ACS Physical Chemistry Au最新文献_第10页

Single Molecule Force Measurements Reveal Energy Stabilization of Theophylline Aptamer RNA Switch Required for Gene Control 单分子力测量揭示了基因控制所需的茶碱适体RNA开关的能量稳定。

IF 4.8

ACS Physical Chemistry Au Pub Date : 2026-03-25 Epub Date: 2026-01-02 DOI: 10.1021/acsphyschemau.5c00109

Favian A. Liu, Brian A. Dawes, William J. Torg, Elena Menichelli, Jennifer C. Petter, Maria Kamenetska

{"title":"Single Molecule Force Measurements Reveal Energy Stabilization of Theophylline Aptamer RNA Switch Required for Gene Control","authors":"Favian A. Liu, Brian A. Dawes, William J. Torg, Elena Menichelli, Jennifer C. Petter, Maria Kamenetska","doi":"10.1021/acsphyschemau.5c00109","DOIUrl":"10.1021/acsphyschemau.5c00109","url":null,"abstract":"RNA aptamers play essential roles in gene regulation,sensing,and therapeutics, relying on ligand-induced kinetic changes for function.The theophylline aptamer has been engineered to regulate syntheticgene networks in response to the presence of the theophylline smallmolecule ligand, but the thermodynamic and kinetic parameters behindtheophylline’s unique function are not known. Here, we useoptical tweezers single-molecule force spectroscopy to measure thefolding dynamics of the theophylline aptamer in the presence and absenceof ligand. We find that theophylline binding does not affect foldingrates but significantly slows unfolding by stabilizing the aptamerby ∼3.6 kBT, or∼2.1 kcal/mol. These results support a conformational selectionmodel of ligand binding and reveal no evidence of large structuralrearrangement upon ligand association. Our findings suggest that theophylline-inducedstabilization, rather than structural remodeling, drives aptamer functionin synthetic biology applications to regulate gene expression. Thiskinetic stabilization supports prior work proposing a kinetic trapmechanism, in which the long-lived, folded ligand-bound state delaysribosome binding and translation. These insights emphasize the kineticbasis of RNA-mediated regulation and inform the future design of ptamer-basedtools in synthetic biology and therapeutics.","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"6 2","pages":"301–307"},"PeriodicalIF":4.8,"publicationDate":"2026-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147575579","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Transient Spin Labeling of Plastics with Chlorine Dioxide 二氧化氯塑料的瞬态自旋标记。

IF 4.8

ACS Physical Chemistry Au Pub Date : 2026-03-25 Epub Date: 2026-03-04 DOI: 10.1021/acsphyschemau.5c00140

Bence G. Márkus, Sándor Kollarics, Kristóf Kály-Kullai, Bernadett Juhász, Dávid Beke, László Forró, Zoltán Noszticzius, Ferenc Simon

{"title":"Transient Spin Labeling of Plastics with Chlorine Dioxide","authors":"Bence G. Márkus, Sándor Kollarics, Kristóf Kály-Kullai, Bernadett Juhász, Dávid Beke, László Forró, Zoltán Noszticzius, Ferenc Simon","doi":"10.1021/acsphyschemau.5c00140","DOIUrl":"10.1021/acsphyschemau.5c00140","url":null,"abstract":"Plastic waste, one of the most critical problems forhumankind,poses severe threats to ecosystems, wildlife, and human health. Tracing,quantifying, and identifying types of plastic waste are crucial tounderstanding its environmental pathways and developing targeted strategiesfor reduction, recycling, and remediation. To contribute to addressingthis global issue, we investigated the spin-labeling capabilitiesof chlorine dioxide (ClO2) radicals introduced into poly(ethyleneterephthalate) and utilized electron spin resonance spectroscopy fordetection. The technique is capable of identifying plastic species,as the unpaired electron of the radical molecule is strongly sensitiveto its local environment through its coupling parameters. Temperature-dependentmeasurements revealed that the molecules are immobilized at low temperaturesand exhibit well-resolved anisotropic and hyperfine spectra that arequantitatively described by a model spin Hamiltonian. Even above themelting point of water, certain degrees of freedom remain restrictedas a result of the polymer matrix. Furthermore, employing a time-seriesmeasurement at room temperature enabled us to determine the diffusioncoefficient of the molecule in the polymer.","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"6 2","pages":"348–355"},"PeriodicalIF":4.8,"publicationDate":"2026-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147575653","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Tutorial on Energy Transfer Mechanisms and Computational Methods in X‑ray Photodynamic Therapy with Metal Nanoclusters 金属纳米团簇X射线光动力治疗中的能量传递机制和计算方法教程。

IF 4.8

ACS Physical Chemistry Au Pub Date : 2026-03-25 Epub Date: 2026-01-01 DOI: 10.1021/acsphyschemau.5c00095

Maxim Laborenz, Sami Malola, Hannu Häkkinen

{"title":"Tutorial on Energy Transfer Mechanisms and Computational Methods in X‑ray Photodynamic Therapy with Metal Nanoclusters","authors":"Maxim Laborenz, Sami Malola, Hannu Häkkinen","doi":"10.1021/acsphyschemau.5c00095","DOIUrl":"10.1021/acsphyschemau.5c00095","url":null,"abstract":"Cancer remains thedeadliest disease for mankind, and hence, theneed for effective, reliable, and functioning cancer treatment iscrucial. A promising minimally invasive oncological treatment calledphotodynamic therapy (PDT) involves irradiation of a photosensitizingdrug injected into the vasculature which in turn transfers energyto the surrounding oxygen, generating heavily cytotoxic reactive oxygenspecies (ROS), either directly or indirectly killing the cell. Althoughsimple in theory, many problems need to be addressed like oxygen wasteand hence resupply, light source delivery to the photosensitizer (PS),or the cancer cell targeting with the PS. Promising new agents totackle multiple issues in PDT are metal nanoclusters (NCs), especiallywith gold as the core. They turn out to accumulate well in cancercells, be very biocompatible, and even function as PS themselves.A less common way to surpass the light source delivery problem isto use X-rays due to low in vivo scattering and absorption cross section,giving rise to what we will call X-ray photodynamic therapy (X-PDT).It shows great potential for demolishing cancer cells, prompted bytheir high energy. The energy transfer in both cases, PDT and X-PDT,from PS or NC to oxygen is poorly understood and the subject of currentresearch. This Tutorial gives an easy to understand introduction toPDT and X-PDT and their different agents, explains the use of metalNCs in both heavily related treatment methods, gives an overview ofthe known elementary transfer mechanisms between the typical contributorsto PDT and X-PDT, and briefly sketches realized and possible simulationstrategies. It aims to give an understanding of where current researchis lacking and thus what new experiments, theories, and simulationsshould be targeted as well as an outlook for possible further theoreticaland computational X-PDT research.","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"6 2","pages":"246–258"},"PeriodicalIF":4.8,"publicationDate":"2026-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147575638","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Nitration Mechanism of Aromatics: Lessons from Born–Oppenheimer Molecular Dynamics 芳烃的硝化机理：波恩-奥本海默分子动力学的启示。

IF 4.8

ACS Physical Chemistry Au Pub Date : 2026-01-28 Epub Date: 2025-11-17 DOI: 10.1021/acsphyschemau.5c00086

Fabio J. F. S. Henrique, Pierre M. Esteves

{"title":"Nitration Mechanism of Aromatics: Lessons from Born–Oppenheimer Molecular Dynamics","authors":"Fabio J. F. S. Henrique, Pierre M. Esteves","doi":"10.1021/acsphyschemau.5c00086","DOIUrl":"10.1021/acsphyschemau.5c00086","url":null,"abstract":"The nitration of aromatic compounds is a fundamentaltransformationin organic chemistry, traditionally understood through the Ingold–Hughespolar mechanism and, more recently, via single-electron transfer (SET)pathways. In this work, Born–Oppenheimer molecular dynamics(BOMD) simulations were employed to explore the mechanistic featuresof toluene nitration in a protic polar medium, specifically a concentratedsulfonitric mixture (HNO3/H2SO4).Simulations at 423 K revealed the spontaneous formation of the nitroniumion (NO2+) via double protonation of HNO3 by H2SO4. Several BOMD trajectorieswere analyzed for the reaction between toluene and NO2+ at 300 K, leading to four different reaction outcomes: (i)no reaction, highlighting nucleophilic rather than protic solvationof NO2+; (ii) nitration at the positions ortho and para via a V-shaped [NO2·ArH]+ SET complex evolving into a σ-complexand ultimately the o- or p-nitrotolueneafter deprotonation; (iii) oxygen transfer resulting in o-cresol and NO, initiated from a Λ-shaped [NO2·ArH]+ SET complex; and (iv) the formation of a cyclohexadienone–NOcomplex via 1,2-hydride shift, also proceeding through a Λ-shaped[NO2·ArH]+ intermediate. Electronic structureanalyses (HOMO/LUMO, spin density, Bader charges) confirmed SET asthe key step in all reacting pathways. No evidence of superelectrophilicsolvation was observed under BOMD conditions. These results reinforcethe role of SET in electrophilic aromatic nitration under stronglyacidic conditions and reveal new oxygen transfer pathways dependenton the spatial orientation of the NO2+ relativeto the aromatic ring.","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"6 1","pages":"103–113"},"PeriodicalIF":4.8,"publicationDate":"2026-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146107440","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Tutorial on WDK-VENUS: A Streamlined and Modular Workflow for High-Temperature Dynamics and Kinetics of Atom–Diatom Collisions WDK-VENUS教程：原子-硅藻碰撞的高温动力学和动力学的流线型和模块化工作流程。

IF 4.8

ACS Physical Chemistry Au Pub Date : 2026-01-28 Epub Date: 2025-12-26 DOI: 10.1021/acsphyschemau.5c00106

Jiawei Yang, Jun Li

{"title":"Tutorial on WDK-VENUS: A Streamlined and Modular Workflow for High-Temperature Dynamics and Kinetics of Atom–Diatom Collisions","authors":"Jiawei Yang, Jun Li","doi":"10.1021/acsphyschemau.5c00106","DOIUrl":"10.1021/acsphyschemau.5c00106","url":null,"abstract":"High-precision dynamic simulations of hypersonic flowsare crucialfor high-temperature aerodynamics, particularly in addressing nonequilibriumeffects in turbulent flows. The quasi-classical trajectory (QCT) method,based on microscopic molecular collisions, is a key approach to tacklethis challenge. By generating state-to-state (StS) integral crosssections (ICSs), QCT simulations enable detailed modeling of high-temperaturethermochemical nonequilibrium flows. However, existing dynamic programsdo not have an automated workflow that converts trajectory data intoreaction rate coefficients. This work introduces WDK-VENUS, a modularQCT workflow for dynamics and kinetics of atom–diatom (A +BC) collisions built upon the VENUS program. The VENUS program isamended to enable handling high rovibrational states. An automatedand efficient bmax test module is introduced.Additionally, an external Python code is provided with four modules:sampling, Gaussian process regression (GPR), model validation, andequilibrium/nonequilibrium rate coefficient calculation. The mainfunction of this workflow is to use GPR machine learning methods tofit models, export large amounts of high-precision ICSs, and calculateequilibrium/nonequilibrium rate coefficients with less human intervention.The modular design of WDK-VENUS simplifies QCT calculations, supportsbatch processing, and integrates Python analysis tools. This workflowis expected to facilitate broader applications in interdisciplinaryfields.","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"6 1","pages":"1–12"},"PeriodicalIF":4.8,"publicationDate":"2026-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146107434","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

When Better Quenching Means Lower Yields: Electrostatic Control of Cage Escape 当更好的淬火意味着更低的产量：静电控制笼逃逸。

IF 4.8

ACS Physical Chemistry Au Pub Date : 2026-01-28 Epub Date: 2025-12-29 DOI: 10.1021/acsphyschemau.5c00103

Alberto Bianco, Mirco Natali, Giacomo Bergamini

{"title":"When Better Quenching Means Lower Yields: Electrostatic Control of Cage Escape","authors":"Alberto Bianco, Mirco Natali, Giacomo Bergamini","doi":"10.1021/acsphyschemau.5c00103","DOIUrl":"10.1021/acsphyschemau.5c00103","url":null,"abstract":"Photoredox catalysis often relies on excited-state quenchingdatato rationalize performance, yet such metrics can obscure the impactof solvent cage escape on overall efficiency. We report a systematicstudy of the effect of electrostatic interactions on the excited-statequenching, cage escape, and back-electron transfer processes in abenchmark system comprising methyl viologen (MV2+) anddifferently carboxylated ruthenium polypyridyl complexes with netcharges from 2+ to 4–. Increasing electrostatic attractionbetween photosensitizer and MV2+ enhances the quenchingrate constant (kq) upto the diffusion limit but simultaneously suppresses cage escape quantumyields, resulting in an inverse correlation between kq and photochemical MV•+ production. Transient absorption spectroscopy confirms that cageescape, rather than quenching or back-electron transfer, governs thequantum yield of product formation. Protonation of carboxylate groupsto yield uniformly 2+ complexes equalizes quenching rates and substantiallyincreases cage escape efficiency for the originally anionic species.These results establish electrostatic control of charge separationas a decisive factor in photoredox catalysis and challenge the practiceof predicting yields solely from quenching experiments. Considerationof both the initial and post-electron-transfer charges of the photocatalyst/quencherpair emerges as a general design principle for maximizing cage escapeand, consequently, photoredox reaction efficiency.","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"6 1","pages":"185–195"},"PeriodicalIF":4.8,"publicationDate":"2026-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146107432","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Unveiled Impact of 211At-Labeled Compounds’ Ability to Form Halogen Bonds on Their In Vivo Stability 2111at标记的化合物形成卤素键的能力对其体内稳定性的影响

IF 4.8

ACS Physical Chemistry Au Pub Date : 2026-01-28 Epub Date: 2025-12-14 DOI: 10.1021/acsphyschemau.5c00091

Samuel D. Mador, Thibault Yssartier, Jean-Yves Le Questel, Gilles Montavon, François Guérard, Nicolas Galland

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Atomic-Scale Insights into Phosphorene-Ionic Liquid Interface with Ab Initio Molecular Dynamics 原子尺度上的磷烯-离子液体界面与从头算分子动力学。

IF 4.8

ACS Physical Chemistry Au Pub Date : 2026-01-28 Epub Date: 2025-12-29 DOI: 10.1021/acsphyschemau.5c00111

Debora Ariana C. da Silva, Guilherme Colherinhas, Eudes Eterno Fileti

{"title":"Atomic-Scale Insights into Phosphorene-Ionic Liquid Interface with Ab Initio Molecular Dynamics","authors":"Debora Ariana C. da Silva, Guilherme Colherinhas, Eudes Eterno Fileti","doi":"10.1021/acsphyschemau.5c00111","DOIUrl":"10.1021/acsphyschemau.5c00111","url":null,"abstract":"The development ofhigh-performance electrodes for supercapacitorsand batteries remains hindered by an incomplete atomic-scale understandingof how material structure and polarization govern electric double-layerformation. In this work, we employ ab initio molecular dynamics (AIMD)simulations to probe the interface between a neutral phosphorene electrodeand the ionic liquid EMIM-BF4, elucidating the mechanismsof charge redistribution and ionic ordering. Key findings includea detailed quantification of phosphorene’s structural flexibility,interplanar P–P distances averaging 0.224 and 0.231 nm withangular fluctuations up to 10°, and the characterization of aweak yet functionally significant electrode–electrolyte interactionenergy of −138.2 kJ mol–1 nm–2 that drives pronounced interfacial ionic layering. Electron densityand Hartree potential profiles reveal alternating regions of chargeaccumulation and depletion extending ∼2.5 nm from the surface,with local electric fields reaching 108 V/m. Under zerobias, no appreciable charge transfer is observed, yet substantiallocal polarization effects underscore the critical role of the ionicliquid in modulating interfacial electrostatics.","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"6 1","pages":"207–214"},"PeriodicalIF":4.8,"publicationDate":"2026-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146106975","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Chemical and Structural Segregation in Quaternary Ni–Cu–Fe-Co Nanoparticles: Atomistic Simulation and Experiment 第四系Ni-Cu-Fe-Co纳米颗粒的化学和结构偏析：原子模拟与实验。

IF 4.8

ACS Physical Chemistry Au Pub Date : 2026-01-28 Epub Date: 2025-12-08 DOI: 10.1021/acsphyschemau.5c00102

Andrey Yu. Kolosov, Nikita Nepsha, Denis Sokolov, Kseniya G. Savina, Dmitry Moskovskikh, Evgenii Beletskii, Saravana Kumar M, Nickolay Yu. Sdobnyakov, Valentin Romanovski

{"title":"Chemical and Structural Segregation in Quaternary Ni–Cu–Fe-Co Nanoparticles: Atomistic Simulation and Experiment","authors":"Andrey Yu. Kolosov, Nikita Nepsha, Denis Sokolov, Kseniya G. Savina, Dmitry Moskovskikh, Evgenii Beletskii, Saravana Kumar M, Nickolay Yu. Sdobnyakov, Valentin Romanovski","doi":"10.1021/acsphyschemau.5c00102","DOIUrl":"10.1021/acsphyschemau.5c00102","url":null,"abstract":"A comprehensive studyof quaternary Ni–Cu–Fe-Co nanoparticleswith sizes ranging from 2,000 to 10,000 atoms (≈10–30nm) was carried out by combining solution combustion synthesis, X-raydiffraction (XRD), transmission electron microscopy (TEM-HAADF-EDS),and atomistic modeling (molecular dynamics and Monte Carlo simulations).Experimental XRD patterns confirmed the predominance of the face-centeredcubic (fcc) structure with broadened reflections,indicative of nanocrystalline domains and partial coexistence of hexagonalclose-packed (hcp) phases. TEM-EDS analysis showed well-defined crystallitesand pronounced surface segregation of Cu (≈25–30%) enrichmentrelative to bulk composition and partial Co enrichment, in contrastto Ni and Fe, which concentrated in the particle cores. Moleculardynamics simulations showed that the melting temperature (Tm) increases with particle size, from 1371–1379(2000 atoms) to 1479–1488 K (10,000 atoms), corresponding toan 8.5% rise. Conversely, crystallization temperatures (Tc) decreasewith faster cooling, e.g., from 1159 at 0.25 to 1086 at 0.75 K/ps,reflecting kinetic effects on solidification. The potential energystabilized from −3.98 (2000 atoms) to −4.06 eV/atom(10,000 atoms), while surface energy decreased from 2320–2361to 2231–2283 mJ/m2, in agreement with experimentalevidence of Cu segregation. These combined experimental and computationalinsights reveal that Ni–Cu–Fe-Co nanoparticles inherentlyform hierarchical, labyrinth-like structures with Cu-rich shells andNi/Fe-dominated cores.","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"6 1","pages":"163–173"},"PeriodicalIF":4.8,"publicationDate":"2026-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146107214","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

π–π Stacking Determines the Selectivity of Unnatural DNA Base Pairs Even without Polymerase π-π堆叠决定了非天然DNA碱基对的选择性，即使没有聚合酶。

IF 4.8

ACS Physical Chemistry Au Pub Date : 2026-01-28 Epub Date: 2025-12-04 DOI: 10.1021/acsphyschemau.5c00100

Zahra Noori, Andreu Bermejo, Josep Maria Bofill, Jordi Poater

{"title":"π–π Stacking Determines the Selectivity of Unnatural DNA Base Pairs Even without Polymerase","authors":"Zahra Noori, Andreu Bermejo, Josep Maria Bofill, Jordi Poater","doi":"10.1021/acsphyschemau.5c00100","DOIUrl":"10.1021/acsphyschemau.5c00100","url":null,"abstract":"Expanding the geneticalphabet requires a mechanisticunderstandingof how synthetic bases are faithfully replicated alongside naturalDNA. We present a quantum chemical study reproducing the experimentallyobserved single-nucleotide incorporation selectivity of Hirao’sunnatural base pairs (UBPs) by the 3′–5′ exonuclease-deficientKlenow fragment of Escherichia coli DNA polymerase I. Our analysis focuses on the highly selective DsPxpair, benchmarking its behavior against canonical Watson–Crickpairs and other UBPs. Strikingly, the observed selectivity emergeswithout explicitly modeling the polymerase, relying solely on computedstacking energies within the DNA helix. Molecular orbital and energy-decompositionanalyses show that both electrostatic and dispersion interactionsstrengthen DsPx’s affinity more, capturing experimental fidelitytrends and explaining its superior performance relative to relatedsystems. We further evaluate other selective UBPs, including QPa,DsPa, and DsPn. Together, these results provide a quantitative frameworkfor UBP incorporation selectivity and highlight the crucial role ofnoncovalent interactions in stabilizing synthetic bases within DNA.By bridging computation and experiment, this work advances designprinciples for synthetic genetic systems and contributes to unravelingthe molecular origins of DNA replication fidelity.","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"6 1","pages":"153–162"},"PeriodicalIF":4.8,"publicationDate":"2026-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146107446","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0