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Ashwood B, Pollum M, Crespo-Hernández CE. Can a Six-Letter Alphabet Increase the Likelihood of Photochemical Assault to the Genetic Code? Chemistry 2016; 22:16648-16656. [PMID: 27723147 DOI: 10.1002/chem.201602160] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Indexed: 12/21/2022]
Abstract
In 2014, two unnatural nucleosides, d5SICS and dNaM, were shown to selectively base pair and replicate with high fidelity in a modified strain of E. coli, thus effectively expanding its genetic alphabet from four to six letters. More recently, a significant reduction in cell proliferation was reported in cells cultured with d5SICS, and putatively with dNaM, upon exposure to brief periods of near-visible radiation. The photosensitizing properties of the lowest-energy excited triplet state of both d5SICS and dNaM were implicated in their cytotoxicity. Importantly, however, the excited-state mechanisms by which near-visible excitation populates the triplet states of d5SICS and dNaM are currently unknown. In this study, steady-state and time-resolved spectroscopies are combined with quantum-chemical calculations in order to reveal the excited-state relaxation mechanisms leading to efficient population of the triplet states in these unnatural nucleosides in solution. It is shown that excitation of d5SICS or dNaM with near-visible light leads overwhelmingly to ultrafast population of their triplet states on the femtosecond time scale. The results presented in this work lend strong support to the proposal that photoexcitation of these unnatural nucleosides can accelerate oxidatively generated damage to DNA and other biomolecules within the cellular environment.
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Affiliation(s)
- Brennan Ashwood
- Department of Chemistry and Center for Chemical Dynamics, Case Western Reserve University, Cleveland, Ohio, 44106, USA
| | - Marvin Pollum
- Department of Chemistry and Center for Chemical Dynamics, Case Western Reserve University, Cleveland, Ohio, 44106, USA
| | - Carlos E Crespo-Hernández
- Department of Chemistry and Center for Chemical Dynamics, Case Western Reserve University, Cleveland, Ohio, 44106, USA.
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52
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Probst M, Aeschimann W, Chau TTH, Langenegger SM, Stocker A, Häner R. Structural insight into DNA-assembled oligochromophores: crystallographic analysis of pyrene- and phenanthrene-modified DNA in complex with BpuJI endonuclease. Nucleic Acids Res 2016; 44:7079-89. [PMID: 27422870 PMCID: PMC5009758 DOI: 10.1093/nar/gkw644] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 07/07/2016] [Accepted: 07/08/2016] [Indexed: 01/13/2023] Open
Abstract
The use of the DNA duplex as a supramolecular scaffold is an established approach for the assembly of chromophore aggregates. In the absence of detailed structural insight, the characterization of thus assembled oligochromophores is, today, largely based on solution-phase spectroscopy. Here, we describe the crystal structures of three DNA-organized chromophore aggregates. DNA hybrids containing non-nucleosidic pyrene and phenanthrene building blocks were co-crystallized with the recently described binding domain of the restriction enzyme BpuJI. Crystal structures of these complexes were determined at 2.7, 1.9 and 1.6 Å resolutions. The structures reveal aromatic stacking interactions between pyrene and/or phenanthrene units within the framework of the B-DNA duplex. In hybrids containing a single modification in each DNA strand near the end of the duplex, the two polyaromatic hydrocarbons are engaged in a face-to-face stacking orientation. Due to crystal packing and steric effects, the terminal GC base pair is disrupted in all three crystal structures, which results in a non-perfect stacking arrangement of the aromatic chromophores in two of the structures. In a hybrid containing a total of three pyrenes, crystal lattice induced end-to-end stacking of individual DNA duplexes leads to the formation of an extended aromatic π-stack containing four co-axially arranged pyrenes. The aromatic planes of the stacked pyrenes are oriented in a parallel way. The study demonstrates the value of co-crystallization of chemically modified DNA with the recombinant binding domain of the restriction enzyme BpuJI for obtaining detailed structural insight into DNA-assembled oligochromophores.
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Affiliation(s)
- Markus Probst
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Walter Aeschimann
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Thi T H Chau
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Simon M Langenegger
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Achim Stocker
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Robert Häner
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
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53
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Mayer C, McInroy GR, Murat P, Van Delft P, Balasubramanian S. An Epigenetics-Inspired DNA-Based Data Storage System. Angew Chem Int Ed Engl 2016; 55:11144-8. [PMID: 27440712 PMCID: PMC5113786 DOI: 10.1002/anie.201605531] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Indexed: 12/22/2022]
Abstract
Biopolymers are an attractive alternative to store and circulate information. DNA, for example, combines remarkable longevity with high data storage densities and has been demonstrated as a means for preserving digital information. Inspired by the dynamic, biological regulation of (epi)genetic information, we herein present how binary data can undergo controlled changes when encoded in synthetic DNA strands. By exploiting differential kinetics of hydrolytic deamination reactions of cytosine and its naturally occurring derivatives, we demonstrate how multiple layers of information can be stored in a single DNA template. Moreover, we show that controlled redox reactions allow for interconversion of these DNA-encoded layers of information. Overall, such interlacing of multiple messages on synthetic DNA libraries showcases the potential of chemical reactions to manipulate digital information on (bio)polymers.
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Affiliation(s)
- Clemens Mayer
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Gordon R McInroy
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Pierre Murat
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Pieter Van Delft
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Shankar Balasubramanian
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
- Cancer Research, UK, Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK.
- School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0SP, UK.
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54
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Stross AE, Iadevaia G, Hunter CA. Mix and match recognition modules for the formation of H-bonded duplexes. Chem Sci 2016; 7:5686-5691. [PMID: 30034707 PMCID: PMC6022071 DOI: 10.1039/c6sc01884j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 05/24/2016] [Indexed: 11/21/2022] Open
Abstract
Oligomeric molecules equipped with complementary H-bond recognition sites form stable duplexes in non-polar solvents. The use of a single H-bond between a good H-bond donor and a good H-bond acceptor as the recognition motif appended to a non-polar backbone leads to an architecture with interchangeable recognition alphabets. The interactions of three different families of H-bond acceptor oligomers (pyridine, pyridine N-oxide or phosphine oxide recognition module) with a family of H-bond donor oligomers (phenol recognition module) are compared. All three donor-acceptor combinations form stable duplexes, where the stability of the 1 : 1 complex increases with increasing numbers of recognition modules. The effective molarity for formation of intramolecular H-bonds that lead to zipping up of the duplex (EM) increases with decreasing flexibility of the recognition modules: 14 mM for the phosphine oxides which are connected to the backbone via a flexible linker; 40 mM for the pyridine N-oxides which have three fewer degrees of torsional freedom, and 80 mM for the pyridines where the geometry of the H-bond is more directional. However, the pyridine-phenol H-bond is an order of magnitude weaker than the other two types of H-bond, so overall the pyridine N-oxides form the most stable duplexes with the highest degree of cooperativity. The results show that it is possible to use different recognition motifs with the same duplex architecture, and this makes it possible to tune overall stabilities of the complexes by varying the components.
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Affiliation(s)
- Alexander E Stross
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK .
| | - Giulia Iadevaia
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK .
| | - Christopher A Hunter
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK .
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55
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Mayer C, McInroy GR, Murat P, Van Delft P, Balasubramanian S. An Epigenetics‐Inspired DNA‐Based Data Storage System. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605531] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Clemens Mayer
- Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Gordon R. McInroy
- Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Pierre Murat
- Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Pieter Van Delft
- Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Shankar Balasubramanian
- Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
- Cancer Research, UK, Cambridge Institute, Li Ka Shing Centre University of Cambridge Robinson Way Cambridge CB2 0RE UK
- School of Clinical Medicine University of Cambridge Cambridge CB2 0SP UK
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56
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Samanta A, Medintz IL. Nanoparticles and DNA - a powerful and growing functional combination in bionanotechnology. NANOSCALE 2016; 8:9037-95. [PMID: 27080924 DOI: 10.1039/c5nr08465b] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Functionally integrating DNA and other nucleic acids with nanoparticles in all their different physicochemical forms has produced a rich variety of composite nanomaterials which, in many cases, display unique or augmented properties due to the synergistic activity of both components. These capabilities, in turn, are attracting greater attention from various research communities in search of new nanoscale tools for diverse applications that include (bio)sensing, labeling, targeted imaging, cellular delivery, diagnostics, therapeutics, theranostics, bioelectronics, and biocomputing to name just a few amongst many others. Here, we review this vibrant and growing research area from the perspective of the materials themselves and their unique capabilities. Inorganic nanocrystals such as quantum dots or those made from gold or other (noble) metals along with metal oxides and carbon allotropes are desired as participants in these hybrid materials since they can provide distinctive optical, physical, magnetic, and electrochemical properties. Beyond this, synthetic polymer-based and proteinaceous or viral nanoparticulate materials are also useful in the same role since they can provide a predefined and biocompatible cargo-carrying and targeting capability. The DNA component typically provides sequence-based addressability for probes along with, more recently, unique architectural properties that directly originate from the burgeoning structural DNA field. Additionally, DNA aptamers can also provide specific recognition capabilities against many diverse non-nucleic acid targets across a range of size scales from ions to full protein and cells. In addition to appending DNA to inorganic or polymeric nanoparticles, purely DNA-based nanoparticles have recently surfaced as an excellent assembly platform and have started finding application in areas like sensing, imaging and immunotherapy. We focus on selected and representative nanoparticle-DNA materials and highlight their myriad applications using examples from the literature. Overall, it is clear that this unique functional combination of nanomaterials has far more to offer than what we have seen to date and as new capabilities for each of these materials are developed, so, too, will new applications emerge.
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Affiliation(s)
- Anirban Samanta
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA. and College of Science, George Mason University, Fairfax, Virginia 22030, USA
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA.
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57
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Iadevaia G, Stross AE, Neumann A, Hunter CA. Mix and match backbones for the formation of H-bonded duplexes. Chem Sci 2016; 7:1760-1767. [PMID: 28936325 PMCID: PMC5592378 DOI: 10.1039/c5sc04467g] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 12/18/2015] [Indexed: 11/21/2022] Open
Abstract
The formation of well-defined supramolecular assemblies involves competition between intermolecular and intramolecular interactions, which is quantified by effective molarity. Formation of a duplex between two oligomers equipped with recognition sites displayed along a non-interacting backbone requires that once one intermolecular interaction has been formed, all subsequent interactions take place in an intramolecular sense. The efficiency of this process is governed by the geometric complementarity and conformational flexibility of the backbone linking the recognition sites. Here we report a series of phosphine oxide H-bond acceptor AA 2-mers and phenol H-bond donor DD 2-mers, where the two recognition sites are connected by isomeric backbone modules that vary in geometry and flexibility. All AA and DD combinations form stable AA·DD duplexes, where two cooperative H-bonds lead to an increase in stability of an order of magnitude compared with the corresponding A·D complexes that can only form one H-bond. For all six possible backbone combinations, the effective molarity for duplex formation is approximately constant (7-20 mM). Thus strict complementarity and high degrees of preorganisation are not required for efficient supramolecular assembly. Provided there is some flexibility, quite different backbone modules can be used interchangeably to construct stable H-bonded duplexes.
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Affiliation(s)
- Giulia Iadevaia
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK .
| | - Alexander E Stross
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK .
| | - Anja Neumann
- Department of Chemistry , University of Sheffield , Sheffield S3 7HF , UK
| | - Christopher A Hunter
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK .
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58
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Bande O, Braddick D, Agnello S, Jang M, Pezo V, Schepers G, Rozenski J, Lescrinier E, Marlière P, Herdewijn P. Base pairing involving artificial bases in vitro and in vivo. Chem Sci 2016; 7:995-1010. [PMID: 29896368 PMCID: PMC5954848 DOI: 10.1039/c5sc03474d] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 10/28/2015] [Indexed: 01/09/2023] Open
Abstract
Herein we report the synthesis of N8-glycosylated 8-aza-deoxyguanosine (N8-8-aza-dG) and 8-aza-9-deaza-deoxyguanosine (N8-8-aza-9-deaza-dG) nucleotides and their base pairing properties with 5-methyl-isocytosine (d-isoCMe), 8-amino-deoxyinosine (8-NH2-dI), 1-N-methyl-8-amino-deoxyinosine (1-Me-8-NH2-dI), 7,8-dihydro-8-oxo-deoxyinosine (8-Oxo-dI), 7,8-dihydro-8-oxo-deoxyadenosine (8-Oxo-dA), and 7,8-dihydro-8-oxo-deoxyguanosine (8-Oxo-dG), in comparison with the d-isoCMe:d-isoG artificial genetic system. As demonstrated by Tm measurements, the N8-8-aza-dG:d-isoCMe base pair formed less stable duplexes as the C:G and d-isoCMe:d-isoG pairs. Incorporation of 8-NH2-dI versus the N8-8-aza-dG nucleoside resulted in a greater reduction in Tm stability, compared to d-isoCMe:d-isoG. Insertion of the methyl group at the N1 position of 8-NH2-dI did not affect duplex stability with N8-8-aza-dG, thus suggesting that the base paring takes place through Hoogsteen base pairing. The cellular interpretation of the nucleosides was studied, whereby a lack of recognition or mispairing of the incorporated nucleotides with the canonical DNA bases indicated the extent of orthogonality in vivo. The most biologically orthogonal nucleosides identified included the 8-amino-deoxyinosines (1-Me-8-NH2-dI and 8-NH2-dI) and N8-8-aza-9-deaza-dG. The 8-oxo modifications mimic oxidative damage ahead of cancer development, and the impact of the MutM mediated recognition of these 8-oxo-deoxynucleosides was studied, finding no significant impact in their in vivo assay.
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Affiliation(s)
- Omprakash Bande
- Medicinal Chemistry , Rega Institute for Medical Research , KU Leuven , Minderbroedersstraat 10 , 3000 Leuven , Belgium . ; Tel: +32 16 337387
| | - Darren Braddick
- iSSB - CNRS FRE3561 , University of Evry-Val-d'Essonne , 5 rue Henri Desbruères, Genopole Campus 1, Bât. 6 , F-91030 Évry Cedex , France
| | - Stefano Agnello
- Medicinal Chemistry , Rega Institute for Medical Research , KU Leuven , Minderbroedersstraat 10 , 3000 Leuven , Belgium . ; Tel: +32 16 337387
| | - Miyeon Jang
- Medicinal Chemistry , Rega Institute for Medical Research , KU Leuven , Minderbroedersstraat 10 , 3000 Leuven , Belgium . ; Tel: +32 16 337387
| | - Valérie Pezo
- iSSB - CNRS FRE3561 , University of Evry-Val-d'Essonne , 5 rue Henri Desbruères, Genopole Campus 1, Bât. 6 , F-91030 Évry Cedex , France
| | - Guy Schepers
- Medicinal Chemistry , Rega Institute for Medical Research , KU Leuven , Minderbroedersstraat 10 , 3000 Leuven , Belgium . ; Tel: +32 16 337387
| | - Jef Rozenski
- Medicinal Chemistry , Rega Institute for Medical Research , KU Leuven , Minderbroedersstraat 10 , 3000 Leuven , Belgium . ; Tel: +32 16 337387
| | - Eveline Lescrinier
- Medicinal Chemistry , Rega Institute for Medical Research , KU Leuven , Minderbroedersstraat 10 , 3000 Leuven , Belgium . ; Tel: +32 16 337387
| | - Philippe Marlière
- iSSB - CNRS FRE3561 , University of Evry-Val-d'Essonne , 5 rue Henri Desbruères, Genopole Campus 1, Bât. 6 , F-91030 Évry Cedex , France
| | - Piet Herdewijn
- iSSB - CNRS FRE3561 , University of Evry-Val-d'Essonne , 5 rue Henri Desbruères, Genopole Campus 1, Bât. 6 , F-91030 Évry Cedex , France
- Medicinal Chemistry , Rega Institute for Medical Research , KU Leuven , Minderbroedersstraat 10 , 3000 Leuven , Belgium . ; Tel: +32 16 337387
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59
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Singleton DG, Hussain R, Siligardi G, Kumar P, Hrdlicka PJ, Berova N, Stulz E. Increased duplex stabilization in porphyrin-LNA zipper arrays with structure dependent exciton coupling. Org Biomol Chem 2016; 14:149-57. [PMID: 26416024 PMCID: PMC4766578 DOI: 10.1039/c5ob01681a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 09/18/2015] [Indexed: 12/23/2022]
Abstract
Porphyrins were attached to LNA uridine building blocks via rigid 5-acetylene or more flexible propargyl-amide linkers and incorporated into DNA strands. The systems show a greatly increased thermodynamic stability when using as little as three porphyrins in a zipper arrangement. Thermodynamic analysis reveals clustering of the strands into more ordered duplexes with both greater negative ΔΔS and ΔΔH values, and less ordered duplexes with small positive ΔΔS differences, depending on the combination of linkers used. The exciton coupling between the porphyrins is dependent on the flanking DNA sequence in the single stranded form, and on the nature of the linker between the nucleobase and the porphyrin in the double stranded form; it is, however, also strongly influenced by intermolecular interactions. This system is suitable for the formation of stable helical chromophore arrays with sequence and structure dependent exciton coupling.
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Affiliation(s)
- Daniel G. Singleton
- School of Chemistry and Institute for Life Sciences , University of Southampton , Highfield , Southampton , SO17 1BJ , UK . ; http://www.southampton.ac.uk/chemistry/about/staff/est.page?
| | - Rohanah Hussain
- Diamond Light Source , Harwell Science and Innovation Campus , Didcot , Oxfordshire OX11 0DE , UK
| | - Giuliano Siligardi
- Diamond Light Source , Harwell Science and Innovation Campus , Didcot , Oxfordshire OX11 0DE , UK
| | - Pawan Kumar
- Department of Chemistry , University of Idaho , Moscow , ID 83844 , USA
| | | | - Nina Berova
- Department of Chemistry , Columbia University , 3000 Broadway , New York , NY 10027 , USA
| | - Eugen Stulz
- School of Chemistry and Institute for Life Sciences , University of Southampton , Highfield , Southampton , SO17 1BJ , UK . ; http://www.southampton.ac.uk/chemistry/about/staff/est.page?
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60
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Bag SS, Talukdar S, Das SK, Pradhan MK, Mukherjee S. Donor/acceptor chromophores-decorated triazolyl unnatural nucleosides: synthesis, photophysical properties and study of interaction with BSA. Org Biomol Chem 2016; 14:5088-108. [DOI: 10.1039/c6ob00500d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We report the syntheses and photophysical properties of some triazolyl donor/acceptor unnatural nucleosides and studies on the interaction of one of the fluorescent nucleosides with BSA.
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Affiliation(s)
- Subhendu Sekhar Bag
- Bio-organic Chemistry Laboratory
- Department of Chemistry
- Indian Institute of Technology Guwahati-781039
- India
| | - Sangita Talukdar
- Bio-organic Chemistry Laboratory
- Department of Chemistry
- Indian Institute of Technology Guwahati-781039
- India
| | - Suman Kalyan Das
- Bio-organic Chemistry Laboratory
- Department of Chemistry
- Indian Institute of Technology Guwahati-781039
- India
| | - Manoj Kumar Pradhan
- Bio-organic Chemistry Laboratory
- Department of Chemistry
- Indian Institute of Technology Guwahati-781039
- India
| | - Soumen Mukherjee
- Bio-organic Chemistry Laboratory
- Department of Chemistry
- Indian Institute of Technology Guwahati-781039
- India
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61
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Tokarenko A, Poštová Slavětínská L, Klepetářová B, Hocek M. Synthesis of Benzene and Pyridine 2′-C-Methyl-C-ribonucleosides and -nucleotides. European J Org Chem 2015. [DOI: 10.1002/ejoc.201501219] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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62
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Chen JL, Bellaousov S, Tubbs JD, Kennedy SD, Lopez MJ, Mathews DH, Turner DH. Nuclear Magnetic Resonance-Assisted Prediction of Secondary Structure for RNA: Incorporation of Direction-Dependent Chemical Shift Constraints. Biochemistry 2015; 54:6769-82. [PMID: 26451676 PMCID: PMC4666457 DOI: 10.1021/acs.biochem.5b00833] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Knowledge
of RNA
structure is necessary to determine structure–function relationships
and to facilitate design of potential therapeutics.
RNA secondary structure prediction can be improved by applying constraints
from nuclear magnetic resonance (NMR) experiments to a dynamic programming
algorithm. Imino proton walks from NOESY spectra reveal double-stranded
regions. Chemical shifts of protons in GH1, UH3, and UH5 of GU pairs,
UH3, UH5, and AH2 of AU pairs, and GH1 of GC pairs were analyzed to
identify constraints for the 5′ to 3′ directionality
of base pairs in helices. The 5′ to 3′ directionality
constraints were incorporated into an NMR-assisted prediction of secondary
structure (NAPSS-CS) program. When it was tested on 18 structures,
including nine pseudoknots, the sensitivity and positive predictive
value were improved relative to those of three unrestrained programs.
The prediction accuracy for the pseudoknots improved the most. The
program also facilitates assignment of chemical shifts to individual
nucleotides, a necessary step for determining three-dimensional structure.
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Affiliation(s)
- Jonathan L Chen
- Department of Chemistry, University of Rochester , Rochester, New York 14627, United States
| | - Stanislav Bellaousov
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry , Rochester, New York 14642, United States
| | - Jason D Tubbs
- Department of Chemistry, University of Rochester , Rochester, New York 14627, United States
| | - Scott D Kennedy
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry , Rochester, New York 14642, United States
| | - Michael J Lopez
- Department of Chemistry, University of Rochester , Rochester, New York 14627, United States
| | - David H Mathews
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry , Rochester, New York 14642, United States.,Center for RNA Biology, University of Rochester , Rochester, New York 14642, United States
| | - Douglas H Turner
- Department of Chemistry, University of Rochester , Rochester, New York 14627, United States.,Center for RNA Biology, University of Rochester , Rochester, New York 14642, United States
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63
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Stross AE, Iadevaia G, Hunter CA. Cooperative duplex formation by synthetic H-bonding oligomers. Chem Sci 2015; 7:94-101. [PMID: 29861969 PMCID: PMC5950798 DOI: 10.1039/c5sc03414k] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 10/15/2015] [Indexed: 01/12/2023] Open
Abstract
Flexible phenol-phosphine oxide oligomers show promise as a new class of synthetic information molecule.
A series of flexible oligomers equipped with phenol H-bond donors and phosphine oxide H-bond acceptors have been synthesised using reductive amination chemistry. H-bonding interactions between complementary oligomers leads to the formation of double-stranded complexes which were characterised using NMR titrations and thermal denaturation experiments. The stability of the duplex increases by one order of magnitude for every H-bonding group added to the chain. Similarly, the enthalpy change for duplex assembly and the melting temperature for duplex denaturation both increase with increasing chain length. These observations indicate that H-bond formation along the oligomers is cooperative despite the flexible backbone, and the effective molarity for intramolecular H-bond formation (14 mM) is sufficient to propagate the formation of longer duplexes using this approach. The product K EM, which is used to quantify chelate cooperativity is 5, which means that each H-bond is more than 80% populated in the assembled duplex. The modular design of these oligomers represents a general strategy for the design of synthetic information molecules that could potentially encode and replicate chemical information in the same way as nucleic acids.
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Affiliation(s)
- Alexander E Stross
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK .
| | - Giulia Iadevaia
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK .
| | - Christopher A Hunter
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK .
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64
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Fakhfakh K, Hughesman CB, Louise Creagh A, Kao V, Haynes C. Calorimetric and Spectroscopic Analysis of the Thermal Stability of Short Duplex DNA-Containing Sugar and Base-Modified Nucleotides. Methods Enzymol 2015; 567:97-127. [PMID: 26794352 DOI: 10.1016/bs.mie.2015.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Base- and sugar-modified analogs of DNA and RNA are finding ever expanding use in medicine and biotechnology as tools to better tailor structured oligonucleotides by altering their thermal stability, nuclease resistance, base-pairing specificity, antisense activity, or cellular uptake. Proper deployment of these chemical modifications generally requires knowledge of how each affects base-pairing properties and thermal stabilities. Here, we describe in detail how differential scanning calorimetry and UV spectroscopy may be used to quantify the melting thermodynamics of short dsDNA containing chemically modified nucleosides in one or both strands. Insights are provided into why and how the presence of highly stable base pairs containing modified nucleosides can alter the nature of calorimetry or melting spectroscopy data, and how each experiment must therefore be conducted to ensure high-quality melting thermodynamics data are obtained. Strengths and weaknesses of the two methods when applied to chemically modified duplexes are also addressed.
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Affiliation(s)
- Kareem Fakhfakh
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada; Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British Columbia, Canada
| | - Curtis B Hughesman
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - A Louise Creagh
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada; Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British Columbia, Canada
| | - Vincent Kao
- Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British Columbia, Canada
| | - Charles Haynes
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada; Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British Columbia, Canada; RES'EAU Water Research Network, Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British Columbia, Canada.
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65
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Haidzinskaya T, Kerchner HA, Liu J, Watson MP. Diastereoselective, Zinc-Catalyzed Alkynylation of α-Bromo Oxocarbenium Ions. Org Lett 2015. [PMID: 26196257 DOI: 10.1021/acs.orglett.5b01838] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have developed a bromination/alkynylation sequence that enables efficient transformation of simple cyclic enol ethers to difunctionalized products. The success of this strategy relies on a highly diastereselective, zinc-catalyzed addition of terminal alkynes to α-bromo oxocarbenium ions, formed in situ via ionization of acetal precursors. Using this method, trans-α-alkynyl-β-halo pyran and furan derivatives can be prepared with high diastereoselectivity and excellent functional group tolerance.
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Affiliation(s)
- Tatsiana Haidzinskaya
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Hilary A Kerchner
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Jixin Liu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Mary P Watson
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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66
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Kore AR, Yang B, Srinivasan B. Short and straightforward synthesis of triphosphates of artificial nucleobase pairs displaying unconventional pairing scheme. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2015; 33:767-73. [PMID: 25372992 DOI: 10.1080/15257770.2014.938754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Concise, facile and efficient synthesis of 5'-O-triphosphates of 6-amino-5-nitro-3-(1'-β-D-2'-deoxyribofuranosyl)-2(1H)-pyridone (dZ) and its Watson-Crick complement 2-amino-8-(1'-β-D-2'-deoxyribofuranosyl)-imidazo[1,2a]-1,3,5-triazin-4(8H)-one (dP) is reported using a one-pot synthetic procedure.
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Affiliation(s)
- Anilkumar R Kore
- a Bioorganic Chemistry Division , Life Sciences Solutions Group, Thermo Fisher Scientific , Austin , TX , USA
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67
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Georgiadis MM, Singh I, Kellett WF, Hoshika S, Benner SA, Richards NGJ. Structural basis for a six nucleotide genetic alphabet. J Am Chem Soc 2015; 137:6947-55. [PMID: 25961938 DOI: 10.1021/jacs.5b03482] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Expanded genetic systems are most likely to work with natural enzymes if the added nucleotides pair with geometries that are similar to those displayed by standard duplex DNA. Here, we present crystal structures of 16-mer duplexes showing this to be the case with two nonstandard nucleobases (Z, 6-amino-5-nitro-2(1H)-pyridone and P, 2-amino-imidazo[1,2-a]-1,3,5-triazin-4(8H)one) that were designed to form a Z:P pair with a standard "edge on" Watson-Crick geometry, but joined by rearranged hydrogen bond donor and acceptor groups. One duplex, with four Z:P pairs, was crystallized with a reverse transcriptase host and adopts primarily a B-form. Another contained six consecutive Z:P pairs; it crystallized without a host in an A-form. In both structures, Z:P pairs fit canonical nucleobase hydrogen-bonding parameters and known DNA helical forms. Unique features include stacking of the nitro group on Z with the adjacent nucleobase ring in the A-form duplex. In both B- and A-duplexes, major groove widths for the Z:P pairs are approximately 1 Å wider than those of comparable G:C pairs, perhaps to accommodate the large nitro group on Z. Otherwise, ZP-rich DNA had many of the same properties as CG-rich DNA, a conclusion supported by circular dichroism studies in solution. The ability of standard duplexes to accommodate multiple and consecutive Z:P pairs is consistent with the ability of natural polymerases to biosynthesize those pairs. This, in turn, implies that the GACTZP synthetic genetic system can explore the entire expanded sequence space that additional nucleotides create, a major step forward in this area of synthetic biology.
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68
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Bartolami E, Gilles A, Dumy P, Ulrich S. Synthesis of α-PNA containing a functionalized triazine as nucleobase analogue. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2015.03.072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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69
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Joo HN, Seo YJ. A multiplex fluorophore molecular beacon: detection of the target sequence using large Stokes shift and multiple emission signal properties. Chem Commun (Camb) 2015; 51:2939-42. [DOI: 10.1039/c4cc08854a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have developed a multiplex fluorophore molecular beacon (mfMB) with fluorophores located at its end to produce unique FRET (Fluorescence Resonance Energy Transfer). It exhibited diverse fluorescence properties depending on the mixing pattern, such as large Stokes shift emission and multiple colors.
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Affiliation(s)
- Han Na Joo
- Department of Chemistry
- Chonbuk National University
- Jeonju 561-756
- South Korea
| | - Young Jun Seo
- Department of Chemistry
- Chonbuk National University
- Jeonju 561-756
- South Korea
- Department of Bioactive Material Sciences
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70
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Zhou F, Wang G, Shi D, Sun Y, Sha L, Qiu Y, Zhang X. One-strand oligonucleotide probe for fluorescent label-free “turn-on” detection of T4 polynucleotide kinase activity and its inhibition. Analyst 2015; 140:5650-5. [DOI: 10.1039/c5an00862j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Thioflavin T (ThT), as one of the most exciting fluorogenic molecules, boasts the “molecular-rotor” ability to induce DNA sequences containing guanine repeats to fold into G-quadruplex structures.
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Affiliation(s)
- Fu Zhou
- Anhui Key Laboratory of Chem-biosensing
- College of Chemistry and Materials Science
- Center for Nanoscience and Nanotechology
- Anhui Normal University
- Wuhu
| | - Guangfeng Wang
- Anhui Key Laboratory of Chem-biosensing
- College of Chemistry and Materials Science
- Center for Nanoscience and Nanotechology
- Anhui Normal University
- Wuhu
| | - Dongmin Shi
- Anhui Key Laboratory of Chem-biosensing
- College of Chemistry and Materials Science
- Center for Nanoscience and Nanotechology
- Anhui Normal University
- Wuhu
| | - Yue Sun
- Anhui Key Laboratory of Chem-biosensing
- College of Chemistry and Materials Science
- Center for Nanoscience and Nanotechology
- Anhui Normal University
- Wuhu
| | - Liang Sha
- Anhui Key Laboratory of Chem-biosensing
- College of Chemistry and Materials Science
- Center for Nanoscience and Nanotechology
- Anhui Normal University
- Wuhu
| | - Yuwei Qiu
- Anhui Key Laboratory of Chem-biosensing
- College of Chemistry and Materials Science
- Center for Nanoscience and Nanotechology
- Anhui Normal University
- Wuhu
| | - Xiaojun Zhang
- Anhui Key Laboratory of Chem-biosensing
- College of Chemistry and Materials Science
- Center for Nanoscience and Nanotechology
- Anhui Normal University
- Wuhu
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71
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Laos R, Thomson JM, Benner SA. DNA polymerases engineered by directed evolution to incorporate non-standard nucleotides. Front Microbiol 2014; 5:565. [PMID: 25400626 PMCID: PMC4215692 DOI: 10.3389/fmicb.2014.00565] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 10/07/2014] [Indexed: 11/13/2022] Open
Abstract
DNA polymerases have evolved for billions of years to accept natural nucleoside triphosphate substrates with high fidelity and to exclude closely related structures, such as the analogous ribonucleoside triphosphates. However, polymerases that can accept unnatural nucleoside triphosphates are desired for many applications in biotechnology. The focus of this review is on non-standard nucleotides that expand the genetic "alphabet." This review focuses on experiments that, by directed evolution, have created variants of DNA polymerases that are better able to accept unnatural nucleotides. In many cases, an analysis of past evolution of these polymerases (as inferred by examining multiple sequence alignments) can help explain some of the mutations delivered by directed evolution.
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Affiliation(s)
- Roberto Laos
- Foundation for Applied Molecular Evolution Gainesville, FL, USA
| | | | - Steven A Benner
- Foundation for Applied Molecular Evolution Gainesville, FL, USA
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72
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Mei H, Ingale SA, Seela F. Imidazolo-dC metal-mediated base pairs: purine nucleosides capture two Ag(+) ions and form a duplex with the stability of a covalent DNA cross-link. Chemistry 2014; 20:16248-57. [PMID: 25336305 DOI: 10.1002/chem.201404422] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Indexed: 12/13/2022]
Abstract
8-Phenylimidazolo-dC ((ph) ImidC, 2) forms metal-mediated DNA base pairs by entrapping two silver ions. To this end, the fluorescent "purine" 2'-deoxyribonucleoside 2 has been synthesised and converted into the phosphoramidite 6. Owing to the ease of nucleobase deprotonation, the new Ag(+) -mediated base pair containing a "purine" skeleton is much stronger than that derived from the pyrrolo- [3,4-d]pyrimidine system ((ph) PyrdC, 1). The silver-mediated (ph) ImidC-(ph) ImidC base pair fits well into the DNA double helix and has the stability of a covalent cross-link. The formation of such artificial metal base pairs might not be limited to DNA but may be applicable to other nucleic acids such as RNA, PNA and GNA as well as other biopolymers.
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Affiliation(s)
- Hui Mei
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster (Germany), Fax: (+49) 251-53406857; Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069 Osnabrück (Germany)
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73
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Zhang F, Mu D, Wang L, Du P, Han F, Zhao Y. Synthesis of Substituted Mono- and Diindole C-Nucleoside Analogues from Sugar Terminal Alkynes by Sequential Sonogashira/Heteroannulation Reaction. J Org Chem 2014; 79:9490-9. [DOI: 10.1021/jo501488x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Fuyi Zhang
- The
College of Chemistry and Molecular Engineering, The Key Laboratory
of Chemical Biology and Organic Chemistry of Henan Province, Zhengzhou University, Zhengzhou, 450001, China
| | - Delong Mu
- The
College of Chemistry and Molecular Engineering, The Key Laboratory
of Chemical Biology and Organic Chemistry of Henan Province, Zhengzhou University, Zhengzhou, 450001, China
| | - Liming Wang
- The
College of Chemistry and Molecular Engineering, The Key Laboratory
of Chemical Biology and Organic Chemistry of Henan Province, Zhengzhou University, Zhengzhou, 450001, China
| | - Pengfei Du
- The
College of Chemistry and Molecular Engineering, The Key Laboratory
of Chemical Biology and Organic Chemistry of Henan Province, Zhengzhou University, Zhengzhou, 450001, China
| | - Fen Han
- The
College of Chemistry and Molecular Engineering, The Key Laboratory
of Chemical Biology and Organic Chemistry of Henan Province, Zhengzhou University, Zhengzhou, 450001, China
| | - Yufen Zhao
- The
College of Chemistry and Molecular Engineering, The Key Laboratory
of Chemical Biology and Organic Chemistry of Henan Province, Zhengzhou University, Zhengzhou, 450001, China
- College
of Chemistry and Chemical Engineering, The Key Laboratory for Chemical
Biology of Fujian Province, Xiamen University, Xiamen, 361005, China
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74
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Wang R, Wang C, Cao Y, Zhu Z, Yang C, Chen J, Qing FL, Tan W. Trifluoromethylated Nucleic Acid Analogues Capable of Self-Assembly through Hydrophobic Interactions. Chem Sci 2014; 5:4076-4081. [PMID: 25285193 PMCID: PMC4180415 DOI: 10.1039/c4sc01162g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
An artificial nucleic acid analogue capable of self-assembly into duplex merely through hydrophobic interactions is presented. The replacement of Watson-Crick hydrogen bonding with strictly hydrophobic interactions has the potential to confer new properties and facilitate the construction of complex DNA nanodevices. To study how the hydrophobic effect works during the self-assembly of nucleic acid bases, we have designed and synthesized a series of fluorinated nucleic acids (FNA) containing 3,5-bis(trifluoromethyl) benzene (F) and nucleic acids incorporating 3,5-dimethylbenzene (M) as hydrophobic base surrogates. Our experiments illustrate that two single-stranded nucleic acid oligomers could spontaneously organize into a duplex entirely by hydrophobic base pairing if the bases were size-complementary and the intermolecular forces were sufficiently strong.
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Affiliation(s)
- RuoWen Wang
- Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, China
| | - Chunming Wang
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yang Cao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhi Zhu
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Chaoyong Yang
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Jianzhong Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Feng-Ling Qing
- Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Science, 345 Lingling Lu, Shanghai, 200032, China
| | - Weihong Tan
- Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, China
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75
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Bag SS, Talukdar S, Das SK. Design and synthesis of triazolyl-donor/acceptor unnatural nucleosides and oligonucleotide probes containing triazolyl-phenanthrene nucleoside. ACTA ACUST UNITED AC 2014; 58:1.32.1-27. [PMID: 25199635 DOI: 10.1002/0471142700.nc0132s58] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
In the context of abasic DNA or DNA duplex stabilization, several unnatural nucleosidic/non-nucleosidic base surrogates have been reported. Toward this end, we have designed and synthesized triazolyl-aromatic donor chomophores as unnatural nucleoside analogs. These modifications display markedly higher thermal stabilization of abasic DNA duplex in comparison to the stabilization offered by other nucleoside/non-nucleoside base surrogates reported in the literature. The same oligonucleotide probe containing triazolylphenanthrene nucleotide also offers very good stability of the self-pair duplex via π-π stacking interaction and hetero-pair duplex via charge transfer interaction when paired against triazolyl acceptor aromatic nucleoside. Moreover, the probe in the reverse sequence containing triazolylphenanthrene nucleotide has shown FRET efficiency in a chimeric DNA duplex. The triazolyl nucleotides would expectedly show stability toward exonuclease activity. This unit describes protocols for chemical synthesis of unnatural triazolyl nucleosides and one oligonucleotide probe. The unit also provides a summary of various thermal and photophysical applications of triazolylphenantherene-containing oligonucleotides.
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Affiliation(s)
- Subhendu Sekhar Bag
- Bio-organic Chemistry Laboratory, Department of Chemistry, Indian Institute of Technology Guwahati, Assam-781039, India
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76
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Grabkowska-Drużyc M, Balzarini J, Piotrowska DG. Design, synthesis, antiviral, and cytostatic evaluation of novel isoxazolidine analogues of C-nucleotides. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2014; 32:682-99. [PMID: 24328565 DOI: 10.1080/15257770.2013.851794] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
5-Aryl-2-methylisoxazolidin-3-yl-3-phosphonates have been synthesised from N-methyl-C-diethoxyphosphorylnitrone and vinyl aryls in good yields. Isoxazolidine phosphonates obtained herein were evaluated for activity against a broad range of DNA and RNA viruses. None of the compounds were endowed with antiviral activity nor cytostatic activity at 100 to 250 μM concentrations.
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77
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Albert SK, Thelu HVP, Golla M, Krishnan N, Chaudhary S, Varghese R. Self-assembly of DNA-oligo(p-phenylene-ethynylene) hybrid amphiphiles into surface-engineered vesicles with enhanced emission. Angew Chem Int Ed Engl 2014; 53:8352-7. [PMID: 24962762 DOI: 10.1002/anie.201403455] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 05/19/2014] [Indexed: 11/09/2022]
Abstract
Surface-addressable nanostructures of linearly π-conjugated molecules play a crucial role in the emerging field of nanoelectronics. Herein, by using DNA as the hydrophilic segment, we demonstrate a solid-phase "click" chemistry approach for the synthesis of a series of DNA-chromophore hybrid amphiphiles and report their reversible self-assembly into surface-engineered vesicles with enhanced emission. DNA-directed surface addressability of the vesicles was demonstrated through the integration of gold nanoparticles onto the surface of the vesicles by sequence-specific DNA hybridization. This system could be converted to a supramolecular light-harvesting antenna by integrating suitable FRET acceptors onto the surface of the nanostructures. The general nature of the synthesis, surface addressability, and biocompatibility of the resulting nanostructures offer great promises for nanoelectronics, energy, and biomedical applications.
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Affiliation(s)
- Shine K Albert
- School of Chemistry, Indian Institute of Science Education and Research-Thiruvananthapuram (IISER-TVM), CET campus, Trivandrum-695016 (India)
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78
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Albert SK, Thelu HVP, Golla M, Krishnan N, Chaudhary S, Varghese R. Self-Assembly of DNA-Oligo(p-phenylene-ethynylene) Hybrid Amphiphiles into Surface-Engineered Vesicles with Enhanced Emission. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201403455] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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79
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Wang G, Chen L, He X, Zhu Y, Zhang X. Detection of polynucleotide kinase activity by using a gold electrode modified with magnetic microspheres coated with titanium dioxide nanoparticles and a DNA dendrimer. Analyst 2014; 139:3895-900. [DOI: 10.1039/c4an00499j] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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80
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Du X, Zhou J, Xu B. Supramolecular hydrogels made of basic biological building blocks. Chem Asian J 2014; 9:1446-72. [PMID: 24623474 PMCID: PMC4024374 DOI: 10.1002/asia.201301693] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Indexed: 12/31/2022]
Abstract
As a consequence of the self-assembly of small organic molecules in water, supramolecular hydrogels are evolving from serendipitous events during organic synthesis to become a new type of materials that hold promise for applications in biomedicine. In this Focus Review, we describe recent advances in the use of basic biological building blocks for creating molecules that act as hydrogelators and the potential applications of the corresponding hydrogels. After introducing the concept of supramolecular hydrogels and defining the scope of this review, we briefly describe the methods for making and characterizing supramolecular hydrogels. We then discuss representative hydrogelators according to the categories of their building blocks, such as amino acids, nucleobases, and saccharides, and highlight the applications of the hydrogels when necessary. Finally, we offer our perspective and outlook on this fast-growing field at the interface of organic chemistry, materials, biology, and medicine. By providing a snapshot for chemists, engineers, and medical scientists, we hope that this Focus Review will contribute to the development of multidisciplinary research on supramolecular hydrogels for a wide range of applications in different fields.
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Affiliation(s)
- Xuewen Du
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA, Fax: (01)781 736 2516
| | - Jie Zhou
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA, Fax: (01)781 736 2516
| | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA, Fax: (01)781 736 2516
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81
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Kervio E, Claasen B, Steiner UE, Richert C. The strength of the template effect attracting nucleotides to naked DNA. Nucleic Acids Res 2014; 42:7409-20. [PMID: 24875480 PMCID: PMC4066754 DOI: 10.1093/nar/gku314] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The transmission of genetic information relies on Watson–Crick base pairing between nucleoside phosphates and template bases in template–primer complexes. Enzyme-free primer extension is the purest form of the transmission process, without any chaperon-like effect of polymerases. This simple form of copying of sequences is intimately linked to the origin of life and provides new opportunities for reading genetic information. Here, we report the dissociation constants for complexes between (deoxy)nucleotides and template–primer complexes, as determined by nuclear magnetic resonance and the inhibitory effect of unactivated nucleotides on enzyme-free primer extension. Depending on the sequence context, Kd′s range from 280 mM for thymidine monophosphate binding to a terminal adenine of a hairpin to 2 mM for a deoxyguanosine monophosphate binding in the interior of a sequence with a neighboring strand. Combined with rate constants for the chemical step of extension and hydrolytic inactivation, our quantitative theory explains why some enzyme-free copying reactions are incomplete while others are not. For example, for GMP binding to ribonucleic acid, inhibition is a significant factor in low-yielding reactions, whereas for amino-terminal DNA hydrolysis of monomers is critical. Our results thus provide a quantitative basis for enzyme-free copying.
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Affiliation(s)
- Eric Kervio
- Institute for Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Birgit Claasen
- Institute for Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Ulrich E Steiner
- Fachbereich Chemie, Universität Konstanz, 78457 Konstanz, Germany
| | - Clemens Richert
- Institute for Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
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82
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Głowacka IE, Balzarini J, Wróblewski AE. Novel acyclic phosphonylated 1,2,3-triazolonucleosides with an acetamidomethyl linker: synthesis and biological activity. Arch Pharm (Weinheim) 2014; 347:506-14. [PMID: 24664932 DOI: 10.1002/ardp.201300468] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 01/28/2014] [Accepted: 01/31/2014] [Indexed: 11/06/2022]
Abstract
A new series of 4-substituted [(1,2,3-triazol-1-yl)acetamido]methylphosphonates as acyclic nucleotide analogs were synthesized from diethyl (2-chloroacetamido)methylphosphonate via azidation followed by 1,3-dipolar cycloaddition with selected alkynes derived from natural nucleobases or their mimetics. All compounds were tested for their antiviral activities against DNA and RNA viruses as well as for cytostatic activity or cytotoxicity. Among all tested compounds, [(1,2,3-triazol-1-yl)acetamido]methylphosphonate 6e substituted with the N(3)-Bz-benzuracil moiety showed activity against the vesicular stomatitis virus (EC50 = 45 µM) in HeLa cell cultures.
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Affiliation(s)
- Iwona E Głowacka
- Bioorganic Chemistry Laboratory, Faculty of Pharmacy, Medical University of Łódź, Łódź, Poland
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83
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Aggarwal N, Arya A, Mathur D, Singh S, Tyagi A, Kumar R, Rana N, Singh R, Prasad AK. Effect of acyl chain length on selective biocatalytic deacylation on O-aryl glycosides and separation of anomers. Bioorg Chem 2014; 53:83-91. [PMID: 24632507 DOI: 10.1016/j.bioorg.2014.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 02/07/2014] [Accepted: 02/11/2014] [Indexed: 11/18/2022]
Abstract
It has been demonstrated that Lipozyme® TL IM (Thermomyces lanuginosus lipase immobilised on silica) can selectively deacylate the ester function involving the C-5' hydroxyl group of α-anomers over the other acyl functions of anomeric mixture of peracylated O-aryl α,β-D-ribofuranoside. The analysis of results of biocatalytic deacylation reaction revealed that the reaction time decreases with the increase in the acyl chain length from C1 to C4. The unique selectivity of Lipozyme® TL IM has been harnessed for the separation of anomeric mixture of peracylated O-aryl α,β-D-ribofuranosides, The lipase mediated selective deacylation methodology has been used for the synthesis of O-aryl α-D-ribofuranosides and O-aryl β-D-ribofuranosides in pure forms, which can be used as chromogenic substrate for the detection of pathogenic microbial parasites containing glycosidases.
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Affiliation(s)
- Neha Aggarwal
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi 110 007, India
| | - Anu Arya
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi 110 007, India
| | - Divya Mathur
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi 110 007, India
| | - Sukhdev Singh
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi 110 007, India
| | - Abhilash Tyagi
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi 110 007, India
| | - Rajesh Kumar
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi 110 007, India
| | - Neha Rana
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi 110 007, India
| | - Rajendra Singh
- CFEES, Brig. S.K. Mazumdar Road, Timarpur, Delhi 110 054, India
| | - Ashok K Prasad
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi 110 007, India.
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84
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Aliakbar Tehrani Z, Jamshidi Z. Watson–Crick versus imidazopyridopyrimidine base pairs: theoretical study on differences in stability and hydrogen bonding strength. Struct Chem 2014. [DOI: 10.1007/s11224-014-0397-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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85
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Yeşilot S, Çoşut B, Alidağı HA, Hacıvelioğlu F, Özpınar GA, Kılıç A. Intramolecular excimer formation in hexakis(pyrenyloxy)cyclotriphosphazene: photophysical properties, crystal structure, and theoretical investigation. Dalton Trans 2014; 43:3428-33. [DOI: 10.1039/c3dt52957f] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A hexakis(pyrenyloxy)cyclotriphosphazene was synthesized by the reaction of N3P3Cl6 with 2-hydroxypyrene, and its excimer emission has been investigated.
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Affiliation(s)
- Serkan Yeşilot
- Department of Chemistry
- Gebze Institute of Technology
- Gebze 41400, Turkey
| | - Bünyemin Çoşut
- Department of Chemistry
- Gebze Institute of Technology
- Gebze 41400, Turkey
| | | | | | - Gül Altınbaş Özpınar
- Department of Chemistry Technology
- Biga Vocational School
- Çanakkale Onsekiz Mart University
- Çanakkale, Turkey
| | - Adem Kılıç
- Department of Chemistry
- Gebze Institute of Technology
- Gebze 41400, Turkey
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86
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Lee DG, Kim IS, Park JW, Seo YJ. Multiplex fluorophore systems on DNA with new diverse fluorescence properties and ability to sense the hybridization dynamics. Chem Commun (Camb) 2014; 50:7273-6. [DOI: 10.1039/c4cc01378f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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87
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Zhang F, Xi Y, Lu Y, Wang L, Liu L, Li J, Zhao Y. Novel syntheses of aryl quinoxaline C-nucleoside analogs by mild and efficient three-component sequential reactions. Chem Commun (Camb) 2014; 50:5771-3. [DOI: 10.1039/c4cc01448k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Novel syntheses of aryl quinoxaline C-nucleoside analogs have been accomplished by mild and efficient three-component sequential reactions in high yields with a wide scope of substrates.
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Affiliation(s)
- Fuyi Zhang
- The College of Chemistry and Molecular Engineering
- The Key Lab of Chemical Biology and Organic Chemistry
- Zhengzhou University
- Zhengzhou 450052, China
| | - Yuan Xi
- The College of Chemistry and Molecular Engineering
- The Key Lab of Chemical Biology and Organic Chemistry
- Zhengzhou University
- Zhengzhou 450052, China
| | - Yanhui Lu
- The College of Chemistry and Molecular Engineering
- The Key Lab of Chemical Biology and Organic Chemistry
- Zhengzhou University
- Zhengzhou 450052, China
| | - Liming Wang
- The College of Chemistry and Molecular Engineering
- The Key Lab of Chemical Biology and Organic Chemistry
- Zhengzhou University
- Zhengzhou 450052, China
| | - Linwei Liu
- The College of Chemistry and Molecular Engineering
- The Key Lab of Chemical Biology and Organic Chemistry
- Zhengzhou University
- Zhengzhou 450052, China
| | - Jinliang Li
- The College of Chemistry and Molecular Engineering
- The Key Lab of Chemical Biology and Organic Chemistry
- Zhengzhou University
- Zhengzhou 450052, China
| | - Yufen Zhao
- The College of Chemistry and Molecular Engineering
- The Key Lab of Chemical Biology and Organic Chemistry
- Zhengzhou University
- Zhengzhou 450052, China
- College of Chemistry and Chemical Engineering
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88
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89
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Abstract
Although both the most popular form of synthetic biology (SB) and chemical synthetic biology (CSB) share the biotechnologically useful aim of making new forms of life, SB does so by using genetic manipulation of extant microorganism, while CSB utilises classic chemical procedures in order to obtain biological structures which are non-existent in nature. The main query concerning CSB is the philosophical question: why did nature do this, and not that? The idea then is to synthesise alternative structures in order to understand why nature operated in such a particular way. We briefly present here some various examples of CSB, including those cases of nucleic acids synthesised with pyranose instead of ribose, and proteins with a reduced alphabet of amino acids; also we report the developing research on the "never born proteins" (NBP) and "never born RNA" (NBRNA), up to the minimal cell project, where the issue is the preparation of semi-synthetic cells that can perform the basic functions of biological cells.
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Affiliation(s)
| | - Pier Luigi Luisi
- Department of Materials, Swiss Federal Institute of Technology Zurich (ETHZ), University of Roma Tre, Italy
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90
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Nicolas L, Angibaud P, Stansfield I, Meerpoel L, Reymond S, Cossy J. Triphenylphosphine: a catalyst for the synthesis of C-aryl furanosides from furanosyl halides. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2013.12.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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91
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Zhang L, Zhou L, Tian J, Li X. Structural, electronic, and photophysical properties of thieno-expanded tricyclic purine analogs: a theoretical study. Phys Chem Chem Phys 2014; 16:4338-49. [DOI: 10.1039/c3cp54505a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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92
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Samanta PK, Pati SK. Structural and magnetic properties of a variety of transition metal incorporated DNA double helices. Chemistry 2013; 20:1760-4. [PMID: 24382746 DOI: 10.1002/chem.201302628] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Revised: 10/30/2013] [Indexed: 12/22/2022]
Abstract
By using density functional theory calculations, the structural, energetic, magnetic, and optical properties for a variety of transition metal (M = Mn, Fe, Co, Ni and Cu) ions incorporated modified-DNA (M-DNA) double helices has been investigated. The DNA is modified with either hydroxypyridone (H) or bis(salicylaldehyde)ethylenediamine (S-en) metalated bases. We find the formation of extended M-O network leading to the ferromagnetic interactions for the case of H-DNA for all the metal ions. More ordered stacking arrangement was found for S-en-DNA. We calculate the exchange coupling constant (J) considering Heisenberg Hamiltonian for quantitative description of magnetic interactions. The ferromagnetic and antiferromagnetic interactions are obtained by varying different transition metal ions. The extent of the magnetic interaction depends on the number of transition metal ions. Optical profiles show peaks below 2 eV, a clear signature of spin-spin coupling.
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Affiliation(s)
- Pralok K Samanta
- Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P. O., Bangalore 560064 (India), Fax: (+91) 80-2208-2766/2767, Hompage: http://www.jncasr.ac.in/pati
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93
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Nicolas L, Izquierdo E, Angibaud P, Stansfield I, Meerpoel L, Reymond S, Cossy J. Cobalt-Catalyzed Diastereoselective Synthesis of C-Furanosides. Total Synthesis of (−)-Isoaltholactone. J Org Chem 2013; 78:11807-14. [DOI: 10.1021/jo401845q] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Lionel Nicolas
- Laboratoire
de Chimie Organique, ESPCI ParisTech, UMR CNRS 7084, 10 rue Vauquelin, 75231 Paris Cedex 05, France
| | - Eva Izquierdo
- Laboratoire
de Chimie Organique, ESPCI ParisTech, UMR CNRS 7084, 10 rue Vauquelin, 75231 Paris Cedex 05, France
| | - Patrick Angibaud
- Janssen Research & Development, a Division of Janssen-Cilag, BP615, Chaussée du Vexin, 27106 Val de Reuil, France
| | - Ian Stansfield
- Janssen Research & Development, a Division of Janssen-Cilag, BP615, Chaussée du Vexin, 27106 Val de Reuil, France
| | - Lieven Meerpoel
- Janssen Research & Development, a Division of Janssen Pharmaceutica N.V., Turnhoutsweg 30, 2340 Beerse, Belgium
| | - Sébastien Reymond
- Laboratoire
de Chimie Organique, ESPCI ParisTech, UMR CNRS 7084, 10 rue Vauquelin, 75231 Paris Cedex 05, France
| | - Janine Cossy
- Laboratoire
de Chimie Organique, ESPCI ParisTech, UMR CNRS 7084, 10 rue Vauquelin, 75231 Paris Cedex 05, France
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94
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Zhang L, Zhu H, Sajimon MC, Stütz JAR, Siegmund K, Richert C, Shafirovich V, Lewis FD. Stabilization of DNA Hairpins by Stilbene Capping of the Terminal Base Pair. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.200600196] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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95
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Abstract
Sequence-controlled polymers are macromolecules in which monomer units of different chemical nature are arranged in an ordered fashion. The most prominent examples are biological and have been studied and used primarily by molecular biologists and biochemists. However, recent progress in protein- and DNA-based nanotechnologies has shown the relevance of sequence-controlled polymers to nonbiological applications, including data storage, nanoelectronics, and catalysis. In addition, synthetic polymer chemistry has provided interesting routes for preparing nonnatural sequence-controlled polymers. Although these synthetic macromolecules do not yet compare in functional scope with their natural counterparts, they open up opportunities for controlling the structure, self-assembly, and macroscopic properties of polymer materials.
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Affiliation(s)
- Jean-François Lutz
- Precision Macromolecular Chemistry Group, Institut Charles Sadron, UPR22-CNRS, 23 rue du Loess, Boîte Postale 84047, 67034 Strasbourg Cedex 2, France
| | - Makoto Ouchi
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - David R. Liu
- Department of Chemistry and Chemical Biology and the Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Mitsuo Sawamoto
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
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96
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Liang J, Nguyen QL, Matsika S. Exciplexes and conical intersections lead to fluorescence quenching in π-stacked dimers of 2-aminopurine with natural purine nucleobases. Photochem Photobiol Sci 2013; 12:1387-400. [PMID: 23625036 PMCID: PMC5006741 DOI: 10.1039/c3pp25449f] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2012] [Accepted: 03/29/2013] [Indexed: 12/26/2022]
Abstract
Fluorescent analogues of the natural DNA bases are useful in the study of nucleic acids' structure and dynamics. 2-Aminopurine (2AP) is a widely used analogue with environmentally sensitive fluorescence behavior. The quantum yield of 2AP has been found to be significantly decreased when engaged in π-stacking interactions with the native bases. We present a theoretical study on fluorescence quenching mechanisms in dimers of 2AP π-stacked with adenine or guanine as in natural DNA. Relaxation pathways on the potential energy surfaces of the first excited states have been computed and reveal the importance of exciplexes and conical intersections in the fluorescence quenching process.
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Affiliation(s)
- JingXin Liang
- Department of Chemistry, Temple University, Philadelphia, PA 19122, USA
| | - Quynh L. Nguyen
- Department of Chemistry, Temple University, Philadelphia, PA 19122, USA
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97
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Laos R, Shaw R, Leal NA, Gaucher E, Benner S. Directed evolution of polymerases to accept nucleotides with nonstandard hydrogen bond patterns. Biochemistry 2013; 52:5288-94. [PMID: 23815560 DOI: 10.1021/bi400558c] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Artificial genetic systems have been developed by synthetic biologists over the past two decades to include additional nucleotides that form additional nucleobase pairs independent of the standard T:A and C:G pairs. Their use in various tools to detect and analyze DNA and RNA requires polymerases that synthesize duplex DNA containing unnatural base pairs. This is especially true for nested polymerase chain reaction (PCR), which has been shown to dramatically lower noise in multiplexed nested PCR if nonstandard nucleotides are used in their external primers. We report here the results of a directed evolution experiment seeking variants of Taq DNA polymerase that can support the nested PCR amplification with external primers containing two particular nonstandard nucleotides, 2-amino-8-(1'-β-d-2'-deoxyribofuranosyl)imidazo[1,2-a]-1,3,5-triazin-4(8H)-one (trivially called P) that pairs with 6-amino-5-nitro-3-(1'-β-d-2'-deoxyribofuranosyl)-2(1H)-pyridone (trivially called Z). Variants emerging from the directed evolution experiments were shown to pause less when challenged in vitro to incorporate dZTP opposite P in a template. Interestingly, several sites involved in the adaptation of Taq polymerases in the laboratory were also found to have displayed "heterotachy" (different rates of change) in their natural history, suggesting that these sites were involved in an adaptive change in natural polymerase evolution. Also remarkably, the polymerases evolved to be less able to incorporate dPTP opposite Z in the template, something that was not selected. In addition to being useful in certain assay architectures, this result underscores the general rule in directed evolution that "you get what you select for".
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Affiliation(s)
- Roberto Laos
- Foundation for Applied Molecular Evolution and The Westheimer Institute of Science and Technology, Gainesville, Florida 32601, United States
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98
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Nakano SI, Uotani Y, Sato Y, Oka H, Fujii M, Sugimoto N. Conformational changes of the phenyl and naphthyl isocyanate-DNA adducts during DNA replication and by minor groove binding molecules. Nucleic Acids Res 2013; 41:8581-90. [PMID: 23873956 PMCID: PMC3794578 DOI: 10.1093/nar/gkt608] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
DNA lesions produced by aromatic isocyanates have an extra bulky group on the nucleotide bases, with the capability of forming stacking interaction within a DNA helix. In this work, we investigated the conformation of the 2′-deoxyadenosine and 2′-deoxycytidine derivatives tethering a phenyl or naphthyl group, introduced in a DNA duplex. The chemical modification experiments using KMnO4 and 1-cyclohexyl-3 -(2-morpholinoethyl) carbodiimide metho-p-toluenesulfonate have shown that the 2′-deoxycytidine lesions form the base pair with guanine while the 2′-deoxyadenosine lesions have less ability of forming the base pair with thymine in solution. Nevertheless, the kinetic analysis shows that these DNA lesions are compatible with DNA ligase and DNA polymerase reactions, as much as natural DNA bases. We suggest that the adduct lesions have a capability of adopting dual conformations, depending on the difference in their interaction energies between stacking of the attached aromatic group and base pairing through hydrogen bonds. It is also presented that the attached aromatic groups change their orientation by interacting with the minor groove binding netropsin, distamycin and synthetic polyamide. The nucleotide derivatives would be useful for enhancing the phenotypic diversity of DNA molecules and for exploring new non-natural nucleotides.
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Affiliation(s)
- Shu-ichi Nakano
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan, Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan, Department of Chemistry, Faculty of Science and Engineering, Konan University, 8-9-1, Okamoto, Higashinada-ku, Kobe, 658-8501, Japan, Molecular Engineering Institute (MEI), Kinki University, 11-6 Kayanomori, Iizuka, Fukuoka, 820-8555, Japan and Department of Environmental and Biological Chemistry, Kinki University, 11-6 Kayanomori, Iizuka, Fukuoka, 820-8555, Japan
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99
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Abstract
For over 20 years, laboratories around the world have been applying the principles of Darwinian evolution to isolate DNA and RNA molecules with specific ligand-binding or catalytic activities. This area of synthetic biology, commonly referred to as in vitro genetics, is made possible by the availability of natural polymerases that can replicate genetic information in the laboratory. Moving beyond natural nucleic acids requires organic chemistry to synthesize unnatural analogues and polymerase engineering to create enzymes that recognize artificial substrates. Progress in both of these areas has led to the emerging field of synthetic genetics, which explores the structural and functional properties of synthetic genetic polymers by in vitro evolution. This review examines recent advances in the Darwinian evolution of artificial genetic polymers and their potential downstream applications in exobiology, molecular medicine, and synthetic biology.
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Affiliation(s)
- John C Chaput
- Center for Evolutionary Medicine and Informatics in the Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-5301, USA.
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100
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Riley KE, Hobza P. On the importance and origin of aromatic interactions in chemistry and biodisciplines. Acc Chem Res 2013; 46:927-36. [PMID: 22872015 DOI: 10.1021/ar300083h] [Citation(s) in RCA: 168] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aromatic systems contain both σ- and π-electrons, which in turn constitute σ- and π-molecular orbitals (MOs). In discussing the properties of these systems, researchers typically refer to the highest occupied and lowest unoccupied MOs, which are π MOs. The characteristic properties of aromatic systems, such as their low ionization potentials and electron affinities, high polarizabilities and stabilities, and small band gaps (in spectroscopy called the N → V1 space), can easily be explained based on their electronic structure. These one-electron properties point to characteristic features of how aromatic systems interact with each other. Unlike hydrogen bonding systems, which primarily interact through electrostatic forces, complexes containing aromatic systems, especially aromatic stacked pairs, are predominantly stabilized by dispersion attraction. The stabilization energy in the benzene dimer is rather small (~2.5 kcal/mol) but strengthens with heteroatom substitution. The stacked interaction of aromatic nucleic acid bases is greater than 10 kcal/mol, and for the most stable stacked pair, guanine and cytosine, it reaches approximately 17 kcal/mol. Although these values do not equal the planar H-bonded interactions of these bases (~29 kcal/mol), stacking in DNA is more frequent than H-bonding and, unlike H-bonding, is not significantly weakened when passing from the gas phase to a water environment. Consequently, the stacking of aromatic systems represents the leading stabilization energy contribution in biomacromolecules and in related nanosystems. Therefore stacking (dispersion) interactions predominantly determine the double helical structure of DNA, which underlies its storage and transfer of genetic information. Similarly, dispersion is the dominant contributor to attractive interactions involving aromatic amino acids within the hydrophobic core of a protein, which is critical for folding. Therefore, understanding the nature of aromatic interactions, which depend greatly on quantum mechanical (QM) calculations, is of key importance in biomolecular science. This Account shows that accurate binding energies for aromatic complexes should be based on computations made at the (estimated) CCSD(T)/complete basis set limit (CBS) level of theory. This method is the least computationally intensive one that can give accurate stabilization energies for all common classes of noncovalent interactions (aromatic-aromatic, H-bonding, ionic, halogen bonding, charge-transfer, etc.). These results allow for direct comparison of binding energies between different interaction types. Conclusions based on lower-level QM calculations should be considered with care.
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Affiliation(s)
- Kevin E. Riley
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 166 10 Prague, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 166 10 Prague, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 771 46 Olomouc, Czech Republic
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