Re-pairing DNA: binding of a ruthenium phi complex to a double mismatch

Tayler D. Prieto Otoya, Kane T. McQuaid, Neil G. Paterson, David J. Cardin, Andrew Kellett and Christine J. Cardin

Chem. Sci., 2024, 15, 9096
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One-shot high-resolution melting curve analysis for KRAS point-mutation discrimination on a digital microfluidics platform

Mingzhong Li, Liang Wan, Man-Kay Law, Li Meng, Yanwei Jia, Pui-In Mak and Rui P. Martins

Lab Chip, 2022, 22, 537
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Nearest-neighbour transition-state analysis for nucleic acid kinetics

Nick A Rejali, Felix D Ye, Aisha M Zuiter, Caroline C Keller and Carl T Wittwer

Nucleic Acids Research, 2021, 49, 4574
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Length-independent and selective sensing of CCG trinucleotide repeat foldings by a monovalency-binding fluorogenic probe

Qingqing Zhang, Xingli Zeng, Qiuda Xu, Rong Lai, Dandan Wang, Xiaoshun Zhou and Yong Shao

Sensors and Actuators B: Chemical, 2024, 401, 135088
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High-throughput DNA melt measurements enable improved models of DNA folding thermodynamics

Yuxi Ke, Eesha Sharma, Hannah K. Wayment-Steele, Winston R. Becker, Anthony Ho, Emil Marklund and William J. Greenleaf

Nat Commun, 2025, 16
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DNA-Templated Modulation in the Photophysical Properties of a Fluorescent Molecular Rotor Auramine O by Varying the DNA Composition

Srikrishna Pramanik, Paritosh Mahato, Ushasi Pramanik, Atanu Nandy, Laxmikanta Khamari, Shivam Shrivastava, Saurabh Rai and Saptarshi Mukherjee

J. Phys. Chem. B, 2022, 126, 2658
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Complete Mesoscopic Parameterization of Single LNA Modifications in DNA Applied to Oncogene Probe Design

Izabela Ferreira, Sofie Slott, Kira Astakhova and Gerald Weber

J. Chem. Inf. Model., 2021, 61, 3615
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In silico Thermodynamic Evaluation of the Effectiveness of RT-LAMP Primers for SARS-CoV-2 Variants Detection

Pâmella Miranda, Pedro A. Alves, Rubens L. do Monte-Neto and Gerald Weber

TOCOVIDJ, 2024, 4
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Staggered intercalation of DNA duplexes with base-pair modulation by two distinct drug molecules induces asymmetric backbone twisting and structure polymorphism

Roshan Satange, Shih-Hao Kao, Ching-Ming Chien, Shan-Ho Chou, Chi-Chien Lin, Stephen Neidle and Ming-Hon Hou

Nucleic Acids Research, 2022, 50, 8867
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Differentiating a Least-Stable Single Nucleotide Mismatch in DNA Via Metal Ion-Mediated Base Pairing and Using Thioflavin T as an Extrinsic Fluorophore

Srikrishna Pramanik, Laxmikanta Khamari and Saptarshi Mukherjee

J. Phys. Chem. Lett., 2021, 12, 2547
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DNA origami enabled assembly of nanophotonic structures and their applications [Invited]

Zhi Zhao, Yutao Han and Yan Liu

Opt. Mater. Express, 2022, 12, 284
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Removal of antibiotic resistant bacteria and genes by post-pyrolysis bio-hybridcarbon/peroxymonosulfate system: Gene-degrading intermediates of bioinformatic identification based on corrected-nanopore sequencing and preference mechanism

Yujie Wang, Jun Ma, Liu Yang, Yuqi Li and Ming Chen

Chemical Engineering Journal, 2023, 460, 141809
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Mesoscopic model confirms strong base pair metal mediated bonding for T–Hg2+–T and weaker for C–Ag+–C

Luciano Gabriel Silva and Gerald Weber

Chemical Physics Letters, 2022, 803, 139847
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Precise Differentiation of Wobble-Type Allele via Ratiometric Design of a Ligase Chain Reaction-Based Electrochemical Biosensor for CYP2C19*2 Genotyping of Clinical Samples

Zhou-Jie Liu, Liang-Yong Yang, Tai-Cheng Lu, Chen Huang, Yu-Qi Liang, Xiong-Wei Xu, Yan-Fang Xu, Meng-Meng Liu, Xin-Hua Lin and Jin-Yuan Chen

Anal. Chem., 2023, 95, 14592
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Deciphering and Predicting Thermal and pH Stabilities of Triplex DNA Under Multifactorial Conditions

Shilong Zhang, Jiqing Shen, Ziyue Guan, Tengshuo Luo, Chengjie Chu, Haoyu Zhu, Jean‐Louis Mergny and Mingpan Cheng

Angewandte Chemie, 2025
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Salt dependent mesoscopic model for RNA at multiple strand concentrations

Izabela Ferreira, Tauanne D. Amarante and Gerald Weber

Biophysical Chemistry, 2021, 271, 106551
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Thermodynamic evaluation of the impact of DNA mismatches in PCR-type SARS-CoV-2 primers and probes

Pâmella Miranda and Gerald Weber

Molecular and Cellular Probes, 2021, 56, 101707
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Biomimetic Hydrogen‐Bonded Base Pairing of Nucleoside Triphosphates in Water by a Tetraphenylethene‐Based Octaimidazolium Cage

Yingjie Li, Lin Cheng, Pingxia Wang, Xuhao Kang, Qingfang Li and Liping Cao

Angewandte Chemie, 2025, 137
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DNA as a perfect quantum computer based on the quantum physics principles

R. Riera Aroche, Y. M. Ortiz García, M. A. Martínez Arellano and A. Riera Leal

Sci Rep, 2024, 14
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Preferential Binding of Epirubicin Hydrochloride with Single Nucleotide Mismatched DNA and Subsequent Sequestration by a Mixed Micelle

Laxmikanta Khamari, Srikrishna Pramanik, Shashi Shekhar, Paritosh Mahato and Saptarshi Mukherjee

J. Phys. Chem. B, 2021, 125, 11660
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Cavity hairpin ThT-light nucleic acid switches: the construction of label- and enzyme-free sensing and imaging platforms

Xinyue Lan, Longjiao Zhu, Yangzi Zhang, Keren Chen, Jia Wang, Zaihui Du, Shuting Li, Xu Chen and Wentao Xu

Nucleic Acids Research, 2023, 51, 3556
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Deciphering and Predicting Thermal and pH Stabilities of Triplex DNA Under Multifactorial Conditions

Shilong Zhang, Jiqing Shen, Ziyue Guan, Tengshuo Luo, Chengjie Chu, Haoyu Zhu, Jean‐Louis Mergny and Mingpan Cheng

Angew Chem Int Ed, 2025
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A pH and Mg2+-Responsive Molecular Switch Based on a Stable DNA Minidumbbell Bearing 5′ and 3′-Overhangs

Jiacheng Zhang, Yang Wang, Liqi Wan, Yuan Liu, Jie Yi, Sik Lok Lam and Pei Guo

ACS Omega, 2021, 6, 28263
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Cation valence dependence of hydrogen bond and stacking potentials in DNA mesoscopic models

Maria Izabel Muniz, Adrian H. Bustos, Sofie Slott, Kira Astakhova and Gerald Weber

Biophysical Chemistry, 2023, 294, 106949
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Structure and Dynamics of dsDNA in Cell-like Environments

Amar Singh, Arghya Maity and Navin Singh

Entropy, 2022, 24, 1587
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All-or-None Selectivity in Probing Polarity-Determined Trinucleotide Repeat Foldings with a Parity Resolution by a Beyond-Size-Matching Ligand

Yun Chang, Xingli Zeng, Shuzhen Peng, Rong Lai, Mujing Yang, Dandan Wang, Xiaoshun Zhou and Yong Shao

Anal. Chem., 2023, 95, 3746
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Non-linear Hamiltonian models for DNA

Marco Zoli

Eur Biophys J, 2022, 51, 431
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Nearest-neighbour parametrization of DNA single, double and triple mismatches at low sodium concentration

Erik de Oliveira Martins and Gerald Weber

Biophysical Chemistry, 2024, 306, 107156
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Models for prediction of single base primer extension efficiency from position and type of single mismatch in primer-template duplex

Myong-Rim Ri, Jin-Sok Kang, Myong-Ryong Ri and Song Nam U

Heliyon, 2023, 9, e18829
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Investigating the interactions of Axitinib, a tyrosine kinase inhibitor, with DNA: experimental studies, molecular docking, and molecular dynamics simulations

Pelin Şenel, Abdullah Al Faysal, Soykan Agar, Mine Yurtsever and Ayşegül Gölcü

Nucleosides, Nucleotides & Nucleic Acids, 2025, 1
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Molecular Dynamics Simulation of Melting of the DNA Duplex with Silver-Mediated Cytosine–Cytosine Base Pair

Elena B. Gusarova and Natalya A. Kovaleva

Computation, 2024, 12, 145
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Backbone Conformational Equilibrium in Mismatched DNA Correlates with Enzyme Activity

M. N. Westwood, A. Pilarski, C. Johnson, S. Mamoud and G. A. Meints

Biochemistry, 2023, 62, 2816
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Targeting DNA mismatches with metal complexes

Natália Kolozsvári and Martin R. Gill

Journal of Inorganic Biochemistry, 2025, 271, 112977
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Enzyme-free and copper-free strategy based on cyclic click chemical-triggered hairpin stacking circuit for accurate detection of circulating microRNAs

Shuang Zhao, Sha Yang, Hanqing Xu, Xiaoqi Tang, Hongwei Wang, Lianyu Yu, Xiaopei Qiu, Yunxia Wang, Mingxuan Gao, Kai Chang and Ming Chen

Analytica Chimica Acta, 2022, 1191, 339282
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A theoretical perspective of the physical properties of different RNA modifications with respect to RNA duplexes

Norman H.L. Chiu, Jennifer H. Simpson, Hongzhou Wang and Bakhos A. Tannous

BBA Advances, 2021, 1, 100025
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Electrochemical quantification based on the interactions of nucleoside analog cladribine with dsDNA via experimental and in-silico studies

Pelin Şenel, Abdullah Al Faysal, Soykan Agar, Mine Yurtsever and Ayşegül Gölcü

International Journal of Biological Macromolecules, 2025, 284, 138083
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Biomimetic Hydrogen‐Bonded Base Pairing of Nucleoside Triphosphates in Water by a Tetraphenylethene‐Based Octaimidazolium Cage

Yingjie Li, Lin Cheng, Pingxia Wang, Xuhao Kang, Qingfang Li and Liping Cao

Angew Chem Int Ed, 2025, 64
DOI: 10.1002/anie.202505732