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Rajani P, Chandra S, Ramanathan N, Sundararajan K, Rao CB. Exploring the conformations of Dibutyl Phosphonate (DBP): A matrix isolation infrared spectroscopic and density functional theory studies. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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2
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Giurgiu C, Fang Z, Aitken HRM, Kim SC, Pazienza L, Mittal S, Szostak JW. Structure–Activity Relationships in Nonenzymatic Template‐Directed RNA Synthesis. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202109714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Constantin Giurgiu
- Howard Hughes Medical Institute Department of Molecular Biology, and Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 USA
- Department of Chemistry and Chemical Biology Harvard University Cambridge MA 02138 USA
| | - Ziyuan Fang
- Howard Hughes Medical Institute Department of Molecular Biology, and Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 USA
- Department of Genetics Harvard Medical School Boston MA 02115 USA
| | - Harry R. M. Aitken
- Howard Hughes Medical Institute Department of Molecular Biology, and Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 USA
- Department of Genetics Harvard Medical School Boston MA 02115 USA
| | - Seohyun Chris Kim
- Howard Hughes Medical Institute Department of Molecular Biology, and Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 USA
- Department of Genetics Harvard Medical School Boston MA 02115 USA
| | - Lydia Pazienza
- Howard Hughes Medical Institute Department of Molecular Biology, and Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 USA
- Department of Chemistry and Chemical Biology Harvard University Cambridge MA 02138 USA
| | - Shriyaa Mittal
- Howard Hughes Medical Institute Department of Molecular Biology, and Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 USA
- Department of Chemistry and Chemical Biology Harvard University Cambridge MA 02138 USA
| | - Jack W. Szostak
- Howard Hughes Medical Institute Department of Molecular Biology, and Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 USA
- Department of Chemistry and Chemical Biology Harvard University Cambridge MA 02138 USA
- Department of Genetics Harvard Medical School Boston MA 02115 USA
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3
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Giurgiu C, Fang Z, Aitken HRM, Kim SC, Pazienza L, Mittal S, Szostak JW. Structure-Activity Relationships in Nonenzymatic Template-Directed RNA Synthesis. Angew Chem Int Ed Engl 2021; 60:22925-22932. [PMID: 34428345 PMCID: PMC8490286 DOI: 10.1002/anie.202109714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Indexed: 11/11/2022]
Abstract
The template-directed synthesis of RNA played an important role in the transition from prebiotic chemistry to the beginnings of RNA based life, but the mechanism of RNA copying chemistry is incompletely understood. We measured the kinetics of template copying with a set of primers with modified 3'-nucleotides and determined the crystal structures of these modified nucleotides in the context of a primer/template/substrate-analog complex. pH-rate profiles and solvent isotope effects show that deprotonation of the primer 3'-hydroxyl occurs prior to the rate limiting step, the attack of the alkoxide on the activated phosphate of the incoming nucleotide. The analogs with a 3 E ribose conformation show the fastest formation of 3'-5' phosphodiester bonds. Among those derivatives, the reaction rate is strongly correlated with the electronegativity of the 2'-substituent. We interpret our results in terms of differences in steric bulk and charge distribution in the ground vs. transition states.
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Affiliation(s)
- Constantin Giurgiu
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Ziyuan Fang
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Harry R M Aitken
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Seohyun Chris Kim
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Lydia Pazienza
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Shriyaa Mittal
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
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4
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Sarkar S, Chandra S, Suryaprasad B, Ramanathan N, Sundararajan K, Suresh A. Conformational topography of tris(2-methylbutyl) phosphate and the influence of methyl branching at the non-hyperconjugative carbon on the conformational landscape: insights from matrix isolation infrared spectroscopy and DFT computations. Phys Chem Chem Phys 2020; 22:24372-24392. [PMID: 33084659 DOI: 10.1039/d0cp03403g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The branching of a methyl group in a linear chain has a profound influence on the conformational morphology as it wields a strong control in reducing a large number of conformations. To unravel the effect of branching on the second non-hyperconjugative carbon atom on the conformational landscape, the conformations of tris(2-methylbutyl)phosphate (T2MBP) were studied using Density Functional Theory (DFT) computations and matrix isolation infrared spectroscopy. Experimentally, T2MBP along with N2/Ar/Kr/Xe gases was effusively expanded and deposited at a low temperature of 12 K, which was subsequently probed using infrared spectroscopy. The computations of all the conformations were accomplished using the B3LYP level of theory with the 6-311++G(d,p) basis set. A dimethyl(2-methylbutyl) phosphate (DM2MBP) prototype, a molecule containing a single 2-methylbutyl moiety, was examined for its conformations. Computations predicted 18 and 9 conformations each for the 'gauche' and 'trans' families, respectively, in which the third branched carbon completely influences the orientation of the fourth carbon, which simplifies the conformational problem of DM2MBP. Of the 18 and 9 bunches each in the 'gauche' and 'trans' families, only 7 and 3 conformations, respectively, became energetically important, which when extrapolated to T2MBP resulted in 343 and 147 conformational possibilities. The factor of degeneracy further reduced these numbers and a total of 168 conformations effectively contribute to the conformational composition of T2MBP in the gas phase. The role of stereo electronic and steric factors prevalent in the conformational clusters of T2MBP was unravelled respectively using natural bond orbital and non-covalent interaction analyses.
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Affiliation(s)
- Subramee Sarkar
- Homi Bhabha National Institute, Materials Chemistry and Metal Fuel Cycle Group, Indira Gandhi Centre for Atomic Research, Kalpakkam 603 102, Tamil Nadu, India.
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5
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Crooke ST, Seth PP, Vickers TA, Liang XH. The Interaction of Phosphorothioate-Containing RNA Targeted Drugs with Proteins Is a Critical Determinant of the Therapeutic Effects of These Agents. J Am Chem Soc 2020; 142:14754-14771. [PMID: 32786803 DOI: 10.1021/jacs.0c04928] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Recent progress in understanding phosphorothioate antisense oligonucleotide (PS-ASO) interactions with proteins has revealed that proteins play deterministic roles in the absorption, distribution, cellular uptake, subcellular distribution, molecular mechanisms of action, and toxicity of PS-ASOs. Similarly, such interactions can alter the fates of many intracellular proteins. These and other advances have opened new avenues for the medicinal chemistry of PS-ASOs and research on all elements of the molecular pharmacology of these molecules. These advances have recently been reviewed. In this Perspective article, we summarize some of those learnings, the general principles that have emerged, and a few of the exciting new questions that can now be addressed.
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Affiliation(s)
- Stanley T Crooke
- Ionis Pharmaceuticals, Inc., Carlsbad, California 92010-6670, United States
| | - Punit P Seth
- Ionis Pharmaceuticals, Inc., Carlsbad, California 92010-6670, United States
| | - Timothy A Vickers
- Ionis Pharmaceuticals, Inc., Carlsbad, California 92010-6670, United States
| | - Xue-Hai Liang
- Ionis Pharmaceuticals, Inc., Carlsbad, California 92010-6670, United States
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Gaweda K, Plazinski W. The systematic influence of solvent on the conformational features of furanosides. Org Biomol Chem 2019; 17:2479-2485. [PMID: 30756110 DOI: 10.1039/c9ob00043g] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The endo- and exo-anomeric effects are the two most recognizable stereoelectronic effects exhibited by carbohydrates. Their presence relies on the interactions between ring substituent(s) and ring oxygen atoms. Here, we report the finding of a new effect that partially controls the conformational properties of furanose rings and can be ascribed to the influence of the solvent on the electronic structure of a molecule. In contrast to anomeric effects, it is not dependent on either presence or absence of ring substituents. Its origins lie in a solvent-induced flux of atomic charges that involves atoms forming the furanose ring. This systematically changes the energy of the whole molecular system and alters the ring-distortion free energies by ∼2.5-6.5 kJ mol-1, favoring the geometries close to the twist 3T2/2T3 conformers and disfavoring the envelope OE/EO-like shapes. This intriguing effect has never been reported before, although it is expected to exist in all furanose rings. Along with more recognized stereoelectronic effects, this phenomenon contributes to a wide applicability of the two-state (north vs. south) model of pseudorotation in furanosides and, in the case of extremely flexible furanose rings, may change the preferred conformation type in comparison with the gas-phase-oriented predictions.
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Affiliation(s)
- Karolina Gaweda
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, ul. Niezapominajek 8, 30-239 Cracow, Poland.
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7
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Saatori SM, Perez TJ, Graham SM. Variable-Temperature NMR Spectroscopy, Conformational Analysis, and Thermodynamic Parameters of Cyclic Adenosine 5'-Diphosphate Ribose Agonists and Antagonists. J Org Chem 2018; 83:2554-2569. [PMID: 29365260 DOI: 10.1021/acs.joc.7b02749] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Cyclic adenosine 5'-diphosphate ribose (cADPR) is a ubiquitous Ca2+-releasing second messenger. Knowledge of its conformational landscape is an essential tool for unraveling the structure-activity relationship (SAR) in cADPR. Variable-temperature 1H NMR spectroscopy, in conjunction with PSEUROT and population analyses, allowed us to determine the conformations and thermodynamic parameters of the furanose rings, γ-bonds (C4'-C5'), and β-bonds (C5'-O5') in the cADPR analogues 2'-deoxy-cADPR, 7-deaza-cADPR, and 8-bromo-cADPR. A significant finding was that, although the analogues are similar to each other and to cADPR itself in terms of overall conformation and population (ΔG°), there were subtle yet important differences in some of thermodynamic properties (ΔH°, ΔS°) associated with each of the conformational equilibria. These differences prompted us to propose a model for cADPR in which the interactions between the A2'-N3, A5″-N3, and H2-R5' atoms serve to fine-tune the N-glycosidic torsion angles (χ).
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Affiliation(s)
- Sarah-Marie Saatori
- Department of Chemistry, St. John's University , 8000 Utopia Parkway, Queens, New York 11439, United States
| | - Tanner J Perez
- Department of Chemistry, St. John's University , 8000 Utopia Parkway, Queens, New York 11439, United States
| | - Steven M Graham
- Department of Chemistry, St. John's University , 8000 Utopia Parkway, Queens, New York 11439, United States
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Abstract
Oligonucleotide-based therapeutics have made rapid progress in the clinic for treatment of a variety of disease indications. Unmodified oligonucleotides are polyanionic macromolecules with poor drug-like properties. Over the past two decades, medicinal chemists have identified a number of chemical modification and conjugation strategies which can improve the nuclease stability, RNA-binding affinity, and pharmacokinetic properties of oligonucleotides for therapeutic applications. In this perspective, we present a summary of the most commonly used nucleobase, sugar and backbone modification, and conjugation strategies used in oligonucleotide medicinal chemistry.
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Affiliation(s)
- W Brad Wan
- Department of Medicinal Chemistry, Ionis Pharmaceuticals , 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Punit P Seth
- Department of Medicinal Chemistry, Ionis Pharmaceuticals , 2855 Gazelle Court, Carlsbad, California 92010, United States
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Wang J, Dong H, Chionh YH, McBee ME, Sirirungruang S, Cunningham RP, Shi PY, Dedon PC. The role of sequence context, nucleotide pool balance and stress in 2'-deoxynucleotide misincorporation in viral, bacterial and mammalian RNA. Nucleic Acids Res 2016; 44:8962-8975. [PMID: 27365049 PMCID: PMC5062971 DOI: 10.1093/nar/gkw572] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 06/06/2016] [Indexed: 11/16/2022] Open
Abstract
The misincorporation of 2′-deoxyribonucleotides (dNs) into RNA has important implications for the function of non-coding RNAs, the translational fidelity of coding RNAs and the mutagenic evolution of viral RNA genomes. However, quantitative appreciation for the degree to which dN misincorporation occurs is limited by the lack of analytical tools. Here, we report a method to hydrolyze RNA to release 2′-deoxyribonucleotide-ribonucleotide pairs (dNrN) that are then quantified by chromatography-coupled mass spectrometry (LC-MS). Using this platform, we found misincorporated dNs occurring at 1 per 103 to 105 ribonucleotide (nt) in mRNA, rRNAs and tRNA in human cells, Escherichia coli, Saccharomyces cerevisiae and, most abundantly, in the RNA genome of dengue virus. The frequency of dNs varied widely among organisms and sequence contexts, and partly reflected the in vitro discrimination efficiencies of different RNA polymerases against 2′-deoxyribonucleoside 5′-triphosphates (dNTPs). Further, we demonstrate a strong link between dN frequencies in RNA and the balance of dNTPs and ribonucleoside 5′-triphosphates (rNTPs) in the cellular pool, with significant stress-induced variation of dN incorporation. Potential implications of dNs in RNA are discussed, including the possibilities of dN incorporation in RNA as a contributing factor in viral evolution and human disease, and as a host immune defense mechanism against viral infections.
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Affiliation(s)
- Jin Wang
- Infectious Disease Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore 138602
| | - Hongping Dong
- Novartis Institute for Tropical Diseases, Singapore 138670
| | - Yok Hian Chionh
- Infectious Disease Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore 138602 Department of Microbiology & Immunology Programme, Center for Life Sciences, National University of Singapore, Singapore 117545
| | - Megan E McBee
- Infectious Disease Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore 138602
| | - Sasilada Sirirungruang
- Infectious Disease Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore 138602
| | - Richard P Cunningham
- Department of Biological Sciences, The University at Albany, Albany, NY 12222, USA
| | - Pei-Yong Shi
- Departments of Biochemistry & Molecular Biology and Phamarcology & Toxicology, and Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Peter C Dedon
- Infectious Disease Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore 138602 Department of Biological Engineering & Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA
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Fox SJ, Gourdain S, Coulthurst A, Fox C, Kuprov I, Essex JW, Skylaris CK, Linclau B. A computational study of vicinal fluorination in 2,3-difluorobutane: implications for conformational control in alkane chains. Chemistry 2015; 21:1682-91. [PMID: 25418601 DOI: 10.1002/chem.201405317] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Indexed: 11/07/2022]
Abstract
A comprehensive conformational analysis of both 2,3-difluorobutane diastereomers is presented based on density functional theory calculations in vacuum and in solution, as well as NMR experiments in solution. While for 1,2-difluoroethane the fluorine gauche effect is clearly the dominant effect determining its conformation, it was found that for 2,3-difluorobutane there is a complex interplay of several effects, which are of similar magnitude but often of opposite sign. As a result, unexpected deviations in dihedral angles, relative conformational energies and populations are observed which cannot be rationalised only by chemical intuition. Furthermore, it was found that it is important to consider the free energies of the various conformers, as these lead to qualitatively different results both in vacuum and in solvent, when compared to calculations based only on the electronic energies. In contrast to expectations, it was found that vicinal syn-difluoride introduction in the butane and by extension, longer hydrocarbon chains, is not expected to lead to an effective stabilisation of the linear conformation. Our findings have implications for the use of the vicinal difluoride motif for conformational control.
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Affiliation(s)
- Stephen J Fox
- Department of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ (UK)
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11
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Seth PP, Swayze EE. Unnatural Nucleoside Analogs for Antisense Therapy. METHODS AND PRINCIPLES IN MEDICINAL CHEMISTRY 2014. [DOI: 10.1002/9783527676545.ch12] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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12
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Plevnik M, Cevec M, Plavec J. NMR structure of 2'-O-(2-methoxyethyl) modified and C5-methylated RNA dodecamer duplex. Biochimie 2013; 95:2385-91. [PMID: 24012551 DOI: 10.1016/j.biochi.2013.08.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 08/26/2013] [Indexed: 10/26/2022]
Abstract
The solution-state structure of 2'-O-(2-methoxyethly) substituted dodecamer r(*CG*CGAA*U*U*CG*C)d(G), 2'-MOE RNA, with all cytosines and uracils methylated at the C5-position has been determined by NMR spectroscopy. The chemical modifications were used to improve the oligonucleotide's drug-like properties. The 2'-MOE group drives pseudorotational equilibrium of the ribofuranose moiety to the N-type conformation and supposedly results in structural preorganization leading to high affinity of a modified oligonucleotide towards its complementary biological target, improved pharmacokinetic and toxicological properties. The high melting temperature of the antiparallel duplex structure adopted by 2'-MOE RNA was explained through the formation of a stable A-form RNA consistent with effective base-pairing and stacking interactions. The comparison of the solution-state structure with the crystal structure of a non-methylated analogue shows an increase in the stacking at the base pair steps for the C5-methylated 2'-MOE RNA duplex. The MOE substituents adopt a well-defined structure in the minor groove with the predominant gauche conformations around the ethylene bond.
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Affiliation(s)
- Miha Plevnik
- Krka, d.d., Šmarješka cesta 6, 8501 Novo mesto, Slovenia
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13
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Taha HA, Richards MR, Lowary TL. Conformational Analysis of Furanoside-Containing Mono- and Oligosaccharides. Chem Rev 2012; 113:1851-76. [DOI: 10.1021/cr300249c] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Hashem A. Taha
- Alberta Glycomics Centre and Department of Chemistry, Gunning−Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2
| | - Michele R. Richards
- Alberta Glycomics Centre and Department of Chemistry, Gunning−Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2
| | - Todd L. Lowary
- Alberta Glycomics Centre and Department of Chemistry, Gunning−Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2
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O’Hagan D. Organofluorine Chemistry: Synthesis and Conformation of Vicinal Fluoromethylene Motifs. J Org Chem 2012; 77:3689-99. [DOI: 10.1021/jo300044q] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- David O’Hagan
- EaStCHEM
School of Chemistry, University of St. Andrews, North Haugh, St. Andrews KY16 9ST, United Kingdom
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Naud S, Macnaughton SJ, Dyson BS, Woollaston DJ, Dallimore JWP, Robertson J. Conformational preferences of oxy-substituents in butenolide–tetrahydropyran spiroacetals and butenolide–piperidine spiro-N,O-acetals. Org Biomol Chem 2012; 10:3506-18. [DOI: 10.1039/c2ob06849d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Seela F, Debelak H, Reuter H, Kastner G, Mikhailopulo IA. 1-Deaza-3′-O-methyladenosine: A Nucleoside with theSyn-conformation in the Solid State and in Solution. ACTA ACUST UNITED AC 2011. [DOI: 10.1080/07328319808004671] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Frank Seela
- a Laboratorium für Organische und Bioorganische Chemie , Institut für Chemie, Universität Osnabrück , Barbarastr 7, D-49069 , Osnabrück , Germany
| | - Harald Debelak
- a Laboratorium für Organische und Bioorganische Chemie , Institut für Chemie, Universität Osnabrück , Barbarastr 7, D-49069 , Osnabrück , Germany
| | - Hans Reuter
- b Anorganische Chemie , Institut für Chemie, Universität Ósnabrück , Barbarastr. 7, D-49069 , Osnabriick , Germany
| | - Guide Kastner
- b Anorganische Chemie , Institut für Chemie, Universität Ósnabrück , Barbarastr. 7, D-49069 , Osnabriick , Germany
| | - Igor A. Mikhailopulo
- c Institute of Bioorganic Chemistry, Byelorussian Academy of Sciences , 220141 , Minsk , Zhodinskaya 5, Byelorussia
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Hunter L, Jolliffe KA, Jordan MJT, Jensen P, Macquart RB. Synthesis and Conformational Analysis of α,β-Difluoro-γ-amino Acid Derivatives. Chemistry 2011; 17:2340-3. [DOI: 10.1002/chem.201003320] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Indexed: 11/07/2022]
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18
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Sharma NK, Ganesh KN. Base dependent pyrrolidine ring pucker in aep-PNA monomers: NMR and PSEUROT analysis. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.09.082] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Gokhale SS, Gogoi K, Kumar VA. Probing Binding Preferences of DNA and RNA: Backbone Chirality of Thioacetamido-Linked Nucleic Acids and iso-Thioacetamido-Linked Nucleic Acids to Differentiate DNA versus RNA Selective Binding. J Org Chem 2010; 75:7431-4. [DOI: 10.1021/jo1014036] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sachin S. Gokhale
- Division Of Organic Chemistry, National Chemical Laboratory, Dr. Homi Bhabha Road, Pune-411008, India
| | - Khirud Gogoi
- Division Of Organic Chemistry, National Chemical Laboratory, Dr. Homi Bhabha Road, Pune-411008, India
| | - Vaijayanti A. Kumar
- Division Of Organic Chemistry, National Chemical Laboratory, Dr. Homi Bhabha Road, Pune-411008, India
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21
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Viazovkina E, Mangos MM, Elzagheid MI, Damha MJ. Solid-phase synthesis of 2'-deoxy-2'-fluoro- beta-D-oligoarabinonucleotides (2'F-ANA) and their phosphorothioate derivatives. ACTA ACUST UNITED AC 2008; Chapter 4:Unit 4.15. [PMID: 18428897 DOI: 10.1002/0471142700.nc0415s10] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
This unit describes the chemical synthesis of 2'-deoxy-2'-fluoro-b-D-oligoarabinonucleotides (2'F-ANA), both with phosphodiester and phosphorothioate linkages. The protocols described herein include araF phosphoramidite preparation, assembly on DNA synthesizers, and final deprotection and purification of oligonucleotides.
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Dowd MK, French AD, Reilly PJ. MM3 Modeling of Ribose and 2-Deoxyribose Ring Puckering. J Carbohydr Chem 2008. [DOI: 10.1080/07328300008544137] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Michael K. Dowd
- a U. S. Department of Agriculture , Southern Regional Research Center , P. O. Box 19687, New Orleans, LA 70179, USA
- b U. S. Department of Agriculture , Southern Regional Research Center , P. O. Box 19687, New Orleans, LA 70179, USA
- c Department of Chemical Engineering , Iowa State University , Ames, IA 50011, USA
| | - Alfred D. French
- a U. S. Department of Agriculture , Southern Regional Research Center , P. O. Box 19687, New Orleans, LA 70179, USA
- b U. S. Department of Agriculture , Southern Regional Research Center , P. O. Box 19687, New Orleans, LA 70179, USA
- c Department of Chemical Engineering , Iowa State University , Ames, IA 50011, USA
| | - Peter J. Reilly
- a U. S. Department of Agriculture , Southern Regional Research Center , P. O. Box 19687, New Orleans, LA 70179, USA
- b U. S. Department of Agriculture , Southern Regional Research Center , P. O. Box 19687, New Orleans, LA 70179, USA
- c Department of Chemical Engineering , Iowa State University , Ames, IA 50011, USA
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Gogoi K, Kumar VA. Chimeric (α-amino acid + nucleoside-β-amino acid)npeptide oligomers show sequence specific DNA/RNA recognition. Chem Commun (Camb) 2008:706-8. [DOI: 10.1039/b716835g] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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24
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Rozners E, Katkevica D, Strömberg R. Oligoribonucleotide analogues containing a mixed backbone of phosphodiester and formacetal internucleoside linkages, together with vicinal 2'-O-methyl groups. Chembiochem 2007; 8:537-45. [PMID: 17300110 DOI: 10.1002/cbic.200600515] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Oligoribonucleotides containing formacetal internucleoside linkages have been prepared and studied by UV melting experiments. In RNA duplexes, the formacetal substitution is stabilizing (Deltat(m)=0 to +0.9 degrees C per modification) at physiological salt concentrations (0.1 M) but destabilizing (Deltat(m)=-0.4 to -0.8 degrees C per modification) at high salt concentrations (1 M); this suggests that reduction of electrostatic repulsion contributes substantially to the stabilization. The presence of 2'-O-Me substituents increases the stabilities of the duplexes (Deltat(m)=+0.5 to +1.1 degrees C per modification). The positive effects of formacetals and 2'-O-Me groups were independent and additive. (1)H NMR studies on monomeric model compounds containing 3'-(ethyl phosphate) or 3'-O-ethoxymethyl groups showed that the formacetal and 2'-O-Me substitutions shift the conformational equilibria of the ribose residues towards the North conformers by 5 to 12 %. Although the preference for the North conformers qualitatively correlates with increased duplex stabilities, changes in thermodynamic parameters (DeltaH degrees and TDeltaS degrees ) for formation of oligonucleotide duplexes and differences in dependence on concentrations of sodium acetate, sodium chloride and sodium perchlorate suggest that solvation effects are also important for the duplex stabilities. Overall the formacetal linkages fit well in A-type RNA duplexes, making them potentially interesting modifications for RNA-based gene-control strategies (e.g., antisense and RNA interference).
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Affiliation(s)
- Eriks Rozners
- Division of Organic and Bioorganic Chemistry, MBB Scheele Laboratory, Karolinska Institutet, 17177 Stockholm, Sweden.
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25
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Buckingham J, Brazier JA, Fisher J, Cosstick R. Incorporation of a S-glycosidic linkage into a glyconucleoside changes the conformational preference of both furanose sugars. Carbohydr Res 2007; 342:16-22. [PMID: 17145047 DOI: 10.1016/j.carres.2006.11.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2006] [Revised: 11/01/2006] [Accepted: 11/07/2006] [Indexed: 11/19/2022]
Abstract
A glyconucleoside containing a thioglycoside linkage, namely 1-(3-S-beta-D-ribofuranosyl-2,3-dideoxy-3-thio-beta-D-ribofuranosyl)-thymine, has been prepared through condensation of a suitably protected derivative of 3'-thiothymidine with an activated ribose sugar. NMR has been used to study the conformation of the S-disaccharide and the unmodified O-disaccharide. A full pseudorotational analysis showed that for the S-disaccharide, the ribose and deoxy ribose sugars have a preference for the south and north pucker, respectively; which is the reverse of what is seen for the O-disaccharide.
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Affiliation(s)
- Joanne Buckingham
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, UK
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26
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Thibaudeau C, Chattopadhyaya J. The Information Transmission from the Nucleobase Drives the Sugar-Phosphate Backbone Conformation in the Nucleotide Wire. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328319808004691] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Christophe Thibaudeau
- a Department of Bioorganic Chemistry , University of Uppsala , Box 581, Biomedical Centre, S-751 23 , Uppsala , Sweden
| | - Jyoti Chattopadhyaya
- a Department of Bioorganic Chemistry , University of Uppsala , Box 581, Biomedical Centre, S-751 23 , Uppsala , Sweden
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27
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Luyten I, Matulic-Adamic J, Beigelman L, Chattopadhyaya J. The Electronic Nature of the Aglycone dictates the Drive of the Pseudorotational Equilibrium of the Pentofuranose Moiety in C-Nucleosides. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328319808004692] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Ingrid Luyten
- a Department of Bioorganic Chemistry , University of Uppsala , Box 581, Biomedical Centre, S-751 23 , Uppsala , Sweden
| | - Jasenka Matulic-Adamic
- b Ribozyme Pharmaceuticals Inc , 2950 Wilderness Place, Boulder , Colorado , 80301 , U.S.A
| | - Leo Beigelman
- b Ribozyme Pharmaceuticals Inc , 2950 Wilderness Place, Boulder , Colorado , 80301 , U.S.A
| | - Jyoti Chattopadhyaya
- a Department of Bioorganic Chemistry , University of Uppsala , Box 581, Biomedical Centre, S-751 23 , Uppsala , Sweden
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28
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Thibaudeau C, Chattopadhyaya J. The Discovery of Intramolecular Stereoelectronic Forces That Drive The Sugar Conformation in Nucleosides and Nucleotides. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328319708002912] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- C. Thibaudeau
- a Department of Bioorganic Chemistry , Box 581 Biomedical Center, Uppsala University , Uppsala , S-751 23 , Sweden
| | - J. Chattopadhyaya
- a Department of Bioorganic Chemistry , Box 581 Biomedical Center, Uppsala University , Uppsala , S-751 23 , Sweden
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Gogoi K, Gunjal AD, Kumar VA. Sugar-thioacetamide backbone in oligodeoxyribonucleosides for specific recognition of nucleic acids. Chem Commun (Camb) 2006:2373-5. [PMID: 16733584 DOI: 10.1039/b603958h] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The amide linkage being shorter than the natural phosphate linkage, an additional atom is introduced into oligodeoxyribonucleosides (ODNs) with sugar-thioacetamide backbone that show very good RNA recognition properties.
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Affiliation(s)
- Khirud Gogoi
- Division of Organic Chemistry (Synthesis), National Chemical Laboratory, Pune, 411008, India
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30
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Gautier A. Phosphate Mimic of Nucleotides, Conformational Influences on the Ribofuranose Conformations. HETEROCYCLES 2006. [DOI: 10.3987/rev-05-sr(t)2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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31
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Fressigné C, Piettre S, Condamine E, Altona C, Gautier A. A C3′ modified nucleotide. The difluorophosphonate function, a phosphate mimic, governs the conformational behaviour of the ribofuranose. Tetrahedron 2005. [DOI: 10.1016/j.tet.2005.03.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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32
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Graham SM, Macaya DJ, Sengupta RN, Turner KB. cADPR analogues: effect of an adenosine 2'- or 3'-methoxy group on conformation. Org Lett 2005; 6:233-6. [PMID: 14723536 DOI: 10.1021/ol036152r] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[structure: see text] The 2'-OMe-A (2) and 3'-OMe-A (3) analogues of the calcium release agent cADPR (1) were prepared and their solution structures studied by NMR spectroscopy. Compared to 1, 2 shows a shift in its A ring conformation and changes in its R ring N:S and gammat:gamma+ ratios, while 3 displays a significant change in the conformation of its A ring gamma-bond.
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Affiliation(s)
- Steven M Graham
- Department of Chemistry, St. John's University, Jamaica, New York 11439, USA.
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33
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Second-generation synthesis of protected phosphonothiodifluoromethylene analogues of nucleoside-3′-phosphates. Tetrahedron 2004. [DOI: 10.1016/j.tet.2004.03.082] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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34
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Olejniczak S, Sobczak M, Potrzebowski MJ, Polak M, Plavec J, Nawrot B. Assignment of absolute configuration at phosphorus of P-chiral diastereomers of deoxyribonucleoside methanephosphonamidates by means of NMR spectroscopy. Tetrahedron 2004. [DOI: 10.1016/j.tet.2004.03.035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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35
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Houseknecht JB, Lowary TL. Oligofuranosides containing conformationally restricted residues: synthesis and conformational analysis. J Org Chem 2002; 67:4150-64. [PMID: 12054950 DOI: 10.1021/jo011127p] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The synthesis of a panel of arabinofuranosyl oligosaccharide analogues (5-13) in which one ring is locked into either the E(3) or OE conformation is described. The E(3)-locked scaffolds 15 and 16 required for the synthesis of 5-10 were prepared in one step from known 1,5-anhydroalditols. A number of routes were explored for the preparation of the OE-locked monosaccharide derivative 17 needed for the preparation of 11-13. The successful synthesis of 17 was achieved in 17 steps from D-arabinose. Subsequent analysis of 5-13 by 1H NMR spectroscopy demonstrated that the locked residue does not exert any detectable influence upon the conformers populated by adjacent conformationally unrestricted furanose rings.
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36
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Acharya P, Chattopadhyaya J. The hydrogen bonding and hydration of 2'-OH in adenosine and adenosine 3'-ethyl phosphate. J Org Chem 2002; 67:1852-65. [PMID: 11895403 DOI: 10.1021/jo010960j] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The 2'-OH group has major structural implications in the recognition, processing, and catalytic properties of RNA. We report here intra- and intermolecular H-bonding of 2'-OH in adenosine 3'-ethyl phosphate (1), 3'-deoxyadenosine (2), and adenosine (3) by both temperature- and concentration-dependent NMR studies, as well as by detailed endo ((3)J(H,H)) and exocyclic ((3)J(H,OH)) coupling constant analyses. We have also examined the nature of hydration and exchange processes of 2'-OH with water by a combination of NOESY and ROESY experiments in DMSO-d(6) containing 2 mol % HOD. The NMR-constrained molecular modeling (by molecular mechanics as well as by ab initio methods both in the gas and solution phase) has been used to characterize the energy minima among the four alternative dihedrals possible from the solution of the Karplus equation for (3)J(H2',OH) and (3)J(H3',OH) to delineate the preferred orientation of 2'-O-H proton in 1 and 2 as well as for 2'/3'-O-H protons in 3. The NMR line shape analysis of 2'-OH gave the DeltaG(H-bond)(298K) of 7.5 kJ mol(-1) for 1 and 8.4 kJ mol(-1) for 3; similar analyses of the methylene protons of 3'-ethyl phosphate moiety in 1 also gave comparable DeltaG(H-bond)(298K) of 7.3 kJ mol(-1). The donor nature of the 2'-OH in the intramolecular H-bonding in 3 is evident from its relatively reduced flexibility [-TDeltaS++](2'-OH) = -17.9(+/-0.5) kJ mol(-1)] because of the loss of conformational freedom owing to the intramolecular 2'O-H...O3' H-bonding, compared to the acceptor 3'-OH in 3 [-TDeltaS++](3'-OH) = -19.8 (+/- 0.6) kJ mol(-1)] at 298 K. The presence of intramolecular 2'-OH...O3' H-bonding in 3 is also corroborated by the existence of weak long-range (4)J(H2',OH3') in 3 (i.e., W conformation of H2'-C2'-C3'-O3'-H) as well as by (3)J(H,OH) dependent orientation of the 2'- and 3'-OH groups. The ROESY spectra for 1 and 3 at 308 K, in DMSO-d(6), show a clear positive ROE contact of both 2'- and 3'-OH with water. The presence of a hydrophilic 3'-phosphate group in 1 causes a much higher water activity in the vicinity of its 2'-OH, which in turn causes the 2'-OH to exchange faster, culminating in a shorter exchange lifetime (tau) for 2'-OH proton with HOD in 1 (tau2'-OH: 489 ms) compared to that in 3 (tau2'-OH: 6897 ms). The activation energy (E(a)) of the exchange with the bound-water for 2'- and 3'-OH in 3 (48.3 and 45.0 kJ mol(-1), respectively) is higher compared to that of 2'-OH in 1 (31.9 kJ mol(-1)), thereby showing that the kinetic availability of hydrated 2'-OH in 1 for any inter- and intramolecular interactions, in general, is owing to the vicinal 3'-phosphate residue. It also suggests that 2'-OH in native RNA can mediate other inter- or intramolecular interactions only in competition with the bound-water, depending upon the specific chemical nature and spatial orientation of other functions with potential for hydrogen bonding in the neighborhood. This availability of the bound water around 2'-OH in RNA would, however, be dictated by whether the vicinal phosphate is exposed to the bulk water or not. This implies that relatively poor hydration around a specific 2'-OH across a polyribonucleotide chain, owing to some hydrophobic microenvironmental pocket around that hydroxyl, may make it more accessible to interact with other donor or acceptor functions for H-bonding interactions, which might then cause the RNA to fold in a specific manner generating a new motif leading to specific recognition and function. Alternatively, a differential hydration of a specific 2'-OH may modulate its nucleophilicity to undergo stereospecific transesterification reaction as encountered in ubiquitous splicing of pre-mRNA to processed RNA or RNA catalysis, in general.
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Affiliation(s)
- Parag Acharya
- Department of Bioorganic Chemistry, Box 581, Biomedical Centre, University of Uppsala, S-751 23 Uppsala, Sweden
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37
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Callam CS, Lowary TL. Synthesis and conformational investigation of methyl 4a-carba-D-arabinofuranosides. J Org Chem 2001; 66:8961-72. [PMID: 11749629 DOI: 10.1021/jo010827r] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The synthesis of carbasugar analogues of methyl alpha-D-arabinofuranoside and methyl beta-D-arabinofuranoside (3 and 4) is reported. The route developed involves the conversion of D-mannose into a suitably protected diene (13), which is then cyclized via olefin metathesis. The resulting cyclopentene (14) is stereoselectively hydrogenated to provide an intermediate that can be used for the synthesis of both targets. Through the use of NMR spectroscopy, we have probed the ring conformation of 3 and 4, as well as the rotamer populations about the C(4)-C(5) and C(1)-O(1) bonds. These studies have demonstrated that there are differences in ring conformation between these carbasugars and their glycoside parents (1 and 2). However, only minor differences are seen in the rotameric equilibrium about the C(4)-C(5) bond in 3 and 4 relative to 1 and 2. In regard to the C(1)-O(1) bond, NOE data from 3 and 4 suggest that the favored position about this bond is similar to that in the glycosides; that is, the methyl group is anti to C(2). However, confirmation of this preference through measurement of (3)J(C,C) between the methyl group and C(2) or C(4a) was not successful.
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Affiliation(s)
- C S Callam
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA
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38
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Improta R, Benzi C, Barone V. Understanding the role of stereoelectronic effects in determining collagen stability. 1. A quantum mechanical study of proline, hydroxyproline, and fluoroproline dipeptide analogues in aqueous solution. J Am Chem Soc 2001; 123:12568-77. [PMID: 11741421 DOI: 10.1021/ja010599i] [Citation(s) in RCA: 120] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The importance of local (intraresidue) effects in determining the stability of the collagen triple helix has been investigated with special reference to the role played by hydroxyproline. To this end the dipeptide analogues of L-proline (ProDA), 4(R)-hydroxy-L-proline (HypDA), and 4(R)-fluoro-L-proline (FlpDA) have been studied by means of quantum mechanical ab initio calculations, taking into account solvent effects by the polarizable continuum model (PCM). Our results confirm that the relative stability of up puckerings of the pyrrolidine ring increases with the electronegativity of the 4(R) substituent (X), whereas down puckerings are favored by 4(S) electronegative substituents. Calculations on model compounds show that this effect is due to the interaction between vicinal C-H bonding and C-X antibonding orbitals. Electronegative substituents on the pyrrolidine ring affect cis-trans isomerism around the peptidic bond, with trans isomers stabilized by 4(R) substituents and cis isomers by 4(S) substituents. Also the hydrogen bonding power of the carbonyl moiety following the pyrrolidine ring is affected by 4(R) substituents, but this effect is tuned by the polarity of the embedding medium. Finally, up puckering favors smaller values of the backbone dihedrals phi and psi. All these results strongly support the proposal that the stability of triple helices containing fluorinated or hydroxylated prolines in Y positions is related to the necessity of having up puckerings in those positions.
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Affiliation(s)
- R Improta
- Dipartimento di Chimica, Università Federico II, Complesso Universitario Monte S. Angelo, Via Cintia, I-80126 Napoli, Italy
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39
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Li ZH, Fan KN, Wong MW. Stereochemistry of Radical Halogenation Reactions. An ab Initio Molecular Orbital Study. J Phys Chem A 2001. [DOI: 10.1021/jp0117056] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zhen-Hua Li
- Department of Chemistry, National University of Singapore, Kent Ridge Crescent, Singapore 119260, and Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Kang-Nian Fan
- Department of Chemistry, National University of Singapore, Kent Ridge Crescent, Singapore 119260, and Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Ming Wah Wong
- Department of Chemistry, National University of Singapore, Kent Ridge Crescent, Singapore 119260, and Department of Chemistry, Fudan University, Shanghai 200433, China
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40
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Jiménez-Barbero J, Demange R, Schenk K, Vogel P. Synthesis and solution conformational analysis of 2,3-anhydro-3-C-[(1R)-2,6-anhydro-1-deoxy-1-fluoro-D-glycero-D-gulo-heptitol-1-C-yl]-beta-D-gulo-furanose: first example of a monofluoromethylene-linked C-disaccharide. J Org Chem 2001; 66:5132-8. [PMID: 11463266 DOI: 10.1021/jo0102462] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Condensation of 2,3,4,6-tetra-O-benzyl-beta-D-glucopyranosylcarbaldehyde with isolevoglucosenone induced by Et(2)AlI, followed by epoxidation, gave an aldol that was fluorinated into a monofluoromethylene C-glucopyranoside that was converted into the title C-disaccharide 1. Its conformational behavior in water has been studied by using a combination of NMR spectroscopy (J and NOE data) and molecular mechanics calculations.
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Affiliation(s)
- J Jiménez-Barbero
- Section de Chimie, Université de Lausanne, BCH, CH-1015 Lausanne-Dorigny, Switzerland
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41
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Acharya P, Thibaudeau C, Chattopadhyaya J. An energetic correlation of ab initio and NMR studies of the 3'-gauche effect in 3'-substituted thymidines. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2001; 20:1229-33. [PMID: 11562991 DOI: 10.1081/ncn-100002524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
A straightforward correlation of our experimental NMR findings on 3'-substituted thymidine derivatives with that of the ab initio calculations shows that (i) the delta Go298kNRM of N reversible S equilibrium in nucleoside can be predicted from the ab initio calculated delta ES-N obtained from 6-311++G** level of theory; (ii) the substituent-dependent steric and stereoelectronic effects on the bias of the two-state N reversible S equilibrium in nucleosides can also be predicted from the ab initio calculations with sufficiently large basis functions, and (iii) the necessity of mimicking the solvation behaviour of the experimental NMR measurement condition in the ab initio calculations of biomolecules is also emphasized.
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Affiliation(s)
- P Acharya
- Department of Bioorganic Chemistry, Box 581, Biomedical Centre, University of Uppsala, S-751 23 Uppsala, Sweden
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42
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Belostotskii AM, Keren-Yeshuah H, Lexner J, Hassner A. New 3'-deoxythymidines bearing a nucleophilic 3'-substituent. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2001; 20:93-101. [PMID: 11303565 DOI: 10.1081/ncn-100001439] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
New potential cancer-driven as well as HIV-driven nucleoside heteroanalogs, such as 3'-thio- and 3'- as well as 5'-selenosubstituted thymidines, have been synthesized. We also report an effective method for the preparation of novel nucleoside derivatives, bis(deoxynucleoside) diselenides, in nearly quantitative yields. The North conformation is significantly populated in the conformational equilibrium for 3'-alpha-alkylthiothymidines.
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43
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Cramer H, Pfleiderer W. Nucleotides LXIV[1]: synthesis hydridization and enzymatic degradation studies of 2'-O-methyloligoribonucleotides and 2'-O-methyl/deoxy gapmers. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2000; 19:1765-77. [PMID: 11200271 DOI: 10.1080/15257770008045458] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
2'-O-Methyloligoribonucleotides, deoxyoligonucleotides and 2'-O-methyl/deoxy gapmers were synthesized using solid phase phosphoramidite chemistry employing the 2-(4-nitrophenyl)ethyl (npe) protection strategy. Melting temperatures of the synthesized oligonucleotides as well as their stability against degradation by several different nucleases were determined. 2'-O-Methyloligoribonucleotides showed the highest melting temperatures (Tm's) whereas 2'-O-methyl/deoxy gapmers revealed either slightly higher or surprizingly no thermal stabilities compared with their deoxy analogs when using self-complementary sequences. Gapmers with four 2'-O-methyl nucleotides on both ends showed about the same stability as all 2'-O-methyloligoribonucleotides against micrococal nuclease, nuclease S1, and snake venom phosphodiesterase.
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Affiliation(s)
- H Cramer
- Fakultät für Chemie, Universität Konstanz, Germany
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44
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D'Souza FW, Ayers JD, McCarren PR, Lowary TL. Arabinofuranosyl Oligosaccharides from Mycobacteria: Synthesis and Effect of Glycosylation on Ring Conformation and Hydroxymethyl Group Rotamer Populations. J Am Chem Soc 2000. [DOI: 10.1021/ja993543l] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Francis W. D'Souza
- Contribution from the Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210
| | - Joseph D. Ayers
- Contribution from the Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210
| | - Patrick R. McCarren
- Contribution from the Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210
| | - Todd L. Lowary
- Contribution from the Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210
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45
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Velikian I, Acharya P, Trifonova A, F�ldesi A, Chattopadhyaya J. The RNA molecular wire: the pH-dependent change of the electronic character of adenin-9-yl is transmitted to drive the sugar and phosphate torsions in adenosine 3?, 5?-bisphosphate. J PHYS ORG CHEM 2000. [DOI: 10.1002/1099-1395(200005)13:5<300::aid-poc245>3.0.co;2-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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46
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Acharya P, Trifonova A, Thibaudeau C, Földesi A, Chattopadhyaya J. Die Übertragung des elektronischen Charakters von Guanin-9-yl bewirkt die Torsionen des Zucker-Phosphat-Rückgrats in Guanosin-3′,5′-bisphosphat. Angew Chem Int Ed Engl 1999. [DOI: 10.1002/(sici)1521-3757(19991216)111:24<3861::aid-ange3861>3.0.co;2-k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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47
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Thibaudeau C, Nishizono N, Sumita Y, Matsuda A, Chattopadhyaya J. Determination of the Group Electronegativity of CF3Group in 3′-O-CF3-Thymidine by1-NMR. ACTA ACUST UNITED AC 1999. [DOI: 10.1080/15257779908041642] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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48
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Belostotskii AM, Lexner J, Hassner A. New nucleoside heteroanalogues: Desoxynucleoside selenocyanates. Tetrahedron Lett 1999. [DOI: 10.1016/s0040-4039(98)02559-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Thibaudeau C, Kumar A, Bekiroglu S, Matsuda A, Marquez VE, Chattopadhyaya J. NMR Conformation of (−)-β-d-Aristeromycin and Its 2‘-Deoxy and 3‘-Deoxy Counterparts in Aqueous Solution. J Org Chem 1998. [DOI: 10.1021/jo980364y] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- C. Thibaudeau
- Department of Bioorganic Chemistry, Box 581, Biomedical Center, University of Uppsala, S-751 23 Uppsala, Sweden, Laboratory of Medicinal Chemistry, DPT, DCT, National Cancer Institute, NIH, Bethesda, Maryland 20892, and Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060, Japan
| | - A. Kumar
- Department of Bioorganic Chemistry, Box 581, Biomedical Center, University of Uppsala, S-751 23 Uppsala, Sweden, Laboratory of Medicinal Chemistry, DPT, DCT, National Cancer Institute, NIH, Bethesda, Maryland 20892, and Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060, Japan
| | - S. Bekiroglu
- Department of Bioorganic Chemistry, Box 581, Biomedical Center, University of Uppsala, S-751 23 Uppsala, Sweden, Laboratory of Medicinal Chemistry, DPT, DCT, National Cancer Institute, NIH, Bethesda, Maryland 20892, and Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060, Japan
| | - A. Matsuda
- Department of Bioorganic Chemistry, Box 581, Biomedical Center, University of Uppsala, S-751 23 Uppsala, Sweden, Laboratory of Medicinal Chemistry, DPT, DCT, National Cancer Institute, NIH, Bethesda, Maryland 20892, and Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060, Japan
| | - V. E. Marquez
- Department of Bioorganic Chemistry, Box 581, Biomedical Center, University of Uppsala, S-751 23 Uppsala, Sweden, Laboratory of Medicinal Chemistry, DPT, DCT, National Cancer Institute, NIH, Bethesda, Maryland 20892, and Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060, Japan
| | - J. Chattopadhyaya
- Department of Bioorganic Chemistry, Box 581, Biomedical Center, University of Uppsala, S-751 23 Uppsala, Sweden, Laboratory of Medicinal Chemistry, DPT, DCT, National Cancer Institute, NIH, Bethesda, Maryland 20892, and Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060, Japan
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Thibaudeau C, Plavec J, Chattopadhyaya J. A New Generalized Karplus-Type Equation Relating Vicinal Proton-Fluorine Coupling Constants to H−C−C−F Torsion Angles. J Org Chem 1998. [DOI: 10.1021/jo980144k] [Citation(s) in RCA: 118] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christophe Thibaudeau
- Department of Bioorganic Chemistry, Box 581, Biomedical Center, University of Uppsala, S-751 23 Uppsala, Sweden, and National Institute of Chemistry, Hajdrihova 19, SI-1115 Ljubljana, Slovenia
| | - Janez Plavec
- Department of Bioorganic Chemistry, Box 581, Biomedical Center, University of Uppsala, S-751 23 Uppsala, Sweden, and National Institute of Chemistry, Hajdrihova 19, SI-1115 Ljubljana, Slovenia
| | - Jyoti Chattopadhyaya
- Department of Bioorganic Chemistry, Box 581, Biomedical Center, University of Uppsala, S-751 23 Uppsala, Sweden, and National Institute of Chemistry, Hajdrihova 19, SI-1115 Ljubljana, Slovenia
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