1
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Abstract
The pyrene-based RNA-fluorescence label 2-(2-pyrenylethynyl) adenosine (2PyA) shows triexponential fluorescence, which depends strongly on the excitation wavelength. Most strikingly, a structured, long-lived fluorescence is observed in solution at room temperature after excitation into the S2 state, which is shifted hypsochromically by 30 nm compared to excitation into the S1 state. This very unusual behavior is investigated in detail with steady-state and time-resolved emission spectroscopy, ultrafast transient absorption spectroscopy, and quantum chemical calculations with both wave functions (CC2-level) and density-functional theory (DFT). 2PyA is found to emit simultaneously from two different intramolecular charge transfer states (mesomeric and twisted, MICT and TICT) which are populated most efficiently via the S1 state and a pyrene-like locally excited (LE) state. Rotational momentum derived from excess excitation energy is required to populate twisted LE configurations. Therefore, the LE state is most efficiently accessible via excitation to the S2. The stabilization of the different substates is related to two distinct reaction coordinates: the adenine-pyrene distance and the adenine-pyrene tilt angle, respectively.
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Affiliation(s)
- Andreas J Reuss
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt , 60438 Frankfurt (Main), Germany
| | - Christian Grünewald
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt , 60438 Frankfurt (Main), Germany
| | - Henrik Gustmann
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt , 60438 Frankfurt (Main), Germany
| | - Joachim W Engels
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt , 60438 Frankfurt (Main), Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt , 60438 Frankfurt (Main), Germany
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2
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Reuss AJ, Grünewald C, Braun M, Engels JW, Wachtveitl J. The Three Possible 2-(Pyrenylethynyl) Adenosines: Rotameric Energy Barriers Govern the Photodynamics of These Structural Isomers. Chemphyschem 2016; 17:1369-76. [PMID: 26635201 DOI: 10.1002/cphc.201500958] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Indexed: 01/22/2023]
Abstract
This article presents a comprehensive study of the photophysics of 2-(2-pyrenylethynyl) adenosine and 2-(4-pyrenylethynyl) adenosine, which are structural isomers of the well-established fluorescent RNA label 2-(1-pyrenylethynyl) adenosine. We performed steady-state and ultrafast transient absorption spectroscopy studies along with time-resolved fluorescence emission experiments in different solvents to work out the interplay of locally excited and charge-transfer states. We found the ultrafast photodynamics to be crucial for the fluorescence decay behavior, which extends up to tens of nanoseconds and is partially multi-exponential. These features in the ultrafast dynamics are indicative of the rotational energy barriers in the first excited state.
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Affiliation(s)
- Andreas J Reuss
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Christian Grünewald
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Markus Braun
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Joachim W Engels
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany.
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3
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Ouahrouch A, Taourirte M, Schols D, Snoeck R, Andrei G, Engels JW, Lazrek HB. Design, Synthesis, and Antiviral Activity of Novel Ribonucleosides of 1,2,3-Triazolylbenzyl-aminophosphonates. Arch Pharm (Weinheim) 2016; 349:30-41. [PMID: 26575425 PMCID: PMC4832832 DOI: 10.1002/ardp.201500292] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [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: 08/19/2015] [Revised: 10/09/2015] [Accepted: 10/14/2015] [Indexed: 01/13/2023]
Abstract
A novel series of ribonucleosides of 1,2,3-triazolylbenzyl-aminophosphonates was synthesized through the Kabachnik-Fields reaction using I2 as catalyst followed by copper-catalyzed cycloaddition of the azide-alkyne reaction (CuAAC). All structures of the newly prepared compounds were characterized by (1) H NMR, (13) C NMR, and HRMS spectra. The structures of 2e, 2f, 3d, and 3g were further confirmed by X-ray diffraction analysis. These compounds were tested against various strains of DNA and RNA viruses; compounds 4b and 4c showed a modest inhibitory activity against respiratory syncytial virus (RSV) and compound 4h displayed modest inhibitory activity against Coxsackie virus B4.
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Affiliation(s)
- Abdelaaziz Ouahrouch
- Department of Chemistry, Faculty of Sciences and Technology Gueliz (FSTG)Laboratory of Bioorganic and Macromolecular ChemistryMarrakeshMorocco
- Department of Chemistry, Faculty of Sciences SemlaliaLaboratory of Biomolecular and Medicinal ChemistryMarrakeshMorocco
- Institute for Organic Chemistry and Chemical BiologyGoethe‐University Frankfurt am MainFrankfurt am MainGermany
| | - Moha Taourirte
- Department of Chemistry, Faculty of Sciences and Technology Gueliz (FSTG)Laboratory of Bioorganic and Macromolecular ChemistryMarrakeshMorocco
| | | | - Robert Snoeck
- Rega Institute for Medical ResearchKU LeuvenLeuvenBelgium
| | | | - Joachim W. Engels
- Institute for Organic Chemistry and Chemical BiologyGoethe‐University Frankfurt am MainFrankfurt am MainGermany
| | - Hassan B. Lazrek
- Department of Chemistry, Faculty of Sciences SemlaliaLaboratory of Biomolecular and Medicinal ChemistryMarrakeshMorocco
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4
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Marimani MD, Ely A, Buff MCR, Bernhardt S, Engels JW, Scherman D, Escriou V, Arbuthnot P. Inhibition of replication of hepatitis B virus in transgenic mice following administration of hepatotropic lipoplexes containing guanidinopropyl-modified siRNAs. J Control Release 2015; 209:198-206. [PMID: 25937322 DOI: 10.1016/j.jconrel.2015.04.042] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 04/24/2015] [Accepted: 04/27/2015] [Indexed: 12/11/2022]
Abstract
Chronic infection with hepatitis B virus (HBV) occurs commonly and complications that arise from persistence of the virus are associated with high mortality. Available licensed drugs have modest curative efficacy and advancing new therapeutic strategies to eliminate the virus is therefore a priority. HBV is susceptible to inactivation by exogenous gene silencers that harness RNA interference (RNAi) and the approach has therapeutic potential. To advance RNAi-based treatment for HBV infection, use in vivo of hepatotropic lipoplexes containing siRNAs with guanidinopropyl (GP) modifications is reported here. Lipoplexes contained polyglutamate, which has previously been shown to facilitate formulation and improve efficiency of the non-viral vectors. GP moieties were included in a previously described anti-HBV siRNA that effectively targeted the conserved viral X sequence. Particles had physical properties that were suitable for use in vivo: average diameter was approximately 50-200 nm and surface charge (zeta potential) was +65 mV. Efficient hepatotropic delivery of labeled siRNA was observed following systemic intravenous injection of the particles into HBV transgenic mice. Good inhibition of markers of viral replication was observed without evidence of toxicity. Efficacy of the GP-modified siRNAs was significantly more durable and formulations made up with chemically modified siRNAs were less immunostimulatory. An RNAi-mediated mechanism was confirmed by demonstrating that HBV mRNA cleavage occurred in vivo at the intended target site. Collectively these data indicate that GP-modified siRNAs formulated in anionic polymer-containing lipoplexes are effective silencers of HBV replication in vivo and have therapeutic potential.
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Affiliation(s)
- Musa D Marimani
- Wits/SA MRC Antiviral Gene Therapy Research Unit, School of Pathology, Health Sciences Faculty, University of the Witwatersrand, Johannesburg, Private Bag 3, Wits 2050, South Africa
| | - Abdullah Ely
- Wits/SA MRC Antiviral Gene Therapy Research Unit, School of Pathology, Health Sciences Faculty, University of the Witwatersrand, Johannesburg, Private Bag 3, Wits 2050, South Africa
| | - Maximilian C R Buff
- Goethe-University, Institute of Organic Chemistry & Chemical Biology, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
| | - Stefan Bernhardt
- Goethe-University, Institute of Organic Chemistry & Chemical Biology, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
| | - Joachim W Engels
- Goethe-University, Institute of Organic Chemistry & Chemical Biology, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
| | - Daniel Scherman
- UTCBS, CNRS UMR8258, INSERM U1022, Université Paris Descartes, Chimie ParisTech, 75006 Paris, France
| | - Virginie Escriou
- UTCBS, CNRS UMR8258, INSERM U1022, Université Paris Descartes, Chimie ParisTech, 75006 Paris, France
| | - Patrick Arbuthnot
- Wits/SA MRC Antiviral Gene Therapy Research Unit, School of Pathology, Health Sciences Faculty, University of the Witwatersrand, Johannesburg, Private Bag 3, Wits 2050, South Africa.
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5
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Ouahrouch A, Taourirte M, Lazrek HB, Engels JW, Bolte M. Crystal structure of 2-benzamido-N-(2,2-di-eth-oxy-eth-yl)benzamide. Acta Crystallogr E Crystallogr Commun 2015; 71:o214-5. [PMID: 25844255 PMCID: PMC4350703 DOI: 10.1107/s2056989015003370] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 02/17/2015] [Indexed: 11/18/2022]
Abstract
In the title compound, C20H24N2O4, both peptide bonds adopt a trans configuration with respect to the -N-H and -C=O groups. The dihedral angle between the aromatic rings is 53.58 (4)°. The mol-ecular conformation is stabilized by an intra-molecular N-H⋯O hydrogen bond. The crystal packing is characterized by zigzag chains of N-H⋯O hydrogen-bonded mol-ecules running along the b-axis direction.
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Affiliation(s)
- Abdelaaziz Ouahrouch
- Laboratory of Bioorganic and Macromolecular Chemistry, Department of Chemistry, Faculty of Sciences and Technology Guéliz (FSTG), BP 549, Marrakech, Morocco
| | - Moha Taourirte
- Laboratory of Bioorganic and Macromolecular Chemistry, Department of Chemistry, Faculty of Sciences and Technology Guéliz (FSTG), BP 549, Marrakech, Morocco
| | - Hassan B. Lazrek
- Laboratory of Biomolecular and Medicinal Chemistry, Department of Chemistry, Faculty of Sciences Semlalia, Marrakech, Morocco
| | - Joachim W. Engels
- Institut für Organische Chemie und Chemische Biologie, Goethe-Universität Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Michael Bolte
- Institut für Anorganische und Analytische Chemie, Goethe-Universität Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
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6
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Ouahrouch A, Ighachane H, Taourirte M, Engels JW, Sedra MH, Lazrek HB. Benzimidazole-1,2,3-triazole hybrid molecules: synthesis and evaluation for antibacterial/antifungal activity. Arch Pharm (Weinheim) 2014; 347:748-55. [PMID: 25088180 PMCID: PMC4225497 DOI: 10.1002/ardp.201400142] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [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: 04/08/2014] [Revised: 06/10/2014] [Accepted: 06/13/2014] [Indexed: 12/31/2022]
Abstract
A novel series of hybrid molecules 4a-i and 5a-i were prepared by condensation of 4-(trimethylsilylethynyl)benzaldehyde 1 with substituted o-phenylenediamines. These in turn were reacted with 2-(azidomethoxy)ethyl acetate in a Cu alkyne-azide cycloaddition (CuAAC) to generate the 1,2,3-triazole pharmacophore under microwave assistance. The newly synthesized compounds were examined for their in vitro antimicrobial activities against Gram-positive and Gram-negative bacteria and the phytopathogenic fungi Verticillium dahliae and Fusarium oxysporum f. sp. albedinis. 2-((4-(4-(5-Trifluoromethyl benzimidazol-2-yl)phenyl)-1,2,3-triazol-1-yl)methoxy)ethanol 5e showed a moderate inhibition of 30% in the Foa sporulation test.
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Affiliation(s)
- Abdelaaziz Ouahrouch
- Laboratory of Bioorganic and Macromolecular Chemistry, Department of Chemistry, Faculty of Sciences and Technology Gueliz (FSTG)Marrakesh, Morocco
- Laboratory of Biomolecular and Medicinal Chemistry, Department of Chemistry, Faculty of Sciences SemlaliaMarrakesh, Morocco
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt am MainFrankfurt am Main, Germany
| | - Hana Ighachane
- Laboratory of Biomolecular and Medicinal Chemistry, Department of Chemistry, Faculty of Sciences SemlaliaMarrakesh, Morocco
- Laboratory of Genetic Phytopathology and Microbial Control, INRAMarrakesh, Morocco
| | - Moha Taourirte
- Laboratory of Bioorganic and Macromolecular Chemistry, Department of Chemistry, Faculty of Sciences and Technology Gueliz (FSTG)Marrakesh, Morocco
| | - Joachim W Engels
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt am MainFrankfurt am Main, Germany
| | - My Hassan Sedra
- Laboratory of Genetic Phytopathology and Microbial Control, INRAMarrakesh, Morocco
| | - Hassan B Lazrek
- Laboratory of Biomolecular and Medicinal Chemistry, Department of Chemistry, Faculty of Sciences SemlaliaMarrakesh, Morocco
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7
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Abstract
The synthesis and use of the new nucleobase-caged nucleotides dT(pHP) and dT(NDEACM) is reported. Through a combination of time and wavelength selectivity four levels of selective uncaging with only two cages, and only two wavelengths, were obtained. The new residue dT(pHP) can be uncaged at 313 nm without the formation of unwanted cyclic pyridine dimers.
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Affiliation(s)
- Alexandre Rodrigues-Correia
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt , Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany
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8
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Trojanowski P, Plötner J, Grünewald C, Graupner FF, Slavov C, Reuss AJ, Braun M, Engels JW, Wachtveitl J. Photo-physical properties of 2-(1-ethynylpyrene)-adenosine: influence of hydrogen bonding on excited state properties. Phys Chem Chem Phys 2014; 16:13875-88. [PMID: 24894337 DOI: 10.1039/c4cp01148a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The photo-physical properties of 2-(1-ethynylpyrene)-adenosine (PyA), a fluorescent probe for RNA dynamics, were examined by solvation studies. The excited-state dynamics display the influence of the vicinity on the spectral features. Combining improved transient absorption and streak camera measurements along with a new analysis method provide a detailed molecular picture of the photophysics. After intramolecular vibrational energy redistribution (IVR), two distinct states are observed. Solvent class (protic/aprotic) and permittivity strongly affect the properties of these states and their population ratio. As a result their emission spectrum is altered, while the fluorescence quantum yield and the overall lifetime remain nearly unchanged. Consequently, the hitherto existing model of the photophysics is herein refined and extended. The findings can serve as basis for improving the information content of measurements with PyA as a label in RNA.
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Affiliation(s)
- P Trojanowski
- Institute for Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438 Frankfurt/Main, Germany.
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9
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Bats JW, Żivković A, Parsch J, Engels JW. Three different fluoro- or chloro-substituted 1'-deoxy-1'-phenyl-β-D-ribofuranoses. Acta Crystallogr C Struct Chem 2014; 70:400-4. [PMID: 24705057 DOI: 10.1107/s2053229614004999] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 03/04/2014] [Indexed: 11/10/2022]
Abstract
Crystal structures are reported for three fluoro- or chloro-substituted 1'-deoxy-1'-phenyl-β-D-ribofuranoses, namely 1'-deoxy-1'-(2,4,5-trifluorophenyl)-β-D-ribofuranose, C11H11F3O4, (I), 1'-deoxy-1'-(2,4,6-trifluorophenyl)-β-D-ribofuranose, C11H11F3O4, (II), and 1'-(4-chlorophenyl)-1'-deoxy-β-D-ribofuranose, C11H13ClO4, (III). The five-membered furanose ring of the three compounds has a conformation between a C2'-endo,C3'-exo twist and a C2'-endo envelope. The ribofuranose groups of (I) and (III) are connected by intermolecular O-H···O hydrogen bonds to six symmetry-related molecules to form double layers, while the ribofuranose group of (II) is connected by O-H···O hydrogen bonds to four symmetry-related molecules to form single layers. The O···O contact distance of the O-H···O hydrogen bonds ranges from 2.7172 (15) to 2.8895 (19) Å. Neighbouring double layers of (I) are connected by a very weak intermolecular C-F···π contact. The layers of (II) are connected by one C-H···O and two C-H···F contacts, while the double layers of (III) are connected by a C-H···Cl contact. The conformations of the molecules are compared with those of seven related molecules. The orientation of the benzene ring is coplanar with the H-C1' bond or bisecting the H-C1'-C2' angle, or intermediate between these positions. The orientation of the benzene ring is independent of the substitution pattern of the ring and depends mainly on crystal-packing effects.
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Affiliation(s)
- Jan W Bats
- Institut für Organische Chemie und Chemische Biologie, Universität Frankfurt, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany
| | - Aleksandra Żivković
- Institut für Organische Chemie und Chemische Biologie, Universität Frankfurt, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany
| | - Jörg Parsch
- Institut für Organische Chemie und Chemische Biologie, Universität Frankfurt, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany
| | - Joachim W Engels
- Institut für Organische Chemie und Chemische Biologie, Universität Frankfurt, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany
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11
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Ouahrouch A, Krim J, Taourirte M, Lazrek HB, Engels JW, Bats JW. Four related diethyl [(arylamino)(4-ethynylphenyl)methyl]phosphonates. Acta Crystallogr C 2013; 69:1157-63. [DOI: 10.1107/s0108270113022981] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 08/15/2013] [Indexed: 11/10/2022] Open
Abstract
Crystal structures are reported for four related diethyl [(arylamino)(4-ethynylphenyl)lmethyl]phosphonate derivatives, namely diethyl [(4-bromoanilino)(4-ethynylphenyl)methyl]phosphonate, C19H21BrNO3P, (I), diethyl ((4-chloro-2-methylanilino){4-[2-(trimethylsilyl)ethynyl]phenyl}methyl)phosphonate, C23H31ClNO3PSi, (II), diethyl ((4-fluoroanilino){4-[2-(trimethylsilyl)ethynyl]phenyl}methyl)phosphonate, C22H29FNO3PSi, (III), and diethyl [(4-ethynylphenyl)(naphthalen-2-ylamino)methyl]phosphonate, C23H24NO3P, (IV). The conformation of the anilinobenzyl group is very similar in all four compounds. The P—C bond has an approximately staggered conformation, with the aniline and ethynylphenyl groups ingauchepositions with respect to the P=O double bond. The two six-membered rings are almost perpendicular. The sums of the valence angles about the N atoms vary from 344 (2) to 351 (2)°. In the crystal structures, molecules of (I), (III) and (IV) are arranged as centrosymmetric or pseudocentrosymmetric dimers connected by two N—H...O=P hydrogen bonds. The molecules of (II) are arranged as centrosymmetric dimers connected by Cmethyl—H...O=P hydrogen bonds. The N—H bond of (II) is not involved in hydrogen bonding.
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12
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Wicke L, Engels JW, Gambari R, Saab AM. Synthesis and Antiproliferative Activity of Quinolone Nucleosides Against the Human Myelogenous Leukemia K‐562 Cell Line. Arch Pharm (Weinheim) 2013; 346:757-65. [DOI: 10.1002/ardp.201300232] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 06/19/2013] [Accepted: 08/07/2013] [Indexed: 11/08/2022]
Affiliation(s)
- Lena Wicke
- Johann Wolfgang Goethe‐UniversitätInstitute of Organic Chemistry and Chemical BiologyFrankfurt am MainGermany
| | - Joachim W. Engels
- Johann Wolfgang Goethe‐UniversitätInstitute of Organic Chemistry and Chemical BiologyFrankfurt am MainGermany
| | - Roberto Gambari
- Department of Life Science and BiotechnologySection of Biochemistry and Molecular BiologyUniversity of FerraraFerraraItaly
| | - Antoine M. Saab
- Faculty of Sciences IIChemistry DepartmentLebanese UniversityFanarBeirutLebanon
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13
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Bats JW, Schell P, Engels JW. 5-[(1R,2R,4R)-2-Meth-oxy-1,7,7-tri-methylbi-cyclo-[2.2.1]hept-2-yl]-1H-tetra-zole. Acta Crystallogr Sect E Struct Rep Online 2013; 69:o1028. [PMID: 24046608 PMCID: PMC3772465 DOI: 10.1107/s1600536813014700] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 05/28/2013] [Indexed: 06/02/2023]
Abstract
The title compound, C12H20N4O, undergoes a phase transition on cooling. The room-temperature structure is tetra-gonal (P43212, Z' = 1), with the meth-oxy-bornyl group being extremely disordered. Below 213 K the structure is ortho-rhom-bic (P212121, Z' = 2), with ordered mol-ecules. The two independent mol-ecules (A and B) have very similar conformations; significant differences only occur for the torsion angles about the Cborn-yl-Ctetra-zole bonds. The independent mol-ecules are approximately related by the pseudo-symmetry relation: xB = -1/4 + yA , yB = 3/4 - xA and zB = 1/4 + zA . In the crystal, mol-ecules are connected by N-H⋯N hydrogen bonds between the tetra-zole groups, forming a pseudo-43 helix parallel to the c-axis direction. The crystal studied was a merohedral twin with a refined twin fraction value of 0.231 (2).
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Affiliation(s)
- Jan W. Bats
- Institut für Organische Chemie und Chemische Biologie, Universität Frankfurt, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany
| | - Peter Schell
- Institut für Organische Chemie und Chemische Biologie, Universität Frankfurt, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany
| | - Joachim W. Engels
- Institut für Organische Chemie und Chemische Biologie, Universität Frankfurt, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany
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14
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Bats JW, Schell P, Engels JW. Biphenyl- and phenylnaphthalenyl-substituted 1H-imidazole-4,5-dicarbonitrile catalysts for the coupling reaction of nucleoside methyl phosphonamidites. Acta Crystallogr C 2013; 69:529-33. [PMID: 23629908 DOI: 10.1107/s0108270113009293] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 04/05/2013] [Indexed: 11/10/2022] Open
Abstract
Crystal structures are reported for three substituted 1H-imidazole-4,5-dicarbonitrile compounds used as catalysts for the coupling reaction of nucleoside methyl phosphonamidites, namely 2-(3',5'-dimethylbiphenyl-2-yl)-1H-imidazole-4,5-dicarbonitrile, C19H14N4, (I), 2-(2',4',6'-trimethylbiphenyl-2-yl)-1H-imidazole-4,5-dicarbonitrile, C20H16N4, (II), and 2-[8-(3,5-dimethylphenyl)naphthalen-1-yl]-1H-imidazole-4,5-dicarbonitrile, C23H16N4, (III). The asymmetric unit of (I) contains two independent molecules with similar conformations. There is steric repulsion between the imidazole group and the terminal phenyl group in all three compounds, resulting in the nonplanarity of the molecules. The naphthalene group of (III) shows significant deviation from planarity. The C-N bond lengths in the imidazole rings range from 1.325 (2) to 1.377 (2) Å. The molecules are connected into zigzag chains by intermolecular N-H···N(imidazole) [for (I)] or N-H····N(cyano) [for (II) and (III)] hydrogen bonds.
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Affiliation(s)
- Jan W Bats
- Institut für Organische Chemie und Chemische Biologie, Universität Frankfurt, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany.
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15
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Robaldo L, Pontiggia R, Di Lella S, Estrin DA, Engels JW, Iribarren AM, Montserrat JM. Conformational States of 2′-C-Methylpyrimidine Nucleosides in Single and Double Nucleic Acid Stranded Structures. J Phys Chem B 2012; 117:57-69. [DOI: 10.1021/jp3081645] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Laura Robaldo
- INGEBI (CONICET), Vuelta de Obligado 2490, Buenos Aires
(1428), Argentina
| | - Rodrigo Pontiggia
- INGEBI (CONICET), Vuelta de Obligado 2490, Buenos Aires
(1428), Argentina
| | - Santiago Di Lella
- Departamento
de Química
Inorgánica, Analítica y Química Física-INQUIMAE,
Fac. de Cs. Exactas y Naturales, UBA, Ciudad
Universitaria, Cap. Fed., Argentina
| | - Darío A. Estrin
- Departamento
de Química
Inorgánica, Analítica y Química Física-INQUIMAE,
Fac. de Cs. Exactas y Naturales, UBA, Ciudad
Universitaria, Cap. Fed., Argentina
| | - Joachim W. Engels
- Institute for Organic Chemistry,
and Chemical Biology, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Adolfo M. Iribarren
- INGEBI (CONICET), Vuelta de Obligado 2490, Buenos Aires
(1428), Argentina
- Laboratorio de Biotransformaciones, Universidad Nacional de Quilmes, Roque Saenz Peña
352 (1876) Bernal, Prov. de Bs. As., Argentina
| | - Javier M. Montserrat
- INGEBI (CONICET), Vuelta de Obligado 2490, Buenos Aires
(1428), Argentina
- Instituto de Ciencias, Universidad Nacional de Gral. Sarmiento, J. M. Gutierrez
1150, Los Polvorines (B1613GSX), Prov. de Bs. As., Argentina
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16
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González-Carmona MA, Quasdorff M, Vogt A, Tamke A, Yildiz Y, Hoffmann P, Lehmann T, Bartenschlager R, Engels JW, Kullak-Ublick GA, Sauerbruch T, Caselmann WH. Inhibition of hepatitis C virus RNA translation by antisense bile acid conjugated phosphorothioate modified oligodeoxynucleotides (ODN). Antiviral Res 2012; 97:49-59. [PMID: 23142319 DOI: 10.1016/j.antiviral.2012.10.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Revised: 10/26/2012] [Accepted: 10/28/2012] [Indexed: 01/22/2023]
Abstract
BACKGROUND The 5'-noncoding region (5'NCR) of the HCV-genome comprises an internal ribosome entry site essential for HCV-translation/replication. Phosphorothioate oligodeoxynucleotides (tS-ODN) complementary to this region can inhibit HCV-translation in vitro. In this study, bile acid conjugated tS-ODN were generated to increase cell-selective inhibition of 5'NCR-dependent HCV-translation. METHODS Different bile acid conjugated tS-ODN complementary to the HCV5'NCR were selected for their inhibitory potential in an in vitro transcription/translation assay. To analyze OATP (organic anion transporting polypeptides)-selective uptake of bile acid conjugated ODN, different hepatoma cells were stably transfected with the OATP1B1-transporter and primary human hepatocytes were used. An adenovirus encoding the HCV5'NCR fused to the luciferase gene (Ad-GFP-NCRluc) was generated to quantify 5'NCR-dependent HCV gene expression in OATP-overexpressing hepatoma cells and in vivo. RESULTS A 17mer phosphorothioate modified ODN (tS-ODN4_13) complementary to HCV5'NCR was able to inhibit 5'NCR-dependent HCV-translation in an in vitro transcription/translation test system by more than 90% and it was also effective in Huh7-cells containing the HCV subgenomic replicon. Conjugation to taurocholate (tS-ODN4_13T) significantly increased selective ODN uptake by primary human hepatocytes and by OATP1B1-expressing HepG2-cells compared to parental HepG2-cells. Correspondingly, tS-ODN4_13T significantly inhibited HCV gene expression in liver-derived OATP1B1-expressing HepG2- or CCL13-cells up to 70% compared to unconjugated tS-ODN and compared to mismatch taurocholate coupled tS-ODN. In vivo, tS-ODN4_13T showed also a trend to block 5'NCR-dependent HCV gene expression. CONCLUSIONS The tested taurocholate conjugated 17mer antisense ODN complementary to HCV5'NCV showed an increased and selective uptake by hepatocytes and liver-derived cells through OATP-mediated transport resulting in enhanced specific inhibition of HCV gene expression in vitro and in vivo. Thus, this novel approach may represent a promising strategy to improve antisense approaches with ODN in the control of hepatitis C infection.
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17
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Ouahrouch A, Taourirte M, Lazrek HB, Bats JW, Engels JW. 2-({4-[4-(1H-Benzimidazol-2-yl)phen-yl]-1H-1,2,3-triazol-1-yl}meth-oxy)ethanol. Acta Crystallogr Sect E Struct Rep Online 2012; 68:o1908. [PMID: 22719663 PMCID: PMC3379465 DOI: 10.1107/s1600536812023410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 05/22/2012] [Indexed: 11/10/2022]
Abstract
In the title molecule, C18H17N5O2, the dihedral angle between the benzene plane and the benzimidazole plane is 19.8 (1)° and the angle between the benzene plane and the triazole plane is 16.7 (1)°. In the crystal, molecules are connected by O—H⋯N hydrogen bonds, forming zigzag chains along the c-axis direction. The chains are connected by bifurcated N—H⋯(N,N) hydrogen bonds into layers parallel to (100). These layers are connected along the a-axis direction by weak C—H⋯O contacts, forming a three-dimensional network.
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18
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Engels JW. Medicinal Chemistry of Nucleic Acids. Edited by Li He Zhang, Zhen Xi and Jyoti Chattopadhyaya. ChemMedChem 2012. [DOI: 10.1002/cmdc.201200073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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19
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20
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Abstract
Stille Coupling is a versatile C-C bond forming reaction with high functional group tolerance under mild conditions. Our on column synthesis concept for RNA modification is based on the incorporation of iodo substituted nucleotide precursors to RNA during automated standard solid phase synthesis via TBDMS-, TC-, and ACE- protecting group strategies. Subsequently, the RNA, still bound on solid support, is ready for orthogonal postsynthetic functionalization via Stille cross-couplings utilizing the advantages of solid phase synthesis. Several monomer test reactions were employed with 2-iodo adenosine and 5-iodo uridine and organostannanes as coupling partners under different conditions, changing the catalyst/ligand system, temperature, and reaction time as well as conventional heating and microwave irradiation. Finally, Stille cross-couplings under optimized conditions were transferred to fully protected 5-mer and 12-mer RNA oligonucleotides on-column. Deprotection and cleavage from solid support resulted in site-specifically labeled oligonucleotides. Derivatizations via Stille cross-couplings were performed initially with vinyltributylstannane as well as later with 2-furanyl-, 2-thiophene-, and benzothiophene-2-tributylstannanes yielding fluorescently functionalized RNA.
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Affiliation(s)
- Lena Wicke
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Max-von-Laue Strasse 7, 60438 Frankfurt am Main, Germany
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21
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Krim J, Taourirte M, Engels JW. Synthesis of 1,4-disubstituted mono and bis-triazolocarbo-acyclonucleoside analogues of 9-(4-hydroxybutyl)guanine by Cu(I)-catalyzed click azide-alkyne cycloaddition. Molecules 2011; 17:179-90. [PMID: 22202806 PMCID: PMC6269037 DOI: 10.3390/molecules17010179] [Citation(s) in RCA: 17] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Revised: 12/09/2011] [Accepted: 12/19/2011] [Indexed: 11/17/2022] Open
Abstract
A series of novel mono-1,2,3-triazole and bis-1,2,3-triazole acyclonucleoside analogues of 9-(4-hydroxybutyl)guanine was prepared via copper(I)-catalyzed 1,3-dipolar cycloaddition of N-9 propargylpurine, N-1-propargylpyrimidines/as-triazine with the azido-pseudo-sugar 4-azidobutylacetate under solvent-free microwave conditions, followed by treatment with K(2)CO(3)/MeOH, or NH(3)/MeOH. All compounds studied in this work were screened for their antiviral activities [against human rhinovirus (HRV) and hepatitis C virus (HCV)] and antibacterial activities against a series of Gram positive and negative bacteria.
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Affiliation(s)
- Jamal Krim
- Laboratoire de Chimie Bioorganique et Macromoléculaire, Faculté des Sciences et Techniques - Guéliz, 40000, Marrakech, Maroc
- Institut für Organische Chemie und Chemische Biologie, J.W. Goethe Universität, Max-von-Laue Str. 7, 60438 Frankfurt am Main, Germany
| | - Moha Taourirte
- Laboratoire de Chimie Bioorganique et Macromoléculaire, Faculté des Sciences et Techniques - Guéliz, 40000, Marrakech, Maroc
| | - Joachim W. Engels
- Institut für Organische Chemie und Chemische Biologie, J.W. Goethe Universität, Max-von-Laue Str. 7, 60438 Frankfurt am Main, Germany
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22
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Brzezinska J, D'Onofrio J, Buff MCR, Hean J, Ely A, Marimani M, Arbuthnot P, Engels JW. Synthesis of 2'-O-guanidinopropyl-modified nucleoside phosphoramidites and their incorporation into siRNAs targeting hepatitis B virus. Bioorg Med Chem 2011; 20:1594-606. [PMID: 22264759 DOI: 10.1016/j.bmc.2011.12.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Revised: 12/12/2011] [Accepted: 12/13/2011] [Indexed: 11/25/2022]
Abstract
Synthetic RNAi activators have shown considerable potential for therapeutic application to silencing of pathology-causing genes. Typically these exogenous RNAi activators comprise duplex RNA of approximately 21 bp with 2 nt overhangs at the 3' ends. To improve efficacy of siRNAs, chemical modification at the 2'-OH group of ribose has been employed. Enhanced stability, gene silencing and attenuated immunostimulation have been demonstrated using this approach. Although promising, efficient and controlled delivery of highly negatively charged nucleic acid gene silencers remains problematic. To assess the potential utility of introducing positively charged groups at the 2' position, our investigations aimed at assessing efficacy of novel siRNAs containing 2'-O-guanidinopropyl (GP) moieties. We describe the formation of all four GP-modified nucleosides using the synthesis sequence of Michael addition with acrylonitrile followed by Raney-Ni reduction and guanidinylation. These precursors were used successfully to generate antihepatitis B virus (HBV) siRNAs. Testing in a cell culture model of viral replication demonstrated that the GP modifications improved silencing. Moreover, thermodynamic stability was not affected by the GP moieties and their introduction into each position of the seed region of the siRNA guide strand did not alter the silencing efficacy of the intended HBV target. These results demonstrate that modification of siRNAs with GP groups confers properties that may be useful for advancing therapeutic application of synthetic RNAi activators.
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Affiliation(s)
- Jolanta Brzezinska
- Goethe-University, Institute of Organic Chemistry & Chemical Biology, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
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23
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Sokočević A, Han S, Engels JW. Biophysical characterization of α-amylase inhibitor Parvulustat (Z-2685) and comparison with Tendamistat (HOE-467). Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 2011; 1814:1383-93. [DOI: 10.1016/j.bbapap.2011.07.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Revised: 07/08/2011] [Accepted: 07/12/2011] [Indexed: 11/25/2022]
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24
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Krstić I, Hänsel R, Romainczyk O, Engels JW, Dötsch V, Prisner TF. Long-Range Distance Measurements on Nucleic Acids in Cells by Pulsed EPR Spectroscopy. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201100886] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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25
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Krstić I, Hänsel R, Romainczyk O, Engels JW, Dötsch V, Prisner TF. Long-range distance measurements on nucleic acids in cells by pulsed EPR spectroscopy. Angew Chem Int Ed Engl 2011; 50:5070-4. [PMID: 21506223 DOI: 10.1002/anie.201100886] [Citation(s) in RCA: 150] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Indexed: 12/18/2022]
Affiliation(s)
- Ivan Krstić
- Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
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26
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Abstract
A or B: RNA-DNA hybrids, key intermediates in gene regulation, were classified by pulsed electron-electron double resonance (PELDOR) in combination with CD spectroscopy into two classes, interpreted as A- and B-like structures. RNase H1 cleavage of these hybrids is in full agreement with these assignments, cleaving the hybrids with A-like geometry preferentially. This combined analytical approach allows the interpretation and eventually the design of more easily cleavable hybrids as needed for the antisense technology.
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Affiliation(s)
- Olga Romainczyk
- Institute of Organic Chemistry and Chemical Biology, Max-von-Laue-Str 7, 60438 Frankfurt am Main, Germany
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27
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Knapp DC, Serva S, D'Onofrio J, Keller A, Lubys A, Kurg A, Remm M, Engels JW. Fluoride-cleavable, fluorescently labelled reversible terminators: synthesis and use in primer extension. Chemistry 2011; 17:2903-15. [PMID: 21294195 PMCID: PMC3110862 DOI: 10.1002/chem.201001952] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Revised: 10/18/2010] [Indexed: 11/08/2022]
Abstract
Fluorescent 2′-deoxynucleotides containing a protecting group at the 3′-O-position are reversible terminators that enable array-based DNA sequencing-by-synthesis (SBS) approaches. Herein, we describe the synthesis and full characterisation of four reversible terminators bearing a 3′-blocking moiety and a linker-dye system that is removable under the same fluoride-based treatment. Each nucleotide analogue has a different fluorophore attached to the base through a fluoride-cleavable linker and a 2-cyanoethyl moiety as the 3′-blocking group, which can be removed by using a fluoride treatment as well. Furthermore, we identified a DNA polymerase, namely, RevertAid M-MuLV reverse transcriptase, which can incorporate the four modified reversible terminators. The synthesised nucleotides and the optimised DNA polymerase were used on CodeLink slides spotted with hairpin oligonucleotides to demonstrate their potential in a cyclic reversible terminating approach.
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Affiliation(s)
- Diana C Knapp
- Institut für Organische Chemie und Chemische Biologie, J.W. Goethe Universität Frankfurt am Main, Max-von-Laue Strasse 7, 60438 Frankfurt am Main, Germany
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28
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Förster U, Grünewald C, Engels JW, Wachtveitl J. Ultrafast dynamics of 1-ethynylpyrene-modified RNA: a photophysical probe of intercalation. J Phys Chem B 2010; 114:11638-45. [PMID: 20707369 DOI: 10.1021/jp103176q] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The photophysics of pyrene attached to an adenine base within RNA single strands and duplexes is examined with respect to the position of the pyrene within the strand and the number of pyrenes attached to one duplex. Compounds with pyrenes intercalating sequence specifically are examined, as well as a doubly modified compound, where the two pyrenes are located close enough to each other for significant excimer interaction. Femtosecond transient absorption measurements and time correlated single photon counting measurements allow a thorough examination of the local influences on the pyrene photophysics. Our results suggest that optical excitation establishes an equilibration between two molecular states of different spectroscopic properties and lifetimes that are coupled only via the excited state as a gateway. One of them is a neutral pyrene-adenine excited state, S*, while the second one is connected to an excited charge transfer state, S*(CT). In all compounds, an ultrafast sub-ps decay from a higher excited state into the lowest excited state S* occurs, and an excited charge transfer species S*(CT) is formed within picoseconds. The fluorescence behavior of the pyrene-modified adenine, however, is strongly dependent on RNA conformation. Both S* and S*(CT) states are fluorescent, and decay within hundreds of picoseconds and approximately 2 ns, respectively. The ratio between S* and S*(CT) fluorescence depends strongly on pyrene intercalation, and it is found that the S* state is quenched selectively upon intercalation of the pyrene into RNA. The doubly modified duplex exhibits an additional fluorescent state with a lifetime of 18.7 ns, which is associated with the pyrene excimer state. This state coexists with a significant population of the pyrene monomer, since the characteristic features of the latter can still be observed. Formation of the excimer occurs on femtosecond time scales. The pyrene label thus provides a sensitive tool to monitor the local structural dynamics of RNA with the chromophore acting as a molecular beacon.
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Affiliation(s)
- Ute Förster
- Institute of Biophysics, Goethe-University Frankfurt, Max-von-Laue-Str. 1, 60438 Frankfurt, Germany
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29
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Haas J, Engels JW. A convenient approach towards 2'-O-modified RNA-oligonucleotides on solid support using universal nucleosides. ACTA ACUST UNITED AC 2010:331-2. [PMID: 18776388 DOI: 10.1093/nass/nrn167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Here we report a novel synthetic pathway for an efficient modification of RNA-oligonucleotides on solid-support using universal nucleosides bearing a 2'-O-aminopropyl-tether.
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Affiliation(s)
- Jens Haas
- Johann Wolfgang Goethe-University Frankfurt, Department of Chemistry, D-60438 Frankfurt am Main, Germany
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30
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Frolow O, Endeward B, Schiemann O, Prisner TF, Engels JW. Nitroxide spin labeled RNA for long range distance measurements by EPR-PELDOR. ACTA ACUST UNITED AC 2010:153-4. [PMID: 18776299 DOI: 10.1093/nass/nrn078] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Long range distance measurement on RNA allow the determination of RNA folds. Here we report the site specific incorporation of nitroxide spin labels at U,C and A by "on column synthesis". PELDOR (Pulsed Electron Double Resonance) measurements of several RNAs in the range of 2-6 nm were successful.
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Affiliation(s)
- O Frolow
- Institut für Organische Chemie und Chemische Biologie (OCCB), Goethe-Universität Frankfurt am Main, Max-von-Laue Str. 7, D-60438 Frankfurt am Main, Germany
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31
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Knapp DC, Keller A, D'Onofrio J, Lubys A, Serva S, Kurg A, Remm M, Kwiatkowski M, Engels JW. Synthesis of four colors fluorescently labelled 3'-O-blocked nucleotides with fluoride cleavable blocking group and linker for array based Sequencing-by-Synthesis applications. ACTA ACUST UNITED AC 2010:345-6. [PMID: 18776395 DOI: 10.1093/nass/nrn174] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Reversible terminators having a fluoride cleavable 3'-O-blocking group are presented. Each nucleotide triphosphate is labelled by a fluorescent dye cleavable by the same reagent. We present here their synthesis, cleavage experiments and polymerase incorporation tests for a possible use in a process of Sequencing-by-Synthesis.
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Affiliation(s)
- Diana C Knapp
- Institut für Organische Chemie und Chemische Biologie, J. W. Goethe Universität Frankfurt am Main, Max-von-Laue Str. 7, D-60438 Frankfurt am Main, Germany
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32
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Knapp DC, D'Onofrio J, Engels JW. Fluorescent labeling of (oligo)nucleotides by a new fluoride cleavable linker capable of versatile attachment modes. Bioconjug Chem 2010; 21:1043-55. [PMID: 20509599 DOI: 10.1021/bc900542f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The development of a fluoride cleavable linker 1 for reversibly labeling (oligo)nucleotides is described here. The linker allows different ways of chemical attachment of a reporter molecule, for example, click chemistry or amide formation. The versatile attachment modes of labels are demonstrated by derivatizations with pyrene and fluorescein. Besides the synthesis of the new linker, we also show the derivatization of iodobenzene as a model compound and a nucleoside to demonstrate the applicability. Further, cleavability studies in solution and on a solid-supported oligonucleotide are shown. The linker can be applied in the synthesis of reversible terminators, useful for new DNA sequencing technologies like cyclic reversibly terminating (CRT) sequencing.
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Affiliation(s)
- Diana C Knapp
- Institut fur Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe Universitat, Frankfurt am Main, Germany
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33
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Förster U, Lommel K, Sauter D, Grünewald C, Engels JW, Wachtveitl J. 2-(1-Ethynylpyrene)-adenosine as a folding probe for RNA - pyrene in or out. Chembiochem 2010; 11:664-72. [PMID: 20183842 DOI: 10.1002/cbic.200900778] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A series of short RNA duplexes containing one or two 1-ethynylpyrene-modified adenine bases was synthesised. The melting behaviour of these duplexes was examined by monitoring temperature-dependent pyrene fluorescence. In the singly modified RNA duplexes, the bases flanking the ethynylpyrene-rA were varied to examine the sequence specificity of the fluorescence change of pyrene upon RNA hybridisation. Because an increase in pyrene fluorescence upon melting of the duplex can be correlated with intercalation of pyrene, and a decrease is usually associated with the position of pyrene outside the strand, a relationship between the flanking bases and the tendency of the dye to intercalate has been established. It was found that pyrene intercalation is less likely to take place if the modified base is flanked only by A-U base pairs. Flanking G-C base pairs, even only in the 5'-direction of the modified base, will favour intercalation. In addition, we examined a doubly modified compound that had a pyrene located on each strand. The spectra indicated that the two pyrenes were close enough for interaction. Upon melting of the strand, a fluorescence blue shift corresponding to the dissociation of the pyrene-pyrene complex could be observed in addition to the intensity effect already known from the singly modified compounds. Two melting curves based on the different properties of the fluorophore could be extracted, leading to different melting points corresponding to the global duplex melting and to the change of local pyrene environment, respectively.
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Affiliation(s)
- Ute Förster
- Institute of Biophysics, Institute of Physical and Theoretical Chemistry, Goethe-University, Max-von-Laue-Strasse 1, 60438 Frankfurt, Germany
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34
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Bramsen JB, Pakula MM, Hansen TB, Bus C, Langkjær N, Odadzic D, Smicius R, Wengel SL, Chattopadhyaya J, Engels JW, Herdewijn P, Wengel J, Kjems J. A screen of chemical modifications identifies position-specific modification by UNA to most potently reduce siRNA off-target effects. Nucleic Acids Res 2010; 38:5761-73. [PMID: 20453030 PMCID: PMC2943616 DOI: 10.1093/nar/gkq341] [Citation(s) in RCA: 137] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Small interfering RNAs (siRNAs) are now established as the preferred tool to inhibit gene function in mammalian cells yet trigger unintended gene silencing due to their inherent miRNA-like behavior. Such off-target effects are primarily mediated by the sequence-specific interaction between the siRNA seed regions (position 2–8 of either siRNA strand counting from the 5′-end) and complementary sequences in the 3′UTR of (off-) targets. It was previously shown that chemical modification of siRNAs can reduce off-targeting but only very few modifications have been tested leaving more to be identified. Here we developed a luciferase reporter-based assay suitable to monitor siRNA off-targeting in a high throughput manner using stable cell lines. We investigated the impact of chemically modifying single nucleotide positions within the siRNA seed on siRNA function and off-targeting using 10 different types of chemical modifications, three different target sequences and three siRNA concentrations. We found several differently modified siRNAs to exercise reduced off-targeting yet incorporation of the strongly destabilizing unlocked nucleic acid (UNA) modification into position 7 of the siRNA most potently reduced off-targeting for all tested sequences. Notably, such position-specific destabilization of siRNA–target interactions did not significantly reduce siRNA potency and is therefore well suited for future siRNA designs especially for applications in vivo where siRNA concentrations, expectedly, will be low.
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Affiliation(s)
- Jesper B Bramsen
- Department of Molecular Biology, University of Aarhus, Arhus, Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, Odense, Denmark.
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35
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Krstić I, Frolow O, Sezer D, Endeward B, Weigand JE, Suess B, Engels JW, Prisner TF. PELDOR spectroscopy reveals preorganization of the neomycin-responsive riboswitch tertiary structure. J Am Chem Soc 2010; 132:1454-5. [PMID: 20078041 DOI: 10.1021/ja9077914] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Pulsed electron double resonance (PELDOR) spectroscopy reveals a prearranged tertiary structure of the 27 nucleotides long engineered neomycin-responsive riboswitch. Measured distances between spin labels at positions U4-U14, U4-U15, U14-U26, and U15-U26 were unchanged upon neomycin binding which implies that the global stem-loop architecture is preserved in the absence and presence of the ligand. On the basis of our results, we infer that low-temperature PELDOR data unambiguously demonstrate the existence of an enthalpically favorable set of RNA conformations ready to bind the ligand without major global rearrangement.
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Affiliation(s)
- Ivan Krstić
- Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Frankfurt am Main, Germany
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36
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Koller AN, Bozilovic J, Engels JW, Gohlke H. Aromatic N versus aromatic F: bioisosterism discovered in RNA base pairing interactions leads to a novel class of universal base analogs. Nucleic Acids Res 2010; 38:3133-46. [PMID: 20081201 PMCID: PMC2875010 DOI: 10.1093/nar/gkp1237] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The thermodynamics of base pairing is of fundamental importance. Fluorinated base analogs are valuable tools for investigating pairing interactions. To understand the influence of direct base-base interactions in relation to the role of water, pairing free energies between natural nucleobases and fluorinated analogs are estimated by potential of mean force calculations. Compared to pairing of AU and GC, pairing involving fluorinated analogs is unfavorable by 0.5-1.0 kcal mol(-1). Decomposing the pairing free energies into enthalpic and entropic contributions reveals fundamental differences for Watson-Crick pairs compared to pairs involving fluorinated analogs. These differences originate from direct base-base interactions and contributions of water. Pairing free energies of fluorinated base analogs with natural bases are less unfavorable by 0.5-1.0 kcal mol(-1) compared to non-fluorinated analogs. This is attributed to stabilizing C-F(...)H-N dipolar interactions and stronger N(...)H-C hydrogen bonds, demonstrating direct and indirect influences of fluorine. 7-methyl-7H-purine and its 9-deaza analog (Z) have been suggested as members of a new class of non-fluorinated base analogs. Z is found to be the least destabilizing universal base in the context of RNA known to date. This is the first experimental evidence for nitrogen-containing heterocylces as bioisosteres of aromatic rings bearing fluorine atoms.
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Affiliation(s)
- Alrun N Koller
- Department of Mathematics and Natural Sciences, Institute of Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-University, 40225 Düsseldorf, Germany
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Wurm JP, Meyer B, Bahr U, Held M, Frolow O, Kötter P, Engels JW, Heckel A, Karas M, Entian KD, Wöhnert J. The ribosome assembly factor Nep1 responsible for Bowen-Conradi syndrome is a pseudouridine-N1-specific methyltransferase. Nucleic Acids Res 2010; 38:2387-98. [PMID: 20047967 PMCID: PMC2853112 DOI: 10.1093/nar/gkp1189] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Nep1 (Emg1) is a highly conserved nucleolar protein with an essential function in ribosome biogenesis. A mutation in the human Nep1 homolog causes Bowen-Conradi syndrome-a severe developmental disorder. Structures of Nep1 revealed a dimer with a fold similar to the SPOUT-class of RNA-methyltransferases suggesting that Nep1 acts as a methyltransferase in ribosome biogenesis. The target for this putative methyltransferase activity has not been identified yet. We characterized the RNA-binding specificity of Methanocaldococcus jannaschii Nep1 by fluorescence- and NMR-spectroscopy as well as by yeast three-hybrid screening. Nep1 binds with high affinity to short RNA oligonucleotides corresponding to nt 910-921 of M. jannaschii 16S rRNA through a highly conserved basic surface cleft along the dimer interface. Nep1 only methylates RNAs containing a pseudouridine at a position corresponding to a previously identified hypermodified N1-methyl-N3-(3-amino-3-carboxypropyl) pseudouridine (m1acp3-Psi) in eukaryotic 18S rRNAs. Analysis of the methylated nucleoside by MALDI-mass spectrometry, HPLC and NMR shows that the methyl group is transferred to the N1 of the pseudouridine. Thus, Nep1 is the first identified example of an N1-specific pseudouridine methyltransferase. This enzymatic activity is also conserved in human Nep1 suggesting that Nep1 is the methyltransferase in the biosynthesis of m1acp3-Psi in eukaryotic 18S rRNAs.
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Affiliation(s)
- Jan Philip Wurm
- Institut für Molekulare Biowissenschaften, Johann-Wolfgang-Goethe-Universität, 60438 Frankfurt/M., Germany
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38
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Müller-Kuller T, Capalbo G, Klebba C, Engels JW, Klein SA. Identification and Characterization of a Highly Efficient Anti-HIV Pol Hammerhead Ribozyme. Oligonucleotides 2009; 19:265-72. [DOI: 10.1089/oli.2008.0150] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Thea Müller-Kuller
- Medizinische Klinik II, der Johann Wolfgang Goethe-Universität, Frankfurt, Germany
| | - Gianni Capalbo
- Medizinische Klinik II, der Johann Wolfgang Goethe-Universität, Frankfurt, Germany
| | - Christian Klebba
- Medizinische Klinik II, der Johann Wolfgang Goethe-Universität, Frankfurt, Germany
| | - Joachim W. Engels
- Institut für Organische Chemie, Johann Wolfgang Goethe-Universität, Frankfurt, Germany
| | - Stefan A. Klein
- Klinikum Bayreuth, Medizinische Klinik IV, Bayreuth, Germany
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Frolow O, Bats JW, Engels JW. 3-Ethynyl-2,2,5,5-tetra-methyl-1-oxyl-3-pyrroline. Acta Crystallogr Sect E Struct Rep Online 2009; 65:o1848. [PMID: 21583548 PMCID: PMC2977453 DOI: 10.1107/s1600536809026725] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Accepted: 07/08/2009] [Indexed: 11/29/2022]
Abstract
The five-membered ring of the title compound, C10H14NO, is almost planar [mean deviation from best plane = 0.006 (1) Å]. The N—O bond is in the plane of the five-membered ring. The molecule is positioned about a pseudo-mirror plane at y = 0.375. In the crystal, molecules are connected by intermolecular C—H⋯O contacts into layers parallel to (010).
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Affiliation(s)
- Olga Frolow
- Institut für Organische Chemie, Universität Frankfurt, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany
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40
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Bramsen JB, Laursen MB, Nielsen AF, Hansen TB, Bus C, Langkjaer N, Babu BR, Højland T, Abramov M, Van Aerschot A, Odadzic D, Smicius R, Haas J, Andree C, Barman J, Wenska M, Srivastava P, Zhou C, Honcharenko D, Hess S, Müller E, Bobkov GV, Mikhailov SN, Fava E, Meyer TF, Chattopadhyaya J, Zerial M, Engels JW, Herdewijn P, Wengel J, Kjems J. A large-scale chemical modification screen identifies design rules to generate siRNAs with high activity, high stability and low toxicity. Nucleic Acids Res 2009; 37:2867-81. [PMID: 19282453 PMCID: PMC2685080 DOI: 10.1093/nar/gkp106] [Citation(s) in RCA: 273] [Impact Index Per Article: 18.2] [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: 11/26/2008] [Revised: 02/09/2009] [Accepted: 02/09/2009] [Indexed: 01/17/2023] Open
Abstract
The use of chemically synthesized short interfering RNAs (siRNAs) is currently the method of choice to manipulate gene expression in mammalian cell culture, yet improvements of siRNA design is expectably required for successful application in vivo. Several studies have aimed at improving siRNA performance through the introduction of chemical modifications but a direct comparison of these results is difficult. We have directly compared the effect of 21 types of chemical modifications on siRNA activity and toxicity in a total of 2160 siRNA duplexes. We demonstrate that siRNA activity is primarily enhanced by favouring the incorporation of the intended antisense strand during RNA-induced silencing complex (RISC) loading by modulation of siRNA thermodynamic asymmetry and engineering of siRNA 3'-overhangs. Collectively, our results provide unique insights into the tolerance for chemical modifications and provide a simple guide to successful chemical modification of siRNAs with improved activity, stability and low toxicity.
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Affiliation(s)
- Jesper B Bramsen
- Department of Molecular Biology, University of Aarhus, Arhus, Nucleic Acid Center, University of Southern Denmark, Odense, Denmark.
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Keller AC, Serva S, Knapp DC, Kwiatkowski M, Engels JW. Synthesis of 3′-O-(2-cyanoethyl)-2′-deoxythymidine-5′-phosphate as a model compound for evaluation of cyanoethyl cleavage. ACTA ACUST UNITED AC 2009. [DOI: 10.1135/cccc2008183] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
An essential and challenging task during the development of our sequencing-by-synthesis (SBS) technique is the evaluation of efficient cyanoethyl (CE) cleavage conditions. For this purpose 3′-O-(2-cyanoethyl)-2′-deoxythymidine-5′-phosphate as a model compound as well as a short DNA oligomer bearing the CE function as terminal group were synthesized and used for various deprotection experiments. As it is already known for 2′-O-CE-protected RNA oligonucleotides, the CE function can be cleaved with tetrabutylammonium fluoride (TBAF) in THF. Indeed, by using 3′-O-(2-cyanoethyl)-2′-deoxythymidine-5′-phosphate as a simple model compound for cleavage tests, we found out that the 3′-O-CE function is quantitatively cleaved with 1 M TBAF in THF. However, the CE group is also cleaved by other small bases like hydroxy groups under alkaline conditions. The CE cleavage with TBAF in THF gives the fastest and quantitative removal of the CE group under mild conditions for our sequencing-by-synthesis (SBS) application. The efficient removal of the 3′-CE group is crucial for the proof-of-principle of our SBS approach using dye-labeled 3′-CE-blocked dNTPs, which is currently under investigation. Herein we describe the application of 3′-O-(2-cyanoethyl)-2′-deoxythymidine-5′-phosphate as model compound for the development of reversible terminators for the SBS technique. Furthermore we suggest that nucleoside phosphates bearing any removable 3′-modification might be suitable model compounds for cleavage studies in a heterogeneous environment comparable to an oligonucleotide/ aprotic solvent system.
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Bats JW, Frolow O, Engels JW. 4-Ethynyl-2,2,6,6-tetra-methyl-1,2,5,6-tetra-hydro-pyridine N-oxide. Acta Crystallogr Sect E Struct Rep Online 2009; 65:o529. [PMID: 21582190 PMCID: PMC2968437 DOI: 10.1107/s1600536809004681] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2009] [Accepted: 02/09/2009] [Indexed: 11/10/2022]
Abstract
The six-membered ring of the title compound, C(11)H(16)NO, has a distorted envelope conformation. The piperidine N atom deviates by 0.128 (1) Å from the plane through its three neighbouring atoms. In the crystal structure, mol-ecules are connected by inter-molecular C(ethyn-yl)-H⋯O contacts to form chains extending in the [10] direction.
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Affiliation(s)
- Jan W Bats
- Institut für Organische Chemie, Universität Frankfurt, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany
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Rehm S, Han S, Hassani I, Sokocevic A, Jonker HRA, Engels JW, Schwalbe H. The high resolution NMR structure of parvulustat (Z-2685) from Streptomyces parvulus FH-1641: comparison with tendamistat from Streptomyces tendae 4158. Chembiochem 2009; 10:119-27. [PMID: 19067455 DOI: 10.1002/cbic.200800547] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The protein parvulustat (Z-2685) from Streptomyces parvulus comprises 78 amino acids and functions as a highly efficient alpha-amylase inhibitor. Parvulustat shares 29.6 % overall amino acid sequence identity to the well-known alpha-amylase inhibitor tendamistat. Among the conserved residues are the two disulfide bridges (C9-C25, C43-C70) and the active-site motif (W16, R17, Y18). Here, we report the high-resolution NMR structure of parvulustat based on NOEs, J couplings, chemical shifts and hydrogen-exchange data. In addition, we studied the dynamical properties of parvulustat by heteronuclear relaxation measurements. We compare the structure of parvulustat with the structure of tendamistat in terms of secondary structure elements, charges and hydrophobicity. The overall structural composition is very similar, but there are distinct differences including the active-site region. These structural and dynamical differences indicate that for parvulustat an induced-fit mechanism for binding to alpha-amylase might take place, since the structure of tendamistat does not change upon binding to alpha-amylase.
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Affiliation(s)
- Stephan Rehm
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann-Wolfgang-Goethe University, Max-von-Laue-Strasse 7, Frankfurt am Main, Germany
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Affiliation(s)
- Hannes Kopitz
- Pharmazeutisches Institut, Christian-Albrechts-Universität zu Kiel, Gutenbergstr. 76, 24118 Kiel, Germany
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Affiliation(s)
- Romualdas Smicius
- Institut für Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe-Universität, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Joachim W. Engels
- Institut für Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe-Universität, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
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Kwon T, Piton N, Grünewald C, Engels JW. Synthesis of pyrene labeled RNA for fluorescence measurements. Nucleosides Nucleotides Nucleic Acids 2008; 26:1381-6. [PMID: 18066787 DOI: 10.1080/15257770701534048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The fluorophores 1-ethynylpyrene and 1-(p-ethynyl-phenylethynyl)-pyrene were attached to RNA through a Sonogashira cross-coupling with 5-iodocytidine either in solution through phosphoamidite synthesis or via on-column conjugation during solid-phase oligonucleotide synthesis. Six probes with the sequence 5'-CUU UUC UUU CUU-3' were derivatized with both fluorophores, whereby the position of the modified cytidine was varied. Fluorescence measurements showed sensitivity of the pyrene group to its environment in the single strands and corresponding duplexes.
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Affiliation(s)
- Taewoo Kwon
- Institut für Organische Chemie und Chemische Biologie (OCCB), Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, D-60438 Frankfurt am Main, Germany
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Abstract
Nucleoside analogues are chemical means to investigate hydrogen bonds, base stacking, and solvation as the three predominant forces that are responsible for the stability of secondary structure of nucleic acids. To obtain deeper insight into the contributions of these interactions to RNA stability apart from the ones exerted by the predominant nucleosides we decided to synthesize some novel nucleic acid analogues where the nucleobases are replaced by fluoroindoles. Fluorinated indoles can be compared to fluorinated benzimidazoles to determine the role of nitrogen in five membered ring system. The synthesis of fluoroindole ribonucleosides is described here.
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Affiliation(s)
- Jelena Bozilović
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Frankfurt am Main, Germany
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48
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Odadzic D, Engels JW. Different strategies for the synthesis of 2'-O-aminoethyl adenosine building blocks. Nucleosides Nucleotides Nucleic Acids 2008; 26:873-7. [PMID: 18058499 DOI: 10.1080/15257770701505295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The chemical modification of the 2'-O-position of nucleosides proved to be of great importance for the RNA stability. Greater stability of RNA duplexes allows a longer half life in the cell and, therefore, a better effect of RNA Interference. Here we investigated the synthesis of 2'-O-aminoethyl adenosine as a cationic modified building block.
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Affiliation(s)
- Dalibor Odadzic
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Frankfurt am Main, Germany
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49
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Nikolaus NV, Bozilović J, Engels JW. Microwave-assisted ribosylation of modified heterocyclic bases by Vorbrüggen method. Nucleosides Nucleotides Nucleic Acids 2008; 26:889-92. [PMID: 18058502 DOI: 10.1080/15257770701505485] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
During the last decades the nucleoside synthesis has proven to be important. The modified silyl-Hilbert-Johnson nucleoside synthesis modified by Vorbrüggen is one of the most often used methods. We have studied N-glycosilation of modifieded heterocyclic bases by Vorbrüggen method with microwave irradiation and we were able to shorten the reaction time and obtain higher yields. The method was demonstrated by fluoroquinolone and purine.
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Affiliation(s)
- Nadja V Nikolaus
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Frankfurt am Main, Germany
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50
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Lazrek HB, Vasseur JJ, Secrist J, Engels JW. A glutaric acid ester as carrier system for sustained delivery of lamuvidine (3TC) dimers. Nucleosides Nucleotides Nucleic Acids 2008; 26:1103-6. [PMID: 18058545 DOI: 10.1080/15257770701519452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
We report the synthesis of homo and heterodimers of 3TC conjugates. All new dimers were screened for their ability to inhibit HIV-1 in MT4 cell line and were compared to AZT alone and showed marked antiviral activity.
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Affiliation(s)
- H B Lazrek
- Faculté des Sciences Semlalia, Laboratoire de Chimie Bio-Organique, Marrakech, Maroc
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