1
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Mandal S, Ganesh KN, Maiti PK. Dynamics of terminal fraying-peeling and hydrogen bonds dictates the sequential vs. cooperative melting pathways of nanoscale DNA and PNA triplexes. NANOSCALE 2024; 16:13029-13040. [PMID: 38904319 DOI: 10.1039/d4nr01104j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Peptide nucleic acids (PNAs) are charge-neutral synthetic DNA/RNA analogues. In many aspects of biology and biotechnology, the details of DNA and PNA melting reaction coordinates are crucial, and their associative/dissociative details remain inadequately understood. In the current study, we have attempted to gain insights into comparative melting pathways and binding affinity of iso-sequences of an 18-mer PNA-DNA-PNA triplex and the analogous DNA-DNA-DNA triplex, and DNA-DNA and PNA-DNA duplexes. It is intriguing that while the DNA-DNA-DNA triplex melts in two sequential steps, the PNA-DNA-PNA triplex melts in a single step and the mechanistic aspects for this difference are still not clear. We report an all-atom molecular dynamics simulation of both complexes in the temperature range of 300 to 500 K with 20 K intervals. Based on the trajectory analysis, we provide evidence that the association and dissociation are dictated by the differences in fraying-peeling effects from either terminus to the center in a zipper pattern among the PNA-DNA-PNA triplex and DNA-DNA-DNA triplexes. These are shown to be governed by the different characteristics of H-bonding, RMSD, and Free Energy Landscape (FEL) as analyzed by PCA, leading to the DNA-DNA-DNA triplex exhibiting sequential melting, while the PNA-DNA-PNA triplex shows cooperative melting of the whole fragment in a single-step. The PNA-DNA-PNA triplex base pairs are thermodynamically more stable than the DNA-DNA-DNA triplex, with the binding affinity of PNA-TFO to the PNA : DNA duplex being higher than that of DNA-TFO to the DNA : DNA duplex. The investigation of the association/dissociation of PNA-TFO to the PNA-DNA duplex has relevance and importance in the emerging effective applications of oligonucleotide therapy.
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Affiliation(s)
- Sandip Mandal
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
| | - Krishna N Ganesh
- Jawaharlal Nehru Center for Advanced Scientific Research (JNCASR), Jakkur, Bengaluru 560064, India.
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
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2
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Peng HC, Mohan S, Huq MT, Bull JA, Michaud T, Piercy TC, Hilber S, Wettasinghe AP, Slinker JD, Kreutz C, Stelling AL. Isotope-Edited Variable Temperature Infrared Spectroscopy for Measuring Transition Temperatures of Single A-T Watson-Crick Base Pairs in DNA Duplexes. Anal Chem 2024; 96:8868-8874. [PMID: 38775341 DOI: 10.1021/acs.analchem.4c00056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
Experimental methods to determine transition temperatures for individual base pair melting events in DNA duplexes are lacking despite intense interest in these thermodynamic parameters. Here, we determine the dimensions of the thymine (T) C2═O stretching vibration when it is within the DNA duplex via isotopic substitutions at other atomic positions in the structure. First, we determined that this stretching state was localized enough to specific atoms in the molecule to make submolecular scale measurements of local structure and stability in high molecular weight complexes. Next, we develop a new isotope-edited variable temperature infrared method to measure melting transitions at various locations in a DNA structure. As an initial test of this "sub-molecular scale thermometer", we applied our T13C2 difference infrared signal to measure location-dependent melting temperatures (TmL) in a DNA duplex via variable temperature attenuated total reflectance Fourier transform infrared (VT-ATR-FTIR) spectroscopy. We report that the TmL of a single Watson-Crick A-T base pair near the end of an A-T rich sequence (poly T) is ∼34.9 ± 0.7°C. This is slightly lower than the TmL of a single base pair near the middle position of the poly T sequence (TmL ∼35.6±0.2°C). In addition, we also report that the TmL of a single Watson-Crick A-T base pair near the end of a 50% G-C sequence (12-mer) is ∼52.5 ± 0.3°C, which is slightly lower than the global melting Tm of the 12-mer sequence (TmL ∼54.0±0.9°C). Our results provide direct physical evidence for end fraying in DNA sequences with our novel spectroscopic methods.
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Affiliation(s)
- Hao-Che Peng
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Shrijaa Mohan
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Muhammad T Huq
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Julie A Bull
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Troy Michaud
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Turner C Piercy
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Stefan Hilber
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck 6020, Austria
| | - Ashan P Wettasinghe
- Department of Physics, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Jason D Slinker
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
- Department of Physics, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck 6020, Austria
| | - Allison L Stelling
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
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3
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Dabin A, Stirnemann G. Atomistic simulations of RNA duplex thermal denaturation: Sequence- and forcefield-dependence. Biophys Chem 2024; 307:107167. [PMID: 38262278 DOI: 10.1016/j.bpc.2023.107167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/26/2023] [Accepted: 12/28/2023] [Indexed: 01/25/2024]
Abstract
Double-stranded RNA is the end-product of template-based replication, and is also the functional state of some biological RNAs. Similarly to proteins and DNA, they can be denatured by temperature, with important physiological and technological implications. Here, we use an in silico strategy to probe the thermal denaturation of RNA duplexes. Following previous results that were obtained on a few different duplexes, and which nuanced the canonical 2-state picture of nucleic acid denaturation, we here specifically address three different aspects that greatly improve our description of the temperature-induced dsRNA separation. First, we investigate the effect of the spatial distribution of weak and strong base-pairs among the duplex sequence. We show that the deviations from the two-state dehybridization mechanism are more pronounced when a strong core is flanked with weak extremities, while duplexes with a weak core but strong extremities exhibit a two-state behavior, which can be explained by the key role played by base fraying. This was later verified by generating artificial hairpin or circular states containing one or two locked duplex extremities, which results in an important reinforcement of the entire HB structure of the duplex and higher melting temperatures. Finally, we demonstrate that our results are little sensitive to the employed combination of RNA and water forcefields. The trends in thermal stability among the different sequences as well as the observed unfolding mechanisms (and the deviations from a two-state scenario) remain the same regardless of the employed atomistic models. However, our study points to possible limitations of recent reparametrizations of the Amber RNA forcefield, which sometimes results in duplexes that readily denature under ambient conditions, in contradiction with available experimental results.
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Affiliation(s)
- Aimeric Dabin
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Université de Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Guillaume Stirnemann
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
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4
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Wadsworth GM, Zahurancik WJ, Zeng X, Pullara P, Lai LB, Sidharthan V, Pappu RV, Gopalan V, Banerjee PR. RNAs undergo phase transitions with lower critical solution temperatures. Nat Chem 2023; 15:1693-1704. [PMID: 37932412 PMCID: PMC10872781 DOI: 10.1038/s41557-023-01353-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 09/19/2023] [Indexed: 11/08/2023]
Abstract
Co-phase separation of RNAs and RNA-binding proteins drives the biogenesis of ribonucleoprotein granules. RNAs can also undergo phase transitions in the absence of proteins. However, the physicochemical driving forces of protein-free, RNA-driven phase transitions remain unclear. Here we report that various types of RNA undergo phase separation with system-specific lower critical solution temperatures. This entropically driven phase separation is an intrinsic feature of the phosphate backbone that requires Mg2+ ions and is modulated by RNA bases. RNA-only condensates can additionally undergo enthalpically favourable percolation transitions within dense phases. This is enabled by a combination of Mg2+-dependent bridging interactions between phosphate groups and RNA-specific base stacking and base pairing. Phase separation coupled to percolation can cause dynamic arrest of RNAs within condensates and suppress the catalytic activity of an RNase P ribozyme. Our work highlights the need to incorporate RNA-driven phase transitions into models for ribonucleoprotein granule biogenesis.
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Affiliation(s)
- Gable M Wadsworth
- Department of Physics, The State University of New York at Buffalo, Buffalo, NY, USA
| | - Walter J Zahurancik
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Xiangze Zeng
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
- Department of Physics, Hong Kong Baptist University, Hong Kong, China
- Teaching and Research Division, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Paul Pullara
- Department of Physics, The State University of New York at Buffalo, Buffalo, NY, USA
| | - Lien B Lai
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Vaishnavi Sidharthan
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA.
| | - Venkat Gopalan
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
| | - Priya R Banerjee
- Department of Physics, The State University of New York at Buffalo, Buffalo, NY, USA.
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5
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Dabin A, Stirnemann G. Toward a Molecular Mechanism of Complementary RNA Duplexes Denaturation. J Phys Chem B 2023. [PMID: 37389985 DOI: 10.1021/acs.jpcb.3c00908] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2023]
Abstract
RNA duplexes are relatively rare but play very important biological roles. As an end-product of template-based RNA replication, they also have key implications for hypothetical primitive forms of life. Unless they are specifically separated by enzymes, these duplexes denature upon a temperature increase. However, mechanistic and kinetic aspects of RNA (and DNA) duplex thermal denaturation remain unclear at the microscopic level. We propose an in silico strategy that probes the thermal denaturation of RNA duplexes and allows for an extensive conformational space exploration along a wide temperature range with atomistic precision. We show that this approach first accounts for the strong sequence and length dependence of the duplexes melting temperature, reproducing the trends seen in the experiments and predicted by nearest-neighbor models. The simulations are then instrumental at providing a molecular picture of the temperature-induced strand separation. The textbook canonical "all-or-nothing" two-state model, very much inspired by the protein folding mechanism, can be nuanced. We demonstrate that a temperature increase leads to significantly distorted but stable structures with extensive base-fraying at the extremities, and that the fully formed duplexes typically do not form around melting. The duplex separation therefore appears as much more gradual than commonly thought.
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Affiliation(s)
- Aimeric Dabin
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, PSL University, Université de Paris, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Guillaume Stirnemann
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, PSL University, Université de Paris, 13 rue Pierre et Marie Curie, 75005, Paris, France
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6
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Rudra S, Chauhan K, Singh AR, Kumar S. Force-induced melting of DNA hairpin: Unfolding pathways and phase diagrams. Phys Rev E 2023; 107:054501. [PMID: 37328992 DOI: 10.1103/physreve.107.054501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 04/27/2023] [Indexed: 06/18/2023]
Abstract
Using the exact enumeration technique, we have studied the force-induced melting of a DNA hairpin on the face centered cubic lattice for two different sequences which differ in terms of loop closing base pairs. The melting profiles obtained from the exact enumeration technique is consistent with the Gaussian network model and Langevin dynamics simulations. Probability distribution analysis based on the exact density of states revealed the microscopic details of the opening of the hairpin. We showed the existence of intermediate states near the melting temperature. We further showed that different ensembles used to model single-molecule force spectroscopy setups may give different force-temperature diagrams. We delineate the possible reasons for the observed discrepancies.
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Affiliation(s)
- Sumitra Rudra
- Department of Physics, Banaras Hindu University, Varanasi 221005, India
| | - Keerti Chauhan
- Department of Physics, Banaras Hindu University, Varanasi 221005, India
| | - Amit Raj Singh
- Department of Physics, Graphic Era Hill University, Dehradun 248002, India
| | - Sanjay Kumar
- Department of Physics, Banaras Hindu University, Varanasi 221005, India
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7
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Kodikara S, Gyawali P, Gleeson JT, Jakli A, Sprunt S, Balci H. Stability of End-to-End Base Stacking Interactions in Highly Concentrated DNA Solutions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:4838-4846. [PMID: 36952670 PMCID: PMC10078606 DOI: 10.1021/acs.langmuir.3c00318] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/09/2023] [Indexed: 06/18/2023]
Abstract
Positionally ordered bilayer liquid crystalline nanostructures formed by gapped DNA (GDNA) constructs provide a practical window into DNA-DNA interactions at physiologically relevant DNA concentrations; concentrations several orders of magnitude greater than those in commonly used biophysical assays. The bilayer structure of these states of matter is stabilized by end-to-end base stacking interactions; moreover, such interactions also promote in-plane positional ordering of duplexes that are separated from each other by less than twice the duplex diameter. The end-to-end stacked as well as in-plane ordered duplexes exhibit distinct signatures when studied via small-angle X-ray scattering (SAXS). This enables analysis of the thermal stability of both the end-to-end and side-by-side interactions. We performed synchrotron SAXS experiments over a temperature range of 5-65 °C on GDNA constructs that differ only by the terminal base-pairs at the blunt duplex ends, resulting in identical side-by-side interactions, while end-to-end base stacking interactions are varied. Our key finding is that bilayers formed by constructs with GC termination transition into the monolayer state at temperatures as much as 30 °C higher than for those with AT termination, while mixed (AT/GC) terminations have intermediate stability. By modeling the bilayer melting in terms of a temperature-dependent reduction in the average fraction of end-to-end paired duplexes, we estimate the stacking free energies in DNA solutions of physiologically relevant concentrations. The free-energies thereby determined are generally smaller than those reported in single-molecule studies, which might reflect the elevated DNA concentrations in our studies.
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Affiliation(s)
- Sineth
G. Kodikara
- Department
of Physics, Kent State University, Kent, Ohio 44242, United States
| | - Prabesh Gyawali
- Department
of Physics, Kent State University, Kent, Ohio 44242, United States
| | - James T. Gleeson
- Department
of Physics, Kent State University, Kent, Ohio 44242, United States
| | - Antal Jakli
- Department
of Physics, Kent State University, Kent, Ohio 44242, United States
- Advanced
Materials and Liquid Crystals Institute, Kent State University, Kent, Ohio 44242, United States
| | - Samuel Sprunt
- Department
of Physics, Kent State University, Kent, Ohio 44242, United States
- Advanced
Materials and Liquid Crystals Institute, Kent State University, Kent, Ohio 44242, United States
| | - Hamza Balci
- Department
of Physics, Kent State University, Kent, Ohio 44242, United States
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8
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Langlois NI, Ma KY, Clark HA. Nucleic acid nanostructures for in vivo applications: The influence of morphology on biological fate. APPLIED PHYSICS REVIEWS 2023; 10:011304. [PMID: 36874908 PMCID: PMC9869343 DOI: 10.1063/5.0121820] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 12/12/2022] [Indexed: 05/23/2023]
Abstract
The development of programmable biomaterials for use in nanofabrication represents a major advance for the future of biomedicine and diagnostics. Recent advances in structural nanotechnology using nucleic acids have resulted in dramatic progress in our understanding of nucleic acid-based nanostructures (NANs) for use in biological applications. As the NANs become more architecturally and functionally diverse to accommodate introduction into living systems, there is a need to understand how critical design features can be controlled to impart desired performance in vivo. In this review, we survey the range of nucleic acid materials utilized as structural building blocks (DNA, RNA, and xenonucleic acids), the diversity of geometries for nanofabrication, and the strategies to functionalize these complexes. We include an assessment of the available and emerging characterization tools used to evaluate the physical, mechanical, physiochemical, and biological properties of NANs in vitro. Finally, the current understanding of the obstacles encountered along the in vivo journey is contextualized to demonstrate how morphological features of NANs influence their biological fates. We envision that this summary will aid researchers in the designing novel NAN morphologies, guide characterization efforts, and design of experiments and spark interdisciplinary collaborations to fuel advancements in programmable platforms for biological applications.
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Affiliation(s)
- Nicole I. Langlois
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, USA
| | - Kristine Y. Ma
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, USA
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9
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Chen F, Nasrabadi H. Molecular Dynamics Simulation of the Thermal Diffusion Effect in n-Alkane Binary Mixtures. J Phys Chem B 2022; 126:10164-10171. [DOI: 10.1021/acs.jpcb.2c05121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
- Fangxuan Chen
- Texas A&M University, 400 Bizzell Street, College Station, Texas77843, United States
| | - Hadi Nasrabadi
- Texas A&M University, 400 Bizzell Street, College Station, Texas77843, United States
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10
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Serrão VHB, Fernandes ADF, Basso LGM, Scortecci JF, Crusca Júnior E, Cornélio ML, de Souza BM, Palma MS, de Oliveira Neto M, Thiemann OH. The Specific Elongation Factor to Selenocysteine Incorporation in Escherichia coli: Unique tRNA Sec Recognition and its Interactions. J Mol Biol 2021; 433:167279. [PMID: 34624294 DOI: 10.1016/j.jmb.2021.167279] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 10/20/2022]
Abstract
Several molecular mechanisms are involved in the genetic code interpretation during translation, as codon degeneration for the incorporation of rare amino acids. One mechanism that stands out is selenocysteine (Sec), which requires a specific biosynthesis and incorporation pathway. In Bacteria, the Sec biosynthesis pathway has unique features compared with the eukaryote pathway as Ser to Sec conversion mechanism is accomplished by a homodecameric enzyme (selenocysteine synthase, SelA) followed by the action of an elongation factor (SelB) responsible for delivering the mature Sec-tRNASec into the ribosome by the interaction with the Selenocysteine Insertion Sequence (SECIS). Besides this mechanism being already described, the sequential events for Sec-tRNASec and SECIS specific recognition remain unclear. In this study, we determined the order of events of the interactions between the proteins and RNAs involved in Sec incorporation. Dissociation constants between SelB and the native as well as unacylated-tRNASec variants demonstrated that the acceptor stem and variable arm are essential for SelB recognition. Moreover, our data support the sequence of molecular events where GTP-activated SelB strongly interacts with SelA.tRNASec. Subsequently, SelB.GTP.tRNASec recognizes the mRNA SECIS to deliver the tRNASec to the ribosome. SelB in complex with its specific RNAs were examined using Hydrogen/Deuterium exchange mapping that allowed the determination of the molecular envelopes and its secondary structural variations during the complex assembly. Our results demonstrate the ordering of events in Sec incorporation and contribute to the full comprehension of the tRNASec role in the Sec amino acid biosynthesis, as well as extending the knowledge of synthetic biology and the expansion of the genetic code.
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Affiliation(s)
- Vitor Hugo Balasco Serrão
- Physics Institute of Sao Carlos, University of Sao Paulo, Trabalhador Sao Carlense Av., 400, São Carlos, SP CEP 13566-590, Brazil; Department of Chemistry and Biochemistry, University California - Santa Cruz, 1156 High St., Santa Cruz, CA 95060, United States
| | - Adriano de Freitas Fernandes
- Physics Institute of Sao Carlos, University of Sao Paulo, Trabalhador Sao Carlense Av., 400, São Carlos, SP CEP 13566-590, Brazil
| | - Luis Guilherme Mansor Basso
- Physical Sciences Laboratory, State University of Northern Rio de Janeiro Darcy Ribeiro - UENF, Av. Alberto Lamego, 2000, 28013-602 Campos dos Goytacazes, RJ, Brazil; Faculty of Science, Philosophy and Letters, University of Sao Paulo, CEP 14040-901 Ribeirão Preto, SP, Brazil
| | - Jéssica Fernandes Scortecci
- Physics Institute of Sao Carlos, University of Sao Paulo, Trabalhador Sao Carlense Av., 400, São Carlos, SP CEP 13566-590, Brazil; Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Science Mall, Vancouver, British Columbia V6T 1Z3, Canada
| | - Edson Crusca Júnior
- Department of Physical Chemistry, Chemistry Institute of the São Paulo State University - UNESP, CEP 14800-900 Araraquara, SP, Brazil
| | - Marinônio Lopes Cornélio
- Physics Department, Institute of Biosciences, Letters and Exact Sciences (IBILCE), São Paulo State University - UNESP, São Jose do Rio Preto, SP, Brazil
| | - Bibiana Monson de Souza
- Department of General and Applied Biology, Institute of Biosciences of Rio Claro, São Paulo State University - UNESP, Rio Claro, SP, Brazil
| | - Mário Sérgio Palma
- Department of General and Applied Biology, Institute of Biosciences of Rio Claro, São Paulo State University - UNESP, Rio Claro, SP, Brazil
| | - Mario de Oliveira Neto
- Bioscience Institute of Universidade Estadual Paulista, Rubião Jr., Botucatu, SP CEP 18618-000, Brazil
| | - Otavio Henrique Thiemann
- Physics Institute of Sao Carlos, University of Sao Paulo, Trabalhador Sao Carlense Av., 400, São Carlos, SP CEP 13566-590, Brazil; Department of Genetics and Evolution, Federal University of São Carlos - UFSCar, 13565-905 São Carlos, SP, Brazil.
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11
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Stein JAC, Ianeselli A, Braun D. Kinetic Microscale Thermophoresis for Simultaneous Measurement of Binding Affinity and Kinetics. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202101261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Julian A. C. Stein
- Systems Biophysics Department of Physics Ludwig-Maximilians-Universität München and Center for NanoScience Amalienstasse 54 80799 München Germany
| | - Alan Ianeselli
- Systems Biophysics Department of Physics Ludwig-Maximilians-Universität München and Center for NanoScience Amalienstasse 54 80799 München Germany
| | - Dieter Braun
- Systems Biophysics Department of Physics Ludwig-Maximilians-Universität München and Center for NanoScience Amalienstasse 54 80799 München Germany
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12
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Stein JAC, Ianeselli A, Braun D. Kinetic Microscale Thermophoresis for Simultaneous Measurement of Binding Affinity and Kinetics. Angew Chem Int Ed Engl 2021; 60:13988-13995. [PMID: 33793031 PMCID: PMC8251828 DOI: 10.1002/anie.202101261] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/16/2021] [Indexed: 12/11/2022]
Abstract
Microscale thermophoresis (MST) is a versatile technique to measure binding affinities of binder-ligand systems, based on the directional movement of molecules in a temperature gradient. We extended MST to measure binding kinetics as well as binding affinity in a single experiment by increasing the thermal dissipation of the sample. The kinetic relaxation fingerprints were derived from the fluorescence changes during thermodynamic re-equilibration of the sample after local heating. Using this method, we measured DNA hybridization on-rates and off-rates in the range 104 -106 m-1 s-1 and 10-4 -10-1 s-1 , respectively. We observed the expected exponential dependence of the DNA hybridization off-rates on salt concentration, strand length and inverse temperature. The measured on-rates showed a linear dependence on salt concentration and weak dependence on strand length and temperature. For biomolecular interactions with large enthalpic contributions, the kinetic MST technique offers a robust, cost-effective and immobilization-free determination of kinetic rates and binding affinity simultaneously, even in crowded solutions.
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Affiliation(s)
- Julian A C Stein
- Systems Biophysics, Department of Physics, Ludwig-Maximilians-Universität München and Center for NanoScience, Amalienstasse 54, 80799, München, Germany
| | - Alan Ianeselli
- Systems Biophysics, Department of Physics, Ludwig-Maximilians-Universität München and Center for NanoScience, Amalienstasse 54, 80799, München, Germany
| | - Dieter Braun
- Systems Biophysics, Department of Physics, Ludwig-Maximilians-Universität München and Center for NanoScience, Amalienstasse 54, 80799, München, Germany
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13
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Monisha K, Bankapur A, Chidangil S, George SD. Laser-induced assembly of biological cells and colloids onto a candle soot coated substrate. Colloids Surf A Physicochem Eng Asp 2021. [DOI: 10.1016/j.colsurfa.2021.126357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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14
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Lu T, Nakashima KK, Spruijt E. Temperature-Responsive Peptide-Nucleotide Coacervates. J Phys Chem B 2021; 125:3080-3091. [PMID: 33757284 PMCID: PMC8020381 DOI: 10.1021/acs.jpcb.0c10839] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Coacervates are a
type of liquid–liquid phase separated
(LLPS) droplets that can serve as models of membraneless organelles
(MLOs) in living cells. Peptide–nucleotide coacervates have
been widely used to mimic properties of ribonucleoprotein (RNP) granules,
but the thermal stability and the role of base stacking is still poorly
understood. Here, we report a systematic investigation of coacervates
formed by five different nucleoside triphosphates (NTPs) with poly-l-lysine and poly-l-arginine as a function of temperature.
All studied combinations exhibit an upper critical solution temperature
(UCST), and a temperature-dependent critical salt concentration, originating
from a significant nonelectrostatic contribution to the mixing free
energy. Both the enthalpic and entropic parts of this nonelectrostatic
interaction decrease in the order G/A/U/C/T, in accordance with nucleobase
stacking free energies. Partitioning of two dyes proves that the local
hydrophobicity inside the peptide–nucleotide coacervates is
different for every nucleoside triphosphate. We derive a simple relation
between the temperature and salt concentration at the critical point
based on a mean-field model of phase separation. Finally, when different
NTPs are mixed with one common oppositely charged peptide, hybrid
coacervates were formed, characterized by a single intermediate UCST
and critical salt concentration. NTPs with lower critical salt concentrations
can remain condensed in mixed coacervates far beyond their original
critical salt concentration. Our results show that NTP-based coacervates
have a strong temperature sensitivity due to base stacking interactions
and that mixing NTPs can significantly influence the stability of
condensates and, by extension, their bioavailability.
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Affiliation(s)
- Tiemei Lu
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Karina K Nakashima
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Evan Spruijt
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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15
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Visone V, Szabó I, Perugino G, Hudecz F, Bánóczi Z, Valenti A. Topoisomerases inhibition and DNA binding mode of daunomycin-oligoarginine conjugate. J Enzyme Inhib Med Chem 2021; 35:1363-1371. [PMID: 32552137 PMCID: PMC7717705 DOI: 10.1080/14756366.2020.1780226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Cancer is a major health issue adsorbing the attention of a biomedical research. To fight this disease, new drugs are developed, specifically tailored to target biological pathways or peculiar components of the tumour cells. Particularly interesting is the use of intercalating agents as drugs capable to bind DNA and inhibit enzymes involved in DNA metabolism. Anthracyclines are the most commonly used anticancer drugs. In particular, daunomycin is used to cancer treatment by exploiting its ability to intercalate DNA and inhibit the activity of DNA topoisomerases implicated in the replication processes. Unfortunately, clinical application of anthracyclines is limited by their side effects. The conjugation with specific carriers could affect the selectivity and reduce side effect by improving stability and/or cellular uptake properties. We here report the biochemical characterisation of a daunomycin oligopeptide conjugate containing six residues of arginine, by the analysis of its fluorescence properties, DNA interaction and topoisomerases inhibitory effects.
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Affiliation(s)
- Valeria Visone
- Institute of Biosciences and BioResources, National Research Council of Italy, Naples, Italy
| | - Ildikó Szabó
- MTA-ELTE Research Group of Peptide Chemistry, Budapest, Hungary
| | - Giuseppe Perugino
- Institute of Biosciences and BioResources, National Research Council of Italy, Naples, Italy
| | - Ferenc Hudecz
- Department of Organic Chemistry, Eötvös Loránd University (ELTE), Budapest, Hungary
| | - Zoltán Bánóczi
- Department of Organic Chemistry, Eötvös Loránd University (ELTE), Budapest, Hungary
| | - Anna Valenti
- Institute of Biosciences and BioResources, National Research Council of Italy, Naples, Italy
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16
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Rydzik AM, Gottschling D, Simon E, Skronska-Wasek W, Rippmann JF, Riether D. Epigenetic Modification 6-Methyladenosine Can Impact the Potency and Specificity of siRNA. Chembiochem 2020; 22:491-495. [PMID: 32936508 DOI: 10.1002/cbic.202000551] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/12/2020] [Indexed: 11/12/2022]
Abstract
The introduction of N6-methyladenosine (m6 A) into siRNA targeting Factor VII impacts its potency in cells and has a significant influence on the selectivity of siRNA, including reduced off-targeting. These effects are dependent on the position of m6 A in the siRNA duplex, with some of the sequences identified as more potent and/or selective than their non-methylated counterpart. These findings broaden the repertoire of available chemical modifications for siRNA therapeutics and imply potential regulatory role of N6-methyladenosine in the RNAi pathways.
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Affiliation(s)
- Anna M Rydzik
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, 88397, Biberach an der Riss, Germany.,Current address: Research and Early Development, Respiratory & Immunology, AstraZeneca, 431 83, Mölndal, Sweden
| | - Dirk Gottschling
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, 88397, Biberach an der Riss, Germany
| | - Eric Simon
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, 88397, Biberach an der Riss, Germany
| | - Wioletta Skronska-Wasek
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, 88397, Biberach an der Riss, Germany
| | - Jörg F Rippmann
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, 88397, Biberach an der Riss, Germany
| | - Doris Riether
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, 88397, Biberach an der Riss, Germany
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17
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Thermophoresis: The Case of Streptavidin and Biotin. Polymers (Basel) 2020; 12:polym12020376. [PMID: 32046223 PMCID: PMC7077373 DOI: 10.3390/polym12020376] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/27/2020] [Accepted: 01/29/2020] [Indexed: 02/02/2023] Open
Abstract
Thermophoretic behavior of a free protein changes upon ligand binding and gives access to information on the binding constants. The Soret effect has also been proven to be a promising tool to gain information on the hydration layer, as the temperature dependence of the thermodiffusion behavior is sensitive to solute–solvent interactions. In this work, we perform systematic thermophoretic measurements of the protein streptavidin (STV) and of the complex STV with biotin (B) using thermal diffusion forced Rayleigh scattering (TDFRS). Our experiments show that the temperature sensitivity of the Soret coefficient is reduced for the complex compared to the free protein. We discuss our data in comparison with recent quasi-elastic neutron scattering (QENS) measurements. As the QENS measurement has been performed in heavy water, we perform additional measurements in water/heavy water mixtures. Finally, we also elucidate the challenges arising from the quantiative thermophoretic study of complex multicomponent systems such as protein solutions.
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18
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Zhang J, Li Y, Qi J, Yu X, Ren H, Zhao X, Xin W, He S, Zheng X, Ma C, Zhang L, Wu B, Zhu D. Circ- calm4 Serves as an miR-337-3p Sponge to Regulate Myo10 (Myosin 10) and Promote Pulmonary Artery Smooth Muscle Proliferation. Hypertension 2020; 75:668-679. [PMID: 32008463 DOI: 10.1161/hypertensionaha.119.13715] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Pulmonary artery smooth muscle cell proliferation is the pathological basis of pulmonary vascular remodeling in hypoxic pulmonary hypertension. Recent studies suggest that circular RNA (circRNA) can regulate various biological processes, including cell proliferation. Therefore, it is possible that circRNA may have important roles in pulmonary artery smooth muscle cell proliferation in hypoxic pulmonary hypertension. In the present study, we aimed to identify functional circRNAs and clarify their roles and mechanisms in pulmonary artery smooth muscle cell proliferation in pulmonary hypertension. RNA sequencing identified 67 circRNAs that were differentially expressed in hypoxic lung tissues of mice. Screening by bioinformatics and quantitative polymerase chain reaction revealed significant elevation of a circRNA derived from alternative splicing of the calmodulin 4 gene (designated circ-calm4). Notably, this circRNA absorbed miR-337-3p. We further identified Myo10 (myosin 10) as a target protein of miR-337-3p. miR-337-3p bound to the 3'-untranslated region of Myo10 mRNA, thereby attenuating the translation of Myo10. Using loss-of-function and gain-of-function approaches, we found that circ-calm4 regulated cell proliferation by regulating the cell cycle. Additionally, we verified the functions of miR-337-3p and Myo10 in hypoxic pulmonary artery smooth muscle. Our results suggested that the circ-calm4/miR-337-3p/Myo10 signal transduction axis modulated the proliferation of pulmonary artery smooth muscle cells at the molecular level, thus establishing potential targets for the early diagnosis and treatment of pulmonary hypertension.
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Affiliation(s)
- Junting Zhang
- From the College of Medical Laboratory Science and Technology (X.Y., X. Zhao, L.Z., C.M., D.Z.), Harbin Medical University (Daqing), China.,Department of Pharmacology, College of Pharmacy (J.Z., Y.L., J.Q., H.R.,W.X., S.H., D.Z.), Harbin Medical University (Daqing), China.,Central Laboratory of Harbin Medical University (Daqing), China (J.Z., Y.L., J.Q., X.Y., H.R., X. Zhao, W.X., S.H., C.M., L.Z., D.Z.).,College of Pharmacy (J.Z., Y.L., J.Q., X.Y., H.R., X. Zhao, W.X., S.H., X. Zheng, C.M., L.Z., D.Z.), Harbin Medical University, China
| | - Yiying Li
- Department of Pharmacology, College of Pharmacy (J.Z., Y.L., J.Q., H.R.,W.X., S.H., D.Z.), Harbin Medical University (Daqing), China.,Central Laboratory of Harbin Medical University (Daqing), China (J.Z., Y.L., J.Q., X.Y., H.R., X. Zhao, W.X., S.H., C.M., L.Z., D.Z.).,College of Pharmacy (J.Z., Y.L., J.Q., X.Y., H.R., X. Zhao, W.X., S.H., X. Zheng, C.M., L.Z., D.Z.), Harbin Medical University, China
| | - Jing Qi
- Department of Pharmacology, College of Pharmacy (J.Z., Y.L., J.Q., H.R.,W.X., S.H., D.Z.), Harbin Medical University (Daqing), China.,Central Laboratory of Harbin Medical University (Daqing), China (J.Z., Y.L., J.Q., X.Y., H.R., X. Zhao, W.X., S.H., C.M., L.Z., D.Z.).,College of Pharmacy (J.Z., Y.L., J.Q., X.Y., H.R., X. Zhao, W.X., S.H., X. Zheng, C.M., L.Z., D.Z.), Harbin Medical University, China
| | - Xiufeng Yu
- Central Laboratory of Harbin Medical University (Daqing), China (J.Z., Y.L., J.Q., X.Y., H.R., X. Zhao, W.X., S.H., C.M., L.Z., D.Z.).,College of Pharmacy (J.Z., Y.L., J.Q., X.Y., H.R., X. Zhao, W.X., S.H., X. Zheng, C.M., L.Z., D.Z.), Harbin Medical University, China
| | - Huanhuan Ren
- Department of Pharmacology, College of Pharmacy (J.Z., Y.L., J.Q., H.R.,W.X., S.H., D.Z.), Harbin Medical University (Daqing), China.,Central Laboratory of Harbin Medical University (Daqing), China (J.Z., Y.L., J.Q., X.Y., H.R., X. Zhao, W.X., S.H., C.M., L.Z., D.Z.).,College of Pharmacy (J.Z., Y.L., J.Q., X.Y., H.R., X. Zhao, W.X., S.H., X. Zheng, C.M., L.Z., D.Z.), Harbin Medical University, China
| | - Xijuan Zhao
- From the College of Medical Laboratory Science and Technology (X.Y., X. Zhao, L.Z., C.M., D.Z.), Harbin Medical University (Daqing), China.,Central Laboratory of Harbin Medical University (Daqing), China (J.Z., Y.L., J.Q., X.Y., H.R., X. Zhao, W.X., S.H., C.M., L.Z., D.Z.).,College of Pharmacy (J.Z., Y.L., J.Q., X.Y., H.R., X. Zhao, W.X., S.H., X. Zheng, C.M., L.Z., D.Z.), Harbin Medical University, China
| | - Wei Xin
- Department of Pharmacology, College of Pharmacy (J.Z., Y.L., J.Q., H.R.,W.X., S.H., D.Z.), Harbin Medical University (Daqing), China.,Central Laboratory of Harbin Medical University (Daqing), China (J.Z., Y.L., J.Q., X.Y., H.R., X. Zhao, W.X., S.H., C.M., L.Z., D.Z.).,College of Pharmacy (J.Z., Y.L., J.Q., X.Y., H.R., X. Zhao, W.X., S.H., X. Zheng, C.M., L.Z., D.Z.), Harbin Medical University, China
| | - Siyu He
- Department of Pharmacology, College of Pharmacy (J.Z., Y.L., J.Q., H.R.,W.X., S.H., D.Z.), Harbin Medical University (Daqing), China.,Central Laboratory of Harbin Medical University (Daqing), China (J.Z., Y.L., J.Q., X.Y., H.R., X. Zhao, W.X., S.H., C.M., L.Z., D.Z.).,College of Pharmacy (J.Z., Y.L., J.Q., X.Y., H.R., X. Zhao, W.X., S.H., X. Zheng, C.M., L.Z., D.Z.), Harbin Medical University, China
| | - Xiaodong Zheng
- Central Laboratory of Harbin Medical University (Daqing), China (J.Z., Y.L., J.Q., X.Y., H.R., X. Zhao, W.X., S.H., C.M., L.Z., D.Z.).,College of Pharmacy (J.Z., Y.L., J.Q., X.Y., H.R., X. Zhao, W.X., S.H., X. Zheng, C.M., L.Z., D.Z.), Harbin Medical University, China
| | - Cui Ma
- From the College of Medical Laboratory Science and Technology (X.Y., X. Zhao, L.Z., C.M., D.Z.), Harbin Medical University (Daqing), China.,Central Laboratory of Harbin Medical University (Daqing), China (J.Z., Y.L., J.Q., X.Y., H.R., X. Zhao, W.X., S.H., C.M., L.Z., D.Z.).,College of Pharmacy (J.Z., Y.L., J.Q., X.Y., H.R., X. Zhao, W.X., S.H., X. Zheng, C.M., L.Z., D.Z.), Harbin Medical University, China
| | - Lixin Zhang
- From the College of Medical Laboratory Science and Technology (X.Y., X. Zhao, L.Z., C.M., D.Z.), Harbin Medical University (Daqing), China.,Central Laboratory of Harbin Medical University (Daqing), China (J.Z., Y.L., J.Q., X.Y., H.R., X. Zhao, W.X., S.H., C.M., L.Z., D.Z.).,College of Pharmacy (J.Z., Y.L., J.Q., X.Y., H.R., X. Zhao, W.X., S.H., X. Zheng, C.M., L.Z., D.Z.), Harbin Medical University, China
| | - Bingxiang Wu
- Department of Cardiovascular Medicine, The Second Affiliated Hospital of Harbin Medical University, China (B.W.)
| | - Daling Zhu
- From the College of Medical Laboratory Science and Technology (X.Y., X. Zhao, L.Z., C.M., D.Z.), Harbin Medical University (Daqing), China.,Department of Pharmacology, College of Pharmacy (J.Z., Y.L., J.Q., H.R.,W.X., S.H., D.Z.), Harbin Medical University (Daqing), China.,Central Laboratory of Harbin Medical University (Daqing), China (J.Z., Y.L., J.Q., X.Y., H.R., X. Zhao, W.X., S.H., C.M., L.Z., D.Z.).,College of Pharmacy (J.Z., Y.L., J.Q., X.Y., H.R., X. Zhao, W.X., S.H., X. Zheng, C.M., L.Z., D.Z.), Harbin Medical University, China.,Key Laboratory of Cardiovascular Medicine Research, Ministry of Education (D.Z.), Harbin Medical University, China.,State Province Key Laboratories of Biomedicine-Pharmaceutics of China (D.Z.)
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19
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Abdelrahman A, Gouda AS, Jørgensen PT, Wengel J. Novel assemblies based on oligonucleotides containing intercalating nucleic acid monomers. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2019; 39:82-96. [PMID: 31674270 DOI: 10.1080/15257770.2019.1683188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
This is the first report exploring the capability of twisted intercalating nucleic acid (TINA) and naphthalene-functionalized non-nucleosidic linkers to stabilize and engage in double-helical structures. Four designs were studied with respect to the formation of duplexes and/or other types of self-assemblies. One of the constructs involving TINA provides a thermostable duplex. The biophysical properties of the individual constructs were investigated by UV thermal melting experiments, circular dichroism, and fluorescence emission spectroscopy. Molecular modeling studies were performed in attempts of explaining the biophysical measurements for the duplex based on the TINA-containing oligonucleotide strands.
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Affiliation(s)
- Asmaa Abdelrahman
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark.,Department of Photochemistry, National Research Centre, Giza, Egypt
| | - Alaa S Gouda
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark.,Department of Chemistry, Faculty of Science, Benha University, Benha, Egypt
| | - Per T Jørgensen
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
| | - Jesper Wengel
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
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20
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Unveiling the druggable RNA targets and small molecule therapeutics. Bioorg Med Chem 2019; 27:2149-2165. [PMID: 30981606 PMCID: PMC7126819 DOI: 10.1016/j.bmc.2019.03.057] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 03/25/2019] [Accepted: 03/29/2019] [Indexed: 12/15/2022]
Abstract
The increasing appreciation for the crucial roles of RNAs in infectious and non-infectious human diseases makes them attractive therapeutic targets. Coding and non-coding RNAs frequently fold into complex conformations which, if effectively targeted, offer opportunities to therapeutically modulate numerous cellular processes, including those linked to undruggable protein targets. Despite the considerable skepticism as to whether RNAs can be targeted with small molecule therapeutics, overwhelming evidence suggests the challenges we are currently facing are not outside the realm of possibility. In this review, we highlight the most recent advances in molecular techniques that have sparked a revolution in understanding the RNA structure-to-function relationship. We bring attention to the application of these modern techniques to identify druggable RNA targets and to assess small molecule binding specificity. Finally, we discuss novel screening methodologies that support RNA drug discovery and present examples of therapeutically valuable RNA targets.
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21
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Ahmed FE, Gouda MM, Hussein LA, Ahmed NC, Vos PW, Mohammad MA. Role of Melt Curve Analysis in Interpretation of Nutrigenomics' MicroRNA Expression Data. Cancer Genomics Proteomics 2018; 14:469-481. [PMID: 29109097 DOI: 10.21873/cgp.20057] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Revised: 10/05/2017] [Accepted: 10/26/2017] [Indexed: 12/23/2022] Open
Abstract
This article illustrates the importance of melt curve analysis (MCA) in interpretation of mild nutrogenomic micro(mi)RNA expression data, by measuring the magnitude of the expression of key miRNA molecules in stool of healthy human adults as molecular markers, following the intake of Pomegranate juice (PGJ), functional fermented sobya (FS), rich in potential probiotic lactobacilli, or their combination. Total small RNA was isolated from stool of 25 volunteers before and following a three-week dietary intervention trial. Expression of 88 miRNA genes was evaluated using Qiagen's 96 well plate RT2 miRNA qPCR arrays. Employing parallel coordinates plots, there was no observed significant separation for the gene expression (Cq) values, using Roche 480® PCR LightCycler instrument used in this study, and none of the miRNAs showed significant statistical expression after controlling for the false discovery rate. On the other hand, melting temperature profiles produced during PCR amplification run, found seven significant genes (miR-184, miR-203, miR-373, miR-124, miR-96, miR-373 and miR-301a), which separated candidate miRNAs that could function as novel molecular markers of relevance to oxidative stress and immunoglobulin function, for the intake of polyphenol (PP)-rich, functional fermented foods rich in lactobacilli (FS), or their combination. We elaborate on these data, and present a detailed review on use of melt curves for analyzing nutigenomic miRNA expression data, which initially appear to show no significant expressions, but are actually more subtle than this simplistic view, necessitating the understanding of the role of MCA for a comprehensive understanding of what the collective expression and MCA data collectively imply.
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Affiliation(s)
- Farid E Ahmed
- GEM Tox Labs, Institute for Research in Biotechnology, Greenville, NC, U.S.A.
| | - Mostafa M Gouda
- Department of Nutrition & Food Science, National Research Centre, Dokki, Cairo, Egypt
| | - Laila A Hussein
- Department of Nutrition & Food Science, National Research Centre, Dokki, Cairo, Egypt
| | - Nancy C Ahmed
- GEM Tox Labs, Institute for Research in Biotechnology, Greenville, NC, U.S.A
| | - Paul W Vos
- Department of Biostatistics, College of Allied Health Sciences, East Carolina University, Greenville, NC, U.S.A
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22
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Increased levels of the long noncoding RNA, HOXA-AS3, promote proliferation of A549 cells. Cell Death Dis 2018; 9:707. [PMID: 29899328 PMCID: PMC5999602 DOI: 10.1038/s41419-018-0725-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 04/26/2018] [Accepted: 05/04/2018] [Indexed: 01/01/2023]
Abstract
Many long noncoding RNAs (lncRNAs) have been identified as powerful regulators of lung adenocarcinoma (LAD). However, the role of HOXA-AS3, a novel lncRNA, in LAD is largely unknown. In this study, we showed that HOXA-AS3 was significantly upregulated in LAD tissues and A549 cells. After knockdown of HOXA-AS3, cell proliferation, migration, and invasion were inhibited. Xenografts derived from A549 cells transfected with shRNA/HOXA-AS3 had significantly lower tumor weights and smaller tumor volumes. We also demonstrated that HOXA-AS3 increased HOXA6 mRNA stability by forming an RNA duplex. In addition, HOXA6 promoted cell proliferation, migration, and invasion in vitro. Using a RNA pull-down assay, we found that HOXA-AS3 bonded with NF110, which regulated the cell localization of HOXA-AS3. Moreover, histone acetylation was involved in upregulation of HOXA-AS3. These results demonstrate that HOXA-AS3 was activated in LAD and supported cancer cell progression. Therefore, inhibition of HOXA-AS3 could be an effective targeted therapy for patients with LAD.
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23
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Di Lecce S, Bresme F. Soret coefficients and thermal conductivities of alkali halide aqueous solutions via non-equilibrium molecular dynamics simulations. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1481960] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Silvia Di Lecce
- Department of Chemistry, Imperial College London, London, UK
| | - Fernando Bresme
- Department of Chemistry, Imperial College London, London, UK
- Department of Chemistry, Norwegian University of Science and Technology, Trondheim, Norway
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24
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Sinha M, Mack H, Coleman TP, Fraley SI. A High-Resolution Digital DNA Melting Platform for Robust Sequence Profiling and Enhanced Genotype Discrimination. SLAS Technol 2018; 23:580-591. [DOI: 10.1177/2472630318769846] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
DNA melting analysis provides a rapid method for genotyping a target amplicon directly after PCR amplification. To transform melt genotyping into a broad-based profiling approach for heterogeneous samples, we previously proposed the integration of universal PCR and melt analysis with digital PCR. Here, we advanced this concept by developing a high-resolution digital melt platform with precise thermal control to accomplish reliable, high-throughput heat ramping of microfluidic chip digital PCR reactions. Using synthetic DNA oligos with defined melting temperatures, we characterized sources of melting variability and minimized run-to-run variations. Within-run comparisons throughout a 20,000-reaction chip revealed that high-melting-temperature sequences were significantly less prone to melt variation. Further optimization using bacterial 16S amplicons revealed a strong dependence of the number of melting transitions on the heating rate during curve generation. These studies show that reliable high-resolution melt curve genotyping can be achieved in digital, picoliter-scale reactions and demonstrate that rate-dependent melt signatures may be useful for enhancing automated melt genotyping.
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Affiliation(s)
- Mridu Sinha
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Clinical Translational Research Institute, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Hannah Mack
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Clinical Translational Research Institute, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Todd P. Coleman
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Stephanie I. Fraley
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Clinical Translational Research Institute, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
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25
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Yang J, Ma XJ, Li L, Wang L, Chen YG, Liu J, Luo Y, Zhuang ZJ, Yang WJ, Zang SF, Shi JP. Berberine ameliorates non-alcoholic steatohepatitis in ApoE -/- mice. Exp Ther Med 2017; 14:4134-4140. [PMID: 29075339 PMCID: PMC5647746 DOI: 10.3892/etm.2017.5051] [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: 05/10/2016] [Accepted: 03/17/2017] [Indexed: 12/19/2022] Open
Abstract
The aim of the present study was to explore the protective effects of Berberine (BBR) against non-alcoholic steatohepatitis (NASH). Male 4-week-old C57BL/6J Apolipoprotein E-deficient (ApoE-/-) mice were divided into the following three groups, which were given different diets: Normal chow diet (SC group); high-fat high-cholesterol diet (HFHC group); and HFHC diet supplemented with BBR (BBR group). Serum biochemical indicators of hepatic function and histological liver tissue changes were evaluated. The expression of neutrophil elastase (NE) and genes involved in the inflammatory response was measured. ApoE-/- mice fed a HFHC diet for 12 weeks developed NASH, characterized by steatosis and liver inflammation. Body weight, and serum triglyceride and cholesterol levels were markedly reduced by BBR. BBR supplementation significantly lowered serum alanine aminotransferase and aspartate aminotransferase levels in mice with HFHC diet-induced NASH, and significantly downregulated hepatic expression and activity of NE, whereas α1-antitrypsin (α1-AT) expression was significantly recovered by BBR (all P<0.05 vs. the HFHC group). Furthermore, treatment with BBR induced a significant reduction in the expression of key genes, including phospoinositide 3-kinase, nuclear factor-κB and interleukin-8, in the C-X-C chemokine receptor type 4 (CXCR4) signaling pathway (all P<0.05 vs. the HFHC group). These results suggest that BBR alleviates NASH in ApoE-/- mice fed a HFHC diet. Restoration of the balance of NE and α1-AT levels, which in turn facilitate the inhibition of the CXCR4 signaling pathways, may be involved in the hepatoprotective effect of BBR. These results indicate that BBR may be a candidate therapeutic agent for the treatment of NASH.
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Affiliation(s)
- Jin Yang
- Center for Translational Medicine, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang 310015, P.R. China
| | - Xiao-Jie Ma
- Center for Translational Medicine, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang 310015, P.R. China
| | - Ling Li
- College of Medical Science, Zhejiang Chinese Medical University, Hangzhou 310053, Zhejiang, P.R. China
| | - Lei Wang
- Center for Translational Medicine, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang 310015, P.R. China
| | - Ying-Gi Chen
- College of Medical Science, Zhejiang Chinese Medical University, Hangzhou 310053, Zhejiang, P.R. China
| | - Jing Liu
- Center for Translational Medicine, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang 310015, P.R. China
| | - Yan Luo
- Center for Translational Medicine, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang 310015, P.R. China
| | - Zhen-Jie Zhuang
- Center for Translational Medicine, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang 310015, P.R. China
| | - Wen-Jun Yang
- Center for Translational Medicine, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang 310015, P.R. China
| | - Shu-Fei Zang
- Center for Translational Medicine, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang 310015, P.R. China
| | - Jun-Ping Shi
- Center for Translational Medicine, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang 310015, P.R. China
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26
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Klepper A, Eng FJ, Doyle EH, El‐Shamy A, Rahman AH, Fiel MI, Avino GC, Lee M, Ye F, Roayaie S, Bansal MB, MacDonald MR, Schiano TD, Branch AD. Hepatitis C virus double-stranded RNA is the predominant form in human liver and in interferon-treated cells. Hepatology 2017; 66:357-370. [PMID: 27642141 PMCID: PMC5573989 DOI: 10.1002/hep.28846] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 08/25/2016] [Accepted: 08/27/2016] [Indexed: 12/25/2022]
Abstract
UNLABELLED Hepatitis C virus (HCV) is unique among RNA viruses in its ability to establish chronic infection in the majority of exposed adults. HCV persists in the liver despite interferon (IFN)-stimulated gene (ISG) induction; robust induction actually predicts treatment failure and viral persistence. It is unclear which forms of HCV RNA are associated with ISG induction and IFN resistance during natural infections. To thoroughly delineate HCV RNA populations, we developed conditions that fully separate the strands of long double-stranded RNA (dsRNA) and allow the released RNAs to be quantified in reverse transcription/polymerase chain reaction assays. These methods revealed that dsRNA, a pathogen-associated molecular pattern (PAMP), comprised 52% (standard deviation, 28%) of the HCV RNA in the livers of patients with chronic infection. HCV dsRNA was proportionally higher in patients with the unfavorable IL28B TT (rs12979860) genotype. Higher ratios of HCV double-stranded to single-stranded RNA (ssRNA) correlated positively with ISG induction. In Huh-7.5 cells, IFN treatment increased the total amount of HCV dsRNA through a process that required de novo viral RNA synthesis and shifted the ratio of viral dsRNA/ssRNA in favor of dsRNA. This shift was blocked by ribavirin (RBV), an antiviral drug that reduces relapse in HCV patients. Northern blotting established that HCV dsRNA contained genome-length minus strands. CONCLUSION HCV dsRNA is the predominant form in the HCV-infected liver and has features of both a PAMP and a genomic reservoir. Interferon treatment increased rather than decreased HCV dsRNA. This unexpected finding suggests that HCV produces dsRNA in response to IFN, potentially to antagonize antiviral defenses. (Hepatology 2017;66:357-370).
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Affiliation(s)
| | | | | | | | | | | | | | - Moonju Lee
- Icahn School of Medicine at Mount SinaiNew YorkNY
| | - Fei Ye
- Icahn School of Medicine at Mount SinaiNew YorkNY
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27
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Cantine MD, Fournier GP. Environmental Adaptation from the Origin of Life to the Last Universal Common Ancestor. ORIGINS LIFE EVOL B 2017; 48:35-54. [PMID: 28685374 DOI: 10.1007/s11084-017-9542-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 06/15/2017] [Indexed: 01/03/2023]
Abstract
Extensive fundamental molecular and biological evolution took place between the prebiotic origins of life and the state of the Last Universal Common Ancestor (LUCA). Considering the evolutionary innovations between these two endpoints from the perspective of environmental adaptation, we explore the hypothesis that LUCA was temporally, spatially, and environmentally distinct from life's earliest origins in an RNA world. Using this lens, we interpret several molecular biological features as indicating an environmental transition between a cold, radiation-shielded origin of life and a mesophilic, surface-dwelling LUCA. Cellularity provides motility and permits Darwinian evolution by connecting genetic material and its products, and thus establishing heredity and lineage. Considering the importance of compartmentalization and motility, we propose that the early emergence of cellularity is required for environmental dispersal and diversification during these transitions. Early diversification and the emergence of ecology before LUCA could be an important pre-adaptation for life's persistence on a changing planet.
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Affiliation(s)
- Marjorie D Cantine
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Gregory P Fournier
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA.
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28
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Lelle M, Freidel C, Kaloyanova S, Tabujew I, Schramm A, Musheev M, Niehrs C, Müllen K, Peneva K. Overcoming drug resistance by cell-penetrating peptide-mediated delivery of a doxorubicin dimer with high DNA-binding affinity. Eur J Med Chem 2017; 130:336-345. [DOI: 10.1016/j.ejmech.2017.02.056] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 02/23/2017] [Accepted: 02/24/2017] [Indexed: 12/15/2022]
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29
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Liberio MS, Sadowski MC, Davis RA, Rockstroh A, Vasireddy R, Lehman ML, Nelson CC. The ascidian natural product eusynstyelamide B is a novel topoisomerase II poison that induces DNA damage and growth arrest in prostate and breast cancer cells. Oncotarget 2016; 6:43944-63. [PMID: 26733491 PMCID: PMC4791278 DOI: 10.18632/oncotarget.6267] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Accepted: 10/08/2015] [Indexed: 12/25/2022] Open
Abstract
As part of an anti-cancer natural product drug discovery program, we recently identified eusynstyelamide B (EB), which displayed cytotoxicity against MDA-MB-231 breast cancer cells (IC50 = 5 μM) and induced apoptosis. Here, we investigated the mechanism of action of EB in cancer cell lines of the prostate (LNCaP) and breast (MDA-MB-231). EB inhibited cell growth (IC50 = 5 μM) and induced a G2 cell cycle arrest, as shown by a significant increase in the G2/M cell population in the absence of elevated levels of the mitotic marker phospho-histone H3. In contrast to MDA-MB-231 cells, EB did not induce cell death in LNCaP cells when treated for up to 10 days. Transcript profiling and Ingenuity Pathway Analysis suggested that EB activated DNA damage pathways in LNCaP cells. Consistent with this, CHK2 phosphorylation was increased, p21CIP1/WAF1 was up-regulated and CDC2 expression strongly reduced by EB. Importantly, EB caused DNA double-strand breaks, yet did not directly interact with DNA. Analysis of topoisomerase II-mediated decatenation discovered that EB is a novel topoisomerase II poison.
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Affiliation(s)
- Michelle S Liberio
- Australian Prostate Cancer Research Centre - Queensland, Institute of Health and Biomedical Innovation, Queensland University of Technology, Princess Alexandra Hospital, Translational Research Institute, Brisbane, Queensland, Australia.,Eskitis Institute for Drug Discovery, Griffith University, Nathan, Queensland, Australia
| | - Martin C Sadowski
- Australian Prostate Cancer Research Centre - Queensland, Institute of Health and Biomedical Innovation, Queensland University of Technology, Princess Alexandra Hospital, Translational Research Institute, Brisbane, Queensland, Australia
| | - Rohan A Davis
- Eskitis Institute for Drug Discovery, Griffith University, Nathan, Queensland, Australia
| | - Anja Rockstroh
- Australian Prostate Cancer Research Centre - Queensland, Institute of Health and Biomedical Innovation, Queensland University of Technology, Princess Alexandra Hospital, Translational Research Institute, Brisbane, Queensland, Australia
| | - Raj Vasireddy
- Australian Prostate Cancer Research Centre - Queensland, Institute of Health and Biomedical Innovation, Queensland University of Technology, Princess Alexandra Hospital, Translational Research Institute, Brisbane, Queensland, Australia
| | - Melanie L Lehman
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Colleen C Nelson
- Australian Prostate Cancer Research Centre - Queensland, Institute of Health and Biomedical Innovation, Queensland University of Technology, Princess Alexandra Hospital, Translational Research Institute, Brisbane, Queensland, Australia
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30
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The novel regulatory ncRNA, NfiS, optimizes nitrogen fixation via base pairing with the nitrogenase gene nifK mRNA in Pseudomonas stutzeri A1501. Proc Natl Acad Sci U S A 2016; 113:E4348-56. [PMID: 27407147 DOI: 10.1073/pnas.1604514113] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Unlike most Pseudomonas, the root-associated bacterium Pseudomonas stutzeri A1501 fixes nitrogen after the horizontal acquisition of a nitrogen-fixing (nif) island. A genome-wide search for small noncoding RNAs (ncRNAs) in P. stutzeri A1501 identified the novel P. stutzeri-specific ncRNA NfiS in the core genome, whose synthesis was significantly induced under nitrogen fixation or sorbitol stress conditions. The expression of NfiS was RNA chaperone Hfq-dependent and activated by the sigma factor RpoN/global nitrogen activator NtrC/nif-specific activator NifA regulatory cascade. The nfiS-deficient mutant displayed reduced nitrogenase activity, as well as increased sensitivity to multiple stresses, such as osmotic and oxidative stresses. Secondary structure prediction and complementation studies confirmed that a stem-loop structure was essential for NfiS to regulate the nitrogenase gene nifK mRNA synthesis and thus nitrogenase activity. Microscale thermophoresis and physiological analysis showed that NfiS directly pairs with nifK mRNA and ultimately enhances nitrogenase activity by increasing the translation efficiency and the half-life of nifK mRNA. Our data also suggest structural and functional divergence of NfiS evolution in diazotrophic and nondiazotrophic backgrounds. It is proposed that NfiS was recruited by nifK mRNA as a novel regulator to integrate the horizontally acquired nif island into host global networks.
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31
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Tan FL, Song RJ, Hu M, Li JH. Metal-Free Oxidative 1,2-Arylmethylation Cascades of N-(Arylsulfonyl)acrylamides Using Peroxides as the Methyl Resource. Org Lett 2016; 18:3198-201. [PMID: 27286238 DOI: 10.1021/acs.orglett.6b01419] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A new, metal-free oxidative 1,2-arylmethylation cascades of N-(arylsulfonyl)acrylamides for the assembly of 2,2-disubstituted-N-arylbutanamides containing an all-carbon quaternary center is presented. This reaction enables the one-step formation of two new C-C bonds through a sequence of methylation/1,4-aryl migration/desulfonylation using an organic peroxide as the methyl resource with a broad substrate scope and excellent functional group tolerance.
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Affiliation(s)
- Fang-Lin Tan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University , Changsha 410082, China
| | - Ren-Jie Song
- Key Laboratory of Jiangxi Province for Persistent Pollutants Control and Resources Recycle, Nanchang Hangkong University , Nanchang 330063, China
| | - Ming Hu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University , Changsha 410082, China
| | - Jin-Heng Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University , Changsha 410082, China.,Key Laboratory of Jiangxi Province for Persistent Pollutants Control and Resources Recycle, Nanchang Hangkong University , Nanchang 330063, China
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32
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Zou S, Toh JDW, Wong KHQ, Gao YG, Hong W, Woon ECY. N(6)-Methyladenosine: a conformational marker that regulates the substrate specificity of human demethylases FTO and ALKBH5. Sci Rep 2016; 6:25677. [PMID: 27156733 PMCID: PMC4860565 DOI: 10.1038/srep25677] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 04/21/2016] [Indexed: 01/08/2023] Open
Abstract
N6-Methyladenosine (m6A) is currently one of the most intensively studied post-transcriptional modifications in RNA. Due to its critical role in epigenetics and physiological links to several human diseases, it is also of tremendous biological and medical interest. The m6A mark is dynamically reversed by human demethylases FTO and ALKBH5, however the mechanism by which these enzymes selectively recognise their target transcripts remains unclear. Here, we report combined biophysical and biochemical studies on the specificity determinants of m6A demethylases, which led to the identification of an m6A-mediated substrate discrimination mechanism. Our results reveal that m6A itself serves as a ‘conformational marker’, which induces different conformational outcomes in RNAs depending on sequence context. This critically impacts its interactions with several m6A-recognising proteins, including FTO and ALKBH5. Remarkably, through the RNA-remodelling effects of m6A, the demethylases were able to discriminate substrates with very similar nucleotide sequences. Our findings provide novel insights into the biological functions of m6A modifications. The mechanism identified in this work is likely of significance to other m6A-recognising proteins.
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Affiliation(s)
- Shui Zou
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore 117 543, Singapore
| | - Joel D W Toh
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore 117 543, Singapore.,Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138 673, Singapore
| | - Kendra H Q Wong
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore 117 543, Singapore
| | - Yong-Gui Gao
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138 673, Singapore.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637 551, Singapore
| | - Wanjin Hong
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138 673, Singapore
| | - Esther C Y Woon
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore 117 543, Singapore
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33
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Wang SK, Su HF, Gu YC, Lin SL, Tan JH, Huang ZS, Ou TM. Complicated behavior of G-quadruplexes and evaluating G-quadruplexes' ligands in various systems mimicking cellular circumstance. Biochem Biophys Rep 2015; 5:439-447. [PMID: 28955851 PMCID: PMC5600415 DOI: 10.1016/j.bbrep.2015.09.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Revised: 09/23/2015] [Accepted: 09/25/2015] [Indexed: 01/09/2023] Open
Abstract
Environments surrounding G-rich sequences remarkably affect the conformations of these structures. A proper evaluation system mimicking the crowded environment in a cell with macromolecules should be developed to perform structural and functional studies on G-quadruplexes. In this study, the topology and stability of a G-quadruplex formed by human telomeric repeat sequences were investigated in a macromolecule-crowded environment created by polyethylene glycol 200 (PEG200), tumor cell extract, and Xenopus laevis egg extract. The interactions between small molecules and telomeric G-quadruplexes were also evaluated in the different systems. The results suggested that the actual behavior of G-quadruplex structures in cells extract is quite different from that in the PEG crowding system, and proteins or other factors in extracts might play a very important role in G-quadruplex structures. Cell-free system was constructed using HL60 cell extract. Topologies and stability of G-quadruplexes were identified in different systems. G-quadruplex’s ligands’ effects were evaluated in different systems.
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Affiliation(s)
- Shi-Ke Wang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Hua-Fei Su
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Yu-Chao Gu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Shu-Ling Lin
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Jia-Heng Tan
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Zhi-Shu Huang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Tian-Miao Ou
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China
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34
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Vélez-Cordero JR, Hernández-Cordero J. On the Motion of Carbon Nanotube Clusters near Optical Fiber Tips: Thermophoresis, Radiative Pressure, and Convection Effects. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:10066-10075. [PMID: 26309145 DOI: 10.1021/acs.langmuir.5b02448] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We analyze the motion of multiwalled carbon nanotubes clusters in water or ethanol upon irradiation with a 975 and 1550 nm laser beam guided by an optical fiber. Upon measuring the velocities of the nanotube clusters in and out of the laser beam cone, we were able to identify thermophoresis, convection and radiation pressure as the main driving forces that determine the equilibrium position of the dispersion at low optical powers: while thermophoresis and convection pull the clusters toward the laser beam axis (negative Soret coefficient), radiation pressure pushes the clusters away from the fiber tip. A theoretical solution for the thermophoretic velocity, which considers interfacial motion and a repulsive potential interaction between the nanotubes and the solvent (hydrophobic interaction), shows that the main mechanism implicated in this type of thermophoresis is the thermal expansion of the fluid, and that the clusters migrate to hotter regions with a characteristic thermal diffusion coefficient D(T) of 9 × 10(-7) cm(2) K(-1) s(-1). We further show that the characteristic length associated with thermophoresis is not that of the nanotube clusters size, O(1) μm, but that corresponding to the microstructure of the clusters, O(1) nm. We finally discuss the role of the formation of gas-liquid interfaces (microbubbles) at high optical powers on the deposition of carbon nanotubes on the optical fiber end faces.
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Affiliation(s)
- J Rodrigo Vélez-Cordero
- Instituto de Física, Universidad Autónoma de San Luis Potosí , Alvaro Obregón 64, 78000 San Luis Potosí, S.L.P., México
- Cátedras CONACyT, Dirección Adjunta de Desarrollo Científico del CONACyT, Av. Insurgentes Sur 1582, México D.F. 03940, México
| | - J Hernández-Cordero
- Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México , Apdo. Postal 70-360, México D.F. 04510, México
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35
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Jerabek-Willemsen M, André T, Wanner R, Roth HM, Duhr S, Baaske P, Breitsprecher D. MicroScale Thermophoresis: Interaction analysis and beyond. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.03.009] [Citation(s) in RCA: 171] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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36
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Nicholson P, Josi C, Kurosawa H, Yamashita A, Mühlemann O. A novel phosphorylation-independent interaction between SMG6 and UPF1 is essential for human NMD. Nucleic Acids Res 2014; 42:9217-35. [PMID: 25053839 PMCID: PMC4132754 DOI: 10.1093/nar/gku645] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Eukaryotic mRNAs with premature translation-termination codons (PTCs) are recognized and eliminated by nonsense-mediated mRNA decay (NMD). NMD substrates can be degraded by different routes that all require phosphorylated UPF1 (P-UPF1) as a starting point. The endonuclease SMG6, which cleaves mRNA near the PTC, is one of the three known NMD factors thought to be recruited to nonsense mRNAs via an interaction with P-UPF1, leading to eventual mRNA degradation. By artificial tethering of SMG6 and mutants thereof to a reporter mRNA combined with knockdowns of various NMD factors, we demonstrate that besides its endonucleolytic activity, SMG6 also requires UPF1 and SMG1 to reduce reporter mRNA levels. Using in vivo and in vitro approaches, we further document that SMG6 and the unique stalk region of the UPF1 helicase domain, along with a contribution from the SQ domain, form a novel interaction and we also show that this region of the UPF1 helicase domain is critical for SMG6 function and NMD. Our results show that this interaction is required for NMD and for the capability of tethered SMG6 to degrade its bound RNA, suggesting that it contributes to the intricate regulation of UPF1 and SMG6 enzymatic activities.
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Affiliation(s)
- Pamela Nicholson
- Department of Chemistry and Biochemistry, University of Berne, Berne, CH-3012, Switzerland
| | - Christoph Josi
- Department of Chemistry and Biochemistry, University of Berne, Berne, CH-3012, Switzerland
| | - Hitomi Kurosawa
- Department of Microbiology, Yokohama City University, School of Medicine, 3-9, Fuku-ura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Akio Yamashita
- Department of Microbiology, Yokohama City University, School of Medicine, 3-9, Fuku-ura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Oliver Mühlemann
- Department of Chemistry and Biochemistry, University of Berne, Berne, CH-3012, Switzerland
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37
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Knez K, Spasic D, Janssen KPF, Lammertyn J. Emerging technologies for hybridization based single nucleotide polymorphism detection. Analyst 2014; 139:353-70. [PMID: 24298558 DOI: 10.1039/c3an01436c] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Detection of single nucleotide polymorphisms (SNPs) is a crucial challenge in the development of a novel generation of diagnostic tools. Accurate detection of SNPs can prove elusive, as the impact of a single variable nucleotide on the properties of a target sequence is limited, even if this sequence consists of only a few nucleotides. New, accurate and facile strategies for the detection of point mutations are therefore absolutely necessary for the increased adoption of point-of-care molecular diagnostics. Currently, PCR and sequencing are mostly applied for diagnosing SNPs. However these methods have serious drawbacks as routine diagnostic tools because of their labour intensity and cost. Several new, more suitable methods can be applied to enable sensitive detection of mutations based on specially designed hybridization probes, mutation recognizing enzymes and thermal denaturation. Here, an overview is presented of the most recent advances in the field of fast and sensitive SNP detection assays with strong potential for integration in point-of-care tests.
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Affiliation(s)
- Karel Knez
- KU Leuven, BIOSYST-MeBioS, Willem de Croylaan 42, Leuven, Belgium.
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38
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Wolff M, Braun D, Nash MA. Detection of thermoresponsive polymer phase transition in dilute low-volume format by microscale thermophoretic depletion. Anal Chem 2014; 86:6797-803. [PMID: 24820008 DOI: 10.1021/ac5008283] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Environmentally responsive polymers are becoming increasingly important in the biomaterials field for use as diagnostic reagents, drug carriers, and tissue engineering scaffolds. Characterizing polymer phase transitions by cloud point curves typically requires large milliliter volumes of sample at high micromolar solution concentrations. Here we present a method based on quantification of thermophoretic Soret diffusion that allows determination of polymer phase transitions using only ~1 μL of liquid at dilute nanomolar concentrations, effectively reducing the amount of sample required by a factor of 10(6). We prepared an oligo(ethylene glycol) (OEG) methyl ether methacrylate copolymer via RAFT polymerization. End-group modification with fluorescent BODIPY-maleimide provided a dye-labeled pOEG-BODIPY conjugate with a lower critical solution temperature (LCST) in the range of ~25-35 °C. Thermophoresis measurements in dilute solution demonstrated a marked change in polymer thermodiffusion in the vicinity of the LCST. We measured the temperature dependence of thermodiffusion and transformed these data sets into sigmoidal curves characterizing the phase transition of the polymer. Finite element modeling suggested a correction to the measured values that brought the transition temperatures measured by thermophoresis into accord with the cloud point curves. Our results demonstrate that observation of polymer thermodiffusion in a low volume dilute format is a facile method for determining polymer phase transition temperatures.
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Affiliation(s)
- Manuel Wolff
- Systems Biophysics, Ludwig-Maximilians-Universität , D-80799 Munich, Germany
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Yang AHJ, Hsieh K, Patterson AS, Ferguson BS, Eisenstein M, Plaxco KW, Soh HT. Accurate zygote-specific discrimination of single-nucleotide polymorphisms using microfluidic electrochemical DNA melting curves. Angew Chem Int Ed Engl 2014; 53:3163-7. [PMID: 24520069 PMCID: PMC3992926 DOI: 10.1002/anie.201310059] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Indexed: 01/17/2023]
Abstract
We report the first electrochemical system for the detection of single-nucleotide polymorphisms (SNPs) that can accurately discriminate homozygous and heterozygous genotypes using microfluidics technology. To achieve this, our system performs real-time melting-curve analysis of surface-immobilized hybridization probes. As an example, we used our sensor to analyze two SNPs in the apolipoprotein E (ApoE) gene, where homozygous and heterozygous mutations greatly affect the risk of late-onset Alzheimer's disease. Using probes specific for each SNP, we simultaneously acquired melting curves for probe-target duplexes at two different loci and thereby accurately distinguish all six possible ApoE allele combinations. Since the design of our device and probes can be readily adapted for targeting other loci, we believe that our method offers a modular platform for the diagnosis of SNP-based diseases and personalized medicine.
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Affiliation(s)
- Allen H. J. Yang
- Department of Mechanical Engineering, University of California Santa Barbara (USA)
| | - Kuangwen Hsieh
- Department of Mechanical Engineering, University of California Santa Barbara (USA)
| | - Adriana S. Patterson
- Department of Chemistry and Biochemistry and Biomolecular Science and Engineering Program, University of California, Santa Barbara (USA)
| | - B. Scott Ferguson
- Department of Mechanical Engineering, University of California Santa Barbara (USA)
| | - Michael Eisenstein
- Department of Mechanical Engineering, University of California Santa Barbara (USA)
| | - Kevin W. Plaxco
- Department of Chemistry and Biochemistry and Biomolecular Science and Engineering Program, University of California, Santa Barbara (USA)
| | - H. Tom Soh
- Materials Department and Department of Mechanical Engineering University of California, Santa Barbara, Santa Barbara, CA 93106 (USA)
- Department of Mechanical Engineering, University of California Santa Barbara (USA)
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Yang AHJ, Hsieh K, Patterson AS, Ferguson BS, Eisenstein M, Plaxco KW, Soh HT. Accurate Zygote-Specific Discrimination of Single-Nucleotide Polymorphisms Using Microfluidic Electrochemical DNA Melting Curves. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201310059] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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41
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Schulz S, Doller A, Pendini NR, Wilce JA, Pfeilschifter J, Eberhardt W. Domain-specific phosphomimetic mutation allows dissection of different protein kinase C (PKC) isotype-triggered activities of the RNA binding protein HuR. Cell Signal 2013; 25:2485-95. [PMID: 23978401 DOI: 10.1016/j.cellsig.2013.08.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 08/06/2013] [Accepted: 08/15/2013] [Indexed: 01/21/2023]
Abstract
The ubiquitous mRNA binding protein human antigen R (HuR) participates in the post-transcriptional regulation of many AU-rich element (ARE)-bearing mRNAs. Previously, by using in vitro kinase assay, we have identified serines (Ser) 158, 221 and 318 as targets of protein kinase C (PKC)-triggered phosphorylation. In this study, we tested whether GFP- or GST-tagged HuR constructs bearing a phosphomimetic Ser (S)-to-Asp (D) substitution at the different PKC target sites, would affect different HuR functions including HuR nucleo-cytoplasmic redistribution and binding to different types of ARE-containing mRNAs. The phosphomimetic GFP-tagged HuR protein bearing a phosphomimetic substitution in the hinge region of HuR (HuR-S221D) showed an increased cytoplasmic abundance when compared to wild-type HuR. Conversely, data from in vitro kinase assay and electrophoretic mobility shift assay (EMSA), implicates that phosphorylation at Ser 221 is not relevant for mRNA binding of HuR. Quantification of in vitro binding affinities of GST-tagged wild-type HuR and corresponding HuR proteins bearing a phosphomimetic substitution in either RRM2 (HuR-S158D) or in RRM3 (HuR-S318D) by microscale thermophoresis (MST) indicates a specific binding of wild-type HuR to type I, II or type III-ARE-oligonucleotides in the high nanomolar range. Interestingly, phosphomimetic mutation at position 158 or 318 had a negative influence on HuR binding to type I- and type II-ARE-mRNAs whereas it significantly enhanced HuR affinity to a type III-ARE substrate. Our data suggest that differential phosphorylation of HuR by PKCs at different HuR domains coordinates subcellular HuR distribution and leads to a preferential binding to U-rich bearing target mRNA.
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Affiliation(s)
- Sebastian Schulz
- pharmazentrum frankfurt/ZAFES, Klinikum der Johann Wolfgang Goethe-Universität, Frankfurt am Main, Germany
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Chursov A, Kopetzky SJ, Bocharov G, Frishman D, Shneider A. RNAtips: Analysis of temperature-induced changes of RNA secondary structure. Nucleic Acids Res 2013; 41:W486-91. [PMID: 23766288 PMCID: PMC3692058 DOI: 10.1093/nar/gkt486] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Although multiple biological phenomena are related to temperature (e.g. elevation of body temperature due to an illness, adaptation to environmental temperature conditions, biology of coldblooded versus warm-blooded organisms), the molecular mechanisms of these processes remain to be understood. Perturbations of secondary RNA structures may play an important role in an organism’s reaction to temperature change—in all organisms from viruses and bacteria to humans. Here, we present RNAtips (temperature-induced perturbation of structure) web server, which can be used to predict regions of RNA secondary structures that are likely to undergo structural alterations prompted by temperature change. The server can also be used to: (i) detect those regions in two homologous RNA sequences that undergo different structural perturbations due to temperature change and (ii) test whether these differences are specific to the particular nucleotide substitutions distinguishing the sequences. The RNAtips web server is freely accessible without any login requirement at http://rnatips.org.
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Affiliation(s)
- Andrey Chursov
- Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftzentrum Weihenstephan, Maximus-von-Imhof-Forum 3, D-85354 Freising, Germany
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43
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Zhang Y, Guo Y, Quirke P, Zhou D. Ultrasensitive single-nucleotide polymorphism detection using target-recycled ligation, strand displacement and enzymatic amplification. NANOSCALE 2013; 5:5027-5035. [PMID: 23636707 PMCID: PMC4576341 DOI: 10.1039/c3nr01010d] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 04/04/2013] [Indexed: 05/29/2023]
Abstract
We report herein the development of a highly sensitive and selective approach for label-free DNA detection by combining target-recycled ligation (TRL), magnetic nanoparticle assisted target capture/separation, and efficient enzymatic amplification. We show that our approach can detect as little as 30 amol (600 fM in 50 μL) of unlabelled single-stranded DNA targets and offer an exquisitely high discrimination ratio (up to >380 fold with background correction) between a perfect-match cancer mutant and its single-base mismatch (wild-type) DNA target. Furthermore, it can quantitate the rare cancer mutant (KRAS codon 12) in a large excess of coexisting wild-type DNAs down to 0.75%. This sensor appears to be well-suited for sensitive SNP detection and a wide range of DNA mutation based diagnostic applications.
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Affiliation(s)
- Yue Zhang
- School of Chemistry and Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , UK . ; ; Fax: +44 (0)113 3436565
| | - Yuan Guo
- School of Chemistry and Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , UK . ; ; Fax: +44 (0)113 3436565
| | - Philip Quirke
- Section of Pathology and Tumour Biology , Leeds Institute of Molecular Medicine , University of Leeds , Wellcome Trust Brenner Building, St James's University Hospital , Leeds LS9 7TF , UK
| | - Dejian Zhou
- School of Chemistry and Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , UK . ; ; Fax: +44 (0)113 3436565
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Eilebrecht S, Wilhelm E, Benecke BJ, Bell B, Benecke AG. HMGA1 directly interacts with TAR to modulate basal and Tat-dependent HIV transcription. RNA Biol 2013; 10:436-44. [PMID: 23392246 DOI: 10.4161/rna.23686] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The transactivating response element (TAR) of human immunodeficiency virus 1 (HIV-1) is essential for promoter transactivation by the viral transactivator of transcription (Tat). The Tat-TAR interaction thereby recruits active positive transcription elongation factor b (P-TEFb) from its inactive, 7SK/HEXIM1-bound form, leading to efficient viral transcription. Here, we show that the 7SK RNA-associating chromatin regulator HMGA1 can specifically bind to the HIV-1 TAR element and that 7SK RNA can thereby compete with TAR. The HMGA1-binding interface of TAR is located within the binding site for Tat and other cellular activators, and we further provide evidence for competition between HMGA1 and Tat for TAR-binding. HMGA1 negatively influences the expression of a HIV-1 promoter-driven reporter in a TAR-dependent manner, both in the presence and in the absence of Tat. The overexpression of the HMGA1-binding substructure of 7SK RNA results in a TAR-dependent gain of HIV-1 promoter activity similar to the effect of the shRNA-mediated knockdown of HMGA1. Our results support a model in which the HMGA1/TAR interaction prevents the binding of transcription-activating cellular co-factors and Tat, subsequently leading to reduced HIV-1 transcription.
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Affiliation(s)
- Sebastian Eilebrecht
- Institut des Hautes Études Scientifiques - Centre National de la Recherche Scientifique; Bures sur Yvette; France & Vaccine Research Institute; Institut Mondor de Recherche Biomédicale; Créteil, France
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Blech M, Peter D, Fischer P, Bauer MM, Hafner M, Zeeb M, Nar H. One Target—Two Different Binding Modes: Structural Insights into Gevokizumab and Canakinumab Interactions to Interleukin-1β. J Mol Biol 2013; 425:94-111. [DOI: 10.1016/j.jmb.2012.09.021] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 09/17/2012] [Accepted: 09/26/2012] [Indexed: 10/27/2022]
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Molecular structure of human GM-CSF in complex with a disease-associated anti-human GM-CSF autoantibody and its potential biological implications. Biochem J 2012; 447:205-15. [PMID: 22839360 DOI: 10.1042/bj20120884] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Polyclonal autoantibodies against human GM-CSF (granulocyte/macrophage colony-stimulating factor) are a hallmark of PAP (pulmonary alveolar proteinosis) and several other reported autoimmune diseases. MB007 is a high-affinity anti-(human GM-CSF) autoantibody isolated from a patient suffering from PAP which shows only modest neutralization of GM-CSF bioactivity. We describe the first crystal structure of a cytokine-directed human IgG1λ autoantibody-binding fragment (Fab) at 1.9 Å (1 Å=0.1 nm) resolution. Its CDR3-H substantially differs from all VH7 germline IgG1 structures reported previously. We derive a reliable model of the antigen-autoantibody complex by using NMR chemical shift perturbation data in combination with computational methods. Superposition of the modelled complex structure with the human GM-CSF-GM-CSF ternary receptor complex reveals only little overlap between receptor and Fab when bound to GM-CSF. Our model provides a structural basis for understanding the mode of action of the MB007 autoantibody.
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Abstract
We investigate the thermal diffusion behavior of aqueous solutions of nucleotides using an infrared thermal diffusion forced Rayleigh scattering (IR-TDFRS) setup. In this work we study 5 nucleotides: cyclic nucleotides adenosine and guanosine monophosphate, 5'-adenosine and 5'-cytidine monophosphate, and also adenosine diphosphate in water. The structures of nucleotides vary systematically, which results in different physical properties such as acidity, solubility, hydrophobicity, and melting point. We discuss the connection between the thermal diffusion behavior and the properties of the different nucleotides. Additionally, as in the case of the alkanes and monoscaccharides, we find a correlation between the thermal diffusion coefficient and the ratio of the thermal expansion coefficient and the kinematic viscosity.
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Affiliation(s)
- Zilin Wang
- ICS-Soft Condensed Matter, Forschungszentrum Jülich GmbH, D-52428 Jülich, Germany.
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Krammer H, Möller FM, Braun D. Thermal, autonomous replicator made from transfer RNA. PHYSICAL REVIEW LETTERS 2012; 108:238104. [PMID: 23003995 DOI: 10.1103/physrevlett.108.238104] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2012] [Indexed: 06/01/2023]
Abstract
Evolving systems rely on the storage and replication of genetic information. Here we present an autonomous, purely thermally driven replication mechanism. A pool of hairpin molecules, derived from transfer RNA replicates the succession of a two-letter code. Energy is first stored thermally in metastable hairpins. Thereafter, energy is released by a highly specific and exponential replication with a duplication time of 30 s, which is much faster than the tendency to produce false positives in the absence of template. Our experiments propose a physical rather than a chemical scenario for the autonomous replication of protein encoding information in a disequilibrium setting.
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Affiliation(s)
- Hubert Krammer
- Systems Biophysics, Physics Department, Center for Nanoscience, Ludwig Maximilians Universität München, Amalienstrasse 54, 80799 München, Germany
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Largy E, Hamon F, Teulade-Fichou MP. A streptavidin paramagnetic-particle based competition assay for the evaluation of the optical selectivity of quadruplex nucleic acid fluorescent probes. Methods 2012; 57:129-37. [PMID: 22406492 DOI: 10.1016/j.ymeth.2012.02.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Revised: 02/18/2012] [Accepted: 02/20/2012] [Indexed: 01/29/2023] Open
Abstract
Although quadruplex nucleic acids are thought to be involved in many biological processes, they are massively overwhelmed by duplex DNA in the cell. Small molecules, able to probe quadruplex nucleic acids with high optical selectivity, could possibly achieve the visualization of these processes. The aim of the method described herein is to evaluate quickly the optical selectivity of quadruplex nucleic acid probes, in isothermal conditions, using widely available materials, small quantities of oligonucleotides and virtually any kind and quantity of biological competitor. The assay relies on the use of streptavidin-coated paramagnetic particles and biotinylated quadruplex forming oligonucleotides, allowing a quick and easy separation of the quadruplex target from the competitor. In the present study, two quadruplex nucleic acids (the DNA and RNA human telomeric repeats) have been used as targets while a duplex DNA oligonucleotide, total DNA, total RNA, another quadruplex nucleic acid and a protein have been used as competitors. The optical selectivity of various probes, displaying different photophysical properties and binding selectivities, has been successfully examined, allowing the identification of a best candidate for further cell microscopy experiments. This assay allows a quick and reliable assessment of the labeling properties of a quadruplex binder in cellular environment conditions. It is an interesting alternative to gel electrophoresis experiments since it is performed in solution, has a well-resolved separation system and allows easy quantifications.
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Affiliation(s)
- Eric Largy
- UMR 176 - Synthèse et Vectorisation de Biomolécules, Institut Curie, Bât. 110-112, Université Paris-Sud, 91405 Orsay, France.
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Jerabek-Willemsen M, Wienken CJ, Braun D, Baaske P, Duhr S. Molecular interaction studies using microscale thermophoresis. Assay Drug Dev Technol 2012; 9:342-53. [PMID: 21812660 DOI: 10.1089/adt.2011.0380] [Citation(s) in RCA: 575] [Impact Index Per Article: 47.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Abstract The use of infrared laser sources for creation of localized temperature fields has opened new possibilities for basic research and drug discovery. A recently developed technology, Microscale Thermophoresis (MST), uses this temperature field to perform biomolecular interaction studies. Thermophoresis, the motion of molecules in temperature fields, is very sensitive to changes in size, charge, and solvation shell of a molecule and thus suited for bioanalytics. This review focuses on the theoretical background of MST and gives a detailed overview on various applications to demonstrate the broad applicability. Experiments range from the quantification of the affinity of low-molecular-weight binders using fluorescently labeled proteins, to interactions between macromolecules and multi-component complexes like receptor containing liposomes. Information regarding experiment and experimental setup is based on the Monolith NT.115 instrument (NanoTemper Technologies GmbH).
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