. Org. Chem., 2010, 75, 1848
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Variable temperature FTIR spectra of polycrystalline purine nucleobases and estimating strengths of individual hydrogen bonds

M. Rozenberg, R. Fausto and I. Reva

Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 2021, 251, 119323
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Prototropic tautomerism and basic molecular principles of hypoxanthine mutagenicity: an exhaustive quantum-chemical analysis

Ol’ha O. Brovarets’ and Dmytro M. Hovorun

Journal of Biomolecular Structure and Dynamics, 2013, 31, 913
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Multi-photon and electron impact ionisation studies of reactivity in adenine–water clusters

B. Barc, M. Ryszka, J.-C. Poully, E. Jabbour Al Maalouf, Z. el Otell, J. Tabet, R. Parajuli, P.J.M. van der Burgt, P. Limão-Vieira, P. Cahillane, M. Dampc, N.J. Mason and S. Eden

International Journal of Mass Spectrometry, 2014, 365-366, 194
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Deoxyinosine mismatch parameters calculated with a mesoscopic model result in uniform hydrogen bonding and strongly variable stacking interactions

Rodolfo Vieira Maximiano and Gerald Weber

Chemical Physics Letters, 2015, 631-632, 87
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Theoretical insights into the nature of intermolecular interactions in cytosine dimer

Żaneta Czyżnikowska and Robert Zaleśny

Biophysical Chemistry, 2009, 139, 137
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Experimental and theoretical rationalization for the base pairing abilities of inosine, guanosine, adenosine, and their corresponding 8‐oxo‐7,8‐dihydropurine, and 8‐bromopurine analogues within A‐form duplexes of RNA

Austin Skinner, Chou‐Hsun Yang, Kazuki Hincks, Haobin Wang and Marino J. E. Resendiz

Biopolymers, 2020, 111
DOI: 10.1002/bip.23410

Characterization of the stacking interactions between DNA or RNA nucleobases and the aromatic amino acids

Lesley R. Rutledge, Lachlan S. Campbell-Verduyn and Stacey D. Wetmore

Chemical Physics Letters, 2007, 444, 167
DOI: 10.1016/j.cplett.2007.06.090