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Pallan PS, Lybrand TP, Rozners E, Abramov M, Schepers G, Eremeeva E, Herdewijn P, Egli M. Conformational Morphing by a DNA Analogue Featuring 7-Deazapurines and 5-Halogenpyrimidines and the Origins of Adenine-Tract Geometry. Biochemistry 2023; 62:2854-2867. [PMID: 37694722 PMCID: PMC11062489 DOI: 10.1021/acs.biochem.3c00327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Several efforts are currently directed at the creation and cellular implementation of alternative genetic systems composed of pairing components that are orthogonal to the natural dA/dT and dG/dC base pairs. In an alternative approach, Watson-Crick-type pairing is conserved, but one or all of the four letters of the A, C, G, and T alphabet are substituted by modified components. Thus, all four nucleobases were altered to create halogenated deazanucleic acid (DZA): dA was replaced by 7-deaza-2'-deoxyadenosine (dzA), dG by 7-deaza-2'-deoxyguanosine (dzG), dC by 5-fluoro-2'-deoxycytidine (FdC), and dT by 5-chloro-2'-deoxyuridine (CldU). This base-pairing system was previously shown to retain function in Escherichia coli. Here, we analyze the stability, hydration, structure, and dynamics of a DZA Dickerson-Drew Dodecamer (DDD) of sequence 5'-FdC-dzG-FdC-dzG-dzA-dzA-CldU-CldU-FdC-dzG-FdC-dzG-3'. Contrary to similar stabilities of DDD and DZA-DDD, osmotic stressing revealed a dramatic loss of hydration for the DZA-DDD relative to that for the DDD. The parent DDD 5'-d(CGCGAATTCGCG)-3' features an A-tract, a run of adenosines uninterrupted by a TpA step, and exhibits a hallmark narrow minor groove. Crystal structures─in the presence of RNase H─and MD simulations show increased conformational plasticity ("morphing") of DZA-DDD relative to that of the DDD. The narrow dzA-tract minor groove in one structure widens to resemble that in canonical B-DNA in a second structure. These changes reflect an indirect consequence of altered DZA major groove electrostatics (less negatively polarized compared to that in DNA) and hydration (reduced compared to that in DNA). Therefore, chemical modifications outside the minor groove that lead to collapse of major groove electrostatics and hydration can modulate A-tract geometry.
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Affiliation(s)
- Pradeep S Pallan
- School of Medicine, Department of Biochemistry, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Terry P Lybrand
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, Binghamton, New York 13902, United States
| | - Mikhail Abramov
- Laboratory of Medicinal Chemistry, KU Leuven, Rega Institute for Medical Research, Minderbroedersstraat 10, Leuven 3000, Belgium
| | - Guy Schepers
- Laboratory of Medicinal Chemistry, KU Leuven, Rega Institute for Medical Research, Minderbroedersstraat 10, Leuven 3000, Belgium
| | - Elena Eremeeva
- Laboratory of Medicinal Chemistry, KU Leuven, Rega Institute for Medical Research, Minderbroedersstraat 10, Leuven 3000, Belgium
| | - Piet Herdewijn
- Laboratory of Medicinal Chemistry, KU Leuven, Rega Institute for Medical Research, Minderbroedersstraat 10, Leuven 3000, Belgium
| | - Martin Egli
- School of Medicine, Department of Biochemistry, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
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Mattelaer HP, Van Hool AS, de Jong F, Van der Auweraer M, Van Meervelt L, Dehaen W, Herdewijn P. New metal-free route towards imidazole substituted uridine. European J Org Chem 2020; 2020:4022-4025. [PMID: 32837299 PMCID: PMC7283795 DOI: 10.1002/ejoc.202000563] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Indexed: 01/24/2023]
Abstract
Nucleosides with a bi(hetero)aryl nucleobase have unique potential applications as antiviral drugs and molecular probes. The need for transition metal catalysis to synthetize these nucleosides from pre-functionalized building blocks and the use of nucleobase protection groups results in expensive and tedious syntheses. Herein we report that 5-imidazolyl-uracil can be obtained by scalable Van Leusen imidazole synthesis and regioselectively introduced on ribose to obtain the desired nucleoside in a 5 step synthesis (total yield 55%). The 5-imidazolyl moiety leads to improved fluorescence properties. The only side-product formed was characterized by 2D-NMR and X-ray crystallography and could be suppressed during synthesis in favor of the desired product.
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Affiliation(s)
| | - Anne-Sophie Van Hool
- Katholieke Universiteit Leuven Rega Institute for Medical Research Medicinal Chemistry BELGIUM
| | - Flip de Jong
- Katholieke Universiteit Leuven Chemistry Department BELGIUM
| | | | | | - Wim Dehaen
- Katholieke Universiteit Leuven Chemistry Department BELGIUM
| | - Piet Herdewijn
- Rega Institute for Medical Research Medicinal Chemistry Herestraat 49 - box 1030 3000 Leuven BELGIUM
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Savitha B, Reddy EK, Kumar CA, Karuvalam RP, Padusha MSA, Bakulev VA, Narasimhamurthy KH, Sajith AM, Joy MN. A modified approach for the site-selective direct C-6 arylation of benzylated uracil. Tetrahedron Lett 2019. [DOI: 10.1016/j.tetlet.2019.151332] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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4
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Patel B, Zunk DM, Grant DG, Rudrawar S. Solid‐Phase Microwave‐Assisted Ligand‐Free Suzuki‐Miyaura Cross‐Coupling of 5‐Iodouridine. ChemistrySelect 2018. [DOI: 10.1002/slct.201703111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Bhautikkumar Patel
- Menzies Health Institute Queensland Griffith University Gold Coast QLD 4222 Australia
- School of Pharmacy and Pharmacology Griffith University Gold Coast QLD 4222 Australia
- Quality Use of Medicines Network Griffith University Gold Coast QLD 4222 Australia
| | - Dr Matthew Zunk
- Menzies Health Institute Queensland Griffith University Gold Coast QLD 4222 Australia
- School of Pharmacy and Pharmacology Griffith University Gold Coast QLD 4222 Australia
- Quality Use of Medicines Network Griffith University Gold Coast QLD 4222 Australia
| | - Dr Gary Grant
- Menzies Health Institute Queensland Griffith University Gold Coast QLD 4222 Australia
- School of Pharmacy and Pharmacology Griffith University Gold Coast QLD 4222 Australia
- Quality Use of Medicines Network Griffith University Gold Coast QLD 4222 Australia
| | - Santosh Rudrawar
- Menzies Health Institute Queensland Griffith University Gold Coast QLD 4222 Australia
- School of Pharmacy and Pharmacology Griffith University Gold Coast QLD 4222 Australia
- Quality Use of Medicines Network Griffith University Gold Coast QLD 4222 Australia
- School of Chemistry The University of Sydney Sydney NSW 2006 Australia
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5
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Rajapaksha SM, Mlsna TE, Pittman CU. A Regioselective Synthesis of 6-Alkyl- and 6-Aryluracils by Cs 2CO 3- or K 3PO 4-Promoted Dimerization of 3-Alkyl- and 3-Aryl-2-Propynamides. J Org Chem 2017; 82:5678-5688. [PMID: 28488857 DOI: 10.1021/acs.joc.7b00508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A regioselective synthesis of 6-alkyl- and 6-aryluracils was developed by the dimerization of 3-alkyl- and 3-aryl-2-propynamides promoted by either Cs2CO3 or K3PO4. A range of 3-aryl-2-propynamides, with both electron-deficient and electron-rich 3-aryl substituents, were successfully reacted in high yields. Cs+ acts as a soft Lewis acid to polarize the carbon-carbon triple bond, and solid K3PO4 interacts with carbonyl oxygen, promoting intermolecular nucleophilic attack by the only weakly nucleophilic amide nitrogen. Experiments were conducted to support the proposed mechanism.
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Affiliation(s)
- Suranga M Rajapaksha
- Department of Chemistry, Mississippi State University , Mississippi State, Mississippi 39762, United States
| | - Todd E Mlsna
- Department of Chemistry, Mississippi State University , Mississippi State, Mississippi 39762, United States
| | - Charles U Pittman
- Department of Chemistry, Mississippi State University , Mississippi State, Mississippi 39762, United States
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Savitha B, Sajith AM, Reddy EK, Kumar CSA, Padusha MSA. Suzuki-Miyaura cross-coupling reaction in water: facile synthesis of (hetero) aryl uracil bases using potassiumorganotrifluoroborates under microwave irradiation. ChemistrySelect 2016. [DOI: 10.1002/slct.201600943] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Bhaskaran Savitha
- Postgraduate and Research Department of Chemistry, Jamal Mohamed College; Bharathidasan University; Tiruchirappalli, Tamil Nadu 620020 India
| | - Ayyiliath M. Sajith
- Postgraduate and Research Department of Chemistry, Kasaragod Government College; Kannur University; Kasaragod, Kerala 671123 India
| | - Eeda Koti Reddy
- Division of Chemistry, Department of Science and Humanities, Vignan‘s Foundation for Science; Technology and Research University-VFSTRU (Vignan University); Vadlamudi, Guntur 522 213, Andhra pradesh India
| | - C. S. Ananda Kumar
- Visvesvaraya Technological University, CPGS, Muddenahalli−562 101 and Centre for Material Science; University of Mysore; Mysuru - 570 006 India
| | - M. Syed Ali Padusha
- Postgraduate and Research Department of Chemistry, Jamal Mohamed College; Bharathidasan University; Tiruchirappalli, Tamil Nadu 620020 India
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Czekański Ł, Hoffmann SK, Barczyński P, Gąsowska A, Bregier-Jarzębowska R, Zalewska A, Goslar J, Ratajczak-Sitarz M, Katrusiak A. Crystal structure and physical properties of 1-methyl-3-(carboxymethyl)benzimidazolium betaine·CuBr2 in crystal and water solution. NEW J CHEM 2016. [DOI: 10.1039/c6nj03192g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Planar CuO2Br2 complex exists in a triclinic unit cell. Single crystal EPR and MO-theory give electron spin density delocalization parameters.
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Affiliation(s)
- Łukasz Czekański
- Faculty of Chemistry
- Adam Mickiewicz University in Poznań
- 61-614 Poznań
- Poland
| | | | - Piotr Barczyński
- Faculty of Chemistry
- Adam Mickiewicz University in Poznań
- 61-614 Poznań
- Poland
| | - Anna Gąsowska
- Faculty of Chemistry
- Adam Mickiewicz University in Poznań
- 61-614 Poznań
- Poland
| | | | - Alina Zalewska
- Faculty of Chemistry
- Adam Mickiewicz University in Poznań
- 61-614 Poznań
- Poland
| | - Janina Goslar
- Institute of Molecular Physics
- Polish Academy of Sciences
- 60-179 Poznań
- Poland
| | | | - Andrzej Katrusiak
- Faculty of Chemistry
- Adam Mickiewicz University in Poznań
- 61-614 Poznań
- Poland
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8
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Mondal B, Hazra S, Roy B. Pd(II)-catalyzed regioselective direct arylation of uracil via oxidative Heck reaction using arylboronic acids. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2013.12.092] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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9
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Enderlin G, Sartori G, Hervé G, Len C. Synthesis of 6-aryluridines via Suzuki–Miyaura cross-coupling reaction at room temperature under aerobic ligand-free conditions in neat water. Tetrahedron Lett 2013. [DOI: 10.1016/j.tetlet.2013.04.066] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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10
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Cheng C, Shih YC, Chen HT, Chien TC. Regioselective arylation of uracil and 4-pyridone derivatives via copper(I) bromide mediated C–H bond activation. Tetrahedron 2013. [DOI: 10.1016/j.tet.2012.11.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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11
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Shih YC, Chien TC. Practical synthesis of 6-aryluridines via palladium(II) acetate catalyzed Suzuki–Miyaura cross-coupling reaction. Tetrahedron 2011. [DOI: 10.1016/j.tet.2011.03.051] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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12
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Pallan PS, Greene EM, Jicman PA, Pandey RK, Manoharan M, Rozners E, Egli M. Unexpected origins of the enhanced pairing affinity of 2'-fluoro-modified RNA. Nucleic Acids Res 2011; 39:3482-95. [PMID: 21183463 PMCID: PMC3082899 DOI: 10.1093/nar/gkq1270] [Citation(s) in RCA: 135] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Revised: 11/19/2010] [Accepted: 11/22/2010] [Indexed: 12/30/2022] Open
Abstract
Various chemical modifications are currently being evaluated for improving the efficacy of short interfering RNA (siRNA) duplexes as antisense agents for gene silencing in vivo. Among the 2'-ribose modifications assessed to date, 2'deoxy-2'-fluoro-RNA (2'-F-RNA) has unique properties for RNA interference (RNAi) applications. Thus, 2'-F-modified nucleotides are well tolerated in the guide (antisense) and passenger (sense) siRNA strands and the corresponding duplexes lack immunostimulatory effects, enhance nuclease resistance and display improved efficacy in vitro and in vivo compared with unmodified siRNAs. To identify potential origins of the distinct behaviors of RNA and 2'-F-RNA we carried out thermodynamic and X-ray crystallographic analyses of fully and partially 2'-F-modified RNAs. Surprisingly, we found that the increased pairing affinity of 2'-F-RNA relative to RNA is not, as commonly assumed, the result of a favorable entropic contribution ('conformational preorganization'), but instead primarily based on enthalpy. Crystal structures at high resolution and osmotic stress demonstrate that the 2'-F-RNA duplex is less hydrated than the RNA duplex. The enthalpy-driven, higher stability of the former hints at the possibility that the 2'-substituent, in addition to its important function in sculpting RNA conformation, plays an underappreciated role in modulating Watson-Crick base pairing strength and potentially π-π stacking interactions.
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Affiliation(s)
- Pradeep S. Pallan
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA, Department of Chemistry, Binghamton University, State University of New York, Binghamton, NY 13902, USA and Department of Drug Discovery, Alnylam Pharmaceuticals, Inc., 300 Third Street, Cambridge, MA 02142, USA
| | - Emily M. Greene
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA, Department of Chemistry, Binghamton University, State University of New York, Binghamton, NY 13902, USA and Department of Drug Discovery, Alnylam Pharmaceuticals, Inc., 300 Third Street, Cambridge, MA 02142, USA
| | - Paul Andrei Jicman
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA, Department of Chemistry, Binghamton University, State University of New York, Binghamton, NY 13902, USA and Department of Drug Discovery, Alnylam Pharmaceuticals, Inc., 300 Third Street, Cambridge, MA 02142, USA
| | - Rajendra K. Pandey
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA, Department of Chemistry, Binghamton University, State University of New York, Binghamton, NY 13902, USA and Department of Drug Discovery, Alnylam Pharmaceuticals, Inc., 300 Third Street, Cambridge, MA 02142, USA
| | - Muthiah Manoharan
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA, Department of Chemistry, Binghamton University, State University of New York, Binghamton, NY 13902, USA and Department of Drug Discovery, Alnylam Pharmaceuticals, Inc., 300 Third Street, Cambridge, MA 02142, USA
| | - Eriks Rozners
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA, Department of Chemistry, Binghamton University, State University of New York, Binghamton, NY 13902, USA and Department of Drug Discovery, Alnylam Pharmaceuticals, Inc., 300 Third Street, Cambridge, MA 02142, USA
| | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA, Department of Chemistry, Binghamton University, State University of New York, Binghamton, NY 13902, USA and Department of Drug Discovery, Alnylam Pharmaceuticals, Inc., 300 Third Street, Cambridge, MA 02142, USA
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Rozners E. Determination of nucleic acid hydration using osmotic stress. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2010; Chapter 7:Unit 7.14. [PMID: 21154532 PMCID: PMC3073695 DOI: 10.1002/0471142700.nc0714s43] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Water plays an important role in structure and molecular recognition of biopolymers. Understanding hydration of biopolymers is a significant problem in structural chemistry and biology. However, hydration is a dynamic process that is difficult to study. While X-ray crystallography, NMR, and molecular modeling have provided structural detail on nucleic acid hydration and valuable insights into water dynamics, the thermodynamic contribution of water molecules to conformational equilibria and recognition of nucleic acids remains poorly understood. This unit describes a thermodynamic analysis of nucleic acid hydration using osmotic stress. Osmotic stress monitors the depression of melting temperature upon decreasing water activity, and calculates the number of thermodynamically unique water molecules associated with the double helix and released from single strands upon melting. Comparison of the number of water molecules released upon melting of nucleic acids with different sequences and chemical modifications provides insights that complement and enhance information obtained by other methods.
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Affiliation(s)
- Eriks Rozners
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, NY 13902, USA, Tel. 1-607-777-2441, Fax 607-777-4478,
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Hocek M, Fojta M. Cross-coupling reactions of nucleoside triphosphates followed by polymerase incorporation. Construction and applications of base-functionalized nucleic acids. Org Biomol Chem 2008; 6:2233-41. [PMID: 18563253 DOI: 10.1039/b803664k] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Construction of functionalized nucleic acids (DNA or RNA) via polymerase incorporation of modified nucleoside triphosphates is reviewed and selected applications of the modified nucleic acids are highlighted. The classical multistep approach for the synthesis of modified NTPs by triphosphorylation of modified nucleosides is compared to the novel approach consisting of direct aqueous cross-coupling reactions of unprotected halogenated nucleoside triphosphates. The combination of cross-coupling of NTPs with polymerase incorporation gives an efficient and straightforward two-step synthesis of modified nucleic acids. Primer extension using biotinylated templates followed by separation using streptavidine-coated magnetic beads and DNA duplex denaturation is used for preparation of modified single stranded oligonucleotides. Examples of using this approach for electrochemical DNA labelling and bioanalytical applications are given.
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Affiliation(s)
- Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic.
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Li F, Pallan PS, Maier MA, Rajeev KG, Mathieu SL, Kreutz C, Fan Y, Sanghvi J, Micura R, Rozners E, Manoharan M, Egli M. Crystal structure, stability and in vitro RNAi activity of oligoribonucleotides containing the ribo-difluorotoluyl nucleotide: insights into substrate requirements by the human RISC Ago2 enzyme. Nucleic Acids Res 2007; 35:6424-38. [PMID: 17881374 PMCID: PMC2095806 DOI: 10.1093/nar/gkm664] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Short interfering RNA (siRNA) duplexes are currently being evaluated as antisense agents for gene silencing. Chemical modification of siRNAs is widely expected to be required for therapeutic applications in order to improve delivery, biostability and pharmacokinetic properties. Beyond potential improvements in the efficacy of oligoribonucleotides, chemical modification may also provide insight into the mechanism of mRNA downregulation mediated by the RNA–protein effector complexes (RNA-induced silencing complex or RISC). We have studied the in vitro activity in HeLa cells of siRNA duplexes against firefly luciferase with substitutions in the guide strand of U for the apolar ribo-2,4-difluorotoluyl nucleotide (rF) [Xia, J. et al. (2006) ACS Chem. Biol., 1, 176–183] as well as of C for rF. Whereas an internal rF:A pair adjacent to the Ago2 (‘slicer’ enzyme) cleavage site did not affect silencing relative to the native siRNA duplex, the rF:G pair and other mismatches such as A:G or A:A were not tolerated. The crystal structure at atomic resolution determined for an RNA dodecamer duplex with rF opposite G manifests only minor deviations between the geometries of rF:G and the native U:G wobble pair. This is in contrast to the previously found, significant deviations between the geometries of rF:A and U:A pairs. Comparison between the structures of the RNA duplex containing rF:G and a new structure of an RNA with A:G mismatches with the structures of standard Watson–Crick pairs in canonical duplex RNA leads to the conclusion that local widening of the duplex formed by the siRNA guide strand and the targeted region of mRNA is the most likely reason for the intolerance of human Ago2 (hAgo2), the RISC endonuclease, toward internal mismatch pairs involving native or chemically modified RNA. Contrary to the influence of shape, the thermodynamic stabilities of siRNA duplexes with single rF:A, A:A, G:A or C:A (instead of U:A) or rF:G pairs (instead of C:G) show no obvious correlation with their activities. However, incorporation of three rF:A pairs into an siRNA duplex leads to loss of activity. Our structural and stability data also shed light on the role of organic fluorine as a hydrogen bond acceptor. Accordingly, UV melting (TM) data, osmotic stress measurements, X-ray crystallography at atomic resolution and the results of semi-empirical calculations are all consistent with the existence of weak hydrogen bonds between fluorine and the H-N1(G) amino group in rF:G pairs of the investigated RNA dodecamers.
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Affiliation(s)
- Feng Li
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, Department of Drug Discovery, Alnylam Pharmaceuticals, Inc., 300 Third Street, Cambridge, MA 02142, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Institute of Organic Chemistry, Center for Molecular Biosciences (CMBI), Leopold-Franzens University, 6020 Innsbruck, Austria
| | - Pradeep S. Pallan
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, Department of Drug Discovery, Alnylam Pharmaceuticals, Inc., 300 Third Street, Cambridge, MA 02142, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Institute of Organic Chemistry, Center for Molecular Biosciences (CMBI), Leopold-Franzens University, 6020 Innsbruck, Austria
| | - Martin A. Maier
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, Department of Drug Discovery, Alnylam Pharmaceuticals, Inc., 300 Third Street, Cambridge, MA 02142, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Institute of Organic Chemistry, Center for Molecular Biosciences (CMBI), Leopold-Franzens University, 6020 Innsbruck, Austria
| | - Kallanthottathil G. Rajeev
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, Department of Drug Discovery, Alnylam Pharmaceuticals, Inc., 300 Third Street, Cambridge, MA 02142, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Institute of Organic Chemistry, Center for Molecular Biosciences (CMBI), Leopold-Franzens University, 6020 Innsbruck, Austria
| | - Steven L. Mathieu
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, Department of Drug Discovery, Alnylam Pharmaceuticals, Inc., 300 Third Street, Cambridge, MA 02142, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Institute of Organic Chemistry, Center for Molecular Biosciences (CMBI), Leopold-Franzens University, 6020 Innsbruck, Austria
| | - Christoph Kreutz
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, Department of Drug Discovery, Alnylam Pharmaceuticals, Inc., 300 Third Street, Cambridge, MA 02142, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Institute of Organic Chemistry, Center for Molecular Biosciences (CMBI), Leopold-Franzens University, 6020 Innsbruck, Austria
| | - Yupeng Fan
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, Department of Drug Discovery, Alnylam Pharmaceuticals, Inc., 300 Third Street, Cambridge, MA 02142, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Institute of Organic Chemistry, Center for Molecular Biosciences (CMBI), Leopold-Franzens University, 6020 Innsbruck, Austria
| | - Jayodita Sanghvi
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, Department of Drug Discovery, Alnylam Pharmaceuticals, Inc., 300 Third Street, Cambridge, MA 02142, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Institute of Organic Chemistry, Center for Molecular Biosciences (CMBI), Leopold-Franzens University, 6020 Innsbruck, Austria
| | - Ronald Micura
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, Department of Drug Discovery, Alnylam Pharmaceuticals, Inc., 300 Third Street, Cambridge, MA 02142, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Institute of Organic Chemistry, Center for Molecular Biosciences (CMBI), Leopold-Franzens University, 6020 Innsbruck, Austria
| | - Eriks Rozners
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, Department of Drug Discovery, Alnylam Pharmaceuticals, Inc., 300 Third Street, Cambridge, MA 02142, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Institute of Organic Chemistry, Center for Molecular Biosciences (CMBI), Leopold-Franzens University, 6020 Innsbruck, Austria
| | - Muthiah Manoharan
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, Department of Drug Discovery, Alnylam Pharmaceuticals, Inc., 300 Third Street, Cambridge, MA 02142, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Institute of Organic Chemistry, Center for Molecular Biosciences (CMBI), Leopold-Franzens University, 6020 Innsbruck, Austria
| | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, Department of Drug Discovery, Alnylam Pharmaceuticals, Inc., 300 Third Street, Cambridge, MA 02142, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Institute of Organic Chemistry, Center for Molecular Biosciences (CMBI), Leopold-Franzens University, 6020 Innsbruck, Austria
- *To whom correspondence should be addressed. +1 615 343 8070+1 615 322 7122
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