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Debiais M, Gimenez Molina A, Müller S, Vasseur JJ, Barvik I, Baraguey C, Smietana M. Design and NMR characterization of reversible head-to-tail boronate-linked macrocyclic nucleic acids. Org Biomol Chem 2022; 20:2889-2895. [PMID: 35319560 DOI: 10.1039/d2ob00232a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Inspired by the ability of boronic acids to bind with compounds containing diol moieties, we envisioned the formation in solution of boronate ester-based macrocycles by the head-to-tail assembly of a nucleosidic precursor that contains both a boronic acid and the natural 2',3'-diol of ribose. DOSY NMR spectroscopy experiments in water and anhydrous DMF revealed the dynamic assembly of this precursor into dimeric and trimeric macrocycles in a concentration-dependent fashion as well as the reversibility of the self-assembly process. NMR experimental values and quantum mechanics calculations provided further insight into the sugar pucker conformation profile of these macrocycles.
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Affiliation(s)
- Mégane Debiais
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, 1919 route de Mende, 34095 Montpellier, France.
| | - Alejandro Gimenez Molina
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, 1919 route de Mende, 34095 Montpellier, France.
| | - Sabine Müller
- University Greifswald, Institute for Biochemistry, Greifswald, Germany
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, 1919 route de Mende, 34095 Montpellier, France.
| | - Ivan Barvik
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, Prague 2, 121 16, Czech Republic
| | - Carine Baraguey
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, 1919 route de Mende, 34095 Montpellier, France.
| | - Michael Smietana
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, 1919 route de Mende, 34095 Montpellier, France.
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2
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Jacobson KA, Salmaso V, Suresh RR, Tosh DK. Expanding the repertoire of methanocarba nucleosides from purinergic signaling to diverse targets. RSC Med Chem 2021; 12:1808-1825. [PMID: 34825182 PMCID: PMC8597424 DOI: 10.1039/d1md00167a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/01/2021] [Indexed: 12/11/2022] Open
Abstract
Nucleoside derivatives are well represented as pharmaceuticals due to their druglike physicochemical properties, and some nucleoside drugs are designed to act on receptors. The purinergic signaling pathways for extracellular nucleosides and nucleotides, consisting of adenosine receptors, P2Y/P2X receptors for nucleotides, and enzymes such as adenosine (ribo)kinase, have been extensively studied. A general modification, i.e. a constrained, bicyclic ring system (bicyclo[3.1.0]hexane, also called methanocarba) substituted in place of a furanose ring, can increase nucleoside/nucleotide potency and/or selectivity at purinergic and antiviral targets and in interactions at diverse and unconventional targets. Compared to other common drug discovery scaffolds containing planar rings, methanocarba nucleosides display greater sp3 character (i.e. more favorable as drug-like molecules) and can manifest as sterically-constrained North (N) or South (S) conformations. Initially weak, off-target interactions of (N)-methanocarba adenosine derivatives were detected as leads that were structurally optimized to enhance activity and selectivity toward target proteins that normally do not recognize nucleosides. By this approach, novel modulators for 5HT2 serotonin and κ-opioid receptors, dopamine (DAT) and ATP-binding cassette (ABC) transporters were found, and previously undetected antiviral activities were revealed. Thus, through methanocarba nucleoside synthesis, structure-activity relationships, and multi-target pharmacology, a robust purinergic receptor scaffold has been repurposed to satisfy the pharmacophoric requirements of various GPCRs, enzymes and transporters.
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Affiliation(s)
- Kenneth A Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health Bethesda MD 20892-0810 USA +301 480 8422 +301 496 9024
| | - Veronica Salmaso
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health Bethesda MD 20892-0810 USA +301 480 8422 +301 496 9024
| | - R Rama Suresh
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health Bethesda MD 20892-0810 USA +301 480 8422 +301 496 9024
| | - Dilip K Tosh
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health Bethesda MD 20892-0810 USA +301 480 8422 +301 496 9024
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3
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Akabane-Nakata M, Erande ND, Kumar P, Degaonkar R, Gilbert JA, Qin J, Mendez M, Woods LB, Jiang Y, Janas M, O’Flaherty DK, Zlatev I, Schlegel M, Matsuda S, Egli M, Manoharan M. siRNAs containing 2'-fluorinated Northern-methanocarbacyclic (2'-F-NMC) nucleotides: in vitro and in vivo RNAi activity and inability of mitochondrial polymerases to incorporate 2'-F-NMC NTPs. Nucleic Acids Res 2021; 49:2435-2449. [PMID: 33577685 PMCID: PMC7969009 DOI: 10.1093/nar/gkab050] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 01/13/2021] [Accepted: 02/07/2021] [Indexed: 02/01/2023] Open
Abstract
We recently reported the synthesis of 2'-fluorinated Northern-methanocarbacyclic (2'-F-NMC) nucleotides, which are based on a bicyclo[3.1.0]hexane scaffold. Here, we analyzed RNAi-mediated gene silencing activity in cell culture and demonstrated that a single incorporation of 2'-F-NMC within the guide or passenger strand of the tri-N-acetylgalactosamine-conjugated siRNA targeting mouse Ttr was generally well tolerated. Exceptions were incorporation of 2'-F-NMC into the guide strand at positions 1 and 2, which resulted in a loss of the in vitro activity. Activity at position 1 was recovered when the guide strand was modified with a 5' phosphate, suggesting that the 2'-F-NMC is a poor substrate for 5' kinases. In mice, the 2'-F-NMC-modified siRNAs had comparable RNAi potencies to the parent siRNA. 2'-F-NMC residues in the guide seed region position 7 and at positions 10, 11 and 12 were well tolerated. Surprisingly, when the 5'-phosphate mimic 5'-(E)-vinylphosphonate was attached to the 2'-F-NMC at the position 1 of the guide strand, activity was considerably reduced. The steric constraints of the bicyclic 2'-F-NMC may impair formation of hydrogen-bonding interactions between the vinylphosphonate and the MID domain of Ago2. Molecular modeling studies explain the position- and conformation-dependent RNAi-mediated gene silencing activity of 2'-F-NMC. Finally, the 5'-triphosphate of 2'-F-NMC is not a substrate for mitochondrial RNA and DNA polymerases, indicating that metabolites should not be toxic.
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Affiliation(s)
| | - Namrata D Erande
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
| | - Pawan Kumar
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
| | - Rohan Degaonkar
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
| | - Jason A Gilbert
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
| | - June Qin
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
| | - Martha Mendez
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
| | - Lauren Blair Woods
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
| | - Yongfeng Jiang
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
| | - Maja M Janas
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
| | - Derek K O’Flaherty
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
| | - Ivan Zlatev
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
| | - Mark K Schlegel
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
| | - Shigeo Matsuda
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
| | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | - Muthiah Manoharan
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
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4
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Nikam RR, Harikrishna S, Gore KR. Synthesis, Structural, and Conformational Analysis of 4′‐
C
‐Alkyl‐2′‐
O
‐Ethyl‐Uridine Modified Nucleosides. European J Org Chem 2021. [DOI: 10.1002/ejoc.202001348] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Rahul R. Nikam
- Department of Chemistry University of Mumbai Mumbai 400098 India
| | - S. Harikrishna
- Center for Structural Biology Vanderbilt University Nashville, Tennessee 37232 United States
| | - Kiran R. Gore
- Department of Chemistry University of Mumbai Mumbai 400098 India
- Department of Chemistry Indian Institute of Technology Kharagpur Kharagpur, West Bengal 721302 India
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5
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Akabane-Nakata M, Kumar P, Erande ND, Matsuda S, Manoharan M. Synthesis of 2'-Fluorinated Northern Methanocarbacyclic (2'-F-NMC) Nucleosides and Their Incorporation Into Oligonucleotides. ACTA ACUST UNITED AC 2020; 80:e103. [PMID: 31985895 DOI: 10.1002/cpnc.103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
This article describes chemical synthesis of 2'-fluorinated Northern methanocarbacyclic (2'-F-NMC) nucleosides and phosphoramidites, based on a bicyclo[3.1.0]hexane scaffold bearing all four natural nucleobases (U, C, A, and G), and their incorporation into oligonucleotides by solid-supported synthesis. This synthesis starts from commercially available cyclopent-2-en-1-one to obtain the fluorinated carbocyclic pseudosugar intermediate (S.13), which can be converted to the uridine intermediate by condensation with isocyanate, followed by cyclization, and to adenine and guanine precursors by microwave-assisted reactions. All four 2'-F-NMC phosphoramidites are synthesized from S.13 in a convergent approach, and the monomers are used for synthesis of 2'-F-NMC-modified oligonucleotides. © 2020 by John Wiley & Sons, Inc. Basic Protocol 1: Preparation of fluorinated carbocyclic pseudosugar intermediate Basic Protocol 2: Preparation of 2'-F-NMC uridine and cytidine phosphoramidites Basic Protocol 3: Preparation of 2'-F-NMC adenosine phosphoramidite Basic Protocol 4: Preparation of 2'-F-NMC guanosine phosphoramidite Basic Protocol 5: Synthesis of oligonucleotides containing 2'-F-NMC.
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Affiliation(s)
| | - Pawan Kumar
- Alnylam Pharmaceuticals, Cambridge, Massachusetts
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6
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Akabane-Nakata M, Kumar P, Das RS, Erande ND, Matsuda S, Egli M, Manoharan M. Synthesis and Biophysical Characterization of RNAs Containing 2'-Fluorinated Northern Methanocarbacyclic Nucleotides. Org Lett 2019; 21:1963-1967. [PMID: 30892051 DOI: 10.1021/acs.orglett.8b04153] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
2'-Fluorinated Northern methanocarbacyclic (2'-F-NMC) nucleosides and phosphoramidites, based on a bicyclo[3.1.0]hexane scaffold bearing all four natural nucleobases (U, C, A, and G), were synthesized to enable exploration of this novel nucleotide modification related to the clinically validated 2'-deoxy-2'-fluororibonucleotides (2'-F-RNA). Biophysical properties of the 2'-F-NMC-containing oligonucleotides were evaluated. A duplex of 2'-F-NMC-modified oligonucleotide with RNA exhibited thermal stability similar to that of the parent RNA duplex, 2'-F-NMC-modified oligonucleotides had higher stability against 5'- and 3'-exonucleolytic degradation than the corresponding oligonucleotides modified with 2'-F-RNA, and 2'-F-NMC-modified oligonucleotides exhibited higher lipophilicity than the corresponding RNA oligonucleotides as well as those modified with 2'-F-RNA.
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Affiliation(s)
- Masaaki Akabane-Nakata
- Alnylam Pharmaceuticals , 300 Third Street , Cambridge , Massachusetts 02142 , United States
| | - Pawan Kumar
- Alnylam Pharmaceuticals , 300 Third Street , Cambridge , Massachusetts 02142 , United States
| | - Rajat S Das
- Alnylam Pharmaceuticals , 300 Third Street , Cambridge , Massachusetts 02142 , United States
| | - Namrata D Erande
- Alnylam Pharmaceuticals , 300 Third Street , Cambridge , Massachusetts 02142 , United States
| | - Shigeo Matsuda
- Alnylam Pharmaceuticals , 300 Third Street , Cambridge , Massachusetts 02142 , United States
| | - Martin Egli
- Department of Biochemistry, School of Medicine , Vanderbilt University , Nashville , Tennessee 37232 , United States
| | - Muthiah Manoharan
- Alnylam Pharmaceuticals , 300 Third Street , Cambridge , Massachusetts 02142 , United States
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7
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Hyde AM, Ashley ER. Organometallic Approaches to [3.1.0] Bicycles in Process Chemistry. TOP ORGANOMETAL CHEM 2019. [DOI: 10.1007/3418_2019_30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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8
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White NA, Sumita M, Marquez VE, Hoogstraten CG. Coupling between conformational dynamics and catalytic function at the active site of the lead-dependent ribozyme. RNA (NEW YORK, N.Y.) 2018; 24:1542-1554. [PMID: 30111534 PMCID: PMC6191710 DOI: 10.1261/rna.067579.118] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 08/02/2018] [Indexed: 06/08/2023]
Abstract
In common with other self-cleaving RNAs, the lead-dependent ribozyme (leadzyme) undergoes dynamic fluctuations to a chemically activated conformation. We explored the connection between conformational dynamics and self-cleavage function in the leadzyme using a combination of NMR spin-relaxation analysis of ribose groups and conformational restriction via chemical modification. The functional studies were performed with a North-methanocarbacytidine modification that prevents fluctuations to C2'-endo conformations while maintaining an intact 2'-hydroxyl nucleophile. Spin-relaxation data demonstrate that the active-site Cyt-6 undergoes conformational exchange attributed to sampling of a minor C2'-endo state with an exchange lifetime on the order of microseconds to tens of microseconds. A conformationally restricted species in which the fluctuations to the minor species are interrupted shows a drastic decrease in self-cleavage activity. Taken together, these data indicate that dynamic sampling of a minor species at the active site of this ribozyme, and likely of related naturally occurring motifs, is strongly coupled to catalytic function. The combination of NMR dynamics analysis with functional probing via conformational restriction is a general methodology for dissecting dynamics-function relationships in RNA.
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Affiliation(s)
- Neil A White
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Minako Sumita
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Victor E Marquez
- Chemical Biology Laboratory, Molecular Discovery Program, Center for Cancer Research, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland 21702, USA
| | - Charles G Hoogstraten
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
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9
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Østergaard ME, Nichols J, Dwight TA, Lima W, Jung ME, Swayze EE, Seth PP. Fluorinated Nucleotide Modifications Modulate Allele Selectivity of SNP-Targeting Antisense Oligonucleotides. MOLECULAR THERAPY. NUCLEIC ACIDS 2017. [PMID: 28624195 PMCID: PMC5363678 DOI: 10.1016/j.omtn.2017.02.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Antisense oligonucleotides (ASOs) have the potential to discriminate between subtle RNA mismatches such as SNPs. Certain mismatches, however, allow ASOs to bind at physiological conditions and result in RNA cleavage mediated by RNase H. We showed that replacing DNA nucleotides in the gap region of an ASO with other chemical modification can improve allele selectivity. Herein, we systematically substitute every position in the gap region of an ASO targeting huntingtin gene (HTT) with fluorinated nucleotides. Potency is determined in cell culture against mutant HTT (mtHTT) and wild-type HTT (wtHTT) mRNA and RNase H cleavage intensities, and patterns are investigated. This study profiled five different fluorinated nucleotides and showed them to have predictable, site-specific effects on RNase H cleavage, and the cleavage patterns were rationalized from a published X-ray structure of human RNase H1. The results herein can be used as a guide for future projects where ASO discrimination of SNPs is important.
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Affiliation(s)
| | - Josh Nichols
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Timothy A Dwight
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Walt Lima
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Michael E Jung
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Eric E Swayze
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Punit P Seth
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
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10
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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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11
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Rohner M, Medina-Molner A, Spingler B. N,N,O and N,O,N Meridional cis Coordination of Two Guanines to Copper(II) by d(CGCGCG)2. Inorg Chem 2016; 55:6130-40. [DOI: 10.1021/acs.inorgchem.6b00672] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Melanie Rohner
- University of Zurich, Department of Chemistry, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Alfredo Medina-Molner
- University of Zurich, Department of Chemistry, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Bernhard Spingler
- University of Zurich, Department of Chemistry, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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12
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Østergaard ME, Dwight T, Berdeja A, Swayze EE, Jung ME, Seth PP. Comparison of duplex stabilizing properties of 2'-fluorinated nucleic acid analogues with furanose and non-furanose sugar rings. J Org Chem 2014; 79:8877-81. [PMID: 25137618 DOI: 10.1021/jo501381q] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We compare the duplex stabilizing properties of 2'-fluorinated nucleic acid analogues with furanose and non-furanose ring systems and dissect the relative contributions of hydration, sugar conformation, and fluorine configuration toward the overall T(m) value. We find that the stabilization imparted by fluorine substitution is additive over that obtained by restricting the conformation of the sugar ring itself. Our studies support further evaluation of fluorinated nucleic acid analogues with non-furanose sugar rings as surrogates of 2'-F RNA for therapeutic antisense applications.
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Affiliation(s)
- Michael E Østergaard
- Department of Medicinal Chemistry, Isis Pharmaceuticals, Inc. , 2855 Gazelle Court, Carlsbad, California 92010, United States
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13
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Luo Z, Dauter M, Dauter Z. Phosphates in the Z-DNA dodecamer are flexible, but their P-SAD signal is sufficient for structure solution. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:1790-800. [PMID: 25004957 PMCID: PMC4089481 DOI: 10.1107/s1399004714004684] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 02/28/2014] [Indexed: 11/11/2022]
Abstract
A large number of Z-DNA hexamer duplex structures and a few oligomers of different lengths are available, but here the first crystal structure of the d(CGCGCGCGCGCG)2 dodecameric duplex is presented. Two synchrotron data sets were collected; one was used to solve the structure by the single-wavelength anomalous dispersion (SAD) approach based on the anomalous signal of P atoms, the other set, extending to an ultrahigh resolution of 0.75 Å, served to refine the atomic model to an R factor of 12.2% and an R(free) of 13.4%. The structure consists of parallel duplexes arranged into practically infinitely long helices packed in a hexagonal fashion, analogous to all other known structures of Z-DNA oligomers. However, the dodecamer molecule shows a high level of flexibility, especially of the backbone phosphate groups, with six out of 11 phosphates modeled in double orientations corresponding to the two previously observed Z-DNA conformations: Z(I), with the phosphate groups inclined towards the inside of the helix, and Z(II), with the phosphate groups rotated towards the outside of the helix.
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Affiliation(s)
- Zhipu Luo
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Miroslawa Dauter
- Leidos Biomedical Research Inc., Basic Research Program, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Zbigniew Dauter
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA
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14
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Thompson A, Marquez VE. Synthesis of a North-methanocarba-thymidine (N-MCT) analog. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2012; Chapter 1:Unit1.29. [PMID: 23255201 PMCID: PMC7477758 DOI: 10.1002/0471142700.nc0129s51] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
A detailed protocol for the synthesis of North-methanocarba-thymidine (N-MCT), a potent antiviral nucleoside with a restricted bicyclo[3.1.0]hexane pseudosugar conformation, is presented. The process is described in two parts. The first basic protocol deals with the synthesis of the carbobicyclic pseudosugar precursor that can be utilized in the syntheses of other bicyclo[3.1.0]hexane nucleosides with natural and non-natural nucleobases. The second basic protocol describes the specific construction of the thymine base in a linear fashion from the carbobicyclic intermediate.
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15
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Ketkar A, Zafar MK, Banerjee S, Marquez VE, Egli M, Eoff RL. Differential furanose selection in the active sites of archaeal DNA polymerases probed by fixed-conformation nucleotide analogues. Biochemistry 2012; 51:9234-44. [PMID: 23050956 DOI: 10.1021/bi301043k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
DNA polymerases select for the incorporation of deoxyribonucleotide triphosphates (dNTPs) using amino acid side-chains that act as a "steric-gate" to bar improper incorporation of rNTPs. An additional factor in the selection of nucleotide substrates resides in the preferred geometry for the furanose moiety of the incoming nucleotide triphosphate. We have probed the role of sugar geometry during nucleotide selection by model DNA polymerases from Sulfolobus solfataricus using fixed conformation nucleotide analogues. North-methanocarba-dATP (N-MC-dATP) locks the central ring into a RNA-type (C2'-exo, North) conformation near a C3'-endo pucker, and South-methanocarba-dATP (S-MC-dATP) locks the central ring system into a (C3'-exo, South) conformation near a C2'-endo pucker. Dpo4 preferentially inserts N-MC-dATP and in the crystal structure of Dpo4 in complex with N-MC-dAMP, the nucleotide analogue superimposes almost perfectly with Dpo4 bound to unmodified dATP. Biochemical assays indicate that the S. solfataricus B-family DNA polymerase Dpo1 can insert and extend from both N-MC-dATP and S-MC-dATP. In this respect, Dpo1 is unexpectedly more tolerant of substrate conformation than Dpo4. The crystal structure of Dpo4 bound to S-MC-dADP shows that poor incorporation of the Southern pucker by the Y-family polymerase results from a hydrogen bond between the 3'-OH group of the nucleotide analogue and the OH group of the steric gate residue, Tyr12, shifting the S-MC-dADP molecule away from the dNTP binding pocket and distorting the base pair at the primer-template junction. These results provide insights into substrate specificity of DNA polymerases, as well as molecular mechanisms that act as a barrier against insertion of rNTPs.
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Affiliation(s)
- Amit Ketkar
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205-7199, United States
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16
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Aviñó A, Mazzini S, Ferreira R, Gargallo R, Marquez VE, Eritja R. The effect on quadruplex stability of North-nucleoside derivatives in the loops of the thrombin-binding aptamer. Bioorg Med Chem 2012; 20:4186-93. [PMID: 22727781 PMCID: PMC3534854 DOI: 10.1016/j.bmc.2012.06.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Revised: 05/31/2012] [Accepted: 06/02/2012] [Indexed: 11/29/2022]
Abstract
Modified thrombin-binding aptamers (TBAs) carrying uridine (U), 2'-deoxy-2'-fluorouridine (FU) and North-methanocarbathymidine (NT) residues in the loop regions were synthesized and analyzed by UV thermal denaturation experiments and CD spectroscopy. The replacement of thymidines in the TGT loop by U and FU results in an increased stability of the antiparallel quadruplex structure described for the TBA while the presence of NT residues in the same positions destabilizes the antiparallel structure. The substitution of the thymidines in the TT loops for U, FU and NT induce a destabilization of the antiparallel quadruplex, indicating the crucial role of these positions. NMR studies on TBAs modified with uridines at the TGT loop also confirm the presence of the antiparallel quadruplex structure. Nevertheless, replacement of two Ts in the TT loops by uridine gives a more complex scenario in which the antiparallel quadruplex structure is present along with other partially unfolded species or aggregates.
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Affiliation(s)
- Anna Aviñó
- Institute for Research in Biomedicine (IRB Barcelona), Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN) and Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, Baldiri Reixac 10, E-08028 Barcelona. Spain
| | - Stefania Mazzini
- Dipartimento di Scienze Molecolari Agroalimentari, Università degli Studi di Milano, via Celoria 2, 20133 Milano, Italy
| | - Ruben Ferreira
- Institute for Research in Biomedicine (IRB Barcelona), Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN) and Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, Baldiri Reixac 10, E-08028 Barcelona. Spain
| | - Raimundo Gargallo
- Department of Analytical Chemistry, University of Barcelona, Diagonal 647, E-08028 Barcelona, Spain
| | - Victor E. Marquez
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland 21702. USA
| | - Ramon Eritja
- Institute for Research in Biomedicine (IRB Barcelona), Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN) and Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, Baldiri Reixac 10, E-08028 Barcelona. Spain
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Martín-Pintado N, Yahyaee-Anzahaee M, Campos-Olivas R, Noronha AM, Wilds CJ, Damha MJ, González C. The solution structure of double helical arabino nucleic acids (ANA and 2'F-ANA): effect of arabinoses in duplex-hairpin interconversion. Nucleic Acids Res 2012; 40:9329-39. [PMID: 22798499 PMCID: PMC3467067 DOI: 10.1093/nar/gks672] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
We report here the first structure of double helical arabino nucleic acid (ANA), the C2′-stereoisomer of RNA, and the 2′-fluoro-ANA analogue (2′F-ANA). A chimeric dodecamer based on the Dickerson sequence, containing a contiguous central segment of arabino nucleotides, flanked by two 2′-deoxy-2′F-ANA wings was studied. Our data show that this chimeric oligonucleotide can adopt two different structures of comparable thermal stabilities. One structure is a monomeric hairpin in which the stem is formed by base paired 2′F-ANA nucleotides and the loop by unpaired ANA nucleotides. The second structure is a bimolecular duplex, with all the nucleotides (2′F-ANA and ANA) forming Watson–Crick base pairs. The duplex structure is canonical B-form, with all arabinoses adopting a pure C2′-endo conformation. In the ANA:ANA segment, steric interactions involving the 2′-OH substituent provoke slight changes in the glycosidic angles and, therefore, in the ANA:ANA base pair geometry. These distortions are not present in the 2′F-ANA:2′F-ANA regions of the duplex, where the –OH substituent is replaced by a smaller fluorine atom. 2′F-ANA nucleotides adopt the C2′-endo sugar pucker and fit very well into the geometry of B-form duplex, allowing for favourable 2′F···H8 interactions. This interaction shares many features of pseudo-hydrogen bonds previously observed in 2′F-ANA:RNA hybrids and in single 2′F-ANA nucleotides.
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Affiliation(s)
- Nerea Martín-Pintado
- Instituto de Química Física Rocasolano, CSIC, C/Serrano 119, 28006 Madrid, Spain
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