Article
Multidisciplinary Sciences
Daniel W. Conroy, Yu Xu, Honglue Shi, Nicole Gonzalez Salguero, Rudra N. Purusottam, Matthew D. Shannon, Hashim M. Al-Hashimi, Christopher P. Jaroniec
Summary: The majority of base pairs in DNA follow the canonical Watson-Crick geometry, but they can also adopt alternative Hoogsteen conformations which are important for biological function and mechanism. This study demonstrates that multidimensional dynamic nuclear polarization-enhanced solid-state NMR can be used as a spectroscopic tool to observe and distinguish between Watson-Crick and Hoogsteen base pairs in various DNA systems.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Microbiology
Adam T. Smiley, Kassidy J. Tompkins, Matthew R. Pawlak, August J. Krueger, Robert L. L. Evans III, Ke Shi, Hideki Aihara, Wendy R. Gordon
Summary: This study investigates the structural and functional dependencies of the Rep protein from Muscovy duck circovirus on ssDNA interaction. It reveals that divalent cations and substrate Watson-Crick base pairing play important roles in Rep-mediated DNA cleavage and rejoining, with a universal requirement for replication initiation in circular Rep-encoding single-stranded DNA viruses.
Article
Chemistry, Multidisciplinary
Jing Jin, Sihao Li, Zhongping Wang, Yan Lu, Xiaoqing Liu, Li Wang
Summary: A series of nucleobases guanine (G) and cytosine (C) pairing configurations have been fabricated on highly oriented pyrolytic graphite (HOPG) surface by controlling the molar ratio of G and C in water solution. The association of C and G nucleobases is governed by Watson-Crick (WC) base pairing, and hydrogen bonding plays a dominant role in the formation of these pairing configurations. The competition between the priority and diversity of hydrogen-bonded configurations bonding between G and C is crucial for the pairing structural polymorphism.
Article
Chemistry, Physical
Ahmed M. Rozza, Imre Bako, Julianna Olah
Summary: Solvation plays a crucial role in maintaining the structure and function of biomolecules. In this study, the hydration patterns of DNA with different base pairings were investigated using molecular dynamics simulation and topological analysis of the hydrogen bond network. It was found that HG base pairing increased the solvation of the major groove and disrupted the water structure in the minor groove, which could contribute to the recognition of specific DNA binding proteins.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Nanoscience & Nanotechnology
Jiulong Zhang, Xiaoyan Sun, Xiufeng Zhao, Lin Liu, Xin Cheng, Chunrong Yang, Haiyang Hu, Mingxi Qiao, Dawei Chen, Xiuli Zhao
Summary: In this study, a versatile noncationic miRNA vector was developed for cancer immunotherapy. The vector can reverse the tumor immunosuppressive microenvironment by downregulating the expression of IDO1. The multifunctional nano-complex not only inhibits tumor growth but also shows remarkable therapeutic effects on distant tumors.
ACS APPLIED MATERIALS & INTERFACES
(2022)
Review
Nanoscience & Nanotechnology
YongDeok Cho, Sung Hun Park, Ji-Hyeok Huh, Ashwin Gopinath, Seungwoo Lee
Summary: This review discusses the current and potential applications of soft quantum nanophotonic devices that combine DNA nanotechnology with chemically synthesizable quantum emitters. By controlling the position and orientation of individual quantum emitters, DNA nanotechnology provides increased reliability and scalability to these devices.
Article
Chemistry, Multidisciplinary
Mark N. K. Afari, Kasper Nurmi, Pasi Virta, Tuomas Lonnberg
Summary: Hairpin oligodeoxynucleotides with a modified residue in the stem were synthesized and reacted with aromatic aldehydes to produce nucleoside analogues. The reaction equilibrium depends on the aldehyde and nucleobase. The modified residue showed the highest affinity and selectivity with 9-formyl-9-deazaadenine.
Article
Chemistry, Physical
Natacha Gillet, Alessio Bartocci, Elise Dumont
Summary: In this study, the sequence dependence of the conformational landscape of the (6-4) photoproduct when embedded in six 25-bp duplexes was evaluated through extensive molecular dynamics simulations. The close sequence pattern was found to impact the conformational landscape around the lesion, inducing different flexibilities upstream and downstream, and REST2 simulations allowed for the exploration of structures potentially important for damaged DNA recognition.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Computer Science, Theory & Methods
Kalpana Mahalingam, Anuran Maity, Palak Pandoh
Summary: This paper investigates WK-palindromes and the mapping theta, as well as the concept of conjugates. The properties of the set of theta-conjugates of a word are explored, along with characterizing words with the same set of conjugates. The distribution of palindromes in the set of conjugates and theta-conjugates is studied, and the structure of words with at least one WK-palindrome in the set C theta(w) is found.
INFORMATION AND COMPUTATION
(2022)
Article
Chemistry, Physical
L. Slocombe, J. S. Al-Khalili, M. Sacchi
Summary: Proton transfer along hydrogen bonds in DNA can lead to short-lived point mutations, with the thermal populations of G*-C* mutations potentially playing a significant role in the replisome.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Mathematics
Jose M. Sempere
Summary: This work analyzes the computational power of Watson-Crick finite automata (WKFA) under restrictions on the transition function, specifically focusing on the maximum length difference between input strands, known as delay. The study shows that WKFA with these restrictions accept languages that form a proper subclass of those accepted by arbitrary WKFA, and introduces the investigation of language classes characterized by WKFAs with bounded delays. Some results are proven through relationships between WKFA and sticker systems.
Article
Chemistry, Medicinal
Andrew H. Kellum, Pradeep S. Pallan, Arman Nilforoushan, Shana J. Sturla, Michael P. Stone, Martin Egli
Summary: O6-Methyl-2'-deoxyguanosine (O6-MeG) is a common DNA lesion that leads to G-to-A mutations during DNA replication. Nucleoside analogs have been developed to interact more favorably with O6-MeG compared to unmodified nucleotides. These analogs form stable pairs with O6-MeG through a combination of H-bonding and stacking.
CHEMICAL RESEARCH IN TOXICOLOGY
(2022)
Review
Chemistry, Multidisciplinary
Hana Dohnalova, Filip Lankas
Summary: The review article discusses recent developments in modeling the mechanical properties of DNA in its B-form, using various models and molecular dynamics simulations. The models are illustrated and critically examined using MD data and Amber force fields.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Karina Belen Sabalette, Liubov Makarova, Marco Marcia
Summary: Long non-coding RNAs (lncRNAs) play important roles in gene expression regulation and diseases. This study focuses on the structural organization of lncRNAs, specifically analyzing the distribution and structure of GU base pairs, a non-canonical interaction. By comparing GU base pairs in lncRNAs with other well-characterized transcripts, the study reveals their involvement in interactions with proteins or miRNAs and their contribution to lncRNA folding. Additionally, the study identifies highly-GU-enriched regions in lncRNAs for future experimental investigation, contributing to a comprehensive understanding of lncRNA functions and molecular mechanisms.
Article
Chemistry, Analytical
Rodtichoti Wannapob, Surachada Chuaychob, Masahiro Fujita, Mizuo Maeda
Summary: Electrochemical impedance spectroscopy (EIS) was utilized to detect non-Watson-Crick base pairs of DNA, where a significant increase in charge-transfer resistance (Rct) was observed for terminal base mismatches but not internal base mismatches. Moreover, unpaired and overhang DNA at the terminal were found to hinder charge transfer to the electrode surface through EIS measurements. Additionally, the steric properties of DNA strands were successfully detected using EIS.
ANALYTICAL SCIENCES
(2021)
Article
Chemistry, Organic
Emma Campbell, Andrea Taladriz-Sender, Olivia Paisley, Alan R. Kennedy, Jacob T. Bush, Glenn A. Burley
Summary: This paper describes a modular approach to prepare tri- and tetracyclic carbazoles via sequential [3 + 2] heteroannulation. The optimization of Pd-catalyzed Buchwald-Hartwig amination followed by C/N-arylation in a one-pot process is established. Mechanistic analyses have identified the origins of the chemo- and regioselective sequential control of both bond-forming steps. The substrate scope is demonstrated by the preparation of a range of tri- and tetracyclic carbazoles, including expedient access to several natural products and anti-cancer agents.
JOURNAL OF ORGANIC CHEMISTRY
(2022)
Article
Nanoscience & Nanotechnology
Carlos J. Bueno-Alejo, Marina Santana Vega, Amanda K. Chaplin, Chloe Farrow, Alexander Axer, Glenn A. Burley, Cyril Dominguez, Hesna Kara, Vasileios Paschalis, Sumera Tubasum, Ian C. Eperon, Alasdair W. Clark, Andrew J. Hudson
Summary: Single-molecule imaging is important for studying the behavior and interactions of biological molecules. However, the irreversible adsorption of components onto surfaces poses a challenge for precise sampling. Interferometric scattering microscopy (iSCAT) can detect the adsorption and desorption of unlabeled proteins on glass surfaces. A surface passivation method using high-density perfluoroalkane brushes allows for continuous monitoring of protein adsorption and desorption without irreversible binding.
ACS APPLIED MATERIALS & INTERFACES
(2022)
Article
Biochemistry & Molecular Biology
Jinnette Tolentino Collado, James N. Iuliano, Katalin Pirisi, Samruddhi Jewlikar, Katrin Adamczyk, Gregory M. Greetham, Michael Towrie, Jeremy R. H. Tame, Stephen R. Meech, Peter J. Tonge, Andras Lukacs
Summary: This study investigates the photoactivation mechanism of OaPAC and reveals the direct connection between BLUF photoactivation and the structural and functional implications on the partner protein. The results demonstrate the formation of an intermediate species on the photoactivation pathway and highlight the essential role of proton transfer in initiating structural reorganization and AC activity.
ACS CHEMICAL BIOLOGY
(2022)
Article
Chemistry, Physical
Sourav Maiti, Sunayana Mitra, Clinton A. Johnson, Kai C. Gronborg, Sean Garrett-Roe, Paul M. Donaldson
Summary: This study investigates the dynamics of excess protons in a protic ionic liquid using visible pump mid-infrared probe spectroscopy. The findings reveal that proton transfer occurs through preformed hydrogen-bonded complexes, and the protons only diffuse a few solvent shells before recombining.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Biochemistry & Molecular Biology
Katharine E. Gilbert, Aini Vuorinen, Arron Aatkar, Peter Pogany, Jonathan Pettinger, Emma K. Grant, Joanna M. Kirkpatrick, Katrin Rittinger, David House, Glenn A. Burley, Jacob T. Bush
Summary: A comprehensive profiling of sulfur(VI) fluoride reactivity is presented, focusing on fragment binders and optimized probes. The reactivity profile of S-VI-Fs is demonstrated through live cell chemoproteomics. The studies provide insights into the hydrolytic stability, protein reactivity, and chemoproteomic utility of S-VI-Fs, offering a valuable guide for designing ligands containing S-VI-Fs and expanding the liganded proteome.
ACS CHEMICAL BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Jiajia Zou, Ashley C. Stammers, Andrea Taladriz-Sender, Jamie M. Withers, Iain Christie, Marina Santana Vega, Badri L. Aekbote, William J. Peveler, David A. Rusling, Glenn A. Burley, Alasdair W. Clark
Summary: An orthogonal, noncovalent approach is presented for the assembly of higher-order DNA origami nanostructures. By incorporating perfluorinated tags into DNA origami tiles, their hierarchical assembly is controlled via fluorous-directed recognition. This integrated catch-and-latch approach combining fluorous effect with base-pairing specificity enables increased assembly efficiency and requires fewer DNA sequences, providing a cheap and efficient means for producing discrete superstructures in DNA nanotechnology.
Article
Chemistry, Analytical
Paul M. Donaldson
Summary: This article explores a spectrophotometric method for determining the relative concentrations of infrared-active analytes with unknown concentration and unknown molar absorption coefficient. The method calculates concentration ratios using infrared absorption and two-dimensional infrared (2D-IR) signals. It provides a simple calculation framework and describes corrections for various factors that may affect the signals. The validity of the method is experimentally confirmed.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Thomas J. Burden, Kathryn P. R. Fernandez, Mary Kagoro, Jonathan B. Eastwood, Theo F. N. Tanner, Adrian C. Whitwood, Ian P. Clark, Michael Towrie, Jean-Philippe Krieger, Jason M. Lynam, Ian J. S. Fairlamb
Summary: Mn(I) C-H functionalization of coumarins allows for rapid assembly of polycyclic pyridinium-containing coumarins, utilizing stable organomanganese reagents in both photochemical and thermal reactions. Cyclomanganated intermediates facilitate the characterization of active Mn(I) carbonyl-containing species and provide insight into the reductive elimination pathway. The obtained products can be further decomplexed to form pi-extended hybrid coumarin-pyridinium compounds.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Chemistry, Multidisciplinary
Katerina Peterkova, Mark Stitch, Rayhaan Z. Boota, Paul A. Scattergood, Paul I. P. Elliott, Michael Towrie, Peter Podbevsek, Janez Plavec, Susan J. Quinn
Summary: G-quadruplexes are important targets in cancer research and understanding their binding with diagnostic probes is crucial for the development of molecular tools. This study investigates the binding of an enantiopure NIR emitting [Os(TAP)(2)(dppz)](2+) complex to G-quadruplex structures formed by human telomere and cMYC sequences in solution using NMR and time-resolved infrared spectroscopy. The results show that the emission response of the complex is sensitive to subtle changes in the binding environment, indicating potential applications in cancer diagnostics.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Chemistry, Physical
Paul M. Donaldson, Russell F. Howe, Alexander P. Hawkins, Mike Towrie, Gregory M. Greetham
Summary: This study presents an experimental approach for measuring high-quality two-dimensional infrared (2D-IR) spectra from scattering pellets of zeolites, titania, and fumed silica. The approach utilizes phase cycling, polarization control, and a bright probe laser beam to suppress scattering. The possible nonlinear signals generated by this approach are found to be limited.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Review
Chemistry, Multidisciplinary
Paul M. Donaldson, Greg M. Greetham, Chris T. Middleton, Bradley M. Luther, Martin T. Zanni, Peter Hamm, Amber T. Krummel
Summary: Ultrafast spectroscopy and imaging have become essential tools for scientists in various fields. The commercialization of advanced spectrometers, such as transient absorption spectrometers and vibrational sum frequency generation spectrometers, has made these measurements available to non-experts in ultrafast spectroscopy. The shift to new Yb-based lasers offers exciting new possibilities in the chemical and physical sciences, with higher efficiency and improved noise characteristics.
ACCOUNTS OF CHEMICAL RESEARCH
(2023)
Article
Chemistry, Multidisciplinary
Frederik Peschke, Andrea Taladriz-Sender, Matthew J. Andrews, Allan J. B. Watson, Glenn A. Burley
Summary: This study demonstrates the use of glutathione (GSH) as a redox modulator to promote a copper-catalyzed (3+2) cycloaddition reaction between an ynamine and an azide. This unique GSH-mediated reactivity gradient is then utilized in the dual sequential bio-orthogonal labeling.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemical Research Methods
Karina Chan, Preethi Soundarya Sathyamurthi, Markus A. Queisser, Michael Mullin, Harry Shrives, Diane M. Coe, Glenn A. Burley
Summary: This manuscript presents a cell-targeted approach to degrade RIPK2 in HER2+ cell lines using an antibody-PROTAC conjugate. The study demonstrates the potential for cell-selective delivery of PROTAC scaffolds by engaging with signature extracellular proteins expressed on the surface of specific cell types.
BIOCONJUGATE CHEMISTRY
(2023)
Article
Chemistry, Analytical
Paul M. Donaldson
Summary: This study explores a spectroscopic method for determining relative concentrations of IR-active analytes with unknown concentration and absorption coefficient. The method is useful for characterizing complex/heterogeneous liquids or solids, studying transient species, and situations where obtaining concentration information is challenging. The concentration ratios of two species are obtained through ratiometric calculations using IR absorption and 2D-IR diagonal bleach signals.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Physical
Paraic M. Keane, Clara Zehe, Fergus E. Poynton, Sandra A. Bright, Sandra Estayalo-Adrian, Stephen J. Devereux, Paul M. Donaldson, Igor V. Sazanovich, Michael Towrie, Stanley W. Botchway, Christine J. Cardin, D. Clive Williams, Thorfinnur Gunnlaugsson, Conor Long, John M. Kelly, Susan J. Quinn
Summary: In this study, the interactions of metal-free TMPyP4 and Pt(ii)TMPyP4 with guanine-containing nucleic acids were investigated using time-resolved infrared spectroscopy (TRIR) for the first time. The results showed that both compounds bound close to guanine, and electron transfer occurred when D(2)TMPyP4 was bound to guanine-containing systems.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)