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Foster PL, Niccum BA, Popodi E, Townes JP, Lee H, MohammedIsmail W, Tang H. Determinants of Base-Pair Substitution Patterns Revealed by Whole-Genome Sequencing of DNA Mismatch Repair Defective Escherichia coli. Genetics 2018; 209:1029-1042. [PMID: 29907647 PMCID: PMC6063221 DOI: 10.1534/genetics.118.301237] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 06/14/2018] [Indexed: 11/18/2022] Open
Abstract
Mismatch repair (MMR) is a major contributor to replication fidelity, but its impact varies with sequence context and the nature of the mismatch. Mutation accumulation experiments followed by whole-genome sequencing of MMR-defective Escherichia coli strains yielded ≈30,000 base-pair substitutions (BPSs), revealing mutational patterns across the entire chromosome. The BPS spectrum was dominated by A:T to G:C transitions, which occurred predominantly at the center base of 5'NAC3'+5'GTN3' triplets. Surprisingly, growth on minimal medium or at low temperature attenuated these mutations. Mononucleotide runs were also hotspots for BPSs, and the rate at which these occurred increased with run length. Comparison with ≈2000 BPSs accumulated in MMR-proficient strains revealed that both kinds of hotspots appeared in the wild-type spectrum and so are likely to be sites of frequent replication errors. In MMR-defective strains transitions were strand biased, occurring twice as often when A and C rather than T and G were on the lagging-strand template. Loss of nucleotide diphosphate kinase increases the cellular concentration of dCTP, which resulted in increased rates of mutations due to misinsertion of C opposite A and T. In an mmr ndk double mutant strain, these mutations were more frequent when the template A and T were on the leading strand, suggesting that lagging-strand synthesis was more error-prone, or less well corrected by proofreading, than was leading strand synthesis.
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Affiliation(s)
- Patricia L Foster
- Department of Biology, Indiana University, Bloomington, Indiana 47405
| | - Brittany A Niccum
- Department of Biology, Indiana University, Bloomington, Indiana 47405
| | - Ellen Popodi
- Department of Biology, Indiana University, Bloomington, Indiana 47405
| | - Jesse P Townes
- Department of Biology, Indiana University, Bloomington, Indiana 47405
| | - Heewook Lee
- School of Informatics, Computing, and Engineering, Indiana University, Bloomington, Indiana 47405
| | - Wazim MohammedIsmail
- School of Informatics, Computing, and Engineering, Indiana University, Bloomington, Indiana 47405
| | - Haixu Tang
- School of Informatics, Computing, and Engineering, Indiana University, Bloomington, Indiana 47405
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102
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Wang Y, Sun Y, Lau C, Lu J. Duplex microRNAs assay based on target-triggered universal reporter hybridization. J Pharm Anal 2018; 8:265-270. [PMID: 30140491 PMCID: PMC6104290 DOI: 10.1016/j.jpha.2018.07.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/09/2018] [Accepted: 07/10/2018] [Indexed: 12/14/2022] Open
Abstract
In this paper, we designed and evaluated a duplex detection strategy for microRNAs (miRNAs) using universal probe-based target-triggered double hybridization and fluorescent microsphere-based assay system (xMAP array). In the absence of target miRNA, reporter DNA cannot hybridize stably with the immobilized capture DNA due to its low melting temperature. Only after adding target miRNA, can reporter probe hybridize with capture probe to form a stable three-component complex. This target-triggered stable hybridization makes this method possible for highly selective and sensitive detection of multiple miRNAs. We exemplified a quantitative detection of duplex miRNAs with a limit of detection of 40 pM. The xMAP array platform holds the potential of extending this approach to simultaneous detection of up to 100 miRNA targets. Considering the simplicity, rapidity and multiplexing, this work promised a potential detection of multiple miRNA biomarkers for early disease diagnosis and prognosis.
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Affiliation(s)
- Yinan Wang
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Yue Sun
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Choiwan Lau
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Jianzhong Lu
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
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103
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Mphahlele MJ, Parbhoo N. Synthesis, Evaluation of Cytotoxicity and Molecular Docking Studies of the 7-Acetamido Substituted 2-Aryl-5-bromo-3-trifluoroacetylindoles as Potential Inhibitors of Tubulin Polymerization. Pharmaceuticals (Basel) 2018; 11:ph11020059. [PMID: 29891753 PMCID: PMC6027433 DOI: 10.3390/ph11020059] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 05/22/2018] [Accepted: 05/25/2018] [Indexed: 02/07/2023] Open
Abstract
The 3-trifluoroacetyl⁻substituted 7-acetamido-2-aryl-5-bromoindoles 5a⁻h were prepared and evaluated for potential antigrowth effect in vitro against human lung cancer (A549) and cervical cancer (HeLa) cells and for the potential to inhibit tubulin polymerization. The corresponding intermediates, namely, the 3-unsubstituted 7-acetyl-2-aryl-5-bromoindole 2a⁻d and 7-acetamido-2-aryl-5-bromoindole 4a⁻d were included in the assays in order to correlate both structural variations and cytotoxicity. No cytotoxicity was observed for compounds 2a⁻d and their 3-trifluoroacetyl⁻substituted derivatives 5a⁻d against both cell lines. The 7-acetamido derivatives 4⁻d exhibited modest cytotoxicity against both cell lines. All of the 3-trifluoroacetyl⁻substituted 7-acetamido-2-aryl-5-bromoindoles 5e⁻h were found to be more active against both cell lines when compared to the chemotherapeutic drug, Melphalan. The most active compound, 5g, induced programmed cell death (apoptosis) in a caspase-dependent manner for both A549 and HeLa cells. Compounds 5e⁻h were found to significantly inhibit tubulin polymerization against indole-3-carbinol and colchicine as reference standards. Molecular docking of 5g into the colchicine-binding site suggests that the compounds bind to tubulin by different type of interactions including pi-alkyl, amide-pi stacked and alkyl interactions as well as hydrogen bonding with the protein residues to elicit anticancer activity.
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Affiliation(s)
- Malose J Mphahlele
- Department of Chemistry, College of Science, Engineering and Technology, University of South Africa, Private Bag X06, Florida 1710, South Africa.
| | - Nishal Parbhoo
- Department of Life & Consumer Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Private Bag X06, Florida 1710, South Africa.
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104
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Raper AT, Reed AJ, Suo Z. Kinetic Mechanism of DNA Polymerases: Contributions of Conformational Dynamics and a Third Divalent Metal Ion. Chem Rev 2018; 118:6000-6025. [DOI: 10.1021/acs.chemrev.7b00685] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Austin T. Raper
- Department of Chemistry and Biochemistry, Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, United States
| | - Andrew J. Reed
- Department of Chemistry and Biochemistry, Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, United States
| | - Zucai Suo
- Department of Chemistry and Biochemistry, Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, United States
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105
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Abstract
We have discovered a well-defined extended conformation of double-stranded DNA, which we call Σ-DNA, using laser-tweezers force-spectroscopy experiments. At a transition force corresponding to free energy change ΔG = 1·57 ± 0·12 kcal (mol base pair)-1 60 or 122 base-pair long synthetic GC-rich sequences, when pulled by the 3'-3' strands, undergo a sharp transition to the 1·52 ± 0·04 times longer Σ-DNA. Intriguingly, the same degree of extension is also found in DNA complexes with recombinase proteins, such as bacterial RecA and eukaryotic Rad51. Despite vital importance to all biological organisms for survival, genome maintenance and evolution, the recombination reaction is not yet understood at atomic level. We here propose that the structural distortion represented by Σ-DNA, which is thus physically inherent to the nucleic acid, is related to how recombination proteins mediate recognition of sequence homology and execute strand exchange. Our hypothesis is that a homogeneously stretched DNA undergoes a 'disproportionation' into an inhomogeneous Σ-form consisting of triplets of locally B-like perpendicularly stacked bases. This structure may ensure improved fidelity of base-pair recognition and promote rejection in case of mismatch during homologous recombination reaction. Because a triplet is the length of a gene codon, we speculate that the structural physics of nucleic acids may have biased the evolution of recombinase proteins to exploit triplet base stacks and also the genetic code.
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106
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Temburnikar K, Seley-Radtke KL. Recent advances in synthetic approaches for medicinal chemistry of C-nucleosides. Beilstein J Org Chem 2018; 14:772-785. [PMID: 29719574 PMCID: PMC5905277 DOI: 10.3762/bjoc.14.65] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 03/06/2018] [Indexed: 12/13/2022] Open
Abstract
C-nucleosides have intrigued biologists and medicinal chemists since their discovery in 1950's. In that regard, C-nucleosides and their synthetic analogues have resulted in promising leads in drug design. Concurrently, advances in chemical syntheses have contributed to structural diversity and drug discovery efforts. Convergent and modular approaches to synthesis have garnered much attention in this regard. Among them nucleophilic substitution at C1' has seen wide applications providing flexibility in synthesis, good yields, the ability to maneuver stereochemistry as well as to incorporate structural modifications. In this review, we describe recent reports on the modular synthesis of C-nucleosides with a focus on D-ribonolactone and sugar modifications that have resulted in potent lead molecules.
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Affiliation(s)
- Kartik Temburnikar
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, 725 N. Wolfe St. Baltimore, MD 21205, United States
| | - Katherine L Seley-Radtke
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, United States
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107
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Vallejo Narváez WE, Jiménez EI, Romero-Montalvo E, Sauza-de la Vega A, Quiroz-García B, Hernández-Rodríguez M, Rocha-Rinza T. Acidity and basicity interplay in amide and imide self-association. Chem Sci 2018; 9:4402-4413. [PMID: 29896381 PMCID: PMC5956980 DOI: 10.1039/c8sc01020j] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 04/05/2018] [Indexed: 12/23/2022] Open
Abstract
Simple acid–base properties explain the differences in amide and imide dimerisation, and represent an alternative to the secondary interactions hypothesis.
Amides dimerise more strongly than imides despite their lower acidity. Such an unexpected result has been rationalised in terms of the Jorgensen Secondary Interactions Hypothesis (JSIH) that involves the spectator (C
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OS) and H-bonded (C
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OHB) carbonyl groups in imides. Notwithstanding the considerable body of experimental and theoretical evidence supporting the JSIH, there are some computational studies which suggest that there might be other relevant intermolecular interactions than those considered in this model. We conjectured that the spectator carbonyl moieties could disrupt the resonance-assisted hydrogen bonds in imide dimers, but our results showed that this was not the case. Intrigued by this phenomenon, we studied the self-association of a set of amides and imides via1H-NMR, 1H-DOSY experiments, DFT calculations, QTAIM topological analyses of the electron density and IQA partitions of the electronic energy. These analyses revealed that there are indeed repulsions of the type OS···OHB in accordance with the JSIH but our data also indicate that the C
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OS group has an overall attraction with the interacting molecule. Instead, we found correlations between self-association strength and simple Brønsted–Lowry acid/base properties, namely, N–H acidities and C
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O basicities. The results in CDCl3 and CCl4 indicate that imides dimerise less strongly than structurally related amides because of the lower basicity of their carbonyl fragments, a frequently overlooked aspect in the study of H-bonding. Overall, the model proposed herein could provide important insights in diverse areas of supramolecular chemistry such as the study of multiple hydrogen-bonded adducts which involve amide or imide functional groups.
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Affiliation(s)
- Wilmer E Vallejo Narváez
- Institute of Chemistry , National Autonomous University of Mexico , Ciudad Universitaria , Circuito Exterior, Del. Coyoacán , Mexico City , 04510 , Mexico . ;
| | - Eddy I Jiménez
- Institute of Chemistry , National Autonomous University of Mexico , Ciudad Universitaria , Circuito Exterior, Del. Coyoacán , Mexico City , 04510 , Mexico . ;
| | - Eduardo Romero-Montalvo
- Institute of Chemistry , National Autonomous University of Mexico , Ciudad Universitaria , Circuito Exterior, Del. Coyoacán , Mexico City , 04510 , Mexico . ;
| | - Arturo Sauza-de la Vega
- Institute of Chemistry , National Autonomous University of Mexico , Ciudad Universitaria , Circuito Exterior, Del. Coyoacán , Mexico City , 04510 , Mexico . ;
| | - Beatriz Quiroz-García
- Institute of Chemistry , National Autonomous University of Mexico , Ciudad Universitaria , Circuito Exterior, Del. Coyoacán , Mexico City , 04510 , Mexico . ;
| | - Marcos Hernández-Rodríguez
- Institute of Chemistry , National Autonomous University of Mexico , Ciudad Universitaria , Circuito Exterior, Del. Coyoacán , Mexico City , 04510 , Mexico . ;
| | - Tomás Rocha-Rinza
- Institute of Chemistry , National Autonomous University of Mexico , Ciudad Universitaria , Circuito Exterior, Del. Coyoacán , Mexico City , 04510 , Mexico . ;
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108
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Negi I, Kathuria P, Sharma P, Wetmore SD. How do hydrophobic nucleobases differ from natural DNA nucleobases? Comparison of structural features and duplex properties from QM calculations and MD simulations. Phys Chem Chem Phys 2018; 19:16365-16374. [PMID: 28657627 DOI: 10.1039/c7cp02576a] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Computational (DFT and MD simulation) methods are employed to systematically characterize the structural and energetic properties of five hydrophobic nucleobases (FEMO, MMO2, NaM, 5SICS and TPT3) that constitute four unnatural base pairs (FEMO:5SICS, MMO2:5SICS, NaM:5SICS and TPT3:NaM). These hydrophobic bases have been recently shown to be replicated when present between natural bases in DNA duplexes, with the highest replication fidelity and efficiency occuring for the TPT3:NaM pair. Our QM calculations suggest that the preferred (anti) glycosidic orientations of nucleosides containing hydrophobic bases are similar to the natural DNA nucleosides despite differences in their chemical structures. However, due to the inability to form interbase hydrogen bonds, hydrophobic base pairs intrinsically prefer nonplanar, distorted geometries, many of which are stabilized through π-π stacking interactions. Furthermore, the intrinsic stacking potential between a hydrophobic and a natural base is similar to that between two natural bases, indicating that the strength of stacking interactions in DNA duplexes containing hydrophobic bases is likely comparable to natural DNA. However, in contrast to the isolated base-pair geometries, our MD simulations suggest that the hydrophobic base pairs adopt variable geometries within DNA, which range from stacked (5SICS:FEMO) to nearly planar (5SICS:NaM and SICS:MMO2) to planar (TPT3:NaM). As a result, the duplex structural features at the site of modification depend on the identity of the hydrophobic base pair, where the TPT3:NaM pair causes the least structural changes compared to natural DNA. Overall, the structural insight obtained from our calculations on DNA containing hydrophobic base pairs explains the experimentally-observed higher fidelity and efficiency during replication of TPT3:NaM compared to other hydrophobic nucleobase pairs. By providing valuable structural information that explains the intrinsic and duplex properties of this class of unnatural nucleobases, the present work may aid the future design of improved hydrophobic analogues.
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Affiliation(s)
- Indu Negi
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh, 160014, India.
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109
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Ren W, Zheng K, Liao C, Yang J, Zhao J. Charge evolution during the unfolding of a single DNA i-motif. Phys Chem Chem Phys 2018; 20:916-924. [PMID: 29230450 DOI: 10.1039/c7cp06235d] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The effective charge and evolution of single chains of a DNA i-motif during its unfolding process are investigated at the single molecule level. Using fluorescence correlation spectroscopy and photon counting histograms, the single chain dimensions and electrical potential of cytosine-rich human telomeric oligonucleotides are monitored, during their unfolding from the i-motif to the random coil state. It is discovered that the effective charge density of the DNA chain is very sensitive to conformation changes and the results remarkably expose the existence of an intermediate state of the unfolding process. A huge difference in pH value exists in the vicinity of the DNA chain and the bulk solution, depending on the salt concentration, as reflected by a down-shift in the pH value of unfolding. The presence of an external salt in the solution helps to stabilize the i-motif structure at low pH values due to the reduction of the effective charge density. It can also destabilize the folded structure in the pH range of the conformation transition due to the elevation of the local pH value, encouraging the deprotonation of the cytosine groups. These results provide new information for understanding the structure and stability of i-motif DNA, and its biological function, as well as the building blocks for smart nanomaterials.
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Affiliation(s)
- Weibin Ren
- Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
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110
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Jawiczuk M. A theoretical study on the hydrogen bond and stability of cytosine and thymine dimers. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2017.11.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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111
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Singh VK, Kumar V, Krishnamachari A. Prediction of replication sites in Saccharomyces cerevisiae genome using DNA segment properties: Multi-view ensemble learning (MEL) approach. Biosystems 2018; 163:59-69. [DOI: 10.1016/j.biosystems.2017.12.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 10/27/2017] [Accepted: 12/07/2017] [Indexed: 10/18/2022]
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112
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Royuela S, García-Garrido E, Martín Arroyo M, Mancheño MJ, Ramos MM, González-Rodríguez D, Somoza Á, Zamora F, Segura JL. Uracil grafted imine-based covalent organic framework for nucleobase recognition. Chem Commun (Camb) 2018; 54:8729-8732. [DOI: 10.1039/c8cc04346a] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An imine-based covalent organic framework (COF) decorated in its cavities with uracil groups has shown selective recognition towards adenine in water.
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Affiliation(s)
- Sergio Royuela
- Departamento de Química Orgánica I
- Facultad de CC. Químicas
- Universidad Complutense de Madrid
- Madrid 28040
- Spain
| | - Eduardo García-Garrido
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia)
- Cantoblanco
- Madrid E-28049
- Spain
| | - Miguel Martín Arroyo
- Departamento de Orgánica
- Facultad de Ciencias
- Universidad Autónoma de Madrid
- Madrid 28049
- Spain
| | - María J. Mancheño
- Departamento de Química Orgánica I
- Facultad de CC. Químicas
- Universidad Complutense de Madrid
- Madrid 28040
- Spain
| | - María M. Ramos
- Departamento de Tecnología Química y Ambiental
- Universidad Rey Juan Carlos
- Madrid 28933
- Spain
| | | | - Álvaro Somoza
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia)
- Cantoblanco
- Madrid E-28049
- Spain
| | - Félix Zamora
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia)
- Cantoblanco
- Madrid E-28049
- Spain
- Departamento de Inorgánica
| | - José L. Segura
- Departamento de Química Orgánica I
- Facultad de CC. Químicas
- Universidad Complutense de Madrid
- Madrid 28040
- Spain
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113
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Electronic properties of DNA: Description of weak interactions in TATA-box-like chains. Biophys Chem 2017; 233:26-35. [PMID: 29287183 DOI: 10.1016/j.bpc.2017.11.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 11/28/2017] [Accepted: 11/28/2017] [Indexed: 11/23/2022]
Abstract
DNA is one of the most important biomolecules since it contains all the genetic information about an organism. The tridimensional structure of DNA is a determinant factor that influences the physiological and biochemical mechanisms by which this molecule carries out its biological functions. It is believed that hydrogen bonds and π-π stacking are the most relevant non-covalent interactions regarding DNA stability. Due to its importance, several theoretical works have been made to describe these interactions, however, most of them often consider only the presence of two nitrogenous bases, having a limited overview of the participation of these in B-DNA stabilization. Furthermore, due to the complexity of the system, there are discrepancies between which involved interaction is more important in duplex stability. Therefore, in this project we describe these interactions considering the effect of chain length on the energy related to both hydrogen bonds and π-π stacking, using as model TATA-box-like chains with n base pairs (n=1 to 14) and taking into consideration two different models: ideal and optimized B-DNA. We have found that there is a cooperative effect on hydrogen bond and π-π stacking mean energies when the presence of other base pairs is considered. In addition, it was found that hydrogen bonds contribute more importantly than π-π stacking to B-DNA stability; nevertheless, the participation of π-π stacking is not negligible: when B-DNA looks for a conformation of lower energy, π-π stacking interaction are the first to be optimized. All work was realized under the framework of DFT using the DMol3 code (M06-L/DNP).
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114
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Derricotte WD, Evangelista FA. Localized Intrinsic Valence Virtual Orbitals as a Tool for the Automatic Classification of Core Excited States. J Chem Theory Comput 2017; 13:5984-5999. [DOI: 10.1021/acs.jctc.7b00493] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Wallace D. Derricotte
- Department of Chemistry and Cherry
L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Francesco A. Evangelista
- Department of Chemistry and Cherry
L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
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115
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Kietrys AM, Velema WA, Kool ET. Fingerprints of Modified RNA Bases from Deep Sequencing Profiles. J Am Chem Soc 2017; 139:17074-17081. [PMID: 29111692 PMCID: PMC5819333 DOI: 10.1021/jacs.7b07914] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Posttranscriptional modifications of RNA bases are not only found in many noncoding RNAs but have also recently been identified in coding (messenger) RNAs as well. They require complex and laborious methods to locate, and many still lack methods for localized detection. Here we test the ability of next-generation sequencing (NGS) to detect and distinguish between ten modified bases in synthetic RNAs. We compare ultradeep sequencing patterns of modified bases, including miscoding, insertions and deletions (indels), and truncations, to unmodified bases in the same contexts. The data show widely varied responses to modification, ranging from no response, to high levels of mutations, insertions, deletions, and truncations. The patterns are distinct for several of the modifications, and suggest the future use of ultradeep sequencing as a fingerprinting strategy for locating and identifying modifications in cellular RNAs.
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Affiliation(s)
- Anna M. Kietrys
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Willem A. Velema
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Eric T. Kool
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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116
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Reiling-Steffensmeier C, Marky LA. Structural Insight into the Unbound State of the DNA Analogue of the PreQ 1 Riboswitch: A Thermodynamic Approach. Biochemistry 2017; 56:6231-6239. [PMID: 29076719 DOI: 10.1021/acs.biochem.7b00596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The preQ1 riboswitch aptamer domain is very dynamic in its unbound state with the ability to form multiple structures: a hairpin, kissing hairpins, and pseudoknot-like structure. The aim of this study is to determine whether the DNA analogue (PreQ1) is able to form structures similar to that of the reported RNA aptamer. Using a thermodynamic approach, we report on structural determination using differential scanning calorimetry under different salt conditions. Further analysis of the primary sequence allowed us to design modified molecules to determine what potential structures are forming in this single-stranded DNA analogue. We found, in a 16 mM Na+ solution, PreQ1 has three transitions with TM values of 14.8, 19.4, and 26.2 °C and a total ΔH of -44.7 kcal/mol. With the increase in salt concentration to 116 mM, there are TM values of 22.3, 28.7, and 38.9 °C and a ΔH of -69.1 kcal/mol, while at 216 mM, the three transitions have TM values of 24.4, 31.6, and 42.9 °C with a total ΔH of -71.5 kcal/mol. Therefore, the increase in enthalpy is due to the formation of additional base-pair stacks. The modified molecules, which would inhibit pseudoknot formation, kissing hairpins, and internal loop interactions, were fully characterized and compared to the native DNA analogue. The analysis of the enthalpy and differential binding of counterions allows us to conclude this single-stranded DNA analogue under physiological conditions is not forming a pseudoknot-like structure. Instead, two potential structures, Compact-Hairpin and Kissing-Complex, are more likely and could be in equilibrium.
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Affiliation(s)
- Calliste Reiling-Steffensmeier
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center , 986025 Nebraska Medical Center, Omaha, Nebraska 68198-6025, United States
| | - Luis A Marky
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center , 986025 Nebraska Medical Center, Omaha, Nebraska 68198-6025, United States
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117
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Yang L, Niu J, Zhan Y, Xu Y, Sun R, Ge J. Fluorescence Responses of the Protonation and Deprotonation Processes between Phenolate and Phenol within Rosamine. CHINESE J CHEM 2017. [DOI: 10.1002/cjoc.201700534] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Ling Yang
- College of Chemistry, Chemical Engineering and Material Science; Soochow University, 199 Ren'Ai Road; Suzhou Jiangsu 215123 China
| | - Jinyun Niu
- School of Radiation Medicine and Protection; Medical College of Soochow University; Suzhou Jiangsu 215123 China
| | - Yanhua Zhan
- College of Chemistry, Chemical Engineering and Material Science; Soochow University, 199 Ren'Ai Road; Suzhou Jiangsu 215123 China
| | - Yujie Xu
- School of Radiation Medicine and Protection; Medical College of Soochow University; Suzhou Jiangsu 215123 China
| | - Ru Sun
- College of Chemistry, Chemical Engineering and Material Science; Soochow University, 199 Ren'Ai Road; Suzhou Jiangsu 215123 China
| | - Jianfeng Ge
- College of Chemistry, Chemical Engineering and Material Science; Soochow University, 199 Ren'Ai Road; Suzhou Jiangsu 215123 China
- Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical, Engineering and Technology; Chinese Academy of Sciences; Suzhou 215163 China
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118
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Ramanathan N, Sankaran K, Sundararajan K. Nitrogen: A New Class of π-Bonding Partner in Hetero π-Stacking Interaction. J Phys Chem A 2017; 121:9081-9091. [DOI: 10.1021/acs.jpca.7b08164] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- N. Ramanathan
- Materials Chemistry & Metal Fuel Cycle Group, ‡Homi Bhabha National Institute, Indira Gandhi Center for Atomic Research, Kalpakkam 603102, Tamil Nadu, India
| | - K. Sankaran
- Materials Chemistry & Metal Fuel Cycle Group, ‡Homi Bhabha National Institute, Indira Gandhi Center for Atomic Research, Kalpakkam 603102, Tamil Nadu, India
| | - K. Sundararajan
- Materials Chemistry & Metal Fuel Cycle Group, ‡Homi Bhabha National Institute, Indira Gandhi Center for Atomic Research, Kalpakkam 603102, Tamil Nadu, India
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119
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Schroeder JW, Yeesin P, Simmons LA, Wang JD. Sources of spontaneous mutagenesis in bacteria. Crit Rev Biochem Mol Biol 2017; 53:29-48. [PMID: 29108429 DOI: 10.1080/10409238.2017.1394262] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Mutations in an organism's genome can arise spontaneously, that is, in the absence of exogenous stress and prior to selection. Mutations are often neutral or deleterious to individual fitness but can also provide genetic diversity driving evolution. Mutagenesis in bacteria contributes to the already serious and growing problem of antibiotic resistance. However, the negative impacts of spontaneous mutagenesis on human health are not limited to bacterial antibiotic resistance. Spontaneous mutations also underlie tumorigenesis and evolution of drug resistance. To better understand the causes of genetic change and how they may be manipulated in order to curb antibiotic resistance or the development of cancer, we must acquire a mechanistic understanding of the major sources of mutagenesis. Bacterial systems are particularly well-suited to studying mutagenesis because of their fast growth rate and the panoply of available experimental tools, but efforts to understand mutagenic mechanisms can be complicated by the experimental system employed. Here, we review our current understanding of mutagenic mechanisms in bacteria and describe the methods used to study mutagenesis in bacterial systems.
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Affiliation(s)
- Jeremy W Schroeder
- a Department of Bacteriology , University of Wisconsin - Madison , Madison , WI , USA
| | - Ponlkrit Yeesin
- a Department of Bacteriology , University of Wisconsin - Madison , Madison , WI , USA
| | - Lyle A Simmons
- b Department of Molecular, Cellular, and Developmental Biology , University of Michigan , Ann Arbor , MI , USA
| | - Jue D Wang
- a Department of Bacteriology , University of Wisconsin - Madison , Madison , WI , USA
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120
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Lee KH, Hamashima K, Kimoto M, Hirao I. Genetic alphabet expansion biotechnology by creating unnatural base pairs. Curr Opin Biotechnol 2017; 51:8-15. [PMID: 29049900 DOI: 10.1016/j.copbio.2017.09.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 09/19/2017] [Indexed: 12/17/2022]
Abstract
Recent studies have made it possible to expand the genetic alphabet of DNA, which is originally composed of the four-letter alphabet with A-T and G-C pairs, by introducing an unnatural base pair (UBP). Several types of UBPs function as a third base pair in replication, transcription, and/or translation. Through the UBP formation, new components with different physicochemical properties from those of the natural ones can be introduced into nucleic acids and proteins site-specifically, providing their increased functionalities. Here, we describe the genetic alphabet expansion technology by focusing on three types of UBPs, which were recently applied to the creations of DNA aptamers that bind to proteins and cells and semi-synthetic organisms containing DNAs with a six-letter alphabet.
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Affiliation(s)
- Kyung Hyun Lee
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, #09-01, Singapore 138669, Singapore
| | - Kiyofumi Hamashima
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, #09-01, Singapore 138669, Singapore
| | - Michiko Kimoto
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, #09-01, Singapore 138669, Singapore
| | - Ichiro Hirao
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, #09-01, Singapore 138669, Singapore.
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121
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Yesudhas D, Anwar MA, Panneerselvam S, Kim HK, Choi S. Evaluation of Sox2 binding affinities for distinct DNA patterns using steered molecular dynamics simulation. FEBS Open Bio 2017; 7:1750-1767. [PMID: 29123983 PMCID: PMC5666385 DOI: 10.1002/2211-5463.12316] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 08/14/2017] [Accepted: 09/05/2017] [Indexed: 11/29/2022] Open
Abstract
Transcription factors (TFs) are gene expression regulators that bind to DNA in a sequence‐specific manner and determine the functional characteristics of the gene. It is worthwhile to study the unique characteristics of such specific TF‐binding pattern in DNA. Sox2 recognizes a 6‐ to 7‐base pair consensus DNA sequence; the central four bases of the binding site are highly conserved, whereas the two to three flanking bases are variable. Here, we attempted to analyze the binding affinity and specificity of the Sox2 protein for distinct DNA sequence patterns via steered molecular dynamics, in which a pulling force is employed to dissociate Sox2 from Sox2–DNA during simulation to study the behavior of a complex under nonequilibrium conditions. The simulation results revealed that the first two stacking bases of the binding pattern have an exclusive impact on the binding affinity, with the corresponding mutant complexes showing greater binding and longer dissociation time than the experimental complexes do. In contrast, mutation of the conserved bases tends to reduce the affinity, and mutation of the complete conserved region disrupts the binding. It might pave the way to identify the most likely binding pattern recognized by Sox2 based on the affinity of each configuration. The α2‐helix of Sox2 was found to be the key player in the Sox2–DNA association. The characterization of Sox2's binding patterns for the target genes in the genome helps in understanding of its regulatory functions.
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Affiliation(s)
- Dhanusha Yesudhas
- Department of Molecular Science and Technology Ajou University Suwon Korea
| | | | | | - Han-Kyul Kim
- Department of Molecular Science and Technology Ajou University Suwon Korea
| | - Sangdun Choi
- Department of Molecular Science and Technology Ajou University Suwon Korea
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122
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Xiao Y, Liu Q, Tang X, Yang Z, Wu L, He Y. Mirror-Image Thymidine Discriminates against Incorporation of Deoxyribonucleotide Triphosphate into DNA and Repairs Itself by DNA Polymerases. Bioconjug Chem 2017; 28:2125-2134. [PMID: 28686433 DOI: 10.1021/acs.bioconjchem.7b00301] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
DNA polymerases are known to recognize preferably d-nucleotides over l-nucleotides during DNA synthesis. Here, we report that several general DNA polymerases catalyze polymerization reactions of nucleotides directed by the DNA template containing an l-thymidine (l-T). The results display that the 5'-3' primer extension of natural nucleotides get to the end at chiral modification site with Taq and Phanta Max DNA polymerases, but the primer extension proceeds to the end of the template catalyzed by Deep Vent (exo-), Vent (exo-), and Therminator DNA polymerases. Furthermore, templating l-nucleoside displays a lag in the deoxyribonucleotide triphosphate (dNTP) incorporation rates relative to natural template by kinetics analysis, and polymerase chain reactions were inhibited with the DNA template containing two or three consecutive l-Ts. Most interestingly, no single base mutation or mismatch mixture corresponding to the location of l-T in the template was found, which is physiologically significant because they provide a theoretical basis on the involvement of DNA polymerase in the effective repair of l-T that may lead to cytotoxicity.
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Affiliation(s)
- Yating Xiao
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences , Beijing 100049, China
| | - Qingju Liu
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences , Beijing 100049, China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, China
| | - Zhenjun Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, China
| | - Li Wu
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences , Beijing 100049, China.,State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, China
| | - Yujian He
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences , Beijing 100049, China.,State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, China
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123
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Hagedorn PH, Hansen BR, Koch T, Lindow M. Managing the sequence-specificity of antisense oligonucleotides in drug discovery. Nucleic Acids Res 2017; 45:2262-2282. [PMID: 28426096 PMCID: PMC5389529 DOI: 10.1093/nar/gkx056] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 01/21/2017] [Indexed: 01/06/2023] Open
Abstract
All drugs perturb the expression of many genes in the cells that are exposed to them. These gene expression changes can be divided into effects resulting from engaging the intended target and effects resulting from engaging unintended targets. For antisense oligonucleotides, developments in bioinformatics algorithms, and the quality of sequence databases, allow oligonucleotide sequences to be analyzed computationally, in terms of the predictability of their interactions with intended and unintended RNA targets. Applying these tools enables selection of sequence-specific oligonucleotides where no- or only few unintended RNA targets are expected. To evaluate oligonucleotide sequence-specificity experimentally, we recommend a transcriptomics protocol where two or more oligonucleotides targeting the same RNA molecule, but with entirely different sequences, are evaluated together. This helps to clarify which changes in cellular RNA levels result from downstream processes of engaging the intended target, and which are likely to be related to engaging unintended targets. As required for all classes of drugs, the toxic potential of oligonucleotides must be evaluated in cell- and animal models before clinical testing. Since potential adverse effects related to unintended targeting are sequence-dependent and therefore species-specific, in vitro toxicology assays in human cells are especially relevant in oligonucleotide drug discovery.
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Affiliation(s)
- Peter H Hagedorn
- Roche Pharmaceutical Discovery and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen, Hørsholm 2970, Denmark.,Center for Computational and Applied Transcriptomics, Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark
| | - Bo R Hansen
- Roche Pharmaceutical Discovery and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen, Hørsholm 2970, Denmark
| | - Troels Koch
- Roche Pharmaceutical Discovery and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen, Hørsholm 2970, Denmark
| | - Morten Lindow
- Roche Pharmaceutical Discovery and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen, Hørsholm 2970, Denmark.,Center for Computational and Applied Transcriptomics, Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark.,The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark
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124
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Mao J, DeSantis C, Bong D. Small Molecule Recognition Triggers Secondary and Tertiary Interactions in DNA Folding and Hammerhead Ribozyme Catalysis. J Am Chem Soc 2017; 139:9815-9818. [PMID: 28691825 DOI: 10.1021/jacs.7b05448] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We have identified tris(2-aminoethyl)amine (tren)-derived scaffolds with two (t2M) or four (t4M) melamine rings that can target oligo T/U domains in DNA/RNA. Unstructured T-rich DNAs cooperatively fold with the tren derivatives to form hairpin-like structures. Both t2M and t4M act as functional switches in a family of hammerhead ribozymes deactivated by stem or loop replacement with a U-rich sequence. Catalysis of bond scission in these hammerhead ribozymes could be restored by putative t2M/t4M refolding of stem secondary structure or tertiary bridging interactions between loop and stem. The simplicity of the t2M/t4M binding site enables programming of allostery in RNAs, recoding oligo-U domains as potential sites for secondary structure or tertiary contact. In combination with a facile and general method for installation of the t2M motif on primary amines, the method described herein streamlines design of synthetic allosteric riboswitches and small molecule-nucleic acid complexes.
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Affiliation(s)
- Jie Mao
- Department of Chemistry and Biochemistry, The Ohio State University , 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Chris DeSantis
- Department of Chemistry and Biochemistry, The Ohio State University , 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Dennis Bong
- Department of Chemistry and Biochemistry, The Ohio State University , 100 West 18th Avenue, Columbus, Ohio 43210, United States
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125
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A Comparative Analysis of Translesion DNA Synthesis Catalyzed by a High-Fidelity DNA Polymerase. J Mol Biol 2017; 429:2308-2323. [PMID: 28601494 DOI: 10.1016/j.jmb.2017.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 06/01/2017] [Accepted: 06/01/2017] [Indexed: 11/20/2022]
Abstract
Translesion DNA synthesis (TLS) is the ability of DNA polymerases to incorporate nucleotides opposite and beyond damaged DNA. TLS activity is an important risk factor for the initiation and progression of genetic diseases such as cancer. In this study, we evaluate the ability of a high-fidelity DNA polymerase to perform TLS with 8-oxo-guanine (8-oxo-G), a highly pro-mutagenic DNA lesion formed by reactive oxygen species. Results of kinetic studies monitoring the incorporation of modified nucleotide analogs demonstrate that the binding affinity of the incoming dNTP is controlled by the overall hydrophobicity of the nucleobase. However, the rate constant for the polymerization step is regulated by hydrogen-bonding interactions made between the incoming nucleotide with 8-oxo-G. Results generated here for replicating the miscoding 8-oxo-G are compared to those published for the replication of the non-instructional abasic site. During the replication of both lesions, binding of the nucleotide substrate is controlled by energetics associated with nucleobase desolvation, whereas the rate constant for the polymerization step is influenced by the physical nature of the DNA lesion, that is, miscoding versus non-instructional. Collectively, these studies highlight the importance of nucleobase desolvation as a key physical feature that enhances the misreplication of structurally diverse DNA lesions.
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126
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Vyas R, Reed AJ, Raper AT, Zahurancik WJ, Wallenmeyer PC, Suo Z. Structural basis for the D-stereoselectivity of human DNA polymerase β. Nucleic Acids Res 2017; 45:6228-6237. [PMID: 28402499 PMCID: PMC5449621 DOI: 10.1093/nar/gkx252] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 03/24/2017] [Accepted: 04/03/2017] [Indexed: 12/20/2022] Open
Abstract
Nucleoside reverse transcriptase inhibitors (NRTIs) with L-stereochemistry have long been an effective treatment for viral infections because of the strong D-stereoselectivity exhibited by human DNA polymerases relative to viral reverse transcriptases. The D-stereoselectivity of DNA polymerases has only recently been explored structurally and all three DNA polymerases studied to date have demonstrated unique stereochemical selection mechanisms. Here, we have solved structures of human DNA polymerase β (hPolβ), in complex with single-nucleotide gapped DNA and L-nucleotides and performed pre-steady-state kinetic analysis to determine the D-stereoselectivity mechanism of hPolβ. Beyond a similar 180° rotation of the L-nucleotide ribose ring seen in other studies, the pre-catalytic ternary crystal structures of hPolβ, DNA and L-dCTP or the triphosphate forms of antiviral drugs lamivudine ((-)3TC-TP) and emtricitabine ((-)FTC-TP) provide little structural evidence to suggest that hPolβ follows the previously characterized mechanisms of D-stereoselectivity. Instead, hPolβ discriminates against L-stereochemistry through accumulation of several active site rearrangements that lead to a decreased nucleotide binding affinity and incorporation rate. The two NRTIs escape some of the active site selection through the base and sugar modifications but are selected against through the inability of hPolβ to complete thumb domain closure.
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Affiliation(s)
- Rajan Vyas
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Andrew J. Reed
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Austin T. Raper
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Walter J. Zahurancik
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Petra C. Wallenmeyer
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Zucai Suo
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
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127
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Kashida H, Asanuma H. Development of Pseudo Base-Pairs on d-Threoninol which Exhibit Various Functions. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2017. [DOI: 10.1246/bcsj.20160371] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Hiromu Kashida
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012
| | - Hiroyuki Asanuma
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603
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128
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Mondal SI, Sen S, Hazra A, Patwari GN. π-Stacked Dimers of Fluorophenylacetylenes: Role of Dipole Moment. J Phys Chem A 2017; 121:3383-3391. [DOI: 10.1021/acs.jpca.7b00209] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sohidul Islam Mondal
- Department
of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India
| | - Saumik Sen
- Department
of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India
| | - Anirban Hazra
- Department
of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, India
| | - G. Naresh Patwari
- Department
of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India
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129
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Bag SS, Das SK. Design, Synthesis and Photophysical Property of a Doubly Widened Fused-Triazolyl-Phenanthrene Unnatural Nucleoside. ChemistrySelect 2017. [DOI: 10.1002/slct.201700392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Subhendu Sekhar Bag
- Bioorganic Chemistry Laboratory; Department of Chemistry; Indian Institute of Technology Guwahati, North Guwhati-; 781039 Assam India
| | - Suman Kalyan Das
- Bioorganic Chemistry Laboratory; Department of Chemistry; Indian Institute of Technology Guwahati, North Guwhati-; 781039 Assam India
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130
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Kilchherr F, Wachauf C, Pelz B, Rief M, Zacharias M, Dietz H. Single-molecule dissection of stacking forces in DNA. Science 2017; 353:353/6304/aaf5508. [PMID: 27609897 DOI: 10.1126/science.aaf5508] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 07/01/2016] [Indexed: 01/01/2023]
Abstract
We directly measured at the single-molecule level the forces and lifetimes of DNA base-pair stacking interactions for all stack sequence combinations. Our experimental approach combined dual-beam optical tweezers with DNA origami components to allow positioning of blunt-end DNA helices so that the weak stacking force could be isolated. Base-pair stack arrays that lacked a covalent backbone connection spontaneously dissociated at average rates ranging from 0.02 to 500 per second, depending on the sequence combination and stack array size. Forces in the range from 2 to 8 piconewtons that act along the helical direction only mildly accelerated the stochastic unstacking process. The free-energy increments per stack that we estimate from the measured forward and backward kinetic rates ranged from -0.8 to -3.4 kilocalories per mole, depending on the sequence combination. Our data contributes to understanding the mechanics of DNA processing in biology, and it is helpful for designing the kinetics of DNA-based nanoscale devices according to user specifications.
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Affiliation(s)
- Fabian Kilchherr
- Labor für Biomolekulare Nanotechnologie, Physik Department and Walter Schottky Institute, Technische Universität München, Am Coulombwall 4a, Garching near Munich, Germany
| | - Christian Wachauf
- Labor für Biomolekulare Nanotechnologie, Physik Department and Walter Schottky Institute, Technische Universität München, Am Coulombwall 4a, Garching near Munich, Germany
| | - Benjamin Pelz
- Lehrstuhl für Molekulare Biophysik, Physik Department, Technische Universität München, James-Franck-Strasse 1, Garching near Munich, Germany
| | - Matthias Rief
- Lehrstuhl für Molekulare Biophysik, Physik Department, Technische Universität München, James-Franck-Strasse 1, Garching near Munich, Germany. Munich Center for Integrated Protein Science, 81377 Munich, Germany
| | - Martin Zacharias
- Lehrstuhl für Theoretische Biophysik, Physik Department, Technische Universität München, James-Franck-Strasse 1, Garching near Munich, Germany. Munich Center for Integrated Protein Science, 81377 Munich, Germany
| | - Hendrik Dietz
- Labor für Biomolekulare Nanotechnologie, Physik Department and Walter Schottky Institute, Technische Universität München, Am Coulombwall 4a, Garching near Munich, Germany. Munich Center for Integrated Protein Science, 81377 Munich, Germany. Institute for Advanced Study, TUM, Germany.
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131
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Olson X, Kotani S, Padilla JE, Hallstrom N, Goltry S, Lee J, Yurke B, Hughes WL, Graugnard E. Availability: A Metric for Nucleic Acid Strand Displacement Systems. ACS Synth Biol 2017; 6:84-93. [PMID: 26875531 PMCID: PMC5259754 DOI: 10.1021/acssynbio.5b00231] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Indexed: 12/20/2022]
Abstract
DNA strand displacement systems have transformative potential in synthetic biology. While powerful examples have been reported in DNA nanotechnology, such systems are plagued by leakage, which limits network stability, sensitivity, and scalability. An approach to mitigate leakage in DNA nanotechnology, which is applicable to synthetic biology, is to introduce mismatches to complementary fuel sequences at key locations. However, this method overlooks nuances in the secondary structure of the fuel and substrate that impact the leakage reaction kinetics in strand displacement systems. In an effort to quantify the impact of secondary structure on leakage, we introduce the concepts of availability and mutual availability and demonstrate their utility for network analysis. Our approach exposes vulnerable locations on the substrate and quantifies the secondary structure of fuel strands. Using these concepts, a 4-fold reduction in leakage has been achieved. The result is a rational design process that efficiently suppresses leakage and provides new insight into dynamic nucleic acid networks.
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Affiliation(s)
- Xiaoping Olson
- Micron
School of Materials Science & Engineering, Department of Chemistry & Biochemistry, and Department of Electrical
& Computer Engineering, Boise State
University, 1910 University
Drive, Boise, Idaho 83725, United States
| | - Shohei Kotani
- Micron
School of Materials Science & Engineering, Department of Chemistry & Biochemistry, and Department of Electrical
& Computer Engineering, Boise State
University, 1910 University
Drive, Boise, Idaho 83725, United States
| | - Jennifer E. Padilla
- Micron
School of Materials Science & Engineering, Department of Chemistry & Biochemistry, and Department of Electrical
& Computer Engineering, Boise State
University, 1910 University
Drive, Boise, Idaho 83725, United States
| | - Natalya Hallstrom
- Micron
School of Materials Science & Engineering, Department of Chemistry & Biochemistry, and Department of Electrical
& Computer Engineering, Boise State
University, 1910 University
Drive, Boise, Idaho 83725, United States
| | - Sara Goltry
- Micron
School of Materials Science & Engineering, Department of Chemistry & Biochemistry, and Department of Electrical
& Computer Engineering, Boise State
University, 1910 University
Drive, Boise, Idaho 83725, United States
| | - Jeunghoon Lee
- Micron
School of Materials Science & Engineering, Department of Chemistry & Biochemistry, and Department of Electrical
& Computer Engineering, Boise State
University, 1910 University
Drive, Boise, Idaho 83725, United States
| | - Bernard Yurke
- Micron
School of Materials Science & Engineering, Department of Chemistry & Biochemistry, and Department of Electrical
& Computer Engineering, Boise State
University, 1910 University
Drive, Boise, Idaho 83725, United States
| | - William L. Hughes
- Micron
School of Materials Science & Engineering, Department of Chemistry & Biochemistry, and Department of Electrical
& Computer Engineering, Boise State
University, 1910 University
Drive, Boise, Idaho 83725, United States
| | - Elton Graugnard
- Micron
School of Materials Science & Engineering, Department of Chemistry & Biochemistry, and Department of Electrical
& Computer Engineering, Boise State
University, 1910 University
Drive, Boise, Idaho 83725, United States
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132
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Mphahlele MJ, Maluleka MM, Rhyman L, Ramasami P, Mampa RM. Spectroscopic, DFT, and XRD Studies of Hydrogen Bonds in N-Unsubstituted 2-Aminobenzamides. Molecules 2017; 22:E83. [PMID: 28054998 PMCID: PMC6155760 DOI: 10.3390/molecules22010083] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 12/24/2016] [Accepted: 12/27/2016] [Indexed: 01/31/2023] Open
Abstract
The structures of the mono- and the dihalogenated N-unsubstituted 2-aminobenzamides were characterized by means of the spectroscopic (¹H-NMR, UV-Vis, FT-IR, and FT-Raman) and X-ray crystallographic techniques complemented with a density functional theory (DFT) method. The hindered rotation of the C(O)-NH₂ single bond resulted in non-equivalence of the amide protons and therefore two distinct resonances of different chemical shift values in the ¹H-NMR spectra of these compounds were observed. 2-Amino-5-bromobenzamide (ABB) as a model confirmed the presence of strong intramolecular hydrogen bonds between oxygen and the amine hydrogen. However, intramolecular hydrogen bonding between the carbonyl oxygen and the amine protons was not observed in the solution phase due to a rapid exchange of these two protons with the solvent and fast rotation of the Ar-NH₂ single bond. XRD also revealed the ability of the amide unit of these compounds to function as a hydrogen bond donor and acceptor simultaneously to form strong intermolecular hydrogen bonding between oxygen of one molecule and the NH moiety of the amine or amide group of the other molecule and between the amine nitrogen and the amide hydrogen of different molecules. DFT calculations using the B3LYP/6-311++G(d,p) basis set revealed that the conformer (A) with oxygen and 2-amine on the same side predominates possibly due to the formation of a six-membered intramolecular ring, which is assisted by hydrogen bonding as observed in the single crystal XRD structure.
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Affiliation(s)
- Malose Jack Mphahlele
- Department of Chemistry, College of Science, Engineering and Technology, University of South Africa, Private Bag X06, Florida 1710, South Africa.
| | - Marole Maria Maluleka
- Department of Chemistry, College of Science, Engineering and Technology, University of South Africa, Private Bag X06, Florida 1710, South Africa.
| | - Lydia Rhyman
- Computational Chemistry Group, Department of Chemistry, Faculty of Science, University of Mauritius, Reduit 80837, Mauritius.
| | - Ponnadurai Ramasami
- Department of Chemistry, College of Science, Engineering and Technology, University of South Africa, Private Bag X06, Florida 1710, South Africa.
| | - Richard Mokome Mampa
- Department of Chemistry, University of Limpopo, Private Bag X1106, Sovenga 0727, South Africa.
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133
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KASHIDA H, ASANUMA H. Development of Pseudo Base Pairs Which Show High DNA Duplex Stabilities and Orthogonality. KOBUNSHI RONBUNSHU 2017. [DOI: 10.1295/koron.2017-0009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Hiromu KASHIDA
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University
- PRESTO, Japan Science and Technology Agency
| | - Hiroyuki ASANUMA
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University
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134
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Hwang JW, Li P, Shimizu KD. Synergy between experimental and computational studies of aromatic stacking interactions. Org Biomol Chem 2016; 15:1554-1564. [PMID: 27878156 DOI: 10.1039/c6ob01985d] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aromatic stacking interactions are one of the most common types of non-covalent interactions. However, their fundamental origins and the ability to accurately predict their stability trends are still an active area of research. The study of aromatic stacking interactions has been particularly challenging. The interaction involves a delicate balance of multiple forces, and the aromatic surfaces can readily adopt different interaction geometries. Thus, the collaborative efforts of theoretical and experimental researchers have been essential to understand and build more accurate predictive models of aromatic stacking interactions.
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Affiliation(s)
- Jung Wun Hwang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA.
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135
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Wagner A, Ortman S, Maxfield R. From the primordial soup to self-driving cars: standards and their role in natural and technological innovation. J R Soc Interface 2016; 13:20151086. [PMID: 26864893 DOI: 10.1098/rsif.2015.1086] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Standards are specifications to which the elements of a technology must conform. Here, we apply this notion to the biochemical 'technologies' of nature, where objects like DNA and proteins, as well as processes like the regulation of gene activity are highly standardized. We introduce the concept of standards with multiple examples, ranging from the ancient genetic material RNA, to Palaeolithic stone axes, and digital electronics, and we discuss common ways in which standards emerge in nature and technology. We then focus on the question of how standards can facilitate technological and biological innovation. Innovation-enhancing standards include those of proteins and digital electronics. They share common features, such as that few standardized building blocks can be combined through standard interfaces to create myriad useful objects or processes. We argue that such features will also characterize the most innovation-enhancing standards of future technologies.
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Affiliation(s)
- Andreas Wagner
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland Swiss Institute of Bioinformatics, Lausanne, Switzerland Santa Fe Institute, Santa Fe, NM, USA
| | - Scott Ortman
- Santa Fe Institute, Santa Fe, NM, USA Department of Anthropology, University of Colorado Boulder, Boulder, CO, USA
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136
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Partlow BP, Bagheri M, Harden JL, Kaplan DL. Tyrosine Templating in the Self-Assembly and Crystallization of Silk Fibroin. Biomacromolecules 2016; 17:3570-3579. [DOI: 10.1021/acs.biomac.6b01086] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Benjamin P. Partlow
- Department
of Biomedical Engineering, Tufts University, 4 Colby Street Medford, Massachusetts 02155, United States
| | - Mehran Bagheri
- Department
of Physics, University of Ottawa, 338L MacDonald Hall, 150 Louis Pasteur Ottawa, Ontario K1N 6N5, Canada
| | - James L. Harden
- Department
of Physics, University of Ottawa, 338L MacDonald Hall, 150 Louis Pasteur Ottawa, Ontario K1N 6N5, Canada
| | - David L. Kaplan
- Department
of Biomedical Engineering, Tufts University, 4 Colby Street Medford, Massachusetts 02155, United States
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137
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Fong CW. Platinum based radiochemotherapies: Free radical mechanisms and radiotherapy sensitizers. Free Radic Biol Med 2016; 99:99-109. [PMID: 27417937 DOI: 10.1016/j.freeradbiomed.2016.07.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 06/18/2016] [Accepted: 07/08/2016] [Indexed: 12/22/2022]
Abstract
The radiosensitizing ability of Pt drugs can in the first instance be predicted based on the ease that they undergo activation by electron attachment accompanied by structural modification prior to forming Pt-DNA adducts. Unlike cisplatin, carboplatin and nedaplatin, oxaliplatin does not undergo a facile dissociative electron transfer reaction when an electron is attached. However, oxaliplatin undergoes a facile nucleophilic assisted proton coupled electron transfer (NAPCET), which may be key element of the success of FOLFOX radiochemotherapy against certain cancers. Under acidic conditions, oxaliplatin is a superior radiosensitizer to cisplatin or carboplatin, in the presence of nucleophiles such as water, chloride ions or thiols. Oxaliplatin may also be activated as a platinating agent and radiosensitizer by a minor hydrogen radical free radical mechanism as well as the more dominant NAPCET mechanism. The radiosensitizing synergism that is shown when oxaliplatin is combined with 5-fluorouracil can be due to the formation of a π complex between the two drugs, which is more potent under acidic conditions. These factors have a bearing on Pt based chemotherapy clinical regimes as well as clinical radiochemotherapy regimes, and could be a basis for optimizing how such drug schedules are administered.
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138
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El-Mellouhi F, Marzouk A, Bentria ET, Rashkeev SN, Kais S, Alharbi FH. Hydrogen Bonding and Stability of Hybrid Organic-Inorganic Perovskites. CHEMSUSCHEM 2016; 9:2648-2655. [PMID: 27604510 DOI: 10.1002/cssc.201600864] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Indexed: 05/13/2023]
Abstract
In the past few years, the efficiency of solar cells based on hybrid organic-inorganic perovskites has exceeded the level needed for commercialization. However, existing perovskites solar cells (PSCs) suffer from several intrinsic instabilities, which prevent them from reaching industrial maturity, and stabilizing PSCs has become a critically important problem. Here we propose to stabilize PSCs chemically by strengthening the interactions between the organic cation and inorganic anion of the perovskite framework. In particular, we show that replacing the methylammonium cation with alternative protonated cations allows an increase in the stability of the perovskite by forming strong hydrogen bonds with the halide anions. This interaction also provides opportunities for tuning the electronic states near the bandgap. These mechanisms should have a universal character in different hybrid organic-inorganic framework materials that are widely used.
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Affiliation(s)
- Fedwa El-Mellouhi
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, P.O. Box 5825, Doha, Qatar.
| | - Asma Marzouk
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, P.O. Box 5825, Doha, Qatar
| | - El Tayeb Bentria
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, P.O. Box 5825, Doha, Qatar
| | - Sergey N Rashkeev
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, P.O. Box 5825, Doha, Qatar.
| | - Sabre Kais
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, P.O. Box 5825, Doha, Qatar
- College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
- Department of Chemistry, Physics, and Birck Nanotechnology Center, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Fahhad H Alharbi
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, P.O. Box 5825, Doha, Qatar
- College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
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139
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Pairas GN, Tsoungas PG. H-Bond: Τhe Chemistry-Biology H-Bridge. ChemistrySelect 2016; 1:4520-4532. [PMID: 32328512 PMCID: PMC7169486 DOI: 10.1002/slct.201600770] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 07/29/2016] [Indexed: 12/19/2022]
Abstract
H-bonding, as a non covalent stabilizing interaction of diverse nature, has a central role in the structure, function and dynamics of chemical and biological processes, pivotal to molecular recognition and eventually to drug design. Types of conventional and non conventional (H-H, dihydrogen, H- π, CH- π, anti- , proton coordination and H-S) H-bonding interactions are discussed as well as features emerging from their interplay, such as cooperativity (σ- and π-) effects and allostery. Its utility in many applications is described. Catalysis, proton and electron transfer processes in various materials or supramolecular architectures of preorganized hosts for guest binding, are front-line technology. The H-bond-related concept of proton transfer (PT) addresses energy issues or deciphering the mechanism of many natural and synthetic processes. PT is also of paramount importance in the functions of cells and is assisted by large complex proteins embedded in membranes. Both intermolecular and intramolecular PT in H-bonded systems has received attention, theoretically and experimentally, using prototype molecules. It is found in rearrangement reactions, protein functions, and enzyme reactions or across proton channels and pumps. Investigations on the competition between intra- and intermolecular H bonding are discussed. Of particular interest is the H-bond furcation, a common phenomenon in protein-ligand binding. Multiple H-bonding (H-bond furcation) is observed in supramolecular structures.
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Affiliation(s)
- George N. Pairas
- Department of PharmacyLaboratory of Medicinal ChemistryUniversity of PatrasGR-265 04PatrasGreece
| | - Petros G. Tsoungas
- Laboratory of BiochemistryHellenic Pasteur Institute127 Vas. Sofias Ave.GR-115 21AthensGreece
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140
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Singh VK, Krishnamachari A. Context based computational analysis and characterization of ARS consensus sequences (ACS) of Saccharomyces cerevisiae genome. GENOMICS DATA 2016; 9:130-6. [PMID: 27508123 PMCID: PMC4971157 DOI: 10.1016/j.gdata.2016.07.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 06/27/2016] [Accepted: 07/06/2016] [Indexed: 01/08/2023]
Abstract
Genome-wide experimental studies in Saccharomyces cerevisiae reveal that autonomous replicating sequence (ARS) requires an essential consensus sequence (ACS) for replication activity. Computational studies identified thousands of ACS like patterns in the genome. However, only a few hundreds of these sites act as replicating sites and the rest are considered as dormant or evolving sites. In a bid to understand the sequence makeup of replication sites, a content and context-based analysis was performed on a set of replicating ACS sequences that binds to origin-recognition complex (ORC) denoted as ORC-ACS and non-replicating ACS sequences (nrACS), that are not bound by ORC. In this study, DNA properties such as base composition, correlation, sequence dependent thermodynamic and DNA structural profiles, and their positions have been considered for characterizing ORC-ACS and nrACS. Analysis reveals that ORC-ACS depict marked differences in nucleotide composition and context features in its vicinity compared to nrACS. Interestingly, an A-rich motif was also discovered in ORC-ACS sequences within its nucleosome-free region. Profound changes in the conformational features, such as DNA helical twist, inclination angle and stacking energy between ORC-ACS and nrACS were observed. Distribution of ACS motifs in the non-coding segments points to the locations of ORC-ACS which are found far away from the adjacent gene start position compared to nrACS thereby enabling an accessible environment for ORC-proteins. Our attempt is novel in considering the contextual view of ACS and its flanking region along with nucleosome positioning in the S. cerevisiae genome and may be useful for any computational prediction scheme.
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141
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Dou B, Yang J, Shi K, Yuan R, Xiang Y. DNA-mediated strand displacement facilitates sensitive electronic detection of antibodies in human serums. Biosens Bioelectron 2016; 83:156-61. [DOI: 10.1016/j.bios.2016.04.044] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 04/05/2016] [Accepted: 04/15/2016] [Indexed: 01/29/2023]
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142
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Holroyd LF, van Mourik T. Stacking of the mutagenic base analogue 5-bromouracil: energy landscapes of pyrimidine dimers in gas phase and water. Phys Chem Chem Phys 2016; 17:30364-70. [PMID: 26507806 DOI: 10.1039/c5cp04612b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The potential energy surfaces of stacked base pairs consisting of cytosine (C), thymine (T), uracil (U) and the mutagenic thymine analogue 5-bromouracil (BrU) have been searched to obtain all possible minima. Minima and transition states were optimised at the counterpoise-corrected M06-2X/6-31+G(d) level, both in the gas phase and in water, modelled by the polarizable continuum model. The stacked dimers studied are BrU/BrU, C/BrU, C/C, C/T, C/U, T/BrU and T/U. Both face-to-back and face-to-face structures were considered. Free energies were calculated at 298.15 K. Together with U/U, T/T and BrU/U results from previous work, these results complete the family consisting of every stacked dimer combination consisting of C, T, U and BrU. The results were used to assess the hypothesis suggested in the literature that BrU stacks stronger than T, which could stabilise the mispair formed by BrU and guanine. In the gas phase, structures of C/BrU, T/BrU and U/BrU with greater zero-point-corrected binding energies than C/T, T/T and U/T, respectively, were found, with differences in favour of BrU of 3.1 kcal mol(-1), 1.7 kcal mol(-1) and 0.5 kcal mol(-1), respectively. However, the structure of these dimers differed considerably from anything encountered in DNA. When only the dimers with the most "DNA-like" twist (±36°) were considered, C/BrU and T/BrU were still more strongly bound than C/T and T/T, by 0.5 kcal mol(-1) and 1.7 kcal mol(-1), respectively. However, when enthalpic and/or solvent contributions were taken into account, the stacking advantage of BrU was reversed in the gas phase and mostly nullified in water. Enhanced stacking therefore does not seem a plausible mechanism for the considerably greater ability of BrU-G mispairs over T-G mispairs to escape enzymatic repair.
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Affiliation(s)
- Leo F Holroyd
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK.
| | - Tanja van Mourik
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK.
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143
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Pfeifer W, Saccà B. From Nano to Macro through Hierarchical Self-Assembly: The DNA Paradigm. Chembiochem 2016; 17:1063-80. [DOI: 10.1002/cbic.201600034] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Wolfgang Pfeifer
- Centre for Medical Biotechnology (ZMB); University of Duisburg-Essen; Universitätstrasse 2 45117 Essen Germany
| | - Barbara Saccà
- Centre for Medical Biotechnology (ZMB); University of Duisburg-Essen; Universitätstrasse 2 45117 Essen Germany
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144
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Ha SH, Ferrell JE. Thresholds and ultrasensitivity from negative cooperativity. Science 2016; 352:990-3. [PMID: 27174675 DOI: 10.1126/science.aad5937] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 04/07/2016] [Indexed: 11/02/2022]
Abstract
Negative cooperativity is a phenomenon in which the binding of one or more molecules of a ligand to a multimeric receptor makes it more difficult for subsequent ligand molecules to bind. Negative cooperativity can make a multimeric receptor's response more graded than it would otherwise be. However, through theory and experimental results, we show that if the ligand binds the receptor with high affinity and can be appreciably depleted by receptor binding, then negative cooperativity produces a qualitatively different type of response: a highly ultrasensitive response with a pronounced threshold. Because ultrasensitivity and thresholds are important for generating various complex systems-level behaviors, including bistability and oscillations, negative cooperativity may be an important ingredient in many types of biological responses.
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Affiliation(s)
- S H Ha
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305-5174, USA
| | - J E Ferrell
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305-5174, USA. Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA
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145
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Jakhlal J, Coantic-Castex S, Denhez C, Petermann C, Martinez A, Harakat D, Guillaume D, Clivio P. 5'- vs. 3'-end sugar conformational control in shaping up dinucleotides. Chem Commun (Camb) 2016; 51:12381-3. [PMID: 26140549 DOI: 10.1039/c5cc04212g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The 5'-end N-sugar puckering is currently believed to govern the intramolecular dinucleotide stacking. We demonstrate that if this 5'-conformation is indeed important in shaping up dinucleotide structures, the 3'-end sugar conformation can either potentiate or cancel the stacking capacity induced by the 5'-end N-sugar conformation.
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Affiliation(s)
- J Jakhlal
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51 rue Cognacq-Jay, F-51096 Reims Cedex, France.
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146
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Woińska M, Grabowsky S, Dominiak PM, Woźniak K, Jayatilaka D. Hydrogen atoms can be located accurately and precisely by x-ray crystallography. SCIENCE ADVANCES 2016; 2:e1600192. [PMID: 27386545 PMCID: PMC4928899 DOI: 10.1126/sciadv.1600192] [Citation(s) in RCA: 173] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 04/28/2016] [Indexed: 05/14/2023]
Abstract
Precise and accurate structural information on hydrogen atoms is crucial to the study of energies of interactions important for crystal engineering, materials science, medicine, and pharmacy, and to the estimation of physical and chemical properties in solids. However, hydrogen atoms only scatter x-radiation weakly, so x-rays have not been used routinely to locate them accurately. Textbooks and teaching classes still emphasize that hydrogen atoms cannot be located with x-rays close to heavy elements; instead, neutron diffraction is needed. We show that, contrary to widespread expectation, hydrogen atoms can be located very accurately using x-ray diffraction, yielding bond lengths involving hydrogen atoms (A-H) that are in agreement with results from neutron diffraction mostly within a single standard deviation. The precision of the determination is also comparable between x-ray and neutron diffraction results. This has been achieved at resolutions as low as 0.8 Å using Hirshfeld atom refinement (HAR). We have applied HAR to 81 crystal structures of organic molecules and compared the A-H bond lengths with those from neutron measurements for A-H bonds sorted into bonds of the same class. We further show in a selection of inorganic compounds that hydrogen atoms can be located in bridging positions and close to heavy transition metals accurately and precisely. We anticipate that, in the future, conventional x-radiation sources at in-house diffractometers can be used routinely for locating hydrogen atoms in small molecules accurately instead of large-scale facilities such as spallation sources or nuclear reactors.
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Affiliation(s)
- Magdalena Woińska
- Biological and Chemical Research Centre, Chemistry Department, University of Warsaw, Zwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Simon Grabowsky
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2–Biologie/Chemie, Universität Bremen, Leobener Str. NW2, 28359 Bremen, Germany
| | - Paulina M. Dominiak
- Biological and Chemical Research Centre, Chemistry Department, University of Warsaw, Zwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre, Chemistry Department, University of Warsaw, Zwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Dylan Jayatilaka
- School of Chemistry and Biochemistry, University of Western Australia, 35 Stirling Highway, Perth, Western Australia 6009, Australia
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147
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Abstract
Base stacking is a key determinant of nucleic acid structures, but the precise origin of the thermodynamic driving force behind the stacking of nucleobases remains open. The rather mild stacking free energy measured experimentally, roughly a kcal/mol depending on the identity of the bases, is physiologically significant because while base stacking confers stability to the genome in its double helix form, the duplex also has to be unwound in order to be replicated or transcribed. A stacking free energy that is either too high or too low will over- or understabilize the genome, impacting the storage of genetic information and also its retrieval. While the molecular origin of stacking driving force has been attributed to many different sources including dispersion, electrostatics, and solvent hydrogen bonding, here we show via a systematic decomposition of the stacking free energy using large-scale computer simulations that the dominant driving force stabilizing base stacking is nonhydrophobic solvent entropy. Counteracting this is the conformational entropic penalty on the sugar-phosphate backbone against stacking, while solvent hydrogen-bonding, charge-charge interactions, and dispersive forces produce only secondary perturbations. Solvent entropic forces and DNA backbone conformational strains therefore work against each other, leading to a very mild composite stacking free energy in agreement with experiments.
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Affiliation(s)
- Chi H Mak
- Department of Chemistry and Center of Applied Mathematical Sciences, University of Southern California , Los Angeles, California 90089, United States
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148
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Hammud HH, El-Dakdouki MH, Sonji N, Sonji G, Bouhadir KH. Interactions of Some Divalent Metal Ions with Thymine and Uracil Thiosemicarbazide Derivatives. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2016; 35:259-76. [PMID: 27049340 DOI: 10.1080/15257770.2016.1143558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The study of interactions between metal ions and nucleobases, nucleosides, nucleotides, or nucleic acids has become an active research area in chemical, biological, and therapeutic fields. In this respect, the coordination behavior of nucleobase derivatives to transition metals was studied in order to get a better understanding about DNA-metal interactions in in vitro and in vivo systems. Two nucleobase derivatives, 3-benzoyl-1-[3-(thymine-1-yl)propamido]thiourea and 3-benzoyl-1-[3-(uracil-1-yl)propamido]thiourea, were synthesized and their dissociation constants were determined at different temperatures and 0.3 ionic strength. Potentiometric studies were carried out on the interaction of the derivatives towards some divalent metals in 50% v/v ethanol-water containing 0.3 mol.dm(-3) KCl, at five different temperatures. The formation constants of the metal complexes for both ligands follow the order: Cu(2+) > Ni(2+) > Co(2+) > Zn(2+) > Pb(2+) > Cd(2+) > Mn(2+). The thermodynamic parameters were estimated; the complexation process has been found to be spontaneous, exothermic, and entropically favorable.
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Affiliation(s)
- Hassan H Hammud
- a Department of Chemistry, Faculty of Science , King Faisal University , Al-Ahsa , Saudi Arabia
| | - Mohammad H El-Dakdouki
- b Department of Chemistry, Faculty of Science , Beirut Arab University , Debbieh , Lebanon
| | - Nada Sonji
- b Department of Chemistry, Faculty of Science , Beirut Arab University , Debbieh , Lebanon
| | - Ghassan Sonji
- b Department of Chemistry, Faculty of Science , Beirut Arab University , Debbieh , Lebanon
| | - Kamal H Bouhadir
- c Department of Chemistry, Faculty of Arts and Sciences , American University of Beirut , Beirut , Lebanon
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149
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Zhang Z, Liu J. Molecularly Imprinted Polymers with DNA Aptamer Fragments as Macromonomers. ACS APPLIED MATERIALS & INTERFACES 2016; 8:6371-6378. [PMID: 26910515 DOI: 10.1021/acsami.6b00461] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Molecularly imprinted polymers (MIPs) are produced in the presence of a template molecule. After removing the template, the cavity can selectively rebind the template. MIPs are attractive functional materials with a low cost and high stability, but traditional MIPs often suffer from low binding affinity. This study employs DNA aptamer fragments as macromonomers to improve MIPs. The DNA aptamer for adenosine was first split into two halves, fluorescently labeled, and copolymerized into MIPs. With a fluorescence quenching assay, the importance of imprinting was confirmed. Further studies were carried out using isothermal titration calorimetry (ITC). Compared to the mixture of the free aptamer fragments, their MIPs doubled the binding affinity. Each free aptamer fragment alone cannot bind adenosine, whereas MIPs containing each fragment are effective binders. We further shortened one of the aptamer fragments, and the DNA length was pushed to as short as six nucleotides, yielding MIPs with a dissociation constant of 27 μM adenosine. This study provides a new method for preparing functional MIP materials by combining high-affinity biopolymer fragments with low-cost synthetic monomers, allowing higher binding affinity and providing a method for signaling binding based on DNA chemistry.
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Affiliation(s)
- Zijie Zhang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
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Petković M, Ristić M, Etinski M. Stability and Anharmonic N–H Stretching Frequencies of 1-Methylthymine Dimers: Hydrogen Bonding versus π-Stacking. J Phys Chem A 2016; 120:1536-44. [DOI: 10.1021/acs.jpca.5b09946] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Milena Petković
- Faculty of Physical Chemistry, University of Belgrade Studentski trg 12-16, 11 158 Belgrade, Serbia
| | - Miroslav Ristić
- Faculty of Physical Chemistry, University of Belgrade Studentski trg 12-16, 11 158 Belgrade, Serbia
| | - Mihajlo Etinski
- Faculty of Physical Chemistry, University of Belgrade Studentski trg 12-16, 11 158 Belgrade, Serbia
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