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Karachevtsev MV, Valeev VA, Karachevtsev VA. Interaction of double-stranded polynucleotide poly(A:U) with graphene/graphene oxide. Eur Phys J E Soft Matter 2021; 44:24. [PMID: 33686498 DOI: 10.1140/epje/s10189-021-00030-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/29/2021] [Indexed: 06/12/2023]
Abstract
Hybrids formed by DNA/RNA and graphene family nanomaterials are considered as potentially useful multifunctional agents in biosensing and nanomedicine. In this work, we study the noncovalent interaction between double-stranded (ds) RNA, polyadenylic:polyuridylic acids (poly(A:U)) and graphene oxide/graphene (GO/Gr) using UV absorption spectroscopy and molecular dynamics (MD) simulations. RNA melting showed that relatively long ds-RNA is adsorbed onto GO (at an ionic strength of [Formula: see text]) at that a large fraction of RNA maintains the duplex structure. It was revealed that this fraction decreases over long time (during a few days), indicating a slow adsorption process of the long polymer. MD simulations showed that the adsorption of duplex (rA)[Formula: see text]: (rU)[Formula: see text] or (rA)[Formula: see text]: (rU)[Formula: see text] on graphene starts with the interaction between [Formula: see text]-systems of graphene and base pairs located at a duplex tail. In contrast to relatively long duplex (rA)[Formula: see text]: (rU)[Formula: see text] which keeps parallel arrangement along the graphene surface, the shorter one ((rA)[Formula: see text]: (rU)[Formula: see text]) always adopts a perpendicular orientation relative to graphene even in case of the initial parallel orientation. It was found out that (rA)[Formula: see text]: (rU)[Formula: see text] forms the stable hybrid with graphene keeping essential fraction of the duplex, while (rA)[Formula: see text]: (rU)[Formula: see text] demonstrates the duplex unzipping into two single strands with time. The interaction energies between adenine/uracil stacked with graphene as well between nucleotides in water environment were determined.
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Affiliation(s)
- Maksym V Karachevtsev
- B. Verkin Institute for Low Temperature Physics and Engineering, National Academy of Sciences of Ukraine, 47, Nauky Ave., Kharkiv, 61103, Ukraine.
| | - Vladimir A Valeev
- B. Verkin Institute for Low Temperature Physics and Engineering, National Academy of Sciences of Ukraine, 47, Nauky Ave., Kharkiv, 61103, Ukraine
| | - Victor A Karachevtsev
- B. Verkin Institute for Low Temperature Physics and Engineering, National Academy of Sciences of Ukraine, 47, Nauky Ave., Kharkiv, 61103, Ukraine
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2
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Regy RM, Dignon GL, Zheng W, Kim YC, Mittal J. Sequence dependent phase separation of protein-polynucleotide mixtures elucidated using molecular simulations. Nucleic Acids Res 2020; 48:12593-12603. [PMID: 33264400 PMCID: PMC7736803 DOI: 10.1093/nar/gkaa1099] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 10/21/2020] [Accepted: 10/27/2020] [Indexed: 12/22/2022] Open
Abstract
Ribonucleoprotein (RNP) granules are membraneless organelles (MLOs), which majorly consist of RNA and RNA-binding proteins and are formed via liquid-liquid phase separation (LLPS). Experimental studies investigating the drivers of LLPS have shown that intrinsically disordered proteins (IDPs) and nucleic acids like RNA and other polynucleotides play a key role in modulating protein phase separation. There is currently a dearth of modelling techniques which allow one to delve deeper into how polynucleotides play the role of a modulator/promoter of LLPS in cells using computational methods. Here, we present a coarse-grained polynucleotide model developed to fill this gap, which together with our recently developed HPS model for protein LLPS, allows us to capture the factors driving protein-polynucleotide phase separation. We explore the capabilities of the modelling framework with the LAF-1 RGG system which has been well studied in experiments and also with the HPS model previously. Further taking advantage of the fact that the HPS model maintains sequence specificity we explore the role of charge patterning on controlling polynucleotide incorporation into condensates. With increased charge patterning we observe formation of structured or patterned condensates which suggests the possible roles of polynucleotides in not only shifting the phase boundaries but also introducing microscopic organization in MLOs.
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Affiliation(s)
- Roshan Mammen Regy
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA 18015, USA
| | - Gregory L Dignon
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA 18015, USA
| | - Wenwei Zheng
- College of Integrative Sciences and Arts, Arizona State University, Mesa, AZ 85212, USA
| | - Young C Kim
- Center for Materials Physics and Technology, Naval Research Laboratory, Washington, DC 20375, USA
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA 18015, USA
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3
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Bentin J, Balme S, Picaud F. Polynucleotide differentiation using hybrid solid-state nanopore functionalizing with α-hemolysin. Soft Matter 2020; 16:1002-1010. [PMID: 31853534 DOI: 10.1039/c9sm01833f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We report results from full atomistic molecular dynamics simulations on the properties of biomimetic nanopores. This latter result was obtained through the direct insertion of an α-hemolysin protein inside a hydrophobic solid-state nanopore. Upon translocation of different DNA strands, we demonstrate here that the theoretical system presents the same discrimination properties as the experimental one obtained previously. This opens an interesting way to promote the stability of a specific protein inside a solid nanopore to develop further biomimetic applications for DNA or protein sequencing.
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Affiliation(s)
- Jérémy Bentin
- Laboratoire de Nanomédecine, Imagerie et Thérapeutique, EA 4662, Université Bourgogne-Franche-Comté (UFR Sciences et Techniques), Centre Hospitalier Universitaire de Besançon, 16 route de Gray, 25030 Besançon, France.
| | - Sébastien Balme
- Institut Européen des Membranes, UMR5635 UM ENSCM CNRS, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Fabien Picaud
- Laboratoire de Nanomédecine, Imagerie et Thérapeutique, EA 4662, Université Bourgogne-Franche-Comté (UFR Sciences et Techniques), Centre Hospitalier Universitaire de Besançon, 16 route de Gray, 25030 Besançon, France.
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4
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Kowiel M, Brzezinski D, Gilski M, Jaskolski M. Conformation-dependent restraints for polynucleotides: the sugar moiety. Nucleic Acids Res 2020; 48:962-973. [PMID: 31799624 PMCID: PMC6954431 DOI: 10.1093/nar/gkz1122] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 11/09/2019] [Accepted: 11/14/2019] [Indexed: 01/01/2023] Open
Abstract
Stereochemical restraints are commonly used to aid the refinement of macromolecular structures obtained by experimental methods at lower resolution. The standard restraint library for nucleic acids has not been updated for over two decades and needs revision. In this paper, geometrical restraints for nucleic acids sugars are derived using information from high-resolution crystal structures in the Cambridge Structural Database. In contrast to the existing restraints, this work shows that different parts of the sugar moiety form groups of covalent geometry dependent on various chemical and conformational factors, such as the type of ribose or the attached nucleobase, and ring puckering or rotamers of the glycosidic (χ) or side-chain (γ) torsion angles. Moreover, the geometry of the glycosidic link and the endocyclic ribose bond angles are functionally dependent on χ and sugar pucker amplitude (τm), respectively. The proposed restraints have been positively validated against data from the Nucleic Acid Database, compared with an ultrahigh-resolution Z-DNA structure in the Protein Data Bank, and tested by re-refining hundreds of crystal structures in the Protein Data Bank. The conformation-dependent sugar restraints presented in this work are publicly available in REFMAC, PHENIX and SHELXL format through a dedicated RestraintLib web server with an API function.
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Affiliation(s)
- Marcin Kowiel
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
| | - Dariusz Brzezinski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
- Institute of Computing Science, Poznan University of Technology, Poznan 60-965, Poland
- Center for Artificial Intelligence and Machine Learning, Poznan University of Technology, Poznan 60-965, Poland
| | - Miroslaw Gilski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan 61-614, Poland
| | - Mariusz Jaskolski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan 61-614, Poland
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5
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Jeong S, Yang D, Beyene AG, Del Bonis-O’Donnell JT, Gest AMM, Navarro N, Sun X, Landry MP. High-throughput evolution of near-infrared serotonin nanosensors. Sci Adv 2019; 5:eaay3771. [PMID: 31897432 PMCID: PMC6920020 DOI: 10.1126/sciadv.aay3771] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 10/30/2019] [Indexed: 05/11/2023]
Abstract
Imaging neuromodulation with synthetic probes is an emerging technology for studying neurotransmission. However, most synthetic probes are developed through conjugation of fluorescent signal transducers to preexisting recognition moieties such as antibodies or receptors. We introduce a generic platform to evolve synthetic molecular recognition on the surface of near-infrared fluorescent single-wall carbon nanotube (SWCNT) signal transducers. We demonstrate evolution of molecular recognition toward neuromodulator serotonin generated from large libraries of ~6.9 × 1010 unique ssDNA sequences conjugated to SWCNTs. This probe is reversible and produces a ~200% fluorescence enhancement upon exposure to serotonin with a K d = 6.3 μM, and shows selective responsivity over serotonin analogs, metabolites, and receptor-targeting drugs. Furthermore, this probe remains responsive and reversible upon repeat exposure to exogenous serotonin in the extracellular space of acute brain slices. Our results suggest that evolution of nanosensors could be generically implemented to develop other neuromodulator probes with synthetic molecular recognition.
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Affiliation(s)
- Sanghwa Jeong
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Darwin Yang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Abraham G. Beyene
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | | | - Anneliese M. M. Gest
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Nicole Navarro
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Xiaoqi Sun
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Markita P. Landry
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
- Innovative Genomics Institute (IGI), Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, Berkeley, CA 94720, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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6
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Wang F, Zhao D, Dong H, Jiang L, Huang L, Liu Y, Li S. THz spectra and corresponding vibrational modes of DNA base pair cocrystals and polynucleotides. Spectrochim Acta A Mol Biomol Spectrosc 2018; 200:195-201. [PMID: 29689511 DOI: 10.1016/j.saa.2018.04.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/26/2018] [Accepted: 04/12/2018] [Indexed: 05/22/2023]
Abstract
The generalized energy-based fragmentation (GEBF) approach has been applied to study the THz spectra and vibrational modes of base pair cocrystals under periodic boundary conditions (denoted as PBC-GEBF). Results of vibrational mode reveal that hydrogen bonds play a pivotal role in the pairing process of base crystals, where most NH and CH bonds stretch to some extent. We also found that hydrogen bonds of a self-made A:T cocrystal completely break in a transition from liquid to the solid state, while self-made C:G cocrystal is different and easier to form a cocrystal, as confirmed by X-ray diffraction (XRD) and terahertz (THz) spectra. Furthermore, we have studied DNA polynucleotides (in both A and B forms) found that the vibrational modes changed a lot during the process of their forming double strand. Despite the key role played by hydrogen bonds, the key contribution originates from collective motions of the main skeleton. A comparative study of the spectra of some stranded fragments suggests that different sequences or forms have similar spectra in THz band. They distinguish from each other mainly in the low-frequency regions, especially below 1 THz. This study would make great contributions to the molecular dynamics model based DNA long-chain structure simulation in the future study.
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Affiliation(s)
- Fang Wang
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, People's Republic of China; School of Electronic and Information Engineering, Sanjiang University, Nanjing 210012, People's Republic of China
| | - Dongbo Zhao
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Hao Dong
- Kuang Yaming Honors School, Nanjing University, 210023, People's Republic of China
| | - Ling Jiang
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Lin Huang
- Forestry College, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Yunfei Liu
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, People's Republic of China.
| | - Shuhua Li
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
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7
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Sulkowska JI, Niewieczerzal S, Jarmolinska AI, Siebert JT, Virnau P, Niemyska W. KnotGenome: a server to analyze entanglements of chromosomes. Nucleic Acids Res 2018; 46:W17-W24. [PMID: 29905836 PMCID: PMC6030981 DOI: 10.1093/nar/gky511] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 05/05/2018] [Accepted: 05/23/2018] [Indexed: 02/03/2023] Open
Abstract
The KnotGenome server enables the topological analysis of chromosome model data using three-dimensional coordinate files of chromosomes as input. In particular, it detects prime and composite knots in single chromosomes, and links between chromosomes. The knotting complexity of the chromosome is presented in the form of a matrix diagram that reveals the knot type of the entire polynucleotide chain and of each of its subchains. Links are determined by means of the Gaussian linking integral and the HOMFLY-PT polynomial. Entangled chromosomes are presented graphically in an intuitive way. It is also possible to relax structure with short molecular dynamics runs before the analysis. KnotGenome is freely available at http://knotgenom.cent.uw.edu.pl/.
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Affiliation(s)
- Joanna I Sulkowska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Szymon Niewieczerzal
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Aleksandra I Jarmolinska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Jonathan T Siebert
- Johannes Gutenberg-Universität Mainz, Institut für Physik, Staudingerweg 9, Mainz, 55128, Germany
| | - Peter Virnau
- Johannes Gutenberg-Universität Mainz, Institut für Physik, Staudingerweg 9, Mainz, 55128, Germany
| | - Wanda Niemyska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Banacha 2, 02-097 Warsaw, Poland
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8
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Tuite EM, Nordén B. Linear and circular dichroism characterization of thionine binding mode with DNA polynucleotides. Spectrochim Acta A Mol Biomol Spectrosc 2018; 189:86-92. [PMID: 28800432 DOI: 10.1016/j.saa.2017.07.064] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 07/25/2017] [Accepted: 07/30/2017] [Indexed: 06/07/2023]
Abstract
The binding mode of thionine (3,7-diamino-5-phenothiazinium) with alternating and non-alternating DNA polynucleotides at low binding ratios was conclusively determined using linear and circular dichroism spectroscopies. The binding to [poly(dG-dC)]2 and poly(dG)·poly(dC) was purely intercalative and was insensitive to ionic strength. Intercalative binding to [poly(dA-dT)]2 is observed at low ionic strength, but a shift of some dye to an non-intercalative mode is observed as the background salt concentration increases. With poly(dA)·poly(dT), intercalative binding is unfavourable, although some dye molecules may intercalate at low ionic strength, and groove binding is strongly promoted with increasing concentration of background salt. However, stacking with bases is observed with single-stranded poly(dA) and with triplex poly(dT)⁎poly(dA)·poly(dT) which suggests that the unusual structure of poly(dA)·poly(dT) precludes intercalation. Thionine behaves similarly to the related dye methylene blue, and small differences may be attributed either to the ability of thionine to form H-bonds that stabilize intercalation or to its improved stacking interactions in the basepair pocket on steric grounds.
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Affiliation(s)
- Eimer Mary Tuite
- School of Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.
| | - Bengt Nordén
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg S-41296, Sweden
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9
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Hyde EI, Callow P, Rajasekar KV, Timmins P, Patel TR, Siligardi G, Hussain R, White SA, Thomas CM, Scott DJ. Intrinsic disorder in the partitioning protein KorB persists after co-operative complex formation with operator DNA and KorA. Biochem J 2017; 474:3121-3135. [PMID: 28760886 PMCID: PMC5577506 DOI: 10.1042/bcj20170281] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 07/26/2017] [Accepted: 07/31/2017] [Indexed: 11/24/2022]
Abstract
The ParB protein, KorB, from the RK2 plasmid is required for DNA partitioning and transcriptional repression. It acts co-operatively with other proteins, including the repressor KorA. Like many multifunctional proteins, KorB contains regions of intrinsically disordered structure, existing in a large ensemble of interconverting conformations. Using NMR spectroscopy, circular dichroism and small-angle neutron scattering, we studied KorB selectively within its binary complexes with KorA and DNA, and within the ternary KorA/KorB/DNA complex. The bound KorB protein remains disordered with a mobile C-terminal domain and no changes in the secondary structure, but increases in the radius of gyration on complex formation. Comparison of wild-type KorB with an N-terminal deletion mutant allows a model of the ensemble average distances between the domains when bound to DNA. We propose that the positive co-operativity between KorB, KorA and DNA results from conformational restriction of KorB on binding each partner, while maintaining disorder.
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Affiliation(s)
- Eva I Hyde
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, U.K.
| | - Philip Callow
- Institut Laue Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble Cedex 9, France
| | | | - Peter Timmins
- Institut Laue Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble Cedex 9, France
| | - Trushar R Patel
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, U.K
| | - Giuliano Siligardi
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, U.K
| | - Rohanah Hussain
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, U.K
| | - Scott A White
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, U.K
| | | | - David J Scott
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, U.K.
- ISIS Neutron and Muon Spallation Source and Research Complex at Harwell, Rutherford Appleton Laboratory, Oxfordshire, U.K
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10
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Shen JW, Li J, Zhao Z, Zhang L, Peng G, Liang L. Molecular dynamics study on the mechanism of polynucleotide encapsulation by chitosan. Sci Rep 2017; 7:5050. [PMID: 28698591 PMCID: PMC5506017 DOI: 10.1038/s41598-017-05197-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 05/25/2017] [Indexed: 11/13/2022] Open
Abstract
The safe and effective delivery of therapeutic genes into target cell interiors is of great importance in gene therapy. Chitosan has been extensively studied as a gene delivery carrier due to its good biocompatibility and biodegradability. Understanding the atomic interaction mechanism between chitosan and DNA is important in the design and application of chitosan-based drug and gene delivery systems. In this work, the interactions between single-stranded polynucleotides and different types of chitosan were systematically investigated by using molecular dynamics (MD) simulation. Our results demonstrate that the functional groups of chitosan, the types of base and length of polynucleotides regulate the interaction behavior between chitosan and polynucleotides. The encapsulation capacity of polynucleotide by chitosan is mainly balanced by two factors: the strength of polynucleotide binding to chitosan and the tendency of self-aggregation of polynucleotide in the solution. For -NH3+ chitosan, due to the strong electrostatic interaction, especially the H-bond between -NH3+ groups in chitosan and phosphate groups in polynucleotide, the aggregation effect could be partially eliminated. The good dispersal capacity of polynucleotides may improve the encapsulation of polynucleotides by chitosan, and hence increase the delivery and transfection efficiency of chitosan-based gene carrier.
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Affiliation(s)
- Jia-Wei Shen
- School of Medicine, Hangzhou Normal University, Hangzhou, 310016, People's Republic of China.
| | - Jiachen Li
- Department of Chemistry, Key Laboratory of Advanced Textile Materials and Manufacturing Technology of Education Ministry, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Zhennan Zhao
- School of Medicine, Hangzhou Normal University, Hangzhou, 310016, People's Republic of China
| | - Li Zhang
- Department of Chemistry, Key Laboratory of Advanced Textile Materials and Manufacturing Technology of Education Ministry, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China.
| | - Guoteng Peng
- Department of Chemistry, Key Laboratory of Advanced Textile Materials and Manufacturing Technology of Education Ministry, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Lijun Liang
- College of Life Information Science and Instrument Engineering, Hangzhou Dianzi University, Hangzhou, 310018, People's Republic of China.
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11
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Saraiva SM, Castro-López V, Pañeda C, Alonso MJ. Synthetic nanocarriers for the delivery of polynucleotides to the eye. Eur J Pharm Sci 2017; 103:5-18. [PMID: 28263915 DOI: 10.1016/j.ejps.2017.03.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 02/28/2017] [Accepted: 03/01/2017] [Indexed: 02/07/2023]
Abstract
This review is a comprehensive analysis of the progress made so far on the delivery of polynucleotide-based therapeutics to the eye, using synthetic nanocarriers. Attention has been addressed to the capacity of different nanocarriers for the specific delivery of polynucleotides to both, the anterior and posterior segments of the eye, with emphasis on their ability to (i) improve the transport of polynucleotides across the different eye barriers; (ii) promote their intracellular penetration into the target cells; (iii) protect them against degradation and, (iv) deliver them in a long-term fashion way. Overall, the conclusion is that despite the advantages that nanotechnology may offer to the area of ocular polynucleotide-based therapies (especially AS-ODN and siRNA delivery), the knowledge disclosed so far is still limited. This fact underlines the necessity of more fundamental and product-oriented research for making the way of the said nanotherapies towards clinical translation.
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Affiliation(s)
- Sofia M Saraiva
- Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Av. Barcelona s/n, Campus Vida, Universidade de Santiago de Compostela, 15706 Santiago de Compostela, Spain
| | - Vanessa Castro-López
- Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Av. Barcelona s/n, Campus Vida, Universidade de Santiago de Compostela, 15706 Santiago de Compostela, Spain
| | - Covadonga Pañeda
- Sylentis, R&D Department, c/Santiago Grisolía 2, 28760 Tres Cantos, Madrid, Spain
| | - María José Alonso
- Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Av. Barcelona s/n, Campus Vida, Universidade de Santiago de Compostela, 15706 Santiago de Compostela, Spain; Department of Pharmacy and Pharmaceutical Technology, School of Pharmacy, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain; Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain.
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12
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Nakamura Y, Yamada S, Nishikawa S, Matsuura K. DNA-modified artificial viral capsids self-assembled from DNA-conjugated β-annulus peptide. J Pept Sci 2017; 23:636-643. [PMID: 28133866 DOI: 10.1002/psc.2967] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 12/15/2016] [Accepted: 12/18/2016] [Indexed: 01/01/2023]
Abstract
β-Annulus peptides from tomato bushy stunt virus conjugated with DNAs (dA20 and dT20 ) at the C-terminal were synthesized. The DNA-modified β-annulus peptides self-assembled into artificial viral capsids with sizes of 45-160 nm. ζ-Potential measurements revealed that the DNAs were coated on the surface of artificial viral capsids. Fluorescence assays indicated that the DNAs on the artificial viral capsids were partially hybridized with the complementary DNAs. Moreover, the DNA-modified artificial viral capsids formed aggregates by adding complementary polynucleotides. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.
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Affiliation(s)
- Yoko Nakamura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, 680-8552, Japan
| | - Saki Yamada
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, 680-8552, Japan
| | - Shoko Nishikawa
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, 680-8552, Japan
| | - Kazunori Matsuura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, 680-8552, Japan
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13
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Rechkunova NI, Lebedeva NA, Lavrik OI. [Tyrosyl-DNA Phosphodiesterase 1 Is a New Player in Repair of Apurinic/Apyrimidinic Sites]. Bioorg Khim 2016; 41:531-8. [PMID: 26762090 DOI: 10.1134/s106816201505012x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Genomic DNA is constantly damaged by the action of exogenous factors and endogenous reactive metabolites. Apurinic/apyrimidinic sites (AP sites), which occur as a result of DNA glycosylase induced or spontaneous hydrolysis of the N-glycosidic bonds, are the most common damages of DNA. The chemical reactivity of AP sites is the cause of DNA breaks, and DNA-protein and DNA-DNA crosslinks. Repair of AP sites is one of the most important mechanisms for maintaining genome stability. Despite the fact that the main participants of the AP site repair are very well studied, the new proteins that could be involved potentially in this process as "back up" players or perform certain specialized functions are being found. This review is dedicated to one of these proteins, tyrosyl-DNA phosphodiesterase 1 (Tdp1), for which we have recently shown that in addition to its main activity of specific cleavage of the tyrosyl-DNA bond formed via a covalent attachment of topoisomerase 1 (Top1) to DNA, Tdp1 is able to initiate the cleavage of the internal AP sites in DNA and their following repair. Tdp1 was discovered in Saccharomyces cerevisiae yeast as an enzyme hydrolyzing the covalent bond between tyrosyl residue of topoisomerase 1 and 3'-phosphate group in DNA. Tdp1 is the major enzyme which carries out the repair of the irreversible complexes of DNA and topoisomerase 1, which appear. in the presence of Top 1 inhibitors, such as camptothecin, therefore Tdp1 is a very important target for the development of inhibitors--anticancer drugs. Besides, Tdp1 hydrolyzes a wide range of 3'-terminal DNA modifications and the 3'-end nucleosides and its derivatives to form a 3'-phosphate. Tdp1 ability to cleave AP sites suggests its involvement in the base excision repair as an alternative enzyme to cleave AP sites instead of AP endonuclease 1--the major enzyme hydrolyzing AP sites in DNA repair process.
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Khan AY, Suresh Kumar G. Spectroscopic studies on the binding interaction of phenothiazinium dyes, azure A and azure B to double stranded RNA polynucleotides. Spectrochim Acta A Mol Biomol Spectrosc 2016; 152:417-425. [PMID: 26241827 DOI: 10.1016/j.saa.2015.07.091] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 07/08/2015] [Accepted: 07/23/2015] [Indexed: 06/04/2023]
Abstract
This manuscript presents spectroscopic characterization of the interaction of two phenothiazinium dyes, azure A and azure B with double stranded (ds) ribonucleic acids, poly(A).poly(U), poly(C).poly(G) and poly(I).poly(C). Absorbance and fluorescence studies revealed that these dyes bind to the RNAs with binding affinities of the order 10(6)M(-1) to poly(A).poly(U), and 10(5)M(-1) to poly(C).poly(G) and poly(I).poly(C), respectively. Fluorescence quenching and viscosity data gave conclusive evidence for the intercalation of the dyes to these RNA duplexes. Circular dichroism results suggested that the conformation of the RNAs was perturbed on interaction and the dyes acquired strong induced optical activity on binding. Azure B bound to all the three RNAs stronger than azure A and the binding affinity varied as poly(A).poly(U)>poly(C).poly(G)>poly(I).poly(C) for both dyes.
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Affiliation(s)
- Asma Yasmeen Khan
- Biophysical Chemistry Laboratory, Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory, Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India.
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15
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Dembska A, Juskowiak B. Pyrene functionalized molecular beacon with pH-sensitive i-motif in a loop. Spectrochim Acta A Mol Biomol Spectrosc 2015; 150:928-933. [PMID: 26123509 DOI: 10.1016/j.saa.2015.06.041] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 06/11/2015] [Indexed: 06/04/2023]
Abstract
In this work, we present a spectral characterization of pH-sensitive system, which combines the i-motif properties with the spatially sensitive fluorescence signal of pyrene molecules attached to hairpin ends. The excimer production (fluorescence max. ∼480 nm) by pyrene labels at the ends of the molecular beacon is driven by pH-dependent i-motif formation in the loop. To illustrate the performance and reversible work of our systems, we performed the experiments with repeatedly pH cycling between pH values of 7.5±0.3 and 6.5±0.3. The sensor gives analytical response in excimer-monomer switching mode in narrow pH range (1.5 pH units) and exhibits high pH resolution (0.1 pH unit).
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Affiliation(s)
- Anna Dembska
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland.
| | - Bernard Juskowiak
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland
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16
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Arteta MY, Berti D, Montis C, Campbell RA, Eriksson C, Clifton LA, Skoda MWA, Soltwedel O, Koutsioubas A, Baglioni P, Nylander T. On the formation of dendrimer/nucleolipids surface films for directed self-assembly. Soft Matter 2015; 11:1973-1990. [PMID: 25626114 DOI: 10.1039/c4sm02712d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We describe the formation and structure of nucleolipid/dendrimer multilayer films controlled by non-covalent interactions to obtain biomaterials that exhibit molecular recognition of nucleic acids. Layers of cationic poly(amidoamine) (PAMAM) dendrimers of generation 4 and the anionic nucleolipids 1,2-dilauroyl-sn-glycero-3-phosphatidylnucleosides (DLPNs) based on uridine (DLPU) and adenosine (DLPA) were first formed at the silica-water interface. The PAMAM/DLPN layers were then exposed to short oligonucleotides, polynucleotides and single stranded DNA (ssDNA). The interfacial properties were characterized using quartz crystal microbalance with dissipation monitoring, attenuated total reflection Fourier transform infrared spectroscopy and neutron reflectometry. Both types of DLPN were found to adsorb as aggregates to preadsorbed PAMAM monolayers with a similar interfacial structure and composition before rinsing with pure aqueous solution. Nucleic acids were found to interact with PAMAM/DLPA layers due to base pairing interactions, while the PAMAM/DLPU layers did not have the same capability. This was attributed to the structure of the DLPA layer, which is formed by aggregates that extend from the interface towards the bulk after rinsing with pure solvent, while the DLPU layer forms compact structures. In complementary experiments using a different protocol, premixed PAMAM/DLPN samples adsorbed to hydrophilic silica only when the mixtures contained positively charged aggregates, which is rationalized in terms of electrostatic forces. The PAMAM/DLPA layers formed from the adsorption of these mixtures also bind ssDNA although in this case the adsorption is mediated by the opposite charges of the film and the nucleic acid rather than specific base pairing. The observed molecular recognition of nucleic acids by dendrimers functionalized via non-covalent interactions with nucleolipids is discussed in terms of biomedical applications such as gene vectors and biosensors.
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Affiliation(s)
- Marianna Yanez Arteta
- Physical Chemistry, Department of Chemistry, Lund University, P. O. Box 124, S-221 00 Lund, Sweden.
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17
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Kosova AA, Lavrik OI, Hodyreva SN. [The role of Ku antigen in the repair of apurinic/apyrimidinic sites in DNA]. Mol Biol (Mosk) 2015; 49:67-74. [PMID: 25916111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Apurinic/apyrimidinic (AP) sites are some of the most frequent lesions in genomic DNA. It is widely accepted that, irrespective of their origin, AP sites are further processed by the base excision repair (BER) machinery, being the central intermediate of this process. Under special conditions, proteins, which recognize AP sites, are able to form covalent adducts with DNA. By combination of the cross-linking technique with mass-spectrometry analysis, Ku antigen (Ku)--the central player in nonhomologous end joining (NHEJ), the pathway of double-strand break (DSB) repair--was identified as a protein reactive to AP sites. Moreover, Ku was shown to be a 5'-dRP/AP lyase that acts near DSBs in NHEJ. The recent studies have demonstrated involvement of Ku in the different stages of BER. Here, Ku roles in NHEJ and BER pathways of DNA repair are overviewed.
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18
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Tang L, Tjong V, Li N, Yingling YG, Chilkoti A, Zauscher S. Enzymatic polymerization of high molecular weight DNA amphiphiles that self-assemble into star-like micelles. Adv Mater 2014; 26:3050-3054. [PMID: 24497034 DOI: 10.1002/adma.201306049] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 12/29/2013] [Indexed: 06/03/2023]
Abstract
High molecular weight ssDNA amphiphiles are synthesized by enzymatic polymerization. These highly asymmetric diblock DNA copolymers self-assemble into "hairy", star-like micelles, shown in the AFM image and the DPD snapshot.
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Affiliation(s)
- Lei Tang
- Dept. of Mechanical Engineering and Materials Science, Duke University, 144 Hudson Hall Box 90300, Durham, North Carolina, 27708, USA
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19
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Cabello-Aguilar S, Balme S, Chaaya AA, Bechelany M, Balanzat E, Janot JM, Pochat-Bohatier C, Miele P, Dejardin P. Slow translocation of polynucleotides and their discrimination by α-hemolysin inside a single track-etched nanopore designed by atomic layer deposition. Nanoscale 2013; 5:9582-9586. [PMID: 24057036 DOI: 10.1039/c3nr03683a] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
We report the formation of a hybrid biological/artificial nanopore by the direct insertion of non-modified α-hemolysin at the entrance of a high aspect ratio (length/diameter) biomimetic nanopore. In this robust hybrid system, the protein exhibits the same polynucleotide discrimination properties as in the biological membrane and the polynucleotide dwell time is strongly increased. This nanopore is very promising for DNA sequencing applications where the high DNA translocation velocity and the fragility of the support are the main bottlenecks.
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Affiliation(s)
- Simon Cabello-Aguilar
- Institut Européen des Membranes, UMR5635 CNRS-UM2-ENSCM, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France.
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20
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Buschmann MD, Merzouki A, Lavertu M, Thibault M, Jean M, Darras V. Chitosans for delivery of nucleic acids. Adv Drug Deliv Rev 2013; 65:1234-70. [PMID: 23872012 PMCID: PMC7103275 DOI: 10.1016/j.addr.2013.07.005] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 05/22/2013] [Accepted: 07/05/2013] [Indexed: 01/19/2023]
Abstract
Alternatives to efficient viral vectors in gene therapy are desired because of their poor safety profiles. Chitosan is a promising non-viral nucleotide delivery vector because of its biocompatibility, biodegradability, low immunogenicity and ease of manufacturing. Since the transfection efficiency of chitosan polyplexes is relatively low compared to viral counterparts, there is an impetus to gain a better understanding of the structure-performance relationship. Recent progress in preparation and characterisation has enabled coupling analysis of chitosans structural parameters that has led to increased TE by tailoring of chitosan's structure. In this review, we summarize the recent advances that have lead to a more rational design of chitosan polyplexes. We present an integrated review of all major areas of chitosan-based transfection, including preparation, chitosan and polyplexes physicochemical characterisation, in vitro and in vivo assessment. In each, we present the obstacles to efficient transfection and the strategies adopted over time to surmount these impediments.
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Affiliation(s)
- Michael D Buschmann
- Dept. Chemical Engineering and Inst. Biomedical Engineering, Ecole Polytechnique, Montreal, QC, Canada.
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21
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Iakushevich LV, Riasik AA. [Dynamics of kinks in inhomogeneous polynucleotide chains]. Biofizika 2013; 58:565-572. [PMID: 24455876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In the present paper the dynamics of the nonlinear conformational excitations--kinks, in inhomogeneous polynucleotide DNA chains is investigated. To calculate the kink rest energy E0 and its length d the method of dynamical interval is used. This makes it possible to take into account that all coefficients of the model dynamic equation--the sine-Gordon equation depend on the sequence of bases. It is shown that the method gives an opportunity to calculate dynamical characteristics of any artificial and real sequences that is important for implementing tasks associated with the search and analysis of functionally important DNA sites.
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22
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Cruz C, Sousa A, Sousa F, Queiroz JA. Study of the specific interaction between L-methionine chromatography support and nucleotides. J Chromatogr B Analyt Technol Biomed Life Sci 2012; 909:1-5. [PMID: 23153636 DOI: 10.1016/j.jchromb.2012.09.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 09/24/2012] [Accepted: 09/27/2012] [Indexed: 02/03/2023]
Abstract
The interaction of L-methionine-agarose with 5'-mononucleotide was investigated by saturation transfer difference (STD)-nuclear magnetic resonance (NMR) spectroscopy. Chromatographic experiments were also performed using homo-oligonucleotides of distinct molecular masses (1-30 nucleotides) to explore the effect of base hydrophobicity, temperature, pH and salt concentration on the retention of homo-oligonucleotides to L-methionine-agarose support. With STD-NMR, the results reveal that hydrophobic residues, such as the CH₃ of thymine and adenine, can preferentially recognise the L-methionine side chain of the support. Also, 5'-TMP led to more contacts with the support, while 5'-UMP presented fewer STD contacts. For 5'-UMP, 5'-CMP and 5'-GMP, the main interaction with the support was through the sugar-phosphate backbone. Similar binding profiles were obtained using chromatographic experiments. Indeed, 5'-TMP had the highest retention time, followed by 5'-GMP, 3'-AMP, 5'-UMP and 5'-CMP. In general, the retention factor of homo-oligonucleotides was higher for ammonium sulphate concentration 1.5 M. For the polyT₃-polyT₃₀ series, the retention time increased by about three-fold, indicating that larger homo-oligonucleotides have more hydrophobic bases, thus enhancing contact with the L-methionine support. The temperature (5, 20 and 35 °C) did not influence homo-oligonucleotide retention. However, the retention time slightly increased when the pH was lower than 9. The STD-NMR technique combined with chromatographic experiments was thus successfully used to screen amino acid-nucleotide interactions.
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Affiliation(s)
- C Cruz
- CICS-UBI-Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal.
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23
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Chakraborty A, Mandal PK, Gautham N. Structure of d(CCGGGACCGG)4 as a four-way junction at 1.6 Å resolution: new insights into solvent interactions. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:1169-74. [PMID: 23027741 PMCID: PMC3497973 DOI: 10.1107/s1744309112034926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2012] [Accepted: 08/07/2012] [Indexed: 06/01/2023]
Abstract
The crystal structure of the decamer sequence d(CCGGGACCGG)(4) has previously been reported at 2.16 Å resolution as a four-way junction. Here, the structure of this sequence is reported at the significantly higher resolution of 1.6 Å, which is the highest resolution reported for a four-way junction. This allowed the unambiguous identification of an extensive hydration network with distinct patterns and solvent-mediated interactions that shed new light on the role of water in the formation and stabilization of junction structures.
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Affiliation(s)
- Arka Chakraborty
- CAS in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai, Tamil Nadu 600 025, India
| | - Pradeep Kumar Mandal
- CAS in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai, Tamil Nadu 600 025, India
| | - Namasivayam Gautham
- CAS in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai, Tamil Nadu 600 025, India
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Abstract
The general notion of an "RNA World" is that, in the early development of life on the Earth, genetic continuity was assured by the replication of RNA and genetically encoded proteins were not involved as catalysts. There is now strong evidence indicating that an RNA World did indeed exist before DNA- and protein-based life. However, arguments regarding whether life on Earth began with RNA are more tenuous. It might be imagined that all of the components of RNA were available in some prebiotic pool, and that these components assembled into replicating, evolving polynucleotides without the prior existence of any evolved macromolecules. A thorough consideration of this "RNA-first" view of the origin of life must reconcile concerns regarding the intractable mixtures that are obtained in experiments designed to simulate the chemistry of the primitive Earth. Perhaps these concerns will eventually be resolved, and recent experimental findings provide some reason for optimism. However, the problem of the origin of the RNA World is far from being solved, and it is fruitful to consider the alternative possibility that RNA was preceded by some other replicating, evolving molecule, just as DNA and proteins were preceded by RNA.
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Affiliation(s)
- Michael P Robertson
- Departments of Chemistry and Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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25
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Tumir LM, Crnolatac I, Deligeorgiev T, Vasilev A, Kaloyanova S, Grabar Branilović M, Tomić S, Piantanida I. Kinetic differentiation between homo- and alternating AT DNA by sterically restricted phosphonium dyes. Chemistry 2012; 18:3859-64. [PMID: 22367738 DOI: 10.1002/chem.201102968] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Indexed: 11/07/2022]
Affiliation(s)
- Lidija-Marija Tumir
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, Bijenička c. 54, P. O. Box 180, 10002 Zagreb, Croatia
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26
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Abstract
Digital gene expression (DGE) profiling techniques are playing an eminent role in the detection, localization, and differential expression quantification of many small RNA species, including microRNAs (1-3). Procedures in small RNA library preparation techniques typically include adapter ligation by RNA ligase, followed by reverse transcription and amplification by PCR. This chapter describes three protocols that were successfully applied to generate small RNA sequencing SOLiD(TM) libraries. The Ambion SREK(TM)-adopted protocol can be readily used for multiplexing samples; the modban-based protocol is cost-efficient, but biased toward certain microRNAs; the poly(A)-based protocol is less biased, but less precise because of the A-tail that is introduced. In summary, each of these protocols has its advantages and disadvantages with respect to the ease of including barcodes, costs, and outcome.
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27
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Iakushevich LV, Kashapova GR, Zakir'ianov FK. [Influence of the periodic field with constant and slowly changing frequency on movement of the DNA kink]. Biofizika 2012; 57:21-26. [PMID: 22567907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The movement of the kink in homogeneous polynucleotide chains of DNA under the influence of three kinds of an external periodic field--with constant, growing and decreasing frequencies is investigated in the work. Dependences of speed and coordinate of the kink from time have been found with the help of McLaughlin and Scott energetic method. Phase trajectories of the kink have been constructed. It has been shown that in the case of external action with constant frequency, the kink aspires to a limiting cycle; in the case of an external field with increasing frequency it tends to a stationary state corresponding to a special point of stable focus type; in the case of an external field with decreasing frequency, the kink transfers from one stationary state (unstable focus) to another (stable focus). The obtained results show the possibility of governing the kink movement by slowly changing frequency.
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Abstract
Recognition of nucleic acids is important for our understanding of nucleic acid structure as well as for our understanding of nucleic acid-protein interactions. In addition to the direct readout mechanisms of nucleic acids such as H-bonding, shape recognition of nucleic acids is being increasingly recognized as playing an equally important role in DNA recognition. Competition dialysis, UV, flourescent intercalator displacement (FID), computational docking, and calorimetry studies were conducted to study the interaction of neomycin with a variety of nucleic acid conformations (shapes). At pH 5.5, the results suggest the following. (1) Neomycin binds three RNA structures [16S A site rRNA, poly(rA)·poly(rA), and poly(rA)·poly(rU)] with high affinities (K(a) ~ 10(7) M(-1)). (2) The binding of neomycin to A-form GC-rich oligomer d(A(2)G(15)C(15)T(2))(2) has an affinity comparable to those of RNA structures. (3) The binding of neomycin to DNA·RNA hybrids shows a 3-fold variance that can be attributed to their structural differences [for poly(dA)·poly(rU), K(a) = 9.4 × 10(6) M(-1), and for poly(rA)·poly(dT), K(a) = 3.1 × 10(6) M(-1)]. (4) The interaction of neomycin with DNA triplex poly(dA)·2poly(dT) yields a binding affinity (K(a)) of 2.4 × 10(5) M(-1). (5) Poly(dA-dT)(2) shows the lowest association constant for all nucleic acids studied (K(a) < 10(5)). (6) Neomycin binds to G-quadruplexes with K(a) values of ~10(4)-10(5) M(-1). (7) Computational studies show that the decrease in major groove width in the B to A transition correlates with increasing neomycin affinity. Neomycin's affinity for various nucleic acid structures can be ranked as follows: RNAs and GC-rich d(A(2)G(15)C(15)T(2))(2) structures > poly(dA)·poly(rU) > poly(rA)·poly(dT) > T·A-T triplex, G-quadruplex, B-form AT-rich, or GC-rich DNA sequences. The results illustrate the first example of a small molecule-based "shape readout" of different nucleic acid conformations.
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Affiliation(s)
- Hongjuan Xi
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina, 29634
| | - Erik Davis
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina, 29634
| | - Nihar Ranjan
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina, 29634
| | - Liang Xue
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina, 29634
| | - David Hyde-Volpe
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina, 29634
| | - Dev P. Arya
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina, 29634
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Saida M, Iles D, Elnefati A, Brinkworth M, Miller D. Key gene regulatory sequences with distinctive ontological signatures associate with differentially endonuclease-accessible mouse sperm chromatin. Reproduction 2011; 142:73-86. [PMID: 21511886 DOI: 10.1530/rep-10-0536] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Using a well-established endonuclease-based chromatin dissection procedure in conjunction with both experimental comparative genome hybridisation (CGH) array profiling and in silico data mining, we show that mouse spermatozoa contain chromatin that is sensitive and resistant to digestion with micrococcal nuclease (MNase). Sequences represented in the micrococcal nuclease digestion solubilised (MNDS) but not the MND insoluble (MNDI) chromatin are strongly enriched in chromosomal regions of high gene density. Furthermore, by fluorescence in situ hybridisation (FISH) analysis, we show that MNDS and MNDI DNAs occupy distinct domains of decondensed mouse sperm nuclei that may also retain abundant histones. More detailed in silico analysis of CGH probe location in relation to known promoters and sequences recognised by CCCTC binding factor (CTCF) shows a significant excess of both in MNDS chromatin. A functional analysis of gene promoters reveals strong ontological signatures for ion transport on methylated promoters associated with CTCF binding sequences in MNDS chromatin. Sensory perception is the only strong ontological signature present in MNDI chromatin, driven by promoters that are not associated with CTCF regardless of their methylation status.
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Affiliation(s)
- Myriam Saida
- Leeds Institute of Genetics, Health and Therapeutics, University of Leeds, Leeds, UK
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30
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Jarak I, Marjanović M, Piantanida I, Kralj M, Karminski-Zamola G. Novel pentamidine derivatives: synthesis, anti-tumor properties and polynucleotide-binding activities. Eur J Med Chem 2011; 46:2807-15. [PMID: 21546133 DOI: 10.1016/j.ejmech.2011.04.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Revised: 03/31/2011] [Accepted: 04/01/2011] [Indexed: 11/18/2022]
Abstract
Novel amidino-substituted conformationally restricted derivatives of pentamidine were synthesized and their antiproliferative activity against several human cancer cell lines determined. It was found that introduction of furandicarboxamide core moiety (9, 10) increases antiproliferative activity as well as selectivity against certain tumor cell lines in comparison with amidino-substituted furan-mono-carboxamide (5, 6). Unlike the furan series where iso-propyl substituted amidine (10) exhibits more potent overall antiproliferative activity and selectivity toward certain cell lines, the same was found for unsubstituted amidines in pyridine series. Amongst all tested compounds the compound 10 is the only one that possesses antiproliferative activity against SW 620 cell line (4 μM). Spectroscopic studies of the interactions of prepared diamidines with double-stranded DNA and RNA polynucleotides show that all compounds preferentially bind into the minor groove of DNA, while most of them intercalate into RNA. The structure-dependant biological activity and the lack of DNA/RNA selective binding suggest that the mechanism of action of the here-presented compounds is controlled not only by the interactions with cellular nucleic acids, but also with other more specific protein targets.
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Affiliation(s)
- Ivana Jarak
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 20, P.O. Box 177, HR-10000 Zagreb, Croatia
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31
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Pang YP, Park JG, Wang S, Vummenthala A, Mishra RK, McLaughlin JE, Di R, Kahn JN, Tumer NE, Janosi L, Davis J, Millard CB. Small-molecule inhibitor leads of ribosome-inactivating proteins developed using the doorstop approach. PLoS One 2011; 6:e17883. [PMID: 21455295 PMCID: PMC3063779 DOI: 10.1371/journal.pone.0017883] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Accepted: 02/16/2011] [Indexed: 11/19/2022] Open
Abstract
Ribosome-inactivating proteins (RIPs) are toxic because they bind to 28S rRNA and depurinate a specific adenine residue from the α-sarcin/ricin loop (SRL), thereby inhibiting protein synthesis. Shiga-like toxins (Stx1 and Stx2), produced by Escherichia coli, are RIPs that cause outbreaks of foodborne diseases with significant morbidity and mortality. Ricin, produced by the castor bean plant, is another RIP lethal to mammals. Currently, no US Food and Drug Administration-approved vaccines nor therapeutics exist to protect against ricin, Shiga-like toxins, or other RIPs. Development of effective small-molecule RIP inhibitors as therapeutics is challenging because strong electrostatic interactions at the RIP•SRL interface make drug-like molecules ineffective in competing with the rRNA for binding to RIPs. Herein, we report small molecules that show up to 20% cell protection against ricin or Stx2 at a drug concentration of 300 nM. These molecules were discovered using the doorstop approach, a new approach to protein•polynucleotide inhibitors that identifies small molecules as doorstops to prevent an active-site residue of an RIP (e.g., Tyr80 of ricin or Tyr77 of Stx2) from adopting an active conformation thereby blocking the function of the protein rather than contenders in the competition for binding to the RIP. This work offers promising leads for developing RIP therapeutics. The results suggest that the doorstop approach might also be applicable in the development of other protein•polynucleotide inhibitors as antiviral agents such as inhibitors of the Z-DNA binding proteins in poxviruses. This work also calls for careful chemical and biological characterization of drug leads obtained from chemical screens to avoid the identification of irrelevant chemical structures and to avoid the interference caused by direct interactions between the chemicals being screened and the luciferase reporter used in screening assays.
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Affiliation(s)
- Yuan-Ping Pang
- Computer-Aided Molecular Design Laboratory, Mayo Clinic, Rochester, Minnesota, United States of America
- * E-mail: (YPP, chemistry); (NET, biology); (CBM, biology)
| | - Jewn Giew Park
- Computer-Aided Molecular Design Laboratory, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Shaohua Wang
- Computer-Aided Molecular Design Laboratory, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Anuradha Vummenthala
- Computer-Aided Molecular Design Laboratory, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Rajesh K. Mishra
- Computer-Aided Molecular Design Laboratory, Mayo Clinic, Rochester, Minnesota, United States of America
| | - John E. McLaughlin
- Department of Plant Biology and Pathology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Rong Di
- Department of Plant Biology and Pathology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Jennifer Nielsen Kahn
- Department of Plant Biology and Pathology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Nilgun E. Tumer
- Department of Plant Biology and Pathology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, New Jersey, United States of America
- * E-mail: (YPP, chemistry); (NET, biology); (CBM, biology)
| | - Laszlo Janosi
- Division of Biochemistry, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Jon Davis
- Division of Biochemistry, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Charles B. Millard
- Division of Biochemistry, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- * E-mail: (YPP, chemistry); (NET, biology); (CBM, biology)
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32
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Turov VV, Chehun VF, Barvinchenko VN, Krupskaya TV, Prylutskyy YI, Scharff P, Ritter U. Low-temperature 1H-NMR spectroscopic study of doxorubicin influence on the hydrated properties of nanosilica modified by DNA. J Mater Sci Mater Med 2011; 22:525-532. [PMID: 21287246 DOI: 10.1007/s10856-011-4237-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Accepted: 01/12/2011] [Indexed: 05/30/2023]
Abstract
The effect of the anticancer drug--doxorubicin (Dox) on hydration properties of a nanocomposite material deposited on silica and modified by small amount of DNA (0.6 wt%) was studied by means of (1)H NMR spectroscopy at low temperatures (in the range of 200-280 K). Signals of either weakly (WAW) or strongly (SAW) associated water, as well as water associated with electrondonor groups of the composite surface (ASW), were observed. The findings reveal that, depending on the temperature and the composition of the dispersion medium, fast molecular exchange takes place between different forms of interphase water. The presence of Dox (0.1-0.2 wt%) in the dispersion medium leads to change of the relative concentrations of different forms of water.
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Affiliation(s)
- V V Turov
- O.O. Chuiko Institute of Surface Chemistry of NAS of Ukraine, Kyiv, Ukraine
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33
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Lebedeva NA, Rechkunova NI, Lavrik OI. AP-site cleavage activity of tyrosyl-DNA phosphodiesterase 1. FEBS Lett 2011; 585:683-6. [PMID: 21276450 DOI: 10.1016/j.febslet.2011.01.032] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Revised: 01/17/2011] [Accepted: 01/19/2011] [Indexed: 11/19/2022]
Abstract
APE-independent base excision repair (BER) pathway plays an important role in the regulation of DNA repair mechanisms. In this study it has been found that recently discovered tyrosyl-DNA phosphodiesterase 1 (Tdp1) catalyzes the AP site cleavage reaction to generate breaks with the 3'- and 5'-phosphate termini. The removal of the 3'-phosphate is performed by polynucleotide kinase phosphatase (PNKP). Tdp1 is known to interact stably with BER proteins: DNA polymerase beta (Pol β), XRCC1, PARP1 and DNA ligase III. The data suggest a role of Tdp1 in the new APE-independent BER pathway in mammals.
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Affiliation(s)
- Natalia A Lebedeva
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
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34
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Wanunu M, Dadosh T, Ray V, Jin J, McReynolds L, Drndić M. Rapid electronic detection of probe-specific microRNAs using thin nanopore sensors. Nat Nanotechnol 2010; 5:807-14. [PMID: 20972437 DOI: 10.1038/nnano.2010.202] [Citation(s) in RCA: 503] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2010] [Accepted: 09/14/2010] [Indexed: 05/24/2023]
Abstract
Small RNA molecules have an important role in gene regulation and RNA silencing therapy, but it is challenging to detect these molecules without the use of time-consuming radioactive labelling assays or error-prone amplification methods. Here, we present a platform for the rapid electronic detection of probe-hybridized microRNAs from cellular RNA. In this platform, a target microRNA is first hybridized to a probe. This probe:microRNA duplex is then enriched through binding to the viral protein p19. Finally, the abundance of the duplex is quantified using a nanopore. Reducing the thickness of the membrane containing the nanopore to 6 nm leads to increased signal amplitudes from biomolecules, and reducing the diameter of the nanopore to 3 nm allows the detection and discrimination of small nucleic acids based on differences in their physical dimensions. We demonstrate the potential of this approach by detecting picogram levels of a liver-specific miRNA from rat liver RNA.
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Affiliation(s)
- Meni Wanunu
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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35
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Tapia MJ, Montserín M, Valente AJM, Burrows HD, Mallavia R. Binding of polynucleotides to conjugated polyelectrolytes and its applications in sensing. Adv Colloid Interface Sci 2010; 158:94-107. [PMID: 19836007 DOI: 10.1016/j.cis.2009.09.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2009] [Revised: 09/10/2009] [Accepted: 09/24/2009] [Indexed: 12/31/2022]
Abstract
We provide a brief overview of the structural characteristics of the main groups of conjugated polyelectrolytes (CPEs) as well as the methods of synthesis and their behaviour in solution. Their tendency to form aggregates in solution, which is one of the key points to be taken into account for them to be used in polynucleotide sensing, is also considered and the various strategies adopted to avoid it will be discussed. These include the synthetic one (with the incorporation of charged and/or bulky substituents), the use of organic co-solvents and the addition of surfactants. The main physical chemical changes (optical, photophysical, electrical conductivity and viscosity) observed upon direct binding between polynucleotide and CPE, the kind of interactions involved and their applicability in sensing are considered as a function of the CPE structural rigidity. Moreover, more complex devices developed in CPE-polynucleotide sensing with the involvement of additional spectroscopic probes to induce Förster resonant energy transfer processes (FRET) or superquenching phenomena are reviewed. Finally, the main CPE applications in biosensing and the potential use of these systems in understanding DNA compaction and possible extension to the construction of supramolecular oligonucleotide structures are summarized.
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Affiliation(s)
- Maria J Tapia
- Departamento de Química, Universidad de Burgos, Plaza Misael Bañuelos, Burgos 09001, Spain.
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36
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Jost D, Everaers R. A unified Poland-Scheraga model of oligo- and polynucleotide DNA melting: salt effects and predictive power. Biophys J 2009; 96:1056-67. [PMID: 18849409 PMCID: PMC2716684 DOI: 10.1529/biophysj.108.134031] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2008] [Accepted: 08/05/2008] [Indexed: 11/18/2022] Open
Abstract
Key biological and nano-technological processes require the partial or complete association and dissociation of complementary DNA strands. We present a variant of the Poland-Scheraga model for DNA melting where we introduce a local, sequence-dependent salt correction of the nearest-neighbor parameters. Furthermore, our formulation accounts for capping and interfacial energies of helical and coiled chain sections. We show that the model reproduces experimental data for melting temperatures over the full experimental range of strand length, strand concentration, and ionic strength of the solution. In particular, we reproduce a phenomenological relation by Frank-Kamenetskii for very long chains using a parameterization based on melting curves for short oligomers. However, we also show that the parameters of the Poland-Scheraga model are still not known with sufficient precision to quantitatively predict the fine structure of melting curves. This formulation of the Poland-Scheraga model opens the possibility to overcome this limitation by optimizing parameters with respect to an extended base of experimental data for short-, medium-, and long-chain melting. We argue that the often-discarded melting data for longer oligomers exhibiting non-two-state transitions could play a particularly important role.
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Affiliation(s)
- Daniel Jost
- Laboratoire de Physique and Centre Blaise Pascal of the École Normale Supérieure de Lyon, Université de Lyon, CNRS UMR 5672, Lyon, France
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37
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Kawano R, Schibel AEP, Cauley C, White HS. Controlling the translocation of single-stranded DNA through alpha-hemolysin ion channels using viscosity. Langmuir 2009; 25:1233-1237. [PMID: 19138164 DOI: 10.1021/la803556p] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Translocation of single-stranded DNA through alpha-hemolysin (alpha-HL) channels is investigated in glycerol/water mixtures containing 1 M KCl. Experiments using glass nanopore membranes as the lipid bilayer support demonstrate that the translocation velocities of poly(deoxyadenylic acid), poly(deoxycytidylic acid), and poly(deoxythymidylic acid) 50-mers are decreased by a factor of approximately 20 in a 63/37 (vol %) glycerol/water mixture, relative to aqueous solutions. The ion conductance of alpha-HL and the entry rate of the polynucleotides into the protein channel also decrease with increasing viscosity. Precise control of translocation parameters by adjusting viscosity provides a potential means to improve sequencing methods based on ion channel recordings.
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Affiliation(s)
- Ryuji Kawano
- Department of Chemistry, University of Utah, 315S. 1400E, Salt Lake City, Utah 84112, USA.
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38
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Peled D, Daube SS, Naaman R. Selective enzymatic labeling to detect packing-induced denaturation of double-stranded DNA at interfaces. Langmuir 2008; 24:11842-11846. [PMID: 18800816 DOI: 10.1021/la801437n] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The adsorption of DNA on surfaces is a widespread procedure and is a common way for fabrication of biosensors, DNA chips, and nanoelectronic devices. Although the biologically relevant and prevailing in vivo structure of DNA is its double-stranded (dsDNA) conformation, the characterization of DNA on surfaces has mainly focused on single-stranded DNA (ssDNA). Studying the structure of dsDNA on surfaces is of invaluable importance to microarray performance since their effectiveness relies on the ability of two DNA molecules to hybridize and remain stable. In addition, many of the enzymatic transactions performed on DNA require dsDNA, rather than ssDNA, as a substrate. However, it is not established that adsorbed dsDNA remains in its structure and does not denature. Here, two methodologies have been developed for distinguishing between surface-adsorbed single- and double-stranded DNA. We demonstrate that, upon formation of a dense monolayer, the nonthiolated strand comprising the dsDNA is released and the monolayer consists of mostly ssDNA. The fraction of dsDNA within the ssDNA monolayer depends on the length of the oligomers. A likely mechanism leading to this rearrangement is discussed.
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Affiliation(s)
- Dana Peled
- Department of Chemical Physics and Chemical Research Support, Weizmann Institute, Rehovot 76100, Israel
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39
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Whittenton J, Harendra S, Pitchumani R, Mohanty K, Vipulanandan C, Thevananther S. Evaluation of asymmetric liposomal nanoparticles for encapsulation of polynucleotides. Langmuir 2008; 24:8533-8540. [PMID: 18597508 DOI: 10.1021/la801133j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Conventional lipid bilayer liposomes have similar inner and outer leaflet compositions; asymmetric liposomes have different lipid leaflet compositions. The goal of this work is to place cationic lipids in the inner leaflet to encapsulate negatively charged polynucleotides and to place neutral/anionic lipids on the outer leaflet to decrease nonspecific cellular uptake/toxicity. Inverse emulsion particles have been developed with a single lipid leaflet of cationic and neutral lipids surrounding an aqueous core containing a negatively charged 21-mer DNA oligo. The particles are accelerated through an oil-water interface, entrapping a second neutral lipid to form oligo encapsulated unilamellar liposome nanoparticles. Inverse emulsion particles can be consistently produced to encapsulate an aqueous environment containing negatively charged oligo. The efficiency of encapsulated liposome formation is low and depends on the hydrocarbon used as the oil phase. Dodecane, mineral oil, and squalene were tested, and squalene, a branched hydrocarbon, yielded the highest efficiency.
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Affiliation(s)
- Jeremiah Whittenton
- Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77204, USA
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40
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IUPAC-IUB joint commission. IUPAC-IUB joint commission on biochemical nomenclature abbreviations and symbols for the description of conformations of polynucleotide chains. ACTA ACUST UNITED AC 2001; Appendix 1:Appendix 1C. [PMID: 18428807 DOI: 10.1002/0471142700.nca01cs00] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This appendix presents nomenclature rules that are as close as possible to the originally published version and are reproduced here with permission from the European Journal of Biochemistry. A web-based version prepared by G.P. Moss is also available.
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41
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Abstract
Water soluble homo-base polynucleotide analogues were synthesized in which polyvinyl alcohol and partially phosphonated polyvinyl alcohol constituted the backbones,onto which were grafted uracil or adenine via 1,3-dioxane spacers formed by acetal formation with the 1,3-diol moieties in PVA. The resulting adenine-PVA polynucleotide analogs exhibited hyperchromic effects, which was not the case for the corresponding uracil compounds. Mixtures of the adenine- and aracil PVA-phosphate polynucleotide analogs in solutions exhibited characteristic S-shaped UV-absorbance vs temperature and melting curves with melting points at approximately 40 degrees C.
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Affiliation(s)
| | - Per Carlsen
- Author to whom correspondence should be addressed; E-Mail:
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42
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Elias B, Creely C, Doorley GW, Feeney MM, Moucheron C, Kirsch-DeMesmaeker A, Dyer J, Grills DC, George MW, Matousek P, Parker AW, Towrie M, Kelly JM. Photooxidation of guanine by a ruthenium dipyridophenazine complex intercalated in a double-stranded polynucleotide monitored directly by picosecond visible and infrared transient absorption spectroscopy. Chemistry 2008; 14:369-75. [PMID: 17886324 DOI: 10.1002/chem.200700564] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Transient species formed by photoexcitation (400 nm) of [Ru(dppz)(tap)2]2+ (1) (dppz = dipyrido[3,2-a:2',3'-c]phenazine; tap=1,4,5,8-tetraazaphenanthrene) in aqueous solution and when intercalated into a double-stranded synthetic polynucleotide, [poly(dG-dC)]2, have been observed on a picosecond timescale by both visible transient absorption (allowing monitoring of the metal complex intermediates) and transient infrared (IR) absorption spectroscopy (allowing direct study of the DNA nucleobases). By contrast with its behavior when free in aqueous solution, excitation of 1 when bound to [poly(dG-dC)]2 causes a strong increase in absorbance at 515 nm due to formation of the reduced complex [Ru(dppz)(tap)2]+ (rate constant=(2.0+/-0.2) x 10(9) s(-1)). The subsequent reformation of 1 proceeds with a rate constant of (1.1+/-0.2) x 10(8) s(-1). When the process is carried out in D2O, the rates of formation and removal of [Ru(dppz)(tap)2]+ are reduced (rate constants (1.5+/-0.3) x 10(9) and (0.7+/-0.2) x 10(8) s(-1) respectively) consistent with proton-coupled electron transfer processes. Picosecond transient IR measurements in the 1540-1720 cm(-1) region in D2O solution confirm that the reduction of 1 intercalated into [poly(dG-dC)]2 is accompanied by bleaching of IR ground-state bands of guanine (1690 cm(-1)) and cytosine (1656 cm(-1)), each with similar rate constants.
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Affiliation(s)
- Benjamin Elias
- Service de Chimie Organique et Photochimie, CP 160/08, Université Libre de Bruxelles, 50 Avenue F.D. Roosevelt, 1050 Bruxelles, Belgium
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Abstract
The binding interactions of three naphthalimide derivatives with heteropoly nucleic acids have been evaluated using fluorescence, absorption and circular dichroism spectroscopies. Mono- and bifunctionalized naphthalimides exhibit sequence-dependent variations in their affinity toward DNA. The heteropoly nucleic acids, [Poly(dA-dT)]2 and [Poly(dG-dC)]2, as well as calf thymus (CT) DNA, were used to understand the factors that govern binding strength and selectivity. Sequence selectivity was addressed by determining the binding constants as a function of polynucleotide composition according to the noncooperative McGhee-von Hippel binding model. Binding affinities toward [poly(dA-dT)](2) were the largest for spermine-substituted naphthalimides (Kb = 2-6 x 10(6) M(-1)). The association constants for complex formation between the cationic naphthalimides and [poly(dG-dC)]2 or CT DNA (58% A-T content) were 2-500 times smaller, depending on the naphthalimide-polynucleotide pair. The binding modes were also assessed using a combination of induced circular dichroism and salt effects to determine whether the naphthalimides associate with DNA through intercalative, electrostatic or groove-binding. The results show that the monofunctionalized spermine and pyridinium-substituted naphthalimides associate with DNA through electrostatic interactions. In contrast, intercalative interactions are predominant in the complex formed between the bifunctionalized spermine compound and all of the polynucleotides.
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Affiliation(s)
- Sun McMasters
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore, MD, USA
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44
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Markarian MZ, Moussallem MD, Jomaa HW, Schlenoff JB. Hydrogen bonding versus ion pairing in polyelectrolyte multilayers with homopolynucleotides. Biomacromolecules 2007; 8:59-64. [PMID: 17206788 DOI: 10.1021/bm0604909] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Homopolynucleotides--poly(adenylic acid), poly(A), and poly(uridylic acid), poly(U)--were assembled, layer-by-layer, into thin films with poly(ethylenimine), PEI. Various combinations and sequences of polynucleotide and PEI were used to highlight contributions of electrostatic versus hydrogen bonding as driving forces for multilayer build-up. Assembly of alternating poly(A) and poly(U) failed to yield growing films, due to excessively strong interactions between these complimentary strands. The surface morphology of multilayers depended on the deposition order and whether films had been annealed by salt. Films assembled from preformed A/U duplexes (having high persistence lengths) were very smooth. Individual adsorption steps, followed by optical waveguide light-mode spectroscopy, showed that only complementary polynucleotides adsorb by H-bonding to the surface of a growing multilayer. In contrast to behavior usually observed for polyelectrolyte multilayer build-up, the films decreased in thickness with increasing salt concentration.
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Affiliation(s)
- Marie Z Markarian
- Department of Chemistry and Biochemistry, Center for Materials Research and Technology, The Florida State University, Tallahassee, Florida 32306, USA
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45
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Hasegawa T, Numata M, Okumura S, Kimura T, Sakurai K, Shinkai S. Carbohydrate-appended curdlans as a new family of glycoclusters with binding properties both for a polynucleotide and lectins. Org Biomol Chem 2007; 5:2404-12. [PMID: 17637960 DOI: 10.1039/b703720a] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Beta-1,3-glucans having carbohydrate-appendages (alpha-D-mannoside, N-acetyl-beta-D-glucosaminide and beta-lactoside) at the C6-position of every repeating unit can be readily prepared from curdlan (a linear beta-1,3-glucan) through regioselective bromination/azidation to afford 6-azido-6-deoxycurdlan followed by chemo-selective Cu(i)-catalyzed [3 + 2]-cycloaddition with various carbohydrate modules having a terminal alkyne. The resultant carbohydrate-appended curdlans can interact with polycytosine to form stable macromolecular complexes consistent with two polysaccharide strands and one polycytosine strand. Furthermore, these macromolecular complexes show strong and specific affinity toward carbohydrate-binding proteins (lectins). Therefore, one can utilize these carbohydrate-appended curdlans as a new family of glycoclusters.
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Affiliation(s)
- Teruaki Hasegawa
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Motooka 744, Nishi-ku, Fukuoka 819-0395, Japan
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46
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Dubrovin EV, Staritsyn SN, Yakovenko SA, Yaminsky IV. Self-assembly effect during the adsorption of polynucleotides on stearic acid langmuir-blodgett monolayer. Biomacromolecules 2007; 8:2258-61. [PMID: 17583947 DOI: 10.1021/bm0702096] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Interaction of polyadenylic acid, poly(A), with stearic acid Langmuir-Blodgett (LB) monolayer was studied in different electrolyte surroundings. For this purpose LB films of stearic acid, transferred on the mica substrate from poly(A) containing subphase, were analyzed with atomic force microscopy (AFM). The density of polynucleotides surface coverage is ruled by the monovalent electrolyte concentration in the subphase that is in good agreement with previous results. Divalent cations in the subphase are needed to stabilize poly(A) molecules on the surface through formation of "salt bridges". At the very low divalent electrolyte concentration polynucleotides adsorb on the LB film to domains in which the effect of self-assembly is observed. Increase of divalent electrolyte concentration leads to the loss of this orientation effect. The explanation of this effect is proposed.
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Affiliation(s)
- Evgeniy V Dubrovin
- Department of Physics of Polymers and Crystals, Faculty of Physics, Moscow State University, Leninskie Gory, Moscow, Russia.
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47
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Li BS, Zhao LF, Zhang C, Hei XH, Li F, Li XB, Shen J, Li YY, Huang Q, Xu SQ. Ultra-sensitive colorimetric method to quantitate hundreds of polynucleotide molecules by gold nanoparticles with silver enhancement. ANAL SCI 2007; 22:1367-70. [PMID: 17038778 DOI: 10.2116/analsci.22.1367] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
An ultra-sensitive colorimetric method to quantitate hundreds of polynucleotide molecules by gold nanoparticles with silver enhancement has been developed. The hybridization products from the target polynucleotides with biotin-labeled probes and gold nanoparticle-functioned oligonucleotides were immobilized to microplates via avidin-biotin system, and the absorbance signals of gold nanoparticles were amplified by silver enhance solution. This sandwich colorimetric assay can detect as few as 600 molecules for single-strand oligonucleotides and as few as 6000 molecules for double-strand polynucleotides in a 50 microL reaction system.
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Affiliation(s)
- Bo-Sheng Li
- MOE Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei Province, China
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48
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Abstract
Electroabsorption spectra were obtained for single-stranded polynucleotides poly(U), poly(C), poly(A), and poly(G) in glycerol/water glass at low temperature, and the differences in permanent dipole moment (Deltamu) and polarizability (Deltaalpha) were estimated for several spectral ranges covering the lowest energy absorption band around 260 nm. In each spectral range, the electrooptical parameters associated with apparent features in the absorption spectrum exhibit distinct values representing either a dominant single transition or the resultant value for a group of a relatively narrow cluster of overlapping transitions. The estimated spacing in energy between electronic origins of these transitions is larger than the electronic coupling within the Coulombic interaction model which is usually adopted in computational studies. The electroabsorption data allow us to distinguish a weak electronic transition associated with a wing in polynucleotide absorption spectra, at an energy below the electronic origin in absorption spectra of monomeric nucleobases. In poly(C) and poly(G), these low-energy transitions are related to increased values of Deltamu and Deltaalpha, possibly indicating a weak involvement of charge resonance in the respective excited states. A model capable of explaining the origin of low-energy excited states, based on the interaction of pipi* and npi* transitions in neighboring bases, is introduced and briefly discussed on the grounds of point dipole interaction.
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Affiliation(s)
- Stanislaw Krawczyk
- Institute of Physics, Maria Curie-Sklodowska University, 20-031 Lublin, Poland.
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49
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Ruiz GT, Juliarena MP, Lezna RO, Wolcan E, Feliz MR, Ferraudi G. Intercalation of fac-[(4,4'-bpy)ReI(CO)3(dppz)]+, dppz = dipyridyl[3,2-a:2'3'-c]phenazine, in polynucleotides. On the UV-vis photophysics of the Re(I) intercalator and the redox reactions with pulse radiolysis-generated radicals. Dalton Trans 2007:2020-9. [PMID: 17502935 DOI: 10.1039/b614970g] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The intercalation of fac-[(4,4'-bpy)Re(I)(CO)3(dppz)]+ (dppz = dipyridyl[3,2-a:2'3'-c]phenazine) in polynucleotides, poly[dAdT]2 and poly[dGdC]2, where A = adenine, G = guanine, C = cytosine and T = thymine, is a major cause of changes in the absorption and emission spectra of the complex. A strong complex-poly[dAdT]2 interaction drives the intercalation process, which has a binding constant, Kb approximately 1.8 x 10(5) M(-1). Pulse radiolysis was used for a study of the redox reactions of e(-)(aq), C*H(2)OH and N3* radicals with the intercalated complex. These radicals exhibited more affinity for the intercalated complex than for the bases. Ligand-radical complexes, fac-[(4,4'-bpy*)Re(I)(CO)3(dppz)] and fac-[(4,4'-bpy)Re(I)(CO)3(dppz *)], were produced by e(-)(aq) and C*H(2)OH, respectively. A Re(II) species, fac-[(4,4'-bpy)Re(II)(CO)3(dppz)](2+), was produced by N3* radicals. The rate of annihilation of the ligand-radical species was second order on the concentration of ligand-radical while the disappearance of the Re(II) complex induced the oxidative cleavage of the polynucleotide strand.
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Affiliation(s)
- G T Ruiz
- INIFTA, Universidad Nacional de La Plata, C. C. 16, Suc. 4, 1900, La Plata, Argentina
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50
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Ikeda M, Hasegawa T, Numata M, Sugikawa K, Sakurai K, Fujiki M, Shinkai S. Instantaneous inclusion of a polynucleotide and hydrophobic guest molecules into a helical core of cationic beta-1,3-glucan polysaccharide. J Am Chem Soc 2007; 129:3979-88. [PMID: 17352476 DOI: 10.1021/ja0684343] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We succeeded in the quantitative and selective introduction of an ammonium cationic group into the C6 position of Curdlan (CUR) by "Click Chemistry", and the obtained cationic Curdlan (CUR-N+) showed good solubility in water. ORD studies suggested that CUR-N+ adopts a single-stranded structure, different from a right-handed, triple-stranded helical structure of beta-1,3-glucan polysaccharides in water. It has been revealed that the polymeric complexes of CUR-N+ with polymeric guest molecules, such as polycytidylic acid (poly(C)), permethyldecasilane (PMDS), and single-walled carbon nanotubes (SWNTs), can be easily obtained by just mixing them in water with sonication. The characterization of the resultant CUR-N+-poly(C) complexes by UV-vis, CD spectroscopic measurements, and AFM and TEM observations revealed that they have stoichiometric, nanosized fibrous structures. From these experimental results as well as our precedent studies (e.g., refs 6 and 23), we propose that the complexation would be driven by the cooperative action of (1) the hydrogen-bonding interaction between the OH group at the C2 position and hydrogen-bonding sites of the cytosine ring (ref 6d), (2) the electrostatic interaction between the ammonium cation and the phosphate anion (ref 23), as well as (3) the background hydrophobic interaction. In addition, the complexed polynucleotide chain showed a strong resistance against enzymatic hydrolysis. Likewise, the dispersion of PMDS and SWNTs in water by CUR-N+ and the fibrous structures of the complexes were confirmed by spectroscopic measurements as well as microscopic observations. These binding properties of CUR-N+, which can proceed spontaneously in water, clearly differ from those of schizophyllan (SPG), which inevitably require a denature-renature process corresponding to a conversion of a triple strand to single strands induced by DMSO or base for inclusion of polymeric guest molecules.
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Affiliation(s)
- Masato Ikeda
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Motooka 744, Nishi-ku, Fukuoka 819-0395, Japan
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