Article
Chemistry, Physical
Xun Gong, Nicholas Renegar, Retsef Levi, Michael S. Strano
Summary: Nanoparticle corona phase design allows for molecular recognition for sensing applications. In this study, the largest DNA-SWCNT PL response library was generated and machine learning techniques were utilized to understand the dependence of molecular recognition and DNA sequence.
NPJ COMPUTATIONAL MATERIALS
(2022)
Article
Multidisciplinary Sciences
Liwei Chen, Jung Eun Park, Peter Paa, Priscilla D. Rajakumar, Hong-Ting Prekop, Yi Ting Chew, Swathi N. Manivannan, Wei Leong Chew
Summary: A new class of base editors, C:G to G:C Base Editors, have been developed in this study to create single-base genomic transversions in human cells, targeting specific genes related to genetic diseases. These editors predominantly perform C:G to G:C editing with high purity and efficiency, showing therapeutic potential for interrogating and correcting human genetic diseases.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Physical
Sergey Stolyar, Roman N. Yaroslavtsev, Anna Tyumentseva, Sergey Komogortsev, Ekaterina S. Tyutrina, Alina T. Saitova, Yulia Gerasimova, Dmitriy A. Velikanov, Michael Rautskii, Rauf S. Iskhakov
Summary: Iron oxide nanoparticles were synthesized through coprecipitation method and the effects of different Fe3O4/tetraethoxysilane ratios on their properties were investigated. The results showed that the magnetite core in nanoparticles had higher magnetization compared to stoichiometric magnetite nanoparticles, which was caused by the interaction with the silicate coating. Additionally, the thickness of the nanoparticle shell was found to be related to the efficiency of DNA isolation.
JOURNAL OF PHYSICAL CHEMISTRY C
(2022)
Article
Chemistry, Physical
Dan Cheng, Shevanuja Theivendran, Jie Tang, Larry Cai, Jun Zhang, Hao Song, Chengzhong Yu
Summary: This study demonstrates that a higher content of hydrogen bonding between phosphonate modified silica nanoparticles and PEI molecules can slow down the dissolution of PEI from freeze-dried solid composites into aqueous solution. By utilizing phosphonated silica nanoparticles, the retention ability of PEI is effectively improved, leading to enhanced transfection efficiency through high DNA binding affinity extracellularly, effective lysosome escape, and high nuclear entry intracellularly.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2022)
Article
Chemistry, Multidisciplinary
Aaron Michelson, Tyler J. Flanagan, Seok-Woo Lee, Oleg Gang
Summary: Continuous nanolattices are promising mechanical meta materials with high strength to-weight ratios. The fabrication of silica frameworks using DNA origami nanolattices demonstrates the potential of lightweight and high-strength nanoarchitected materials.
CELL REPORTS PHYSICAL SCIENCE
(2023)
Article
Multidisciplinary Sciences
Hongmiao Hu, Shu Tian, Guohui Xie, Rui Liu, Nana Wang, Sisi Li, Yuehui He, Jiamu Du
Summary: TEM1 combinatorically recognizes the FT gene 5'-UTR by binding to both the AP2 and B3 domains, recruiting the PRC2 to deposit H3K27me3 at the FT 5'-UTR, thereby precisely regulating the floral transition.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Biochemistry & Molecular Biology
Oleg Tutanov, Svetlana Tamkovich
Summary: Circulating DNA has been proven to be a valuable tool in translational medicine. This review aims to shed light on the association of circulating DNA with different proteins, its origins and forms of circulation, biological effects, and the clinical potential of circulating tumor deoxyribonucleoprotein complexes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Frank DiMaio, Ryan McHugh
Summary: The study introduces a machine learning model, RoseTTAFoldNA, capable of accurately predicting structures of protein-DNA and protein-RNA complexes, particularly for protein families lacking structural information.
Article
Biochemistry & Molecular Biology
Wan Yang, Vijay Singh Gondil, Dehua Luo, Jin He, Hongping Wei, Hang Yang
Summary: The study involves incorporating silica-binding peptide and anti-staphylococcal lysin into functional coatings to kill Staphylococcus aureus and prevent biofilm formation. SiBP1-ClyF-functionalized coatings effectively kill MRSA strains and support normal growth of mammalian cells on surfaces.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Editorial Material
Genetics & Heredity
Surag Nair, Arjun Barrett, Daofeng Li, Brian J. Raney, Brian T. Lee, Peter Kerpedjiev, Vivekanandan Ramalingam, Anusri Pampari, Fritz Lekschas, Ting Wang, Maximilian Haeussler, Anshul Kundaje
Summary: High-throughput experimental platforms revolutionize the analysis of the biochemical and functional properties of biological sequences. However, existing genome browser tracks are not suitable for visualizing high-resolution DNA sequence features.
Article
Biotechnology & Applied Microbiology
Luke W. Koblan, Mandana Arbab, Max W. Shen, Jeffrey A. Hussmann, Andrew V. Anzalone, Jordan L. Doman, Gregory A. Newby, Dian Yang, Beverly Mok, Joseph M. Replogle, Albert Xu, Tyler A. Sisley, Jonathan S. Weissman, Britt Adamson, David R. Liu
Summary: Engineered CGBEs paired with machine learning models have been developed to enable efficient and high-purity base editing, correcting disease-related SNVs with precision and increasing editing efficiency. Matching a set of base editors to target sequences can further enhance transversion base editing efficiency.
NATURE BIOTECHNOLOGY
(2021)
Article
Microbiology
Yizhao Luan, Zehua Tang, Yao He, Zhi Xie
Summary: In this study, evidence was provided showing that coevolving residues in TF domains contribute to DNA binding specificity. It was demonstrated that the coevolving residues are more likely to coevolve with other TF subclass-determining sites and mutation of these coevolving residues could significantly reduce the stability of the TF-DNA complex. Overall, this study expands our understanding of the interaction among coevolving residues in TFs and their importance in transcriptional regulation.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biochemistry & Molecular Biology
Chang Lu, Anand Lopez, Jinkai Zheng, Juewen Liu
Summary: This study examined the possibility of using DNA intrinsic fluorescence to study aptamer binding. The results showed that DNA hybridization led to a decrease in fluorescence, while specific aptamers induced fluorescence increases. The length of the terminal stem had an impact on the fluorescence change for certain aptamers, while others failed to produce a fluorescence change.
Article
Chemistry, Multidisciplinary
Tianshi Yu, Chanin Nantasenamat, Supicha Kachenton, Nuttapat Anuwongcharoen, Theeraphon Piacham
Summary: This study used cheminformatic analysis and machine learning modeling to investigate the chemical space, scaffolds, structure-activity relationship, and landscape of human androgen receptor antagonists. The findings revealed differences in physicochemical properties between potent/active class molecules and intermediate/inactive class molecules. Low scaffold diversity was observed, especially in the potent/active class molecules, indicating the need for developing molecules with novel scaffolds. The study also identified significant activity cliff generators and provided insights and guidelines for the development of novel androgen receptor antagonists.
Article
Biochemistry & Molecular Biology
Saaz Sakrikar, Amy K. Schmid
Summary: Histone proteins in eukaryotes, originating from archaea, have been found to have alternative functions in regulating gene expression and maintaining cell morphology in halophilic archaea. Specifically, the histone-like protein HpyA plays a key role in growth and morphology under reduced salinity conditions, binding DNA to regulate ion uptake and indirectly activate other pathways in response to salt levels.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Chemistry, Physical
Heydar Hamzi, Ali Rajabpour, Edgar Roldan, Ali Hassanali
Summary: In this study, the thermal relaxation of amino acids in water and in protein lysozyme was investigated using molecular dynamics simulations. The results showed that the relaxation times of the amino acids in water were influenced by the size of hydrocarbon side chain for hydrophobic amino acids, and the number of hydrogen bonds did not significantly affect the time scales for hydrophilic amino acids. Additionally, the thermal relaxation of amino acids in the protein was found to slow down by up to five times compared to that in water, primarily due to the size of the hydrophobic side chain.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Chemistry, Physical
Edward Danquah Donkor, Alessandro Laio, Ali Hassanali
Summary: Machine-learning is widely used in molecular simulations, and in this study, we focus on using the Smooth Overlap of Atomic Positions (SOAP) descriptors to study the properties of liquid water. By comparing SOAP with standard order parameters, we find that they are not entirely equivalent. Additionally, we elucidate the role of metaparameters in the SOAP definition for encoding chemical information.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Unmesh Mondal, Ivan Girotto, Ali Hassanali, Prasenjit Ghosh
Summary: In this study, we investigated the temperature-dependent double proton transfer (DPT) in the molecular crystals of terephthalic acid (TPA) using path integral molecular dynamics simulations. Our results confirm the occurrence of a DPT-induced order-to-disorder transition in TPA crystals, which is sensitive to nuclear quantum effects. Our simulations reveal the presence of both L and R tautomers of TPA as well as positively and negatively charged pairs of TPA molecules. The DPT in TPA crystals likely proceeds through tunneling at low temperatures and through activated hopping at room temperature, as supported by the analysis of the electronic structure.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Physical
Jenelle Fortunato, Yun Kyung Shin, Michael A. A. Spencer, Adri C. T. van Duin, Veronica Augustyn
Summary: This study investigates the proton-coupled electron transfer mechanisms in transition metal oxides in aqueous acidic electrolytes. The competition for protons and electrons among different processes is found to significantly influence electrochemical properties. The use of an acidic buffered electrolyte (H3PO4) increases the Coulombic efficiency and specific capacity, improving the electrode performance.
JOURNAL OF PHYSICAL CHEMISTRY C
(2023)
Article
Chemistry, Physical
Karen Mohammadtabar, Enrique Guerrero, Sergio Romero Garcia, Yun Kyung Shin, Adri C. T. van Duin, David A. Strubbe, Ashlie Martini
Summary: The properties of MoS2 can be improved through Ni doping, and a new force field called ReaxFF is developed to describe this material. The force field parameters are optimized to match the DFT calculations of Ni-doped MoS2 at different doping sites and under different strains. The force field can successfully model the phase transition of Ni-doped MoS2 from amorphous to crystalline, and it can be used for further investigations of Ni-doped MoS2 using reactive molecular dynamics simulations.
JOURNAL OF PHYSICAL CHEMISTRY C
(2023)
Article
Chemistry, Physical
Jaehoon Yang, Sherwin J. Singer
Summary: In this letter, a new method for calculating free energy differences (FEDs) between multiple thermodynamic states using energy probability densities is introduced. Existing methods such as BAR, MBAR, and WHAM require iterative solution of nonlinear equations, while our method solves linear equations to obtain FEDs. For the classic two-state problem, the statistical error of our method matches that of BAR under common conditions.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Multidisciplinary Sciences
Adu Offei-Danso, Uriel N. Morzan, Alex Rodriguez, Ali Hassanali, Asja Jelic
Summary: In this study, the authors investigate the collective nature of reorientational dynamics in water. They find that large angular fluctuations involve a highly cooperative dynamics of many water molecules in the hydrogen-bond network. They propose a mechanism involving a cascade of hydrogen-bond fluctuations underlying angular jumps, providing new insights into the interpretation of spectroscopies and reorientational dynamics of water.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Solana Di Pino, Yamila A. Peerez A. Sirkin, Uriel N. Morzan, Veronica M. Sanchez, Ali Hassanali, Damian A. Scherlis
Summary: Nanoconfinement effects on water dissociation and reactivity at interfaces, pores, or aerosols remain controversial. Using ab initio simulations, we demonstrate that water dissociation is conserved intact to unexpectedly small length-scales, down to aggregates of only a dozen molecules or pores of widths below 2 nm. This work provides a fundamental description of water dissociation at different scales with implications on reactivity at the air-liquid interface.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Physical
Colin K. Egan, Ali Hassanali
Summary: This study analyzes the thermodynamics of synergistic interfacial adsorption effects between anionic dodecyl sulfate (DS-) and polar hexaethylene glycol monododecyl ether (C12E6) surfactants using free energy decompositions and the potential distribution theorem. The analysis reveals that the synergistic adsorption is mainly driven by van der Waals stabilization between DS- and C12E6, as well as competing energetic and entropic effects caused by changes in the interfacial water structure.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Yongjian Yang, Yun Kyung Shin, Hideaki Ooe, Xinyang Yin, Xueyi Zhang, Adri C. T. van Duin, Yasuhiro Murase, John C. Mauro
Summary: Aqueous stability is crucial for the application of MOF materials in humid conditions. We have developed a ReaxFF force field for simulating the reaction of ZIFs with water. By considering the energy barrier for a hydrolysis reaction, the simulation results are in agreement with the experiments. MOFs with open structures and large pores are found to be unstable, while ZIFs with the -NO2 functional groups exhibit higher water stability.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Multidisciplinary
Giulia Sormani, Aruna Korde, Alex Rodriguez, Melissa Denecke, Ali Hassanali
Summary: In recent years, the use of Zirconium-89 (Zr-89) as a radionuclide in nuclear medicine for cancer diagnostic imaging and drug discovery has increased. Our research reveals a different coordination structure of the Zr-DFO complex, which is contrary to the conventional belief. Through molecular dynamics simulations and free energy calculations, we find that thermal fluctuations lead to an open hexadentate chelate structure of the Zr-DFO complex, while a stable and closely packed structure is formed by binding with 4HMS.
Article
Multidisciplinary Sciences
Khatereh Azizi, Matteo Gori, Uriel Morzan, Ali Hassanali, Philip Kurian
Summary: The microscopic origins of terahertz (THz) vibrational modes in biological systems are actively investigated. Recent experiments have shown a pronounced mode at around 0.3 THz in fluorophore-decorated bovine serum albumin (BSA) protein under optical pumping. Molecular dynamics simulations and information theory techniques indicate that optical excitations can alter specific THz vibrational modes, leading to a multiscale response.
Article
Multidisciplinary Sciences
Khatereh Azizi, Alessandro Laio, Ali Hassanali
Summary: According to traditional physical chemistry wisdom, solvent cavities tightly wrap around solutes, practically coinciding with their van der Waals surface. However, this study challenges this notion by demonstrating that the cavities surrounding 20 amino acids deviate significantly from the molecular surface. Remarkably, the shape of the cavity alone can predict solvation free energy, entropy, enthalpy, and hydrophobicity, without explicitly considering solute-solvent interactions involving the different chemical moieties of the amino acid in the prediction model.
Article
Chemistry, Multidisciplinary
M. Monti, E. Scarel, A. Hassanali, M. Stener, S. Marchesan
Summary: This study uncovers the conformational differences that drive self-assembly of dipeptides into distinct outcomes. Through in silico and experimental data, the electronic circular dichroism (ECD) spectra of self-assembling dipeptides were analyzed, revealing the importance of folded or extended conformers in the self-assembly process.
CHEMICAL COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Jonathan R. Chin, Marshall B. Frye, Derrick Shao-Heng Liu, Maria Hilse, Ian C. Graham, Jeffrey Shallenberger, Ke Wang, Roman Engel-Herbert, Mengyi Wang, Yun Kyung Shin, Nadire Nayir, Adri C. T. van Duin, Lauren M. Garten
Summary: Self-limiting stoichiometry promotes the growth of SnSe thin films by maintaining film stoichiometry and controlling crystallographic orientation. Results show that self-limiting stoichiometry can increase the lateral scale of SnSe layers, providing a promising avenue for device fabrication.
