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Novikova D, Sagaidak A, Vorona S, Tribulovich V. A Visual Compendium of Principal Modifications within the Nucleic Acid Sugar Phosphate Backbone. Molecules 2024; 29:3025. [PMID: 38998973 PMCID: PMC11243533 DOI: 10.3390/molecules29133025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 07/14/2024] Open
Abstract
Nucleic acid chemistry is a huge research area that has received new impetus due to the recent explosive success of oligonucleotide therapy. In order for an oligonucleotide to become clinically effective, its monomeric parts are subjected to modifications. Although a large number of redesigned natural nucleic acids have been proposed in recent years, the vast majority of them are combinations of simple modifications proposed over the past 50 years. This review is devoted to the main modifications of the sugar phosphate backbone of natural nucleic acids known to date. Here, we propose a systematization of existing knowledge about modifications of nucleic acid monomers and an acceptable classification from the point of view of chemical logic. The visual representation is intended to inspire researchers to create a new type of modification or an original combination of known modifications that will produce unique oligonucleotides with valuable characteristics.
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Affiliation(s)
- Daria Novikova
- Laboratory of Molecular Pharmacology, St. Petersburg State Institute of Technology, St. Petersburg 190013, Russia
| | - Aleksandra Sagaidak
- Laboratory of Molecular Pharmacology, St. Petersburg State Institute of Technology, St. Petersburg 190013, Russia
| | - Svetlana Vorona
- Laboratory of Molecular Pharmacology, St. Petersburg State Institute of Technology, St. Petersburg 190013, Russia
| | - Vyacheslav Tribulovich
- Laboratory of Molecular Pharmacology, St. Petersburg State Institute of Technology, St. Petersburg 190013, Russia
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2
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Hoogstraten CG, Terrazas M, Aviñó A, White NA, Sumita M. Dynamics-Function Analysis in Catalytic RNA Using NMR Spin Relaxation and Conformationally Restricted Nucleotides. Methods Mol Biol 2021; 2167:183-202. [PMID: 32712921 DOI: 10.1007/978-1-0716-0716-9_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
A full understanding of biomolecular function requires an analysis of both the dynamic properties of the system of interest and the identification of those dynamics that are required for function. We describe NMR methods based on metabolically directed specific isotope labeling for the identification of molecular disorder and/or conformational transitions on the RNA backbone ribose groups. These analyses are complemented by the use of synthetic covalently modified nucleotides constrained to a single sugar pucker, which allow functional assessment of dynamics by selectively removing a minor conformer identified by NMR from the structural ensemble.
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Affiliation(s)
- Charles G Hoogstraten
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA.
| | - Montserrat Terrazas
- Institute for Advanced Chemistry of Catalonia (IQAC), Spanish Council for Scientific Research (CSIC), Barcelona, Spain.,Joint IRB-BSC Program in Computational Biology, The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Anna Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC), Spanish Council for Scientific Research (CSIC), Barcelona, Spain.,Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona, Spain
| | - Neil A White
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA.,Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA
| | - Minako Sumita
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA.,Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, IL, USA
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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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Riccardi C, Napolitano E, Platella C, Musumeci D, Montesarchio D. G-quadruplex-based aptamers targeting human thrombin: Discovery, chemical modifications and antithrombotic effects. Pharmacol Ther 2020; 217:107649. [PMID: 32777331 DOI: 10.1016/j.pharmthera.2020.107649] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 07/29/2020] [Indexed: 02/07/2023]
Abstract
First studies on thrombin-inhibiting DNA aptamers were reported in 1992, and since then a large number of anticoagulant aptamers has been discovered. TBA - also named HD1, a 15-mer G-quadruplex (G4)-forming oligonucleotide - is the best characterized thrombin binding aptamer, able to specifically recognize the protein exosite I, thus inhibiting the conversion of soluble fibrinogen into insoluble fibrin strands. Unmodified nucleic acid-based aptamers, in general, and TBA in particular, exhibit limited pharmacokinetic properties and are rapidly degraded in vivo by nucleases. In order to improve the biological performance of aptamers, a widely investigated strategy is the introduction of chemical modifications in their backbone at the level of the nucleobases, sugar moieties or phosphodiester linkages. Besides TBA, also other thrombin binding aptamers, able to adopt a well-defined G4 structure, e.g. mixed duplex/quadruplex sequences, as well as homo- and hetero-bivalent constructs, have been identified and optimized. Considering the growing need of new efficient anticoagulant agents associated with the strong therapeutic potential of these thrombin inhibitors, the research on thrombin binding aptamers is still a very hot and intriguing field. Herein, we comprehensively described the state-of-the-art knowledge on the DNA-based aptamers targeting thrombin, especially focusing on the optimized analogues obtained by chemically modifying the oligonucleotide backbone, and their biological performances in therapeutic applications.
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Affiliation(s)
- Claudia Riccardi
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; Department of Advanced Medical and Surgical Sciences, 2(nd) Division of Neurology, Center for Rare Diseases and InterUniversity Center for Research in Neurosciences, University of Campania Luigi Vanvitelli, via Sergio Pansini, 5, I-80131 Naples, Italy.
| | - Ettore Napolitano
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy.
| | - Chiara Platella
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy.
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; Institute of Biostructures and Bioimages, CNR, via Mezzocannone 16, I-80134 Naples, Italy.
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy.
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5
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Slanina T, Ayub R, Toldo J, Sundell J, Rabten W, Nicaso M, Alabugin I, Fdez Galván I, Gupta AK, Lindh R, Orthaber A, Lewis RJ, Grönberg G, Bergman J, Ottosson H. Impact of Excited-State Antiaromaticity Relief in a Fundamental Benzene Photoreaction Leading to Substituted Bicyclo[3.1.0]hexenes. J Am Chem Soc 2020; 142:10942-10954. [PMID: 32456426 PMCID: PMC7497645 DOI: 10.1021/jacs.9b13769] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
![]()
Benzene exhibits a rich photochemistry
which can provide access
to complex molecular scaffolds that are difficult to access with reactions
in the electronic ground state. While benzene is aromatic in its ground
state, it is antiaromatic in its lowest ππ* excited
states. Herein, we clarify to what extent relief of excited-state
antiaromaticity (ESAA) triggers a fundamental benzene photoreaction:
the photoinitiated nucleophilic addition of solvent to benzene in
acidic media leading to substituted bicyclo[3.1.0]hex-2-enes. The
reaction scope was probed experimentally, and it was found that silyl-substituted
benzenes provide the most rapid access to bicyclo[3.1.0]hexene derivatives,
formed as single isomers with three stereogenic centers in yields
up to 75% in one step. Two major mechanism hypotheses, both involving
ESAA relief, were explored through quantum chemical calculations and
experiments. The first mechanism involves protonation of excited-state
benzene and subsequent rearrangement to bicyclo[3.1.0]hexenium cation,
trapped by a nucleophile, while the second involves photorearrangement
of benzene to benzvalene followed by protonation and nucleophilic
addition. Our studies reveal that the second mechanism is operative.
We also clarify that similar ESAA relief leads to puckering of S1-state silabenzene and pyridinium ion, where the photorearrangement
of the latter is of established synthetic utility. Finally, we identified
causes for the limitations of the reaction, information that should
be valuable in explorations of similar photoreactions. Taken together,
we reveal how the ESAA in benzene and 6π-electron heterocycles
trigger photochemical distortions that provide access to complex three-dimensional
molecular scaffolds from simple reactants.
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Affiliation(s)
- Tomáš Slanina
- Department of Chemistry - Ångström Laboratory, Uppsala University, SE-751 20, Uppsala, Sweden.,Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo námĕstí 2, 16610 Prague 6, Czech Republic
| | - Rabia Ayub
- Department of Chemistry - Ångström Laboratory, Uppsala University, SE-751 20, Uppsala, Sweden
| | - Josene Toldo
- Department of Chemistry - Ångström Laboratory, Uppsala University, SE-751 20, Uppsala, Sweden
| | - Johan Sundell
- Medicinal Chemistry, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Wangchuk Rabten
- Department of Chemistry - Ångström Laboratory, Uppsala University, SE-751 20, Uppsala, Sweden
| | - Marco Nicaso
- Department of Chemistry - Ångström Laboratory, Uppsala University, SE-751 20, Uppsala, Sweden
| | - Igor Alabugin
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
| | - Ignacio Fdez Galván
- Department of Chemistry - BMC, Uppsala University, SE-751 23 Uppsala, Sweden
| | - Arvind K Gupta
- Department of Chemistry - Ångström Laboratory, Uppsala University, SE-751 20, Uppsala, Sweden
| | - Roland Lindh
- Department of Chemistry - BMC, Uppsala University, SE-751 23 Uppsala, Sweden.,Uppsala Center for Computational Chemistry - UC3, Uppsala University, SE-751 23 Uppsala Sweden
| | - Andreas Orthaber
- Department of Chemistry - Ångström Laboratory, Uppsala University, SE-751 20, Uppsala, Sweden
| | - Richard J Lewis
- Medicinal Chemistry, Research and Early Development Respiratory, Inflammation and Autoimmune, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Gunnar Grönberg
- Medicinal Chemistry, Research and Early Development Respiratory, Inflammation and Autoimmune, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Joakim Bergman
- Medicinal Chemistry, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Henrik Ottosson
- Department of Chemistry - Ångström Laboratory, Uppsala University, SE-751 20, Uppsala, Sweden
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6
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7
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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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8
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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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9
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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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10
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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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11
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12
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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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13
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Pallan PS, Marquez VE, Egli M. The conformationally constrained N-methanocarba-dT analogue adopts an unexpected C4'-exo sugar pucker in the structure of a DNA hairpin. Biochemistry 2012; 51:2639-41. [PMID: 22409313 DOI: 10.1021/bi300215k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Incorporation of a bicyclo[3.1.0]hexane scaffold into the nucleoside sugar was devised to lock the embedded cyclopentane ring in conformations that mimic the furanose North and South sugar puckers. To analyze the effects of North-methanocarba-2'-deoxythymidine (N-MCdT) on the B-form DNA, we crystallized d(CGCGAA[mcTmcT]CGCG) with two N-MCdTs. Instead of a duplex, the 12mer forms a tetraloop hairpin, whereby loop N-MCdTs adopt the C4'-exo pucker (NE; P = 50°). Thus, the bicyclic framework does not limit the pucker to the anticipated C2'-exo range (NNW; P = -18°).
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Affiliation(s)
- Pradeep S Pallan
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232, United States
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14
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Terrazas M, Ocampo SM, Perales JC, Marquez VE, Eritja R. Effect of north bicyclo[3.1.0]hexane 2'-deoxy-pseudosugars on RNA interference: a novel class of siRNA modification. Chembiochem 2011; 12:1056-65. [PMID: 21452187 DOI: 10.1002/cbic.201000791] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Indexed: 01/15/2023]
Abstract
North bicyclo methanocarba thymidine (T(N)) nucleosides were substituted into siRNAs to investigate the effect of bicyclo[3.1.0]hexane 2'-deoxy-pseudosugars on RNA interference activity. Here we provide evidence that these modified siRNAs are compatible with the intracellular RNAi machinery. We studied the effect of the T(N) modification in a screen involving residue-specific changes in an siRNA targeting Renilla luciferase and we applied the most effective pattern of modification to the knockdown of murine tumor necrosis factor (TNF-α). We also showed that incorporation of T(N) units into siRNA duplexes increased their thermal stabilities, substantially enhanced serum stabilities, and decreased innate immunostimulation. Comparative RNAi studies involving the T(N) substitution and locked nucleic acids (LNAs) showed that the gene-silencing activities of T(N) -modified siRNAs were comparable to those obtained with the LNA modification. An advantage of the North 2'-deoxy-methanocarba modification is that it may be explored further in the future by changing the 2'-position. The results from these studies suggest that this modification might be valuable for the development of siRNAs for therapeutic applications.
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Affiliation(s)
- Montserrat Terrazas
- Institute for Research in Biomedicine, CIBER-BBN, Spanish Research Council, Barcelona, Spain.
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15
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Saneyoshi H, Mazzini S, Aviñó A, Portella G, González C, Orozco M, Marquez VE, Eritja R. Conformationally rigid nucleoside probes help understand the role of sugar pucker and nucleobase orientation in the thrombin-binding aptamer. Nucleic Acids Res 2009; 37:5589-601. [PMID: 19620215 PMCID: PMC2761269 DOI: 10.1093/nar/gkp598] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Modified thrombin-binding aptamers carrying 2′-deoxyguanine (dG) residues with locked North- or South-bicyclo[3.1.0]hexane pseudosugars were synthesized. Individual 2′-deoxyguanosines at positions dG5, dG10, dG14 and dG15 of the aptamer were replaced by these analogues where the North/anti and South/syn conformational states were confined. It was found that the global structure of the DNA aptamer was, for the most part, very accommodating. The substitution at positions 5, 10 and 14 with a locked South/syn-dG nucleoside produced aptamers with the same stability and global structure as the innate, unmodified one. Replacing position 15 with the same South/syn-dG nucleoside induced a strong destabilization of the aptamer, while the antipodal North/anti-dG nucleoside was less destabilizing. Remarkably, the insertion of a North/anti-dG nucleoside at position 14, where both pseudosugar conformation and glycosyl torsion angle are opposite with respect to the native structure, led to the complete disruption of the G-tetraplex structure as detected by NMR and confirmed by extensive molecular dynamics simulations. We conclude that conformationally locked bicyclo[3.1.0]hexane nucleosides appear to be excellent tools for studying the role of key conformational parameters that are critical for the formation of a stable, antiparallel G-tetrad DNA structures.
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Affiliation(s)
- Hisao Saneyoshi
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA, DISMA, Universita’ degli Studi di Milano. Via Celoria 2, I-20133 Milano, Italy, Institute for Research in Biomedicine, IQAC-CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Baldiri Reixac 15, E-08028 Barcelona, Joint IRB-BSC program on Computational Biology. Institute for Research in Biomedicine, Baldiri Reixac 10-12, E-08028 Barcelona and Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Department of Biochemistry, University of Barcelona, Diagonal 647, 08028 Barcelona, Instituto de Química Física Rocasolano. CSIC, C/Serrano, 119, 28006 Madrid, Spain
| | - Stefania Mazzini
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA, DISMA, Universita’ degli Studi di Milano. Via Celoria 2, I-20133 Milano, Italy, Institute for Research in Biomedicine, IQAC-CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Baldiri Reixac 15, E-08028 Barcelona, Joint IRB-BSC program on Computational Biology. Institute for Research in Biomedicine, Baldiri Reixac 10-12, E-08028 Barcelona and Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Department of Biochemistry, University of Barcelona, Diagonal 647, 08028 Barcelona, Instituto de Química Física Rocasolano. CSIC, C/Serrano, 119, 28006 Madrid, Spain
| | - Anna Aviñó
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA, DISMA, Universita’ degli Studi di Milano. Via Celoria 2, I-20133 Milano, Italy, Institute for Research in Biomedicine, IQAC-CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Baldiri Reixac 15, E-08028 Barcelona, Joint IRB-BSC program on Computational Biology. Institute for Research in Biomedicine, Baldiri Reixac 10-12, E-08028 Barcelona and Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Department of Biochemistry, University of Barcelona, Diagonal 647, 08028 Barcelona, Instituto de Química Física Rocasolano. CSIC, C/Serrano, 119, 28006 Madrid, Spain
| | - Guillem Portella
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA, DISMA, Universita’ degli Studi di Milano. Via Celoria 2, I-20133 Milano, Italy, Institute for Research in Biomedicine, IQAC-CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Baldiri Reixac 15, E-08028 Barcelona, Joint IRB-BSC program on Computational Biology. Institute for Research in Biomedicine, Baldiri Reixac 10-12, E-08028 Barcelona and Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Department of Biochemistry, University of Barcelona, Diagonal 647, 08028 Barcelona, Instituto de Química Física Rocasolano. CSIC, C/Serrano, 119, 28006 Madrid, Spain
| | - Carlos González
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA, DISMA, Universita’ degli Studi di Milano. Via Celoria 2, I-20133 Milano, Italy, Institute for Research in Biomedicine, IQAC-CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Baldiri Reixac 15, E-08028 Barcelona, Joint IRB-BSC program on Computational Biology. Institute for Research in Biomedicine, Baldiri Reixac 10-12, E-08028 Barcelona and Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Department of Biochemistry, University of Barcelona, Diagonal 647, 08028 Barcelona, Instituto de Química Física Rocasolano. CSIC, C/Serrano, 119, 28006 Madrid, Spain
| | - Modesto Orozco
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA, DISMA, Universita’ degli Studi di Milano. Via Celoria 2, I-20133 Milano, Italy, Institute for Research in Biomedicine, IQAC-CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Baldiri Reixac 15, E-08028 Barcelona, Joint IRB-BSC program on Computational Biology. Institute for Research in Biomedicine, Baldiri Reixac 10-12, E-08028 Barcelona and Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Department of Biochemistry, University of Barcelona, Diagonal 647, 08028 Barcelona, Instituto de Química Física Rocasolano. CSIC, C/Serrano, 119, 28006 Madrid, Spain
| | - Víctor E. Marquez
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA, DISMA, Universita’ degli Studi di Milano. Via Celoria 2, I-20133 Milano, Italy, Institute for Research in Biomedicine, IQAC-CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Baldiri Reixac 15, E-08028 Barcelona, Joint IRB-BSC program on Computational Biology. Institute for Research in Biomedicine, Baldiri Reixac 10-12, E-08028 Barcelona and Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Department of Biochemistry, University of Barcelona, Diagonal 647, 08028 Barcelona, Instituto de Química Física Rocasolano. CSIC, C/Serrano, 119, 28006 Madrid, Spain
- *To whom correspondence should be addressed. Tel: +34 93 4039942; Fax: +34 93 2045904;
| | - Ramon Eritja
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA, DISMA, Universita’ degli Studi di Milano. Via Celoria 2, I-20133 Milano, Italy, Institute for Research in Biomedicine, IQAC-CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Baldiri Reixac 15, E-08028 Barcelona, Joint IRB-BSC program on Computational Biology. Institute for Research in Biomedicine, Baldiri Reixac 10-12, E-08028 Barcelona and Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Department of Biochemistry, University of Barcelona, Diagonal 647, 08028 Barcelona, Instituto de Química Física Rocasolano. CSIC, C/Serrano, 119, 28006 Madrid, Spain
- *To whom correspondence should be addressed. Tel: +34 93 4039942; Fax: +34 93 2045904;
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Obika S, Kodama T, Sugaya K, Baba T, Imanishi T. Synthesis of a Novel trans-3’,4’-BNA Monomer Bearing a 4,8-Dioxa-5-azabicyclo[5.3.0]decane Skeleton. HETEROCYCLES 2009. [DOI: 10.3987/com-08-s(d)58] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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17
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Obika S, Kodama T, Sugaya K, Harada Y, Mitsuoka Y, Imanishi T. Synthesis and Properties of 2’-Deoxy-trans-3’,4’-BNA with S-Type Sugar Puckering. HETEROCYCLES 2009. [DOI: 10.3987/com-08-s(f)99] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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18
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Julien KR, Sumita M, Chen PH, Laird-Offringa IA, Hoogstraten CG. Conformationally restricted nucleotides as a probe of structure-function relationships in RNA. RNA (NEW YORK, N.Y.) 2008; 14:1632-1643. [PMID: 18596252 PMCID: PMC2491483 DOI: 10.1261/rna.866408] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2008] [Accepted: 04/17/2008] [Indexed: 05/26/2023]
Abstract
We introduce the use of commercially available locked nucleic acids (LNAs) as a functional probe in RNA. LNA nucleotides contain a covalent linkage that restricts the pseudorotation phase of the ribose to C3'-endo (A-form). Introduction of an LNA at a single site thus allows the role of ribose structure and dynamics in RNA function to be assessed. We apply LNA probing at multiple sites to analyze self-cleavage in the lead-dependent ribozyme (leadzyme), thermodynamic stability in the UUCG tetraloop, and the kinetics of recognition of U1A protein by U1 snRNA hairpin II. In the leadzyme, locking a single guanosine residue into the C3'-endo pucker increases the catalytic rate by a factor of 20, despite the fact that X-ray crystallographic and NMR structures of the leadzyme ground state reported a C2'-endo conformation at this site. These results strongly suggest that a conformational change at this position is critical for catalytic function. Functional insights obtained in all three systems demonstrate the highly general applicability of LNA probing in analysis of the role of ribose orientation in RNA structure, dynamics, and function.
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Affiliation(s)
- Kristine R Julien
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
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19
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Maderia M, Shenoy S, Van QN, Marquez VE, Barchi JJ. Biophysical studies of DNA modified with conformationally constrained nucleotides: comparison of 2'-exo (north) and 3'-exo (south) 'locked' templates. Nucleic Acids Res 2007; 35:1978-91. [PMID: 17341464 PMCID: PMC1895885 DOI: 10.1093/nar/gkm025] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The biophysical properties of oligodeoxyribonucleotides (ODNs) selectively modified with conformationally ‘locked’ bicyclo[3.1.0]hexane pseudosugars (Maier,M.A., Choi,Y., Gaus,H., Barchi,J.J. Jr, Marquez,V.E., Manoharan,M. (2004) Synthesis and characterization of oligonucleotides containing conformationally constrained bicyclo[3.1.0]hexane pseudosugar analogs Nucleic Acids Res., 32, 3642–3650) have been studied by various techniques. Six separate synthetic ODNs based on the Dickerson Drew dodecamer sequence (CGCGAAT*T*CGCG) were examined where each one (or both) of the thymidines (T*) were substituted with a bicyclic pseudosugar locked in either a North (2′-exo) or South (3′-exo) ring pucker. Circular dichroism spectroscopy, differential scanning calorimetry and 1H NMR spectroscopy were used to examine the duplex stability and conformational properties of the ODNs. Replacement of one or both thymidines with North-locked sugars (RNA-like) into the dodecamer did not greatly affect duplex formation or melt temperatures but distinct differences in thermodynamic parameters were observed. In contrast, incorporation of South-locked sugar derivatives that were predicted to stabilize this standard B-DNA, had the unexpected effect of causing a conformational equilibrium between different duplex forms at specific strand and salt concentrations. Our data and those of others suggest that although DNA can tolerate modifications with RNA-like (North) nucleotides, a more complicated spectrum of changes emerges with modifications restricted to South (DNA-like) puckers.
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Affiliation(s)
- Melissa Maderia
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702 USA, Molecular Targets Development Program and Laboratory of Proteomics and Analytical Technologies, SAIC-Frederick, Inc., Frederick, MD 21702 USA
| | - Shilpa Shenoy
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702 USA, Molecular Targets Development Program and Laboratory of Proteomics and Analytical Technologies, SAIC-Frederick, Inc., Frederick, MD 21702 USA
| | - Que N. Van
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702 USA, Molecular Targets Development Program and Laboratory of Proteomics and Analytical Technologies, SAIC-Frederick, Inc., Frederick, MD 21702 USA
| | - Victor E. Marquez
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702 USA, Molecular Targets Development Program and Laboratory of Proteomics and Analytical Technologies, SAIC-Frederick, Inc., Frederick, MD 21702 USA
| | - Joseph J. Barchi
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702 USA, Molecular Targets Development Program and Laboratory of Proteomics and Analytical Technologies, SAIC-Frederick, Inc., Frederick, MD 21702 USA
- *To whom correspondence should be addressed. +1 301 846 5905+1 301 846 6033
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20
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Maderia M, Wu J, Bax A, Shenoy S, O'Keefe B, Marquez VE, Barchi JJ. Engineering DNA topology with locked nucleosides: a structural study. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2005; 24:687-90. [PMID: 16248015 DOI: 10.1081/ncn-200060256] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
DNA dodecamers modified with nucleotide building blocks based on a bicyclo[3. 1.0]hexane system that effectively locks the ribose template into an RNA-like or North (N) conformation were analyzed by various biophysical techniques including high field nuclear magnetic resonance (NMR). Replacement of either one or both of the center thymidines in the Dickerson Drew dodecamer (CGCGAAT*T*CGCG) caused a progressive shift in the bending propensity of the double helix as shown by a newly developed rapid technique that compares the residual dipolar coupling (RDC) values of the modified duplexes with those previously determined for the native DNA.
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Affiliation(s)
- Melissa Maderia
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
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21
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Wu Z, Maderia M, Barchi JJ, Marquez VE, Bax A. Changes in DNA bending induced by restricting nucleotide ring pucker studied by weak alignment NMR spectroscopy. Proc Natl Acad Sci U S A 2004; 102:24-8. [PMID: 15618396 PMCID: PMC544063 DOI: 10.1073/pnas.0408498102] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Changes in bending of the DNA helix axis caused by the introduction of conformationally locked nucleotide analogs into the center region of the palindromic Dickerson dodecamer, d(CGCGAATTCGCG)(2), have been studied by NMR measurement of residual one-bond (13)C-(1)H dipolar couplings. Thymidine analogs, in which the deoxyribose was substituted by bicyclo[3.1.0]hexane, were incorporated in the T7, T8, and T7T8 positions. These nucleotide analogs restrict the ring pucker to the C2'-exo or "north" conformation, instead of C2'-endo or "south," which dominates in regular B-form DNA. For all three oligomers, bending toward the major groove is found relative to the native molecule. The effects are additive with bending of 5 +/- 1 degrees per locked nucleotide. Measurement of the change in bending is more accurate than measurement of the bending angle itself and requires far fewer experimental data.
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Affiliation(s)
- Zhengrong Wu
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
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Horton JR, Ratner G, Banavali NK, Huang N, Choi Y, Maier MA, Marquez VE, MacKerell AD, Cheng X. Caught in the act: visualization of an intermediate in the DNA base-flipping pathway induced by HhaI methyltransferase. Nucleic Acids Res 2004; 32:3877-86. [PMID: 15273274 PMCID: PMC506793 DOI: 10.1093/nar/gkh701] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Rotation of a DNA or RNA nucleotide out of the double helix and into a protein pocket ('base flipping') is a mechanistic feature common to some DNA/RNA-binding proteins. Here, we report the structure of HhaI methyltransferase in complex with DNA containing a south-constrained abasic carbocyclic sugar at the target site in the presence of the methyl donor byproduct AdoHcy. Unexpectedly, the locked south pseudosugar appears to be trapped in the middle of the flipping pathway via the DNA major groove, held in place primarily through Van der Waals contacts with a set of invariant amino acids. Molecular dynamics simulations indicate that the structural stabilization observed with the south-constrained pseudosugar will not occur with a north-constrained pseudosugar, which explains its lowered binding affinity. Moreover, comparison of structural transitions of the sugar and phosphodiester backbone observed during computational studies of base flipping in the M.HhaI-DNA-AdoHcy ternary complex indicate that the south-constrained pseudosugar induces a conformation on the phosphodiester backbone that corresponds to that of a discrete intermediate of the base-flipping pathway. As previous crystal structures of M.HhaI ternary complex with DNA displayed the flipped sugar moiety in the antipodal north conformation, we suggest that conversion of the sugar pucker from south to north beyond the middle of the pathway is an essential part of the mechanism through which flipping must proceed to reach its final destination. We also discuss the possibility of the south-constrained pseudosugar mimicking a transition state in the phosphodiester and sugar moieties that occurs during DNA base flipping in the presence of M.HhaI.
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Affiliation(s)
- John R Horton
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA
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