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Mondal M, Gao YQ. Atomistic Insights into Sequence-Mediated Spontaneous Association of Short RNA Chains. Biochemistry 2024. [PMID: 39377398 DOI: 10.1021/acs.biochem.4c00293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/09/2024]
Abstract
RNA-RNA association and phase separation appear to be essential for the assembly of stress granules and underlie RNA foci formation in repeat expansion disorders. RNA molecules are found to play a significant role in gene-regulatory functions via condensate formation among themselves or with RNA-binding proteins. The interplay between driven versus spontaneous processes is likely to be an important factor for controlling the formation of RNA-mediated biomolecular condensate. However, the sequence-specific interactions and molecular mechanisms that drive the spontaneous RNA-RNA association and help to form RNA-mediated phase-separated condensate remain unclear. With microseconds-long atomistic molecular simulations here, we report how essential aspects of RNA chains, namely, base composition, metal ion binding, and hydration properties, contribute to the association of the series of simplest biologically relevant homopolymeric and heteropolymeric short RNA chains. We show that spontaneous processes make the key contributions governed by the sequence-intrinsic properties of RNA chains, where the definite roles of base-specific hydrogen bonding and stacking interactions are prominent in the association of the RNA chains. Purine versus pyrimidine contents of RNA chains can directly influence the association properties of RNA chains by modulating hydrogen bonding and base stacking interactions. This study determines the impact of ionic environment in sequence-specific spontaneous association of short RNA chains, hydration features, and base-specific interactions of Na+, K+, and Mg2+ ions with RNA chains.
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Affiliation(s)
- Manas Mondal
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, 518107 Shenzhen, China
| | - Yi Qin Gao
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, 518107 Shenzhen, China
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, 100871 Beijing, China
- Biomedical Pioneering Innovation Center, Peking University, 100871 Beijing, China
- Changping Laboratory, Beijing 102200, China
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Bennett D, Chen X, Walker GJ, Stelzer-Braid S, Rawlinson WD, Hibbert DB, Tilley RD, Gooding JJ. Machine Learning Color Feature Analysis of a High Throughput Nanoparticle Conjugate Sensing Assay. Anal Chem 2023; 95:6550-6558. [PMID: 37036670 DOI: 10.1021/acs.analchem.2c05292] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
Plasmonic nanoparticles are finding applications within the single molecule sensing field in a "dimer" format, where interaction of the target with hairpin DNA causes a decrease in the interparticle distance, leading to a localized surface plasmon resonance shift. While this shift may be detected using spectroscopy, achieving statistical relevance requires the measurement of thousands of nanoparticle dimers and the timescales required for spectroscopic analysis are incompatible with point-of-care devices. However, using dark-field imaging of the dimer structures, simultaneous digital analysis of the plasmonic resonance shift after target interaction of thousands of dimer structures may be achieved in minutes. The main challenge of this digital analysis on the single-molecule scale was the occurrence of false signals caused by non-specifically bound clusters of nanoparticles. This effect may be reduced by digitally separating dimers from other nanoconjugate types. Variation in image intensity was observed to have a discernible impact on the color analysis of the nanoconjugate constructs and thus the accuracy of the digital separation. Color spaces wherein intensity may be uncoupled from the color information (hue, saturation, and value (HSV) and luminance, a* vector, and b* vector (LAB) were contrasted to a color space which cannot uncouple intensity (RGB) to train a classifier algorithm. Each classifier algorithm was validated to determine which color space produced the most accurate digital separation of the nanoconjugate types. The LAB-based learning classifier demonstrated the highest accuracy for digitally separating nanoparticles. Using this classifier, nanoparticle conjugates were monitored for their plasmonic color shift after interaction with a synthetic RNA target, resulting in a platform with a highly accurate yes/no response with a true positive rate of 88% and a true negative rate of 100%. The sensor response of tested single stranded RNA (ssRNA) samples was well above control responses for target concentrations in the range of 10 aM-1 pM.
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Affiliation(s)
- Danielle Bennett
- School of Chemistry, The University of New South Wales, Sydney, New South Wales 2052, Australia
- Australian Centre for Nanomedicine, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Xueqian Chen
- School of Chemistry, The University of New South Wales, Sydney, New South Wales 2052, Australia
- Australian Centre for Nanomedicine, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Gregory J Walker
- The Virology Research Laboratory, The University of New South Wales, The Prince of Wales Hospital, Sydney, New South Wales 2052, Australia
| | - Sacha Stelzer-Braid
- The Virology Research Laboratory, The University of New South Wales, The Prince of Wales Hospital, Sydney, New South Wales 2052, Australia
| | - William D Rawlinson
- The Virology Research Laboratory, The University of New South Wales, The Prince of Wales Hospital, Sydney, New South Wales 2052, Australia
| | - D Brynn Hibbert
- School of Chemistry, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Richard D Tilley
- School of Chemistry, The University of New South Wales, Sydney, New South Wales 2052, Australia
- Electron Microscope Unit, Mark Wainwright Analytical Centre, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - J Justin Gooding
- School of Chemistry, The University of New South Wales, Sydney, New South Wales 2052, Australia
- Australian Centre for Nanomedicine, The University of New South Wales, Sydney, New South Wales 2052, Australia
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3
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Mondal M, Gao YQ. Sequence‐dependent clustering properties of nucleotides fragments in an ionic solution. J CHIN CHEM SOC-TAIP 2023. [DOI: 10.1002/jccs.202200425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Manas Mondal
- Institute of Systems and Physical Biology Shenzhen Bay Laboratory Shenzhen China
| | - Yi Qin Gao
- Institute of Systems and Physical Biology Shenzhen Bay Laboratory Shenzhen China
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering Peking University Beijing China
- Biomedical Pioneering Innovation Center Peking University Beijing China
- Beijing Advanced Innovation Center for Genomics Peking University Beijing China
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Mitra S, Kundagrami A. Polyelectrolyte complexation of two oppositely charged symmetric polymers: A minimal theory. J Chem Phys 2023; 158:014904. [PMID: 36610965 DOI: 10.1063/5.0128904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Interplay of Coulomb interaction energy, free ion entropy, and conformational elasticity is a fascinating aspect in polyelectrolytes (PEs). We develop a theory for complexation of two oppositely charged PEs, a process known to be the precursor to the formation of complex coacervates in PE solutions, to explore the underlying thermodynamics of complex formation, at low salts. The theory considers general degrees of solvent polarity and dielectricity within an implicit solvent model, incorporating a varying Coulomb strength. Explicit calculation of the free energy of complexation and its components indicates that the entropy of free counterions and salt ions and the Coulomb enthalpy of bound ion-pairs dictate the equilibrium of PE complexation. This helps decouple the self-consistent dependency of charge and size of the uncomplexed parts of the polyions, derive an analytical expression for charge, and evaluate the free energy components as functions of chain overlap. Complexation is observed to be driven by enthalpy gain at low Coulomb strengths, driven by entropy gain of released counterions but opposed by enthalpy loss due to reduction of ion-pairs at moderate Coulomb strengths, and progressively less favorable due to enthalpy loss at even higher Coulomb strengths. The total free energy of the system is found to decrease linearly with an overlap of chains. Thermodynamic predictions from our model are in good quantitative agreement with simulations in literature.
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Affiliation(s)
- Soumik Mitra
- Department of Physical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, India
| | - Arindam Kundagrami
- Department of Physical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, India
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5
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Li S, Li F, Dong Y, Song N, Pan L, Yang D. Synthesis and Catalytic Property of Ribonucleoside-Derived Carbon Dots. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2106269. [PMID: 35266630 DOI: 10.1002/smll.202106269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 01/26/2022] [Indexed: 06/14/2023]
Abstract
Exploring appropriate precursors has been proposed to be a promising strategy for the creation of artificial enzymes that are emerging as alternatives of natural enzymes. Herein, inspired by the catalytic activities of ribose nucleic acid, using ribonucleosides as precursors including adenosine, guanosine, cytidine, and uridine, respectively, four carbonic aggregates, namely, carbon dots (A-CDs, G-CDs, C-CDs, and U-CDs) to mimic artificial enzymes are synthesized. All the CDs show a planar graphene-like structure and thus can intercalatively bind with DNA double helix. Different from the other three CDs, the uridine-derived U-CDs exhibit unique catalytic property, which can mediate the topological transformation of DNA from supercoiled to nicked open-circular conformation. U-CDs can catalyze oxidation of O2 to generate singlet oxygen 1 O2 via a Haber-Weiss reaction, and consequently mediate oxidative cleavage of phosphate backbone in DNA and release the torsional energy stored in supercoiled DNA. Explorations reveal that the unique highly active oxygenated species, namely, quinone groups that are on the edge of U-CDs, play a key role in the catalytic production of 1 O2 . This work represents a new insight that using natural biomolecules in living systems as precursors can create new species beyond life.
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Affiliation(s)
- Shuai Li
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P. R. China
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, 315201, P. R. China
| | - Feng Li
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P. R. China
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, 315201, P. R. China
| | - Yuhang Dong
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P. R. China
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, 315201, P. R. China
| | - Nachuan Song
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P. R. China
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, 315201, P. R. China
| | - Li Pan
- Tianjin Key Laboratory of Composite & Functional Materials, School of Materials Science and Engineering, Tianjin University, Tianjin, 300072, P. R. China
| | - Dayong Yang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P. R. China
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, 315201, P. R. China
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Srivastava S, Chhabra A, Gang O. Effect of mono- and multi-valent ionic environments on the in-lattice nanoparticle-grafted single-stranded DNA. SOFT MATTER 2022; 18:526-534. [PMID: 34908083 DOI: 10.1039/d1sm01171e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Polyelectrolyte (PE) chains respond in a complex manner to multivalent salt environments, and this behavior depends on pH, temperature, and the presence of specific counter ions. Although much work has been done to understand the behaviour of free PE chains, it is important to reveal their behaviour on a nanoparticle's surface, where surface constraints, particle geometry, and multi-chain environment can affect their behaviour and contribute to particles' assembly states. Our work investigates, using in situ small-angle X-ray scattering (SAXS), the morphology of PE (single-stranded DNA) chains grafted onto the surface of spherical gold nanoparticles assembled in a lattice in the presence of monovalent, divalent and trivalent salts. For divalent salts, the DNA brush length was found to decrease at a faster rate with salt concentration than in the monovalent salt environment, while trivalent salts led to chain collapse. Using a power law analysis and the modified Daoud-Cotton model, we have obtained insight into the mechanism of a nanoparticle-grafted chain's response to ionic environments. Our analysis suggests that the decrease in brush length is due to the conventional electrostatic screening for monovalent systems, whereas for divalent systems both electrostatic screening and divalent ion bridging must be considered.
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Affiliation(s)
- Sunita Srivastava
- Department of Physics, Indian Institute of Technology Bombay, Mumbai, 400076, India.
| | - Anuj Chhabra
- Center for Nanoscience, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Oleg Gang
- Center for Functional Nanomaterials Brookhaven National Laboratory Upton, NY 11973, USA.
- Department of Chemical Engineering Columbia University New York, NY 10027, USA
- Department of Applied Physics and Applied Mathematics Columbia University New York, NY 10027, USA
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7
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Dewangan JK, Basu N, Chowdhury M. Cationic surfactant-directed structural control of NaCl crystals from evaporating sessile droplets. SOFT MATTER 2021; 18:62-79. [PMID: 34878487 DOI: 10.1039/d1sm01357b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We report morphological regulation of NaCl (sodium chloride) crystals through the evaporative crystallisation process of microdroplets containing a cationic surfactant CTAB (cetyltrimethylammonium bromide). Various fascinating evaporative salt morphologies are observed using different combinations of salt (CNaCl) and surfactant (CCTAB) concentrations. Each observed morphology is carefully explained by the interplaying physical phenomena, such as crystallisation, micellisation, evaporative dewetting, and surface adsorption of anionic couneterions. Salt morphologies are investigated for low (CNaCl = 0.1 (M)), intermediate (CNaCl = 0.5 (M)) and high (CNaCl = 2 (M)) concentrations, whereas surfactant concentrations are varied four orders of magnitudes (from 0.0001 (M) to 0.1 (M)). Interestingly, we observe a threshold in CCTAB at 0.001 (M), beyond which the peripheral rings of dried deposits are found to be composed of CTAB for CNaCl = 0.1 (M), while the same is seen to be made up of NaCl for CNaCl = 2 (M). We have explained the morphological evolution by the process of competitive surface adsorption phenomenon between Cl- and Br- counter ions. Such a detailed study of saline droplet crystallisation in the presence of a cationic surfactant underpins the fundamental understanding of the crystallisation process. In addition, it may further impact application sectors where crystallisation of saline solution plays an important role, especially in the presence of additives.
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Affiliation(s)
- Jayant K Dewangan
- Lab of Soft Interfaces, Department of Metallurgical Engineering and Materials Science, Indian Institute of Technology Bombay, Mumbai 400076, India.
| | - Nandita Basu
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Mithun Chowdhury
- Lab of Soft Interfaces, Department of Metallurgical Engineering and Materials Science, Indian Institute of Technology Bombay, Mumbai 400076, India.
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Sarkar S, Maity A, Chakrabarti R. In Silico Elucidation of Molecular Picture of Water-Choline Chloride Mixture. J Phys Chem B 2021; 125:13212-13228. [PMID: 34812630 DOI: 10.1021/acs.jpcb.1c06636] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Choline chloride (ChCl) is a component of several deep eutectic solvents (DESs) having numerous applications. Recent studies have reported manifold promising use of aqueous choline chloride solution as an alternative to DES, where water plays the role of the hydrogen-bond donor. The characteristic physical properties of the DESs and aqueous DES originate from the "inter-" and intraspecies hydrogen-bond network formed by the constituents. However, a detailed molecular-level picture of choline chloride and water mixture is largely lacking in the literature. This motivates us to carry out extensive all-atom molecular dynamics simulations of the ChCl-water mixture of varying compositions. Our analyses clearly show an overall increase in the interspecies association with an increase in ChCl concentration. At higher concentrations, the trimethylammonium groups of choline are stabilized by a nonpolar interaction, whereas the hydroxyl groups preferentially interact with water. Chloride ions are found to be involved in two types of interactions: one where chloride ions intercalate two or more choline cations, and the other one where they are surrounded by five to six water molecules forming solvated chloride ions. However, the relative fractions of these two types of associations depend on the concentration of ChCl in the mixture. Another important structural aspect is the disruption of the hydrogen-bonded water network due to the presence of both choline cations and chloride ions. However, chloride ions participate to partially restore the tetrahedral arrangement of partners around water molecules.
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Affiliation(s)
- Soham Sarkar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
| | - Atanu Maity
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
| | - Rajarshi Chakrabarti
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
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9
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Maity A, Choudhury AR, Chakrabarti R. Effect of Stapling on the Thermodynamics of mdm2-p53 Binding. J Chem Inf Model 2021; 61:1989-2000. [PMID: 33830760 DOI: 10.1021/acs.jcim.1c00219] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Protein-protein interaction (PPI) is one of the key regulatory features driving biomolecular processes and hence is targeted for designing therapeutics against diseases. Small peptides are a new and emerging class of therapeutics owing to their high specificity and low toxicity. For achieving efficient targeting of the PPI, amino acid side chains are often stapled together, resulting in the rigidification of these peptides. Exploring the scope of these peptides demands a comprehensive understanding of their working principle. In this work, two stapled p53 peptides have been considered to delineate their binding mechanism with mdm2 using computational approaches. The addition of stapling agent protects the secondary structure of the peptides even in the case of thermal and chemical denaturation. Although the introduction of a stapling agent increases the hydrophobicity of the peptide, the enthalpic stabilization decreases. This is overcome by the lowering of the entropic penalty, and the overall binding affinity improves. The mechanistic insights into the benefit of peptide stapling can be adopted for further improvement of peptide therapeutics.
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Affiliation(s)
- Atanu Maity
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Asha Rani Choudhury
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Rajarshi Chakrabarti
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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10
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Stellwagen E, Stellwagen NC. Electrophoretic Mobility of DNA in Solutions of High Ionic Strength. Biophys J 2020; 118:2783-2789. [PMID: 32445623 DOI: 10.1016/j.bpj.2020.02.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 02/06/2020] [Accepted: 02/27/2020] [Indexed: 12/11/2022] Open
Abstract
The free-solution mobilities of small single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) have been measured by capillary electrophoresis in solutions containing 0.01-1.0 M sodium acetate. The mobility of dsDNA is greater than that of ssDNA at all ionic strengths because of the greater charge density of dsDNA. The mobilities of both ssDNA and dsDNA decrease with increasing ionic strength until approaching plateau values at ionic strengths greater than ∼0.6 M. Hence, ssDNA and dsDNA appear to interact in a similar manner with the ions in the background electrolyte. For dsDNA, the mobilities predicted by the Manning electrophoresis equation are reasonably close to the observed mobilities, using no adjustable parameters, if the average distance between phosphate residues (the b parameter) is taken to be 1.7 Å. For ssDNA, the predicted mobilities are close to the observed mobilities at ionic strengths ≤0.01 M if the b-value is taken to be 4.1 Å. The predicted and observed mobilities diverge strongly at higher ionic strengths unless the b-value is reduced significantly. The results suggest that ssDNA strands exist as an ensemble of relatively compact conformations at high ionic strengths, with b-values corresponding to the relatively short phosphate-phosphate distances through space.
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Li F, Li S, Guo X, Dong Y, Yao C, Liu Y, Song Y, Tan X, Gao L, Yang D. Chiral Carbon Dots Mimicking Topoisomerase I To Mediate the Topological Rearrangement of Supercoiled DNA Enantioselectively. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202002904] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Feng Li
- Frontier Science Center for Synthetic BiologyKey Laboratory of Systems Bioengineering (MOE)School of Chemical Engineering and TechnologyTianjin University Tianjin 300350 P. R. China
| | - Shuai Li
- Frontier Science Center for Synthetic BiologyKey Laboratory of Systems Bioengineering (MOE)School of Chemical Engineering and TechnologyTianjin University Tianjin 300350 P. R. China
| | - Xiaocui Guo
- Frontier Science Center for Synthetic BiologyKey Laboratory of Systems Bioengineering (MOE)School of Chemical Engineering and TechnologyTianjin University Tianjin 300350 P. R. China
| | - Yuhang Dong
- Frontier Science Center for Synthetic BiologyKey Laboratory of Systems Bioengineering (MOE)School of Chemical Engineering and TechnologyTianjin University Tianjin 300350 P. R. China
| | - Chi Yao
- Frontier Science Center for Synthetic BiologyKey Laboratory of Systems Bioengineering (MOE)School of Chemical Engineering and TechnologyTianjin University Tianjin 300350 P. R. China
| | - Yangping Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and DiagnosticsSchool of PharmacyTianjin Medical University Tianjin 300070 P. R. China
| | - Yuguang Song
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and DiagnosticsSchool of PharmacyTianjin Medical University Tianjin 300070 P. R. China
| | - Xiaoli Tan
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and DiagnosticsSchool of PharmacyTianjin Medical University Tianjin 300070 P. R. China
| | - Lizeng Gao
- CAS Engineering Laboratory for NanozymeInstitute of BiophysicsChinese Academy of Sciences Beijing 100101 P. R. China
| | - Dayong Yang
- Frontier Science Center for Synthetic BiologyKey Laboratory of Systems Bioengineering (MOE)School of Chemical Engineering and TechnologyTianjin University Tianjin 300350 P. R. China
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Li F, Li S, Guo X, Dong Y, Yao C, Liu Y, Song Y, Tan X, Gao L, Yang D. Chiral Carbon Dots Mimicking Topoisomerase I To Mediate the Topological Rearrangement of Supercoiled DNA Enantioselectively. Angew Chem Int Ed Engl 2020; 59:11087-11092. [DOI: 10.1002/anie.202002904] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Indexed: 12/21/2022]
Affiliation(s)
- Feng Li
- Frontier Science Center for Synthetic BiologyKey Laboratory of Systems Bioengineering (MOE)School of Chemical Engineering and TechnologyTianjin University Tianjin 300350 P. R. China
| | - Shuai Li
- Frontier Science Center for Synthetic BiologyKey Laboratory of Systems Bioengineering (MOE)School of Chemical Engineering and TechnologyTianjin University Tianjin 300350 P. R. China
| | - Xiaocui Guo
- Frontier Science Center for Synthetic BiologyKey Laboratory of Systems Bioengineering (MOE)School of Chemical Engineering and TechnologyTianjin University Tianjin 300350 P. R. China
| | - Yuhang Dong
- Frontier Science Center for Synthetic BiologyKey Laboratory of Systems Bioengineering (MOE)School of Chemical Engineering and TechnologyTianjin University Tianjin 300350 P. R. China
| | - Chi Yao
- Frontier Science Center for Synthetic BiologyKey Laboratory of Systems Bioengineering (MOE)School of Chemical Engineering and TechnologyTianjin University Tianjin 300350 P. R. China
| | - Yangping Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and DiagnosticsSchool of PharmacyTianjin Medical University Tianjin 300070 P. R. China
| | - Yuguang Song
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and DiagnosticsSchool of PharmacyTianjin Medical University Tianjin 300070 P. R. China
| | - Xiaoli Tan
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and DiagnosticsSchool of PharmacyTianjin Medical University Tianjin 300070 P. R. China
| | - Lizeng Gao
- CAS Engineering Laboratory for NanozymeInstitute of BiophysicsChinese Academy of Sciences Beijing 100101 P. R. China
| | - Dayong Yang
- Frontier Science Center for Synthetic BiologyKey Laboratory of Systems Bioengineering (MOE)School of Chemical Engineering and TechnologyTianjin University Tianjin 300350 P. R. China
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14
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Stacking geometry between two sheared Watson-Crick basepairs: Computational chemistry and bioinformatics based prediction. Biochim Biophys Acta Gen Subj 2020; 1864:129600. [PMID: 32179130 DOI: 10.1016/j.bbagen.2020.129600] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 03/05/2020] [Accepted: 03/11/2020] [Indexed: 11/21/2022]
Abstract
BACKGROUND Molecular modeling of RNA double helices is possible using most probable values of basepair parameters obtained from crystal structure database. The A:A w:wC non-canonical basepair, involving Watson-Crick edges of two Adenines in cis orientation, appears quite frequently in database. Bimodal distribution of its Shear, due to two different H-bonding schemes, introduces the confusion in assigning most the probable value. Its effect is pronounced when the A:A w:wC basepair stacks on Sheared wobble G:U W:WC basepairs. METHODS We employed molecular dynamics simulations of three possible double helices with GAG, UAG and GAU sequence motifs at their centers and quantum chemical calculation for non-canonical A:A w:wC basepair stacked on G:U W:WC basepair. RESULTS We noticed stable structures of GAG motif with specifically negative Shear of the A:A basepair but stabilities of the other motifs were not found with A:A w:wC basepairing. Hybrid DFT-D and MP2 stacking energy analyses on dinucleotide step sequences, A:A w:wC::G:U W:WC and A:A w:wC::U:G W:WC reveal that viable orientation of A:A::G:U prefers one of the H-bonding modes with negative Shear, supported by crystal structure database. The A:A::U:G dinucleotide, however, prefers structure with only positive Shear. CONCLUSIONS The quantum chemical calculations explain why MD simulations of GAG sequence motif only appear stable. In the cases of the GAU and UAG motifs "tug of war" situation between positive and negative Shears of A:A w:wC basepair induces conformational plasticity. GENERAL SIGNIFICANCE We have projected comprehensive reason behind the promiscuous nature of A:A w:wC basepair which brings occasional structural plasticity.
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Maity A, Sarkar S, Theeyancheri L, Chakrabarti R. Choline Chloride as a Nano‐Crowder Protects HP‐36 from Urea‐Induced Denaturation: Insights from Solvent Dynamics and Protein‐Solvent Interactions. Chemphyschem 2020; 21:552-567. [DOI: 10.1002/cphc.201901078] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 01/22/2020] [Indexed: 12/27/2022]
Affiliation(s)
- Atanu Maity
- Department of ChemistryIndian Institute of Technology Bombay Powai Mumbai 400076 India
| | - Soham Sarkar
- Department of ChemistryIndian Institute of Technology Bombay Powai Mumbai 400076 India
| | - Ligesh Theeyancheri
- Department of ChemistryIndian Institute of Technology Bombay Powai Mumbai 400076 India
| | - Rajarshi Chakrabarti
- Department of ChemistryIndian Institute of Technology Bombay Powai Mumbai 400076 India
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