1
|
Kawamoto Y, Wu Y, Takahashi Y, Takakura Y. Development of nucleic acid medicines based on chemical technology. Adv Drug Deliv Rev 2023; 199:114872. [PMID: 37244354 DOI: 10.1016/j.addr.2023.114872] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/01/2023] [Accepted: 05/12/2023] [Indexed: 05/29/2023]
Abstract
Oligonucleotide-based therapeutics have attracted attention as an emerging modality that includes the modulation of genes and their binding proteins related to diseases, allowing us to take action on previously undruggable targets. Since the late 2010s, the number of oligonucleotide medicines approved for clinical uses has dramatically increased. Various chemistry-based technologies have been developed to improve the therapeutic properties of oligonucleotides, such as chemical modification, conjugation, and nanoparticle formation, which can increase nuclease resistance, enhance affinity and selectivity to target sites, suppress off-target effects, and improve pharmacokinetic properties. Similar strategies employing modified nucleobases and lipid nanoparticles have been used for developing coronavirus disease 2019 mRNA vaccines. In this review, we provide an overview of the development of chemistry-based technologies aimed at using nucleic acids for developing therapeutics over the past several decades, with a specific emphasis on the structural design and functionality of chemical modification strategies.
Collapse
Affiliation(s)
- Yusuke Kawamoto
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan.
| | - You Wu
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Yuki Takahashi
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Yoshinobu Takakura
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan.
| |
Collapse
|
2
|
Das G, Harikrishna S, Gore KR. Influence of Sugar Modifications on the Nucleoside Conformation and Oligonucleotide Stability: A Critical Review. CHEM REC 2022; 22:e202200174. [PMID: 36048010 DOI: 10.1002/tcr.202200174] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/16/2022] [Indexed: 12/15/2022]
Abstract
Ribofuranose sugar conformation plays an important role in the structure and dynamics of functional nucleic acids such as siRNAs, AONs, aptamers, miRNAs, etc. To improve their therapeutic potential, several chemical modifications have been introduced into the sugar moiety over the years. The stability of the oligonucleotide duplexes as well as the formation of stable and functional protein-oligonucleotide complexes are dictated by the conformation and dynamics of the sugar moiety. In this review, we systematically categorise various ribofuranose sugar modifications employed in DNAs and RNAs so far. We discuss different stereoelectronic effects imparted by different substituents on the sugar ring and how these effects control sugar puckering. Using this data, it would be possible to predict the precise use of chemical modifications and design novel sugar-modified nucleosides for therapeutic oligonucleotides that can improve their physicochemical properties.
Collapse
Affiliation(s)
- Gourav Das
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal-721302, India
| | - S Harikrishna
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Kiran R Gore
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal-721302, India
| |
Collapse
|
3
|
Wang Y, Liu X, Shehabat M, Chim N, Chaput JC. Transliteration of synthetic genetic enzymes. Nucleic Acids Res 2021; 49:11438-11446. [PMID: 34634814 PMCID: PMC8599711 DOI: 10.1093/nar/gkab923] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/07/2021] [Accepted: 09/27/2021] [Indexed: 01/23/2023] Open
Abstract
Functional nucleic acids lose activity when their sequence is prepared in the backbone architecture of a different genetic polymer. The only known exception to this rule is a subset of aptamers whose binding mechanism involves G-quadruplex formation. We refer to such examples as transliteration-a synthetic biology concept describing cases in which the phenotype of a nucleic acid molecule is retained when the genotype is written in a different genetic language. Here, we extend the concept of transliteration to include nucleic acid enzymes (XNAzymes) that mediate site-specific cleavage of an RNA substrate. We show that an in vitro selected 2'-fluoroarabino nucleic acid (FANA) enzyme retains catalytic activity when its sequence is prepared as α-l-threofuranosyl nucleic acid (TNA), and vice versa, a TNA enzyme that remains functional when its sequence is prepared as FANA. Structure probing with DMS supports the hypothesis that FANA and TNA enzymes having the same primary sequence can adopt similarly folded tertiary structures. These findings provide new insight into the sequence-structure-function paradigm governing biopolymer folding.
Collapse
Affiliation(s)
- Yajun Wang
- College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, China
| | - Xiaolin Liu
- College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, China
| | - Mouhamad Shehabat
- Departments of Pharmaceutical Sciences, University of California, Irvine, CA 92697, USA
| | - Nicholas Chim
- Departments of Pharmaceutical Sciences, University of California, Irvine, CA 92697, USA
| | - John C Chaput
- Departments of Pharmaceutical Sciences, University of California, Irvine, CA 92697, USA.,Department of Chemistry, University of California, Irvine, CA 92697, USA.,Department of Molecular Biology and Biochemistry, University of California, CA 92697, USA.,Department of Chemical and Biomolecular Engineering, University of California, CA 92697, USA
| |
Collapse
|
4
|
Mattelaer CA, Mattelaer HP, Rihon J, Froeyen M, Lescrinier E. Efficient and Accurate Potential Energy Surfaces of Puckering in Sugar-Modified Nucleosides. J Chem Theory Comput 2021; 17:3814-3823. [PMID: 34000809 DOI: 10.1021/acs.jctc.1c00270] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Puckering of the sugar unit in nucleosides and nucleotides is an important structural aspect that directly influences the helical structure of nucleic acids. The preference for specific puckering modes in nucleic acids can be analyzed via in silico conformational analysis, but the large amount of conformations and the accuracy of the analysis leads to an extensive amount of computational time. In this paper, we show that the combination of geometry optimizations with the HF-3c method with single point energies at the RI-MP2 level results in accurate results for the puckering potential energy surface (PES) of DNA and RNA nucleosides while significantly reducing the necessary computational time. Applying this method to a series of known xeno nucleic acids (XNAs) allowed us to rapidly explore the puckering PES of each of the respective nucleosides and to explore the puckering PES of six-membered modified XNA (HNA and β-homo-DNA) for the first time.
Collapse
Affiliation(s)
- Charles-Alexandre Mattelaer
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 - Box 1041, 3000 Leuven, Belgium
| | - Henri-Philippe Mattelaer
- Campus Drie Eiken, Laboratory of Medicinal Chemistry, UAntwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Jérôme Rihon
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 - Box 1041, 3000 Leuven, Belgium
| | - Matheus Froeyen
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 - Box 1041, 3000 Leuven, Belgium
| | - Eveline Lescrinier
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 - Box 1041, 3000 Leuven, Belgium
| |
Collapse
|
5
|
Liczner C, Duke K, Juneau G, Egli M, Wilds CJ. Beyond ribose and phosphate: Selected nucleic acid modifications for structure-function investigations and therapeutic applications. Beilstein J Org Chem 2021; 17:908-931. [PMID: 33981365 PMCID: PMC8093555 DOI: 10.3762/bjoc.17.76] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/14/2021] [Indexed: 12/16/2022] Open
Abstract
Over the past 25 years, the acceleration of achievements in the development of oligonucleotide-based therapeutics has resulted in numerous new drugs making it to the market for the treatment of various diseases. Oligonucleotides with alterations to their scaffold, prepared with modified nucleosides and solid-phase synthesis, have yielded molecules with interesting biophysical properties that bind to their targets and are tolerated by the cellular machinery to elicit a therapeutic outcome. Structural techniques, such as crystallography, have provided insights to rationalize numerous properties including binding affinity, nuclease stability, and trends observed in the gene silencing. In this review, we discuss the chemistry, biophysical, and structural properties of a number of chemically modified oligonucleotides that have been explored for gene silencing.
Collapse
Affiliation(s)
- Christopher Liczner
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Kieran Duke
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Gabrielle Juneau
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Martin Egli
- Department of Biochemistry, Vanderbilt Institute of Chemical Biology, and Center for Structural Biology, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Christopher J Wilds
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
| |
Collapse
|
6
|
Gruenke PR, Alam KK, Singh K, Burke DH. 2'-fluoro-modified pyrimidines enhance affinity of RNA oligonucleotides to HIV-1 reverse transcriptase. RNA (NEW YORK, N.Y.) 2020; 26:1667-1679. [PMID: 32732393 PMCID: PMC7566575 DOI: 10.1261/rna.077008.120] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 07/24/2020] [Indexed: 06/01/2023]
Abstract
Nucleic acid aptamers can be chemically modified to enhance function, but modifying previously selected aptamers can have nontrivial structural and functional consequences. We present a reselection strategy to evaluate the impact of several modifications on preexisting aptamer pools. RNA aptamer libraries with affinity to HIV-1 reverse transcriptase (RT) were retranscribed with 2'-F, 2'-OMe, or 2'-NH2 pyrimidines and subjected to three additional selection cycles. RT inhibition was observed for representative aptamers from several structural families identified by high-throughput sequencing when transcribed with their corresponding modifications. Thus, reselection identified specialized subsets of aptamers that tolerated chemical modifications from unmodified preenriched libraries. Inhibition was the strongest with the 2'-F-pyrimidine (2'-FY) RNAs, as compared to inhibition by the 2'-OMeY and 2'-NH2Y RNAs. Unexpectedly, a diverse panel of retroviral RTs were strongly inhibited by all 2'-FY-modified transcripts, including sequences that do not inhibit those RTs as unmodified RNA. The magnitude of promiscuous RT inhibition was proportional to mole fraction 2'-FY in the transcript. RT binding affinity by 2'-FY transcripts was more sensitive to salt concentration than binding by unmodified transcripts, indicating that interaction with retroviral RTs is more ionic in character for 2'-FY RNA than for unmodified 2'-OH RNA. These surprising features of 2'-FY-modified RNA may have general implications for applied aptamer technologies.
Collapse
Affiliation(s)
- Paige R Gruenke
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, USA
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA
| | - Khalid K Alam
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, USA
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA
| | - Kamal Singh
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA
- Department of Veterinary Pathobiology, University of Missouri, Columbia, Missouri 65211, USA
| | - Donald H Burke
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, USA
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri 65211, USA
- Department of Biological Engineering, University of Missouri, Columbia, Missouri 65211, USA
| |
Collapse
|
7
|
Hardwick JS, Haugland MM, El-Sagheer AH, Ptchelkine D, Beierlein FR, Lane AN, Brown T, Lovett JE, Anderson EA. 2'-Alkynyl spin-labelling is a minimally perturbing tool for DNA structural analysis. Nucleic Acids Res 2020; 48:2830-2840. [PMID: 32052020 PMCID: PMC7102949 DOI: 10.1093/nar/gkaa086] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 01/28/2020] [Accepted: 02/10/2020] [Indexed: 02/06/2023] Open
Abstract
The determination of distances between specific points in nucleic acids is essential to understanding their behaviour at the molecular level. The ability to measure distances of 2-10 nm is particularly important: deformations arising from protein binding commonly fall within this range, but the reliable measurement of such distances for a conformational ensemble remains a significant challenge. Using several techniques, we show that electron paramagnetic resonance (EPR) spectroscopy of oligonucleotides spin-labelled with triazole-appended nitroxides at the 2' position offers a robust and minimally perturbing tool for obtaining such measurements. For two nitroxides, we present results from EPR spectroscopy, X-ray crystal structures of B-form spin-labelled DNA duplexes, molecular dynamics simulations and nuclear magnetic resonance spectroscopy. These four methods are mutually supportive, and pinpoint the locations of the spin labels on the duplexes. In doing so, this work establishes 2'-alkynyl nitroxide spin-labelling as a minimally perturbing method for probing DNA conformation.
Collapse
Affiliation(s)
- Jack S Hardwick
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Marius M Haugland
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Afaf H El-Sagheer
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
- Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez 43721, Egypt
| | - Denis Ptchelkine
- Weatherall Institute of Molecular Medicine, Department of Oncology, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DS, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Frank R Beierlein
- Computer-Chemistry-Center and Interdisciplinary Center for Molecular Materials, Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nägelsbachstrasse 25, 91052 Erlangen, Germany
| | - Andrew N Lane
- Center for Environmental and Systems Biochemistry and Department of Toxicology & Cancer Biology, The University of Kentucky, 789 S. Limestone St., Lexington, KY 40536, USA
| | - Tom Brown
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Janet E Lovett
- SUPA School of Physics and Astronomy and BSRC, University of St Andrews, North Haugh, St Andrews KY16 9SS, UK
| | - Edward A Anderson
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| |
Collapse
|
8
|
Dow BJ, Malik SS, Drohat AC. Defining the Role of Nucleotide Flipping in Enzyme Specificity Using 19F NMR. J Am Chem Soc 2019; 141:4952-4962. [PMID: 30841696 DOI: 10.1021/jacs.9b00146] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A broad range of proteins employ nucleotide flipping to recognize specific sites in nucleic acids, including DNA glycosylases, which remove modified nucleobases to initiate base excision repair. Deamination, a pervasive mode of damage, typically generates lesions that are recognized by glycosylases as being foreign to DNA. However, deamination of 5-methylcytosine (mC) generates thymine, a canonical DNA base, presenting a challenge for damage recognition. Nevertheless, repair of mC deamination is important because the resulting G·T mispairs cause C → T transition mutations, and mC is abundant in all three domains of life. Countering this threat are three types of glycosylases that excise thymine from G·T mispairs, including thymine DNA glycosylase (TDG). These enzymes must minimize excision of thymine that is not generated by mC deamination, in A·T pairs and in polymerase-generated G·T mispairs. TDG preferentially removes thymine from DNA contexts in which cytosine methylation is prevalent, including CG and one non-CG site. This remarkable context specificity could be attained through modulation of nucleotide flipping, a reversible step that precedes base excision. We tested this idea using fluorine NMR and DNA containing 2'-fluoro-substituted nucleotides. We find that dT nucleotide flipping depends on DNA context and is efficient only in contexts known to feature cytosine methylation. We also show that a conserved Ala residue limits thymine excision by hindering nucleotide flipping. A linear free energy correlation reveals that TDG attains context specificity for thymine excision through modulation of nucleotide flipping. Our results provide a framework for characterizing nucleotide flipping in nucleic acids using 19F NMR.
Collapse
Affiliation(s)
- Blaine J Dow
- Department of Biochemistry and Molecular Biology , University of Maryland School of Medicine , Baltimore , Maryland 21201 , United States
| | - Shuja S Malik
- Department of Biochemistry and Molecular Biology , University of Maryland School of Medicine , Baltimore , Maryland 21201 , United States
| | - Alexander C Drohat
- Department of Biochemistry and Molecular Biology , University of Maryland School of Medicine , Baltimore , Maryland 21201 , United States
| |
Collapse
|
9
|
Haase L, Karg B, Weisz K. Manipulating DNA G-Quadruplex Structures by Using Guanosine Analogues. Chembiochem 2019; 20:985-993. [PMID: 30511814 DOI: 10.1002/cbic.201800642] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Indexed: 12/22/2022]
Abstract
The ability to control the folding topology of DNA G-quadruplexes allows for rational design of quadruplex-based scaffolds for potential use in various therapeutic and technological applications. By exploiting the distinct conformational properties of some base- and sugar-modified guanosine surrogates, conformational transitions can be induced through their judicious incorporation at specific sites in the quadruplex core. Changes may involve tetrad polarity inversions with conservation of the global fold or complete refolding to new topologies. Reliable predictions relating to low-energy conformers formed upon specific chemical perturbations of the system and the rational design of modified sequences suffer from our still limited understanding of the subtle interplay of various favorable and unfavorable interactions within a particular quadruplex scaffold. However, aided by an increasing number of systematic substitution experiments and high-resolution structures of modified quadruplex variants, critical interactions, in addition to glycosidic bond angle propensities, are starting to emerge as important contributors to modification-driven quadruplex refolding.
Collapse
Affiliation(s)
- Linn Haase
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| | - Beatrice Karg
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| | - Klaus Weisz
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| |
Collapse
|
10
|
Parui S, Jana B. Factors Promoting the Formation of Clathrate-Like Ordering of Water in Biomolecular Structure at Ambient Temperature and Pressure. J Phys Chem B 2019; 123:811-824. [PMID: 30605607 DOI: 10.1021/acs.jpcb.8b11172] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Clathrate hydrate forms when a hydrophobic molecule is entrapped inside a water cage or cavity. Although biomolecular structures also have hydrophobic patches, clathrate-like water is found in only a limited number of biomolecules. Also, while clathrate hydrates form at low temperature and moderately higher pressure, clathrate-like water is observed in biomolecular structure at ambient temperature and pressure. These indicate presence of other factors along with hydrophobic environment behind the formation of clathrate-like water in biomolecules. In the current study, we presented a systematic approach to explore the factors behind the formation of clathrate-like water in biomolecules by means of molecular dynamics simulation of a model protein, maxi, which is a naturally occurring nanopore and has clathrate-like water inside the pore. Removal of either confinement or hydrophobic environment results in the disappearance of clathrate-like water ordering, indicating a coupled role of these two factors. Apart from these two factors, clathrate-like water ordering also requires anchoring groups that can stabilize the clathrate-like water through hydrogen bonding. Our results uncover crucial factors for the stabilization of clathrate-like ordering in biomolecular structure which can be used for the development of new biomolecular structure promoting clathrate formation.
Collapse
Affiliation(s)
- Sridip Parui
- School of Chemical Sciences , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032 , India
| | - Biman Jana
- School of Chemical Sciences , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032 , India
| |
Collapse
|
11
|
Frei S, Katolik AK, Leumann CJ. Synthesis, biophysical properties, and RNase H activity of 6'-difluoro[4.3.0]bicyclo-DNA. Beilstein J Org Chem 2019; 15:79-88. [PMID: 30680042 PMCID: PMC6334804 DOI: 10.3762/bjoc.15.9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/13/2018] [Indexed: 12/25/2022] Open
Abstract
Here we present the synthesis, the biophysical properties, and the RNase H profile of 6'-difluorinated [4.3.0]bicyclo-DNA (6'-diF-bc4,3-DNA). The difluorinated thymidine phosphoramidite building block was synthesized starting from an already known gem-difluorinated tricyclic glycal. This tricyclic siloxydifluorocyclopropane was converted into the [4.3.0]bicyclic nucleoside via cyclopropane ring-opening through the addition of an electrophilic iodine during the nucleosidation step followed by reduction. The gem-difluorinated bicyclic nucleoside was then converted into the corresponding phosphoramidite building block which was incorporated into oligonucleotides. Thermal denaturation experiments of these oligonucleotides hybridized to complementary DNA or RNA disclosed a significant destabilization of both duplex types (ΔT m/mod = -1.6 to -5.5 °C). However, in the DNA/RNA hybrid the amount of destabilization could be reduced by multiple insertions of the modified unit. In addition, CD spectroscopy of the oligonucleotides hybridized to RNA showed a similar structure than the natural DNA/RNA duplex. Furthermore, since the structural investigation on the nucleoside level by X-ray crystallography and ab initio calculations pointed to a furanose conformation in the southern region, a RNase H cleavage assay was conducted. This experiment revealed that the oligonucleotide containing five modified units was able to elicit the RNase H-mediated cleavage of the complementary RNA strand.
Collapse
Affiliation(s)
- Sibylle Frei
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Adam K Katolik
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Christian J Leumann
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| |
Collapse
|
12
|
Peters JP, Kowal EA, Pallan PS, Egli M, Maher LJ. Comparative analysis of inosine-substituted duplex DNA by circular dichroism and X-ray crystallography. J Biomol Struct Dyn 2018; 36:2753-2772. [PMID: 28818035 PMCID: PMC6251417 DOI: 10.1080/07391102.2017.1369164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Leveraging structural biology tools, we report the results of experiments seeking to determine if the different mechanical properties of DNA polymers with base analog substitutions can be attributed, at least in part, to induced changes from classical B-form DNA. The underlying hypothesis is that different inherent bending and twisting flexibilities may characterize non-canonical B-DNA, so that it is inappropriate to interpret mechanical changes caused by base analog substitution as resulting simply from 'electrostatic' or 'base stacking' influences without considering the larger context of altered helical geometry. Circular dichroism spectra of inosine-substituted oligonucleotides and longer base-substituted DNAs in solution indicated non-canonical helical conformations, with the degree of deviation from a standard B-form geometry depending on the number of I⋅C pairs. X-ray diffraction of a highly inosine-substituted DNA decamer crystal (eight I⋅C and two A⋅T pairs) revealed an A-tract-like conformation with a uniformly narrow minor groove, reduced helical rise, and the majority of sugars adopting a C1'-exo (southeastern) conformation. This contrasts with the standard B-DNA geometry with C2'-endo sugar puckers (south conformation). In contrast, the crystal structure of a decamer with only four I⋅C pairs has a geometry similar to that of the reference duplex with eight G⋅C and two A⋅T pairs. The unique crystal geometry of the inosine-rich duplex is noteworthy given its unusual CD signature in solution and the altered mechanical properties of some inosine-containing DNAs.
Collapse
Affiliation(s)
- Justin P. Peters
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, 200 First St. SW, Rochester, MN 55905, USA
| | - Ewa A. Kowal
- Department of Biochemistry, Vanderbilt University School of Medicine, 607 Light Hall, Nashville, TN 37232, USA
| | - Pradeep S. Pallan
- Department of Biochemistry, Vanderbilt University School of Medicine, 607 Light Hall, Nashville, TN 37232, USA
| | - Martin Egli
- Department of Biochemistry, Vanderbilt University School of Medicine, 607 Light Hall, Nashville, TN 37232, USA
| | - L. James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, 200 First St. SW, Rochester, MN 55905, USA,To whom correspondence should be addressed at
| |
Collapse
|
13
|
Malek-Adamian E, Patrascu MB, Jana SK, Martínez-Montero S, Moitessier N, Damha MJ. Adjusting the Structure of 2'-Modified Nucleosides and Oligonucleotides via C4'-α-F or C4'-α-OMe Substitution: Synthesis and Conformational Analysis. J Org Chem 2018; 83:9839-9849. [PMID: 29963864 DOI: 10.1021/acs.joc.8b01329] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We report the first syntheses of three nucleoside analogues, namely, 2',4'-diOMe-rU, 2'-OMe,4'-F-rU, and 2'-F,4'-OMe-araU, via stereoselective introduction of fluorine or methoxy functionalities at the C4'-α-position of a 4',5'-olefinic intermediate. Conformational analyses of these nucleosides and comparison to other previously reported 2',4'-disubstituted nucleoside analogues make it possible to evaluate the effect of fluorine and methoxy substitution on the sugar pucker, as assessed by NMR, X-ray diffraction, and computational methods. We found that C4'-α-F/OMe substituents reinforce the C3'-endo ( north) conformation of 2'-OMe-rU. Furthermore, the predominant C2'-endo ( south/ east) conformation of 2'-F-araU switches to C3'-endo upon introduction of these substituents at C4'. The nucleoside analogues were incorporated into DNA and RNA oligonucleotides via standard phosphoramidite chemistry, and their effects on the thermal stability of homo- and heteroduplexes were assessed via UV thermal melting experiments. We found that 4'-substituents can modulate the binding affinity of the parent 2'-modified oligomers, inducing a mildly destabilizing or stabilizing effect depending on the duplex type. This study expands the spectrum of oligonucleotide modifications available for rational design of oligonucleotide therapeutics.
Collapse
Affiliation(s)
- Elise Malek-Adamian
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec , Canada H3A 0B8
| | - Mihai Burai Patrascu
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec , Canada H3A 0B8
| | - Sunit Kumar Jana
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec , Canada H3A 0B8
| | - Saúl Martínez-Montero
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec , Canada H3A 0B8
| | - Nicolas Moitessier
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec , Canada H3A 0B8
| | - Masad J Damha
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec , Canada H3A 0B8
| |
Collapse
|
14
|
Schröder AS, Parsa E, Iwan K, Traube FR, Wallner M, Serdjukow S, Carell T. 2'-(R)-Fluorinated mC, hmC, fC and caC triphosphates are substrates for DNA polymerases and TET-enzymes. Chem Commun (Camb) 2018; 52:14361-14364. [PMID: 27905578 DOI: 10.1039/c6cc07517g] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A deeper investigation of the chemistry that occurs on the newly discovered epigenetic DNA bases 5-hydroxymethyl-(hmdC), 5-formyl-(fdC), and 5-carboxy-deoxycytidine (cadC) requires chemical tool compounds, which are able to dissect the different potential reaction pathways in cells. Here we report that the 2'-(R)-fluorinated derivatives F-hmdC, F-fdC, and F-cadC, which are resistant to removal by base excision repair, are good substrates for DNA polymerases and TET enzymes. This result shows that the fluorinated compounds are ideal tool substances to investigate potential C-C-bond cleaving reactions in the context of active demethylation.
Collapse
Affiliation(s)
- A S Schröder
- Center for Integrated Protein Science, Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377 Munich, Germany.
| | - E Parsa
- Center for Integrated Protein Science, Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377 Munich, Germany.
| | - K Iwan
- Center for Integrated Protein Science, Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377 Munich, Germany.
| | - F R Traube
- Center for Integrated Protein Science, Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377 Munich, Germany.
| | - M Wallner
- Center for Integrated Protein Science, Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377 Munich, Germany.
| | - S Serdjukow
- Center for Integrated Protein Science, Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377 Munich, Germany.
| | - T Carell
- Center for Integrated Protein Science, Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377 Munich, Germany.
| |
Collapse
|
15
|
Evich M, Spring-Connell AM, Germann MW. Impact of modified ribose sugars on nucleic acid conformation and function. HETEROCYCL COMMUN 2017. [DOI: 10.1515/hc-2017-0056] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
AbstractThe modification of the ribofuranose in nucleic acids is a widespread method of manipulating the activity of nucleic acids. These alterations, however, impact the local conformation and chemical reactivity of the sugar. Changes in the conformation and dynamics of the sugar moiety alter the local and potentially global structure and plasticity of nucleic acids, which in turn contributes to recognition, binding of ligands and enzymatic activity of proteins. This review article introduces the conformational properties of the (deoxy)ribofuranose ring and then explores sugar modifications and how they impact local and global structure and dynamics in nucleic acids.
Collapse
Affiliation(s)
- Marina Evich
- Georgia State University, Department of Chemistry, 50 Decatur St. SE, Atlanta, GA 30303, USA
| | | | - Markus W. Germann
- Georgia State University, Department of Chemistry, 50 Decatur St. SE, Atlanta, GA 30303, USA
- Georgia State University, Department of Biology, P.O. 4010, Atlanta, GA 30303, USA
- Georgia State University, Neuroscience Institute, P.O. 5030, Atlanta, GA 30303, USA
| |
Collapse
|
16
|
Istrate A, Katolik A, Istrate A, Leumann CJ. 2'β-Fluoro-Tricyclo Nucleic Acids (2'F-tc-ANA): Thermal Duplex Stability, Structural Studies, and RNase H Activation. Chemistry 2017; 23:10310-10318. [PMID: 28477335 DOI: 10.1002/chem.201701476] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Indexed: 01/16/2023]
Abstract
We describe the synthesis, thermal stability, structural and RNase H activation properties of 2'β-fluoro-tricyclo nucleic acids (2'F-tc-ANA). Three 2'F-tc-ANA nucleosides (T, 5Me C and A) were synthesized starting from a previously described fluorinated tricyclo sugar intermediate. NMR analysis and quantum mechanical calculations indicate that 2'F-tc-ANA nucleosides prefer sugar conformations in the East and South regions of the pseudorotational cycle. UV-melting experiments revealed that non-consecutive insertions of 2'F-tc-ANA units in DNA reduce the affinity to DNA and RNA complements. However, an oligonucleotide with five contiguous 2'F-tc-ANA-T insertions exhibits increased affinity to complementary RNA. Moreover, a fully modified 10-mer 2'F-tc-ANA oligonucleotide paired to both DNA (+1.6 °C/mod) and RNA (+2.5 °C/mod) with significantly higher affinity compared to corresponding unmodified DNA, and similar affinity compared to corresponding tc-DNA. In addition, CD spectroscopy and molecular dynamics simulations indicate that the conformation of the 2'F-tc-ANA/RNA duplex is similar to that of a DNA/RNA duplex. Moreover, in some sequence contexts, 2'F-tc-ANA promotes RNase H-mediated cleavage of a complementary RNA strand. Taken together, 2'F-tc-ANA represents a nucleic acid analogue that offers the advantage of high RNA affinity while maintaining the ability to activate RNase H, and can be considered a prospective candidate for gene silencing applications.
Collapse
Affiliation(s)
- Alena Istrate
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Adam Katolik
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Andrei Istrate
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Christian J Leumann
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| |
Collapse
|
17
|
Pidugu LS, Flowers JW, Coey CT, Pozharski E, Greenberg MM, Drohat AC. Structural Basis for Excision of 5-Formylcytosine by Thymine DNA Glycosylase. Biochemistry 2016; 55:6205-6208. [PMID: 27805810 DOI: 10.1021/acs.biochem.6b00982] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thymine DNA glycosylase (TDG) is a base excision repair enzyme with key functions in epigenetic regulation. Performing a critical step in a pathway for active DNA demethylation, TDG removes 5-formylcytosine and 5-carboxylcytosine, oxidized derivatives of 5-methylcytosine that are generated by TET (ten-eleven translocation) enzymes. We determined a crystal structure of TDG bound to DNA with a noncleavable (2'-fluoroarabino) analogue of 5-formyldeoxycytidine flipped into its active site, revealing how it recognizes and hydrolytically excises fC. Together with previous structural and biochemical findings, the results illustrate how TDG employs an adaptable active site to excise a broad variety of nucleobases from DNA.
Collapse
Affiliation(s)
- Lakshmi S Pidugu
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine , Baltimore, Maryland 21201, United States
| | - Joshua W Flowers
- Department of Chemistry, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Christopher T Coey
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine , Baltimore, Maryland 21201, United States
| | - Edwin Pozharski
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine , Baltimore, Maryland 21201, United States.,Center for Biomolecular Therapeutics, Institute for Bioscience and Biotechnology Research , Rockville, Maryland 20850, United States
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Alexander C Drohat
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine , Baltimore, Maryland 21201, United States
| |
Collapse
|
18
|
Coey CT, Malik SS, Pidugu LS, Varney KM, Pozharski E, Drohat AC. Structural basis of damage recognition by thymine DNA glycosylase: Key roles for N-terminal residues. Nucleic Acids Res 2016; 44:10248-10258. [PMID: 27580719 PMCID: PMC5137436 DOI: 10.1093/nar/gkw768] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 08/20/2016] [Accepted: 08/22/2016] [Indexed: 11/13/2022] Open
Abstract
Thymine DNA Glycosylase (TDG) is a base excision repair enzyme functioning in DNA repair and epigenetic regulation. TDG removes thymine from mutagenic G·T mispairs arising from deamination of 5-methylcytosine (mC), and it processes other deamination-derived lesions including uracil (U). Essential for DNA demethylation, TDG excises 5-formylcytosine and 5-carboxylcytosine, derivatives of mC generated by Tet (ten-eleven translocation) enzymes. Here, we report structural and functional studies of TDG82-308, a new construct containing 29 more N-terminal residues than TDG111-308, the construct used for previous structures of DNA-bound TDG. Crystal structures and NMR experiments demonstrate that most of these N-terminal residues are disordered, for substrate- or product-bound TDG82-308 Nevertheless, G·T substrate affinity and glycosylase activity of TDG82-308 greatly exceeds that of TDG111-308 and is equivalent to full-length TDG. We report the first high-resolution structures of TDG in an enzyme-substrate complex, for G·U bound to TDG82-308 (1.54 Å) and TDG111-308 (1.71 Å), revealing new enzyme-substrate contacts, direct and water-mediated. We also report a structure of the TDG82-308 product complex (1.70 Å). TDG82-308 forms unique enzyme-DNA interactions, supporting its value for structure-function studies. The results advance understanding of how TDG recognizes and removes modified bases from DNA, particularly those resulting from deamination.
Collapse
Affiliation(s)
- Christopher T Coey
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Shuja S Malik
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Lakshmi S Pidugu
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Kristen M Varney
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.,University of Maryland Marlene and Stewart Greenebaum Cancer Center, Baltimore, MD 21201, USA.,Center for Biomolecular Therapeutics, Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
| | - Edwin Pozharski
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA .,University of Maryland Marlene and Stewart Greenebaum Cancer Center, Baltimore, MD 21201, USA.,Center for Biomolecular Therapeutics, Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
| | - Alexander C Drohat
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA .,University of Maryland Marlene and Stewart Greenebaum Cancer Center, Baltimore, MD 21201, USA
| |
Collapse
|
19
|
Schröder AS, Kotljarova O, Parsa E, Iwan K, Raddaoui N, Carell T. Synthesis of (R)-Configured 2′-Fluorinated mC, hmC, fC, and caC Phosphoramidites and Oligonucleotides. Org Lett 2016; 18:4368-71. [DOI: 10.1021/acs.orglett.6b02110] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Arne S. Schröder
- Center
for Integrated Protein
Science, Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstraße
5-13, 81377 Munich, Germany
| | - Olga Kotljarova
- Center
for Integrated Protein
Science, Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstraße
5-13, 81377 Munich, Germany
| | - Edris Parsa
- Center
for Integrated Protein
Science, Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstraße
5-13, 81377 Munich, Germany
| | - Katharina Iwan
- Center
for Integrated Protein
Science, Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstraße
5-13, 81377 Munich, Germany
| | - Nada Raddaoui
- Center
for Integrated Protein
Science, Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstraße
5-13, 81377 Munich, Germany
| | - Thomas Carell
- Center
for Integrated Protein
Science, Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstraße
5-13, 81377 Munich, Germany
| |
Collapse
|
20
|
Lima WF, De Hoyos CL, Liang XH, Crooke ST. RNA cleavage products generated by antisense oligonucleotides and siRNAs are processed by the RNA surveillance machinery. Nucleic Acids Res 2016; 44:3351-63. [PMID: 26843429 PMCID: PMC4838368 DOI: 10.1093/nar/gkw065] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 01/25/2016] [Indexed: 01/22/2023] Open
Abstract
DNA-based antisense oligonucleotides (ASOs) elicit cleavage of the targeted RNA by the endoribonuclease RNase H1, whereas siRNAs mediate cleavage through the RNAi pathway. To determine the fates of the cleaved RNA in cells, we lowered the levels of the factors involved in RNA surveillance prior to treating cells with ASOs or siRNA and analyzed cleavage products by RACE. The cytoplasmic 5' to 3' exoribonuclease XRN1 was responsible for the degradation of the downstream cleavage products generated by ASOs or siRNA targeting mRNAs. In contrast, downstream cleavage products generated by ASOs targeting nuclear long non-coding RNA Malat 1 and pre-mRNA were degraded by nuclear XRN2. The downstream cleavage products did not appear to be degraded in the 3' to 5' direction as the majority of these products contained intact poly(A) tails and were bound by the poly(A) binding protein. The upstream cleavage products of Malat1 were degraded in the 3' to 5' direction by the exosome complex containing the nuclear exoribonuclease Dis3. The exosome complex containing Dis3 or cytoplasmic Dis3L1 degraded mRNA upstream cleavage products, which were not bound by the 5'-cap binding complex and, consequently, were susceptible to degradation in the 5' to 3' direction by the XRN exoribonucleases.
Collapse
Affiliation(s)
- Walt F Lima
- Ionis Pharmaceuticals Inc., Carlsbad, CA, USA
| | | | | | | |
Collapse
|
21
|
Yurenko YP, Novotný J, Sklenář V, Marek R. Substituting CF2 for O4' in Components of Nucleic Acids: Towards Systems with Reduced Propensity to Form Abasic Lesions. Chemistry 2015; 21:17933-43. [PMID: 26493955 DOI: 10.1002/chem.201502977] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Indexed: 01/22/2023]
Abstract
Intrinsic structural features and energetics of nucleotides containing variously fluorinated sugars as potential building blocks of DNA duplexes and quadruplexes are explored systematically using the modern methods of density functional theory (DFT) and quantum chemical topology (QCT). Our results suggest that fluorination at the 2'-β or 2'-α,β positions somewhat stabilizes in vacuo the AI relative to the BI conformations. In contrast, substitution of the CF2 group for the O4' atom (O4'-CF2 modification) leads to a preference of the BI relative to AI DNA-like conformers. All the studied modifications result in a noticeable increase in the stability of the glycosidic bond [estimated by the relaxed force constants (RFC) approach], with particularly encouraging results for the O4'-CF2 derivative. Consequently, the O4'-CF2 modified systems are suggested and explored as promising scaffolds for the development of duplex and quadruplex structures with reduced propensity to form abasic lesions and to undergo DNA damage.
Collapse
Affiliation(s)
- Yevgen P Yurenko
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno (Czech Republic).
| | - Jan Novotný
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno (Czech Republic)
| | - Vladimir Sklenář
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno (Czech Republic).,National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno (Czech Republic).,Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno (Czech Republic)
| | - Radek Marek
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno (Czech Republic). .,National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno (Czech Republic). .,Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno (Czech Republic).
| |
Collapse
|
22
|
Alves Ferreira-Bravo I, Cozens C, Holliger P, DeStefano JJ. Selection of 2'-deoxy-2'-fluoroarabinonucleotide (FANA) aptamers that bind HIV-1 reverse transcriptase with picomolar affinity. Nucleic Acids Res 2015; 43:9587-99. [PMID: 26476448 PMCID: PMC4751925 DOI: 10.1093/nar/gkv1057] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 10/02/2015] [Indexed: 11/17/2022] Open
Abstract
Using a Systematic Evolution of Ligands by Exponential Enrichment (SELEX) protocol capable of selecting xeno-nucleic acid (XNA) aptamers, a 2′-deoxy-2′-fluoroarabinonucleotide (FANA) aptamer (referred to as FA1) to HIV-1 reverse transcriptase (HIV-1 RT) was selected. FA1 bound HIV-1 RT with KD,app values in the low pM range under different ionic conditions. Comparisons to published HIV-1 RT RNA and DNA aptamers indicated that FA1 bound at least as well as these aptamers. FA1 contained a 20 nucleotide 5′ DNA sequence followed by a 57 nucleotide region of FANA nucleotides. Removal of the fourteen 5′ DNA nucleotides did not affect binding. FA1's predicted structure was composed of four stems and four loops. All stem nucleotides could be modified to G-C base pairs (14 total changes) with a small effect on binding. Eliminating or altering most loop sequences reduced or abolished tight binding. Overall, results suggested that the structure and the sequence of FA1 were important for binding. FA1 showed strong inhibition of HIV-1 RT in extension assays while no specific binding to avian myeloblastosis or Moloney murine leukemia RTs was detected. A complete DNA version of FA1 showed low binding to HIV-1 RT, emphasizing the unique properties of FANA in HIV-1 RT binding.
Collapse
Affiliation(s)
- Irani Alves Ferreira-Bravo
- Cell Biology and Molecular Genetics, Bioscience Research Building, University of Maryland, College Park, MD 20742, USA Maryland Pathogen Research Institute, College Park, MD 20742, USA
| | - Christopher Cozens
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Jeffrey J DeStefano
- Cell Biology and Molecular Genetics, Bioscience Research Building, University of Maryland, College Park, MD 20742, USA Maryland Pathogen Research Institute, College Park, MD 20742, USA
| |
Collapse
|
23
|
Moreno PMD, Pêgo AP. Therapeutic antisense oligonucleotides against cancer: hurdling to the clinic. Front Chem 2014; 2:87. [PMID: 25353019 PMCID: PMC4196572 DOI: 10.3389/fchem.2014.00087] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Accepted: 09/23/2014] [Indexed: 12/11/2022] Open
Abstract
Under clinical development since the early 90's and with two successfully approved drugs (Fomivirsen and Mipomersen), oligonucleotide-based therapeutics has not yet delivered a clinical drug to the market in the cancer field. Whilst many pre-clinical data has been generated, a lack of understanding still exists on how to efficiently tackle all the different challenges presented for cancer targeting in a clinical setting. Namely, effective drug vectorization, careful choice of target gene or synergistic multi-gene targeting are surely decisive, while caution must be exerted to avoid potential toxic, often misleading off-target-effects. Here a brief overview will be given on the nucleic acid chemistry advances that established oligonucleotide technologies as a promising therapeutic alternative and ongoing cancer related clinical trials. Special attention will be given toward a perspective on the hurdles encountered specifically in the cancer field by this class of therapeutic oligonucleotides and a view on possible avenues for success is presented, with particular focus on the contribution from nanotechnology to the field.
Collapse
Affiliation(s)
- Pedro M D Moreno
- Instituto de Engenharia Biomédica, Nanobiomaterials for Targeted Therapies Group Porto, Portugal
| | - Ana P Pêgo
- Instituto de Engenharia Biomédica, Nanobiomaterials for Targeted Therapies Group Porto, Portugal ; Faculdade de Engenharia, Universidade do Porto Porto, Portugal ; Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto Porto, Portugal
| |
Collapse
|
24
|
Sarell CJ, Karamanos TK, White SJ, Bunka DHJ, Kalverda AP, Thompson GS, Barker AM, Stockley PG, Radford SE. Distinguishing closely related amyloid precursors using an RNA aptamer. J Biol Chem 2014; 289:26859-26871. [PMID: 25100729 PMCID: PMC4175327 DOI: 10.1074/jbc.m114.595066] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Although amyloid fibrils assembled in vitro commonly involve a single protein, fibrils formed in vivo can contain multiple protein sequences. The amyloidogenic protein human β2-microglobulin (hβ2m) can co-polymerize with its N-terminally truncated variant (ΔN6) in vitro to form hetero-polymeric fibrils that differ from their homo-polymeric counterparts. Discrimination between the different assembly precursors, for example by binding of a biomolecule to one species in a mixture of conformers, offers an opportunity to alter the course of co-assembly and the properties of the fibrils formed. Here, using hβ2m and its amyloidogenic counterpart, ΔΝ6, we describe selection of a 2'F-modified RNA aptamer able to distinguish between these very similar proteins. SELEX with a N30 RNA pool yielded an aptamer (B6) that binds hβ2m with an EC50 of ∼200 nM. NMR spectroscopy was used to assign the (1)H-(15)N HSQC spectrum of the B6-hβ2m complex, revealing that the aptamer binds to the face of hβ2m containing the A, B, E, and D β-strands. In contrast, binding of B6 to ΔN6 is weak and less specific. Kinetic analysis of the effect of B6 on co-polymerization of hβ2m and ΔN6 revealed that the aptamer alters the kinetics of co-polymerization of the two proteins. The results reveal the potential of RNA aptamers as tools for elucidating the mechanisms of co-assembly in amyloid formation and as reagents able to discriminate between very similar protein conformers with different amyloid propensity.
Collapse
Affiliation(s)
- Claire J Sarell
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Theodoros K Karamanos
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Simon J White
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - David H J Bunka
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Arnout P Kalverda
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Gary S Thompson
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Amy M Barker
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.
| |
Collapse
|
25
|
Jung ME, Dwight TA, Vigant F, Østergaard ME, Swayze EE, Seth PP. Synthesis and duplex-stabilizing properties of fluorinated N-methanocarbathymidine analogues locked in the C3'-endo conformation. Angew Chem Int Ed Engl 2014; 53:9893-7. [PMID: 25044699 DOI: 10.1002/anie.201405283] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Indexed: 11/11/2022]
Abstract
The efficient synthesis, antiviral activity, and duplex-stabilizing properties of both isomers of the 2'-fluoro analogue of Northern methanocarbathymidine (N-MCT), 2 and 3, are reported. We show that 2'-F incorporation on the N-MCT scaffold has a strong stabilizing effect on duplex thermal stability.
Collapse
Affiliation(s)
- Michael E Jung
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 (USA).
| | | | | | | | | | | |
Collapse
|
26
|
Jung ME, Dwight TA, Vigant F, Østergaard ME, Swayze EE, Seth PP. Synthesis and Duplex-Stabilizing Properties of FluorinatedN-Methanocarbathymidine Analogues Locked in the C3′-endoConformation. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201405283] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
27
|
Dramatic effect of furanose C2' substitution on structure and stability: directing the folding of the human telomeric quadruplex with a single fluorine atom. J Am Chem Soc 2013; 135:5344-7. [PMID: 23521511 DOI: 10.1021/ja401954t] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Human telomeric DNA quadruplexes can adopt different conformations in solution. We have found that arabinose, 2'F-arabinose, and ribose substitutions stabilize the propeller parallel G-quadruplex form over competing conformers, allowing NMR structural determination of this particularly significant nucleic acid structure. 2'F-arabinose substitution provides the greatest stabilization as a result of electrostatic (F-CH---O4') and pseudo-hydrogen-bond (F---H8) stabilizing interactions. In contrast, 2'F-rG substitution provokes a dramatic destabilization of the quadruplex structure due to unfavorable electrostatic repulsion between the phosphate and the 2'-F.
Collapse
|
28
|
Baranowski D, Golankiewicz B, Folkman W, Popenda M. 2-Methylwyosine, a nucleoside with restricted anti conformation in the east region enforced by nucleobase moiety modification: synthesis and conformational analysis by NMR and molecular dynamics. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2013; 31:707-19. [PMID: 23067123 DOI: 10.1080/15257770.2012.724133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We synthesized a new 2-methyl derivative of wyosine using a multistep procedure starting from guanosine. We examined different synthetic paths and optimized the conditions for each step. Based on MD calculations and analysis of the (3) J (HH) and J (C1'H1') of the ribose moiety, we discovered that the sugar part adopted conformation specific for the East region rarely occurring in solution. This unusual conformational preference is probably due to steric repulsions between the methyl group at position 2 and the 5'-CH(2)OH group. We observed that N-glycosidic bond stability weakened 14-fold upon the introduction of the methyl group in position 2 compared with wyosine.
Collapse
Affiliation(s)
- Daniel Baranowski
- Laboratory of Nucleoside Chemistry, Institute of Bioorganic Chemistry PAS, Poznan, Poland.
| | | | | | | |
Collapse
|
29
|
Deleavey GF, Damha MJ. Designing chemically modified oligonucleotides for targeted gene silencing. ACTA ACUST UNITED AC 2012; 19:937-54. [PMID: 22921062 DOI: 10.1016/j.chembiol.2012.07.011] [Citation(s) in RCA: 423] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2012] [Revised: 06/28/2012] [Accepted: 07/02/2012] [Indexed: 02/07/2023]
Abstract
Oligonucleotides (ONs), and their chemically modified mimics, are now routinely used in the laboratory as a means to control the expression of fundamentally interesting or therapeutically relevant genes. ONs are also under active investigation in the clinic, with many expressing cautious optimism that at least some ON-based therapies will succeed in the coming years. In this review, we will discuss several classes of ONs used for controlling gene expression, with an emphasis on antisense ONs (AONs), small interfering RNAs (siRNAs), and microRNA-targeting ONs (anti-miRNAs). This review provides a current and detailed account of ON chemical modification strategies for the optimization of biological activity and therapeutic application, while clarifying the biological pathways, chemical properties, benefits, and limitations of oligonucleotide analogs used in nucleic acids research.
Collapse
Affiliation(s)
- Glen F Deleavey
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, QC H3A 0B8, Canada.
| | | |
Collapse
|
30
|
Zhao L, Pence MG, Christov PP, Wawrzak Z, Choi JY, Rizzo CJ, Egli M, Guengerich FP. Basis of miscoding of the DNA adduct N2,3-ethenoguanine by human Y-family DNA polymerases. J Biol Chem 2012; 287:35516-35526. [PMID: 22910910 DOI: 10.1074/jbc.m112.403253] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
N(2),3-Ethenoguanine (N(2),3-εG) is one of the exocyclic DNA adducts produced by endogenous processes (e.g. lipid peroxidation) and exposure to bioactivated vinyl monomers such as vinyl chloride, which is a known human carcinogen. Existing studies exploring the miscoding potential of this lesion are quite indirect because of the lability of the glycosidic bond. We utilized a 2'-fluoro isostere approach to stabilize this lesion and synthesized oligonucleotides containing 2'-fluoro-N(2),3-ε-2'-deoxyarabinoguanosine to investigate the miscoding potential of N(2),3-εG by Y-family human DNA polymerases (pols). In primer extension assays, pol η and pol κ replicated through N(2),3-εG, whereas pol ι and REV1 yielded only 1-base incorporation. Steady-state kinetics revealed that dCTP incorporation is preferred opposite N(2),3-εG with relative efficiencies in the order of pol κ > REV1 > pol η ≈ pol ι, and dTTP misincorporation is the major miscoding event by all four Y-family human DNA pols. Pol ι had the highest dTTP misincorporation frequency (0.71) followed by pol η (0.63). REV1 misincorporated dTTP and dGTP with much lower frequencies. Crystal structures of pol ι with N(2),3-εG paired to dCTP and dTTP revealed Hoogsteen-like base pairing mechanisms. Two hydrogen bonds were observed in the N(2),3-εG:dCTP base pair, whereas only one appears to be present in the case of the N(2),3-εG:dTTP pair. Base pairing mechanisms derived from the crystal structures explain the slightly favored dCTP insertion for pol ι in steady-state kinetic analysis. Taken together, these results provide a basis for the mutagenic potential of N(2),3-εG.
Collapse
Affiliation(s)
- Linlin Zhao
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146; Department of Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Matthew G Pence
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146; Department of Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Plamen P Christov
- Department of Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146; Department of Chemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Zdzislaw Wawrzak
- Northwestern University Synchrotron Research Center, Life Sciences Collaborative Access Team, Argonne, Illinois 60439
| | - Jeong-Yun Choi
- Division of Pharmacology, Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Gyeonggi-do 440-746, Republic of Korea
| | - Carmelo J Rizzo
- Department of Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146; Department of Chemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Martin Egli
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146; Department of Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146; Department of Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146.
| |
Collapse
|
31
|
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.
Collapse
Affiliation(s)
- Nerea Martín-Pintado
- Instituto de Química Física Rocasolano, CSIC, C/Serrano 119, 28006 Madrid, Spain
| | | | | | | | | | | | | |
Collapse
|
32
|
Onizuka K, Yeo J, David SS, Beal PA. NEIL1 binding to DNA containing 2'-fluorothymidine glycol stereoisomers and the effect of editing. Chembiochem 2012; 13:1338-48. [PMID: 22639086 DOI: 10.1002/cbic.201200139] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Indexed: 11/06/2022]
Abstract
Thymine glycol (Tg), one of the oxidized bases formed in DNA by reactive oxygen species, is repaired by the DNA glycosylases such as NEIL1, NTH1 and Endo III. In our recent studies, we showed that NEIL1's catalytic efficiency and lesion specificity are regulated by an RNA-editing adenosine deamination reaction. In this study, we synthesized oligodeoxynucleotides containing 2'-fluorothymidine glycol with either ribo or arabino configuration and investigated the binding of these modified DNAs with the unedited and edited forms of human NEIL1 along with E. coli Endo III. For the two forms of hNEIL1, binding affinities to FTg-containing DNA were similar indicating that the editing effect is more subtle than to simply alter substrate affinity. While the NEIL1-binding to FTg-containing DNAs was largely insensitive to C5 and 2' stereochemistry, a preference was observed for the FTg-G pair over the FTg-A pair. In addition, we found that optimal binding is observed with Endo III and duplex DNA with riboFTg(5S) paired with dG. The modified DNAs reported here will provide useful tools for further characterizing the interaction between DNA repair glycosylases and thymine glycol containing DNA.
Collapse
Affiliation(s)
- Kazumitsu Onizuka
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | | | | | | |
Collapse
|
33
|
Seth PP, Yu J, Jazayeri A, Pallan PS, Allerson CR, Østergaard ME, Liu F, Herdewijn P, Egli M, Swayze EE. Synthesis and antisense properties of fluoro cyclohexenyl nucleic acid (F-CeNA), a nuclease stable mimic of 2'-fluoro RNA. J Org Chem 2012; 77:5074-85. [PMID: 22591005 DOI: 10.1021/jo300594b] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We report the design and synthesis of 2'-fluoro cyclohexenyl nucleic acid (F-CeNA) pyrimidine phosphoramidites and the synthesis and biophysical, structural, and biological evaluation of modified oligonucleotides. The synthesis of the nucleoside phosphoramidites was accomplished in multigram quantities starting from commercially available methyl-D-mannose pyranoside. Installation of the fluorine atom was accomplished using nonafluorobutanesulfonyl fluoride, and the cyclohexenyl ring system was assembled by means of a palladium-catalyzed Ferrier rearrangement. Installation of the nucleobase was carried out under Mitsunobu conditions followed by standard protecting group manipulations to provide the desired pyrimidine phosphoramidites. Biophysical evaluation indicated that F-CeNA shows behavior similar to that of a 2'-modified nucleotide, and duplexes with RNA showed slightly lower duplex thermostability as compared to that of the more rigid 3'-fluoro hexitol nucleic acid (FHNA). However, F-CeNA modified oligonucleotides were significantly more stable against digestion by snake venom phosphodiesterases (SVPD) as compared to unmodified DNA, 2'-fluoro RNA (FRNA), 2'-methoxyethyl RNA (MOE), and FHNA modified oligonucleotides. Examination of crystal structures of a modified DNA heptamer duplex d(GCG)-T*-d(GCG):d(CGCACGC) by X-ray crystallography indicated that the cyclohexenyl ring system exhibits both the (3)H(2) and (2)H(3) conformations, similar to the C3'-endo/C2'-endo conformation equilibrium seen in natural furanose nucleosides. In the (2)H(3) conformation, the equatorial fluorine engages in a relatively close contact with C8 (2.94 Å) of the 3'-adjacent dG nucleotide that may represent a pseudo hydrogen bond. In contrast, the cyclohexenyl ring of F-CeNA was found to exist exclusively in the (3)H(2) (C3'-endo like) conformation in the crystal structure of the modified A-form DNA decamer duplex [d(GCGTA)-T*-d(ACGC)](2.) In an animal experiment, a 16-mer F-CeNA gapmer ASO showed similar RNA affinity but significantly improved activity compared to that of a sequence matched MOE ASO, thus establishing F-CeNA as a useful modification for antisense applications.
Collapse
Affiliation(s)
- Punit P Seth
- Isis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, California 92010, United States.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Abstract
Metal ions play a key role in nucleic acid structure and activity. Elucidation of the rules that govern the binding of metal ions is therefore an essential step for better understanding of the nucleic acid functions. This review is as an update to a preceding one (Metal Ions Biol. Syst., 1996, 32, 91-134), in which we offered a general view of metal ion interactions with mono-, di-, tri-, and oligonucleotides in the solid state, based on their crystal structures reported before 1994. In this chapter, we survey all the crystal structures of metal ion complexes with nucleotides involving oligonucleotides reported after 1994 and we have tried to uncover new characteristic metal bonding patterns for mononucleotides and oligonucleotides with A-RNA and A/B/Z-DNA fragments that form duplexes. We do not cover quadruplexes, duplexes with metal-mediated base-pairs, tRNAs, rRNAs in ribosome, ribozymes, and nucleic acid-drug and -protein complexes. Factors that affect metal binding to mononucleotides and oligonucleotide duplexes are also dealt with.
Collapse
|
35
|
Abstract
Numerous chemically modified oligonucleotides have been developed so far and show their own unique chemical properties and pharmacodynamic/pharmacokinetic characteristics. Among all non-natural nucleotides, to the best of our knowledge, only five chemistries are currently being tested in clinical trials: phosphorothioate, 2´-O-methyl RNA, 2´-O-methoxyethyl RNA, 2´,4´-bridged nucleic acid/locked nucleic acid and the phosphorodiamidate morpholino oligomer. Since phosphorothioate modification can improve the pharmacokinetics of oligonucleotides, this modification is currently used in combination with all other modifications except phosphorodiamidate morpholino oligomer. For the treatment of metabolic, cardiovascular, cancer and other systemic diseases, the phosphorothioate class of drugs is obviously helpful, while superior efficacies can be observed in phosphorodiamidate morpholino oligomer compared to other classes of oligonucleotides for the treatment of Duchenne muscular dystrophy. Which properties of antisense molecules are actually essential for clinical applications? In this article, we provide an overview of the medicinal chemistry of existing non-natural antisense molecules, as well as their clinical applications, to discuss which properties of antisense oligonuculeotides affect therapeutic potency.
Collapse
|
36
|
Maiti A, Drohat AC. Dependence of substrate binding and catalysis on pH, ionic strength, and temperature for thymine DNA glycosylase: Insights into recognition and processing of G·T mispairs. DNA Repair (Amst) 2011; 10:545-53. [PMID: 21474392 DOI: 10.1016/j.dnarep.2011.03.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Revised: 03/04/2011] [Accepted: 03/08/2011] [Indexed: 11/29/2022]
Abstract
Repair of G·T mismatches arising from deamination of 5-methylcytosine (m(5)C) involves excision of thymine and restoration of a G·C pair via base excision repair (BER). Thymine DNA glycosylase (TDG) is one of two mammalian enzymes that can specifically remove thymine from G·T mispairs. While TDG can excise other bases, it maintains stringent specificity for a CpG context, suggesting deaminated m(5)C is an important biological substrate. Recent studies reveal TDG is essential for embryogenesis; it helps to maintain an active chromatin complex and initiates BER to counter aberrant de novo CpG methylation, which may involve excision of actively deaminated m(5)C. The relatively weak G·T activity of TDG has been implicated in the hypermutability of CpG sites, which largely involves C→T transitions arising from m(5)C deamination. Thus, it is important to understand how TDG recognizes and process substrates, particularly G·T mispairs. Here, we extend our detailed studies of TDG by examining the dependence of substrate binding and catalysis on pH, ionic strength, and temperature. Catalytic activity is relatively constant for pH 5.5-9, but falls sharply for pH>9 due to severely weakened substrate binding, and, potentially, ionization of the target base. Substrate binding and catalysis diminish sharply with increasing ionic strength, particularly for G·T substrates, due partly to effects on nucleotide flipping. TDG aggregates rapidly and irreversibly at 37°C, but can be stabilized by specific and nonspecific DNA. The temperature dependence of catalysis reveals large and unexpected differences for G·U and G·T substrates, where G·T activity exhibits much steeper temperature dependence. The results suggest that reversible nucleotide flipping is much more rapid for G·T substrates, consistent with our previous findings that steric effects limit the active-site lifetime of thymine, which may account for the relatively weak G·T activity. Our findings provide important insight into catalysis by TDG, particularly for mutagenic G·T mispairs.
Collapse
Affiliation(s)
- Atanu Maiti
- Department of Biochemistry and Molecular Biology, Greenebaum Cancer Center, School of Medicine, University of Maryland, Baltimore, 21201, USA
| | | |
Collapse
|
37
|
Morgan MT, Maiti A, Fitzgerald ME, Drohat AC. Stoichiometry and affinity for thymine DNA glycosylase binding to specific and nonspecific DNA. Nucleic Acids Res 2010; 39:2319-29. [PMID: 21097883 PMCID: PMC3064789 DOI: 10.1093/nar/gkq1164] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Deamination of 5-methylcytosine to thymine creates mutagenic G·T mispairs, contributing to cancer and genetic disease. Thymine DNA glycosylase (TDG) removes thymine from these G·T lesions, and follow-on base excision repair yields a G·C pair. A previous crystal structure revealed TDG (catalytic domain) bound to abasic DNA product in a 2:1 complex, one subunit at the abasic site and the other bound to undamaged DNA. Biochemical studies showed TDG can bind abasic DNA with 1:1 or 2:1 stoichiometry, but the dissociation constants were unknown, as was the stoichiometry and affinity for binding substrates and undamaged DNA. We showed that 2:1 binding is dispensable for G·U activity, but its role in G·T repair was unknown. Using equilibrium binding anisotropy experiments, we show that a single TDG subunit binds very tightly to G·U mispairs and abasic (G·AP) sites, and somewhat less tightly G·T mispairs. Kinetics experiments show 1:1 binding provides full G·T activity. TDG binds undamaged CpG sites with remarkable affinity, modestly weaker than G·T mispairs, and exhibits substantial affinity for nonspecific DNA. While 2:1 binding is observed for large excess TDG concentrations, our findings indicate that a single TDG subunit is fully capable of locating and processing G·U or G·T lesions.
Collapse
Affiliation(s)
- Michael T Morgan
- Department of Biochemistry and Molecular Biology and Greenebaum Cancer Center, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
| | | | | | | |
Collapse
|
38
|
Deleavey GF, Watts JK, Alain T, Robert F, Kalota A, Aishwarya V, Pelletier J, Gewirtz AM, Sonenberg N, Damha MJ. Synergistic effects between analogs of DNA and RNA improve the potency of siRNA-mediated gene silencing. Nucleic Acids Res 2010; 38:4547-57. [PMID: 20413581 PMCID: PMC2910058 DOI: 10.1093/nar/gkq181] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Revised: 02/28/2010] [Accepted: 03/01/2010] [Indexed: 12/28/2022] Open
Abstract
We report that combining a DNA analog (2'F-ANA) with rigid RNA analogs [2'F-RNA and/or locked nucleic acid (LNA)] in siRNA duplexes can produce gene silencing agents with enhanced potency. The favored conformations of these two analogs are different, and combining them in a 1-1 pattern led to reduced affinity, whereas alternating short continuous regions of individual modifications increased affinity relative to an RNA:RNA duplex. Thus, the binding affinity at key regions of the siRNA duplex could be tuned by changing the pattern of incorporation of DNA-like and RNA-like nucleotides. These heavily or fully modified duplexes are active against a range of mRNA targets. Effective patterns of modification were chosen based on screens using two sequences targeting firefly luciferase. We then applied the most effective duplex designs to the knockdown of the eIF4E binding proteins 4E-BP1 and 4E-BP2. We identified modified duplexes with potency comparable to native siRNA. Modified duplexes showed dramatically enhanced stability to serum nucleases, and were characterized by circular dichroism and thermal denaturation studies. Chemical modification significantly reduced the immunostimulatory properties of these siRNAs in human peripheral blood mononuclear cells.
Collapse
Affiliation(s)
- Glen F. Deleavey
- Department of Chemistry, McGill University, Montréal, QC, Canada H3A 2K6, Department of Biochemistry and Goodman Cancer Center, McGill University, Montreal, QC, Canada H3A 1A3, Department of Biochemistry and Goodman Cancer Center, McIntyre Medical Sciences Building, McGill University, Montreal, QC, Canada H3G 1Y6 and Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Jonathan K. Watts
- Department of Chemistry, McGill University, Montréal, QC, Canada H3A 2K6, Department of Biochemistry and Goodman Cancer Center, McGill University, Montreal, QC, Canada H3A 1A3, Department of Biochemistry and Goodman Cancer Center, McIntyre Medical Sciences Building, McGill University, Montreal, QC, Canada H3G 1Y6 and Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Tommy Alain
- Department of Chemistry, McGill University, Montréal, QC, Canada H3A 2K6, Department of Biochemistry and Goodman Cancer Center, McGill University, Montreal, QC, Canada H3A 1A3, Department of Biochemistry and Goodman Cancer Center, McIntyre Medical Sciences Building, McGill University, Montreal, QC, Canada H3G 1Y6 and Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Francis Robert
- Department of Chemistry, McGill University, Montréal, QC, Canada H3A 2K6, Department of Biochemistry and Goodman Cancer Center, McGill University, Montreal, QC, Canada H3A 1A3, Department of Biochemistry and Goodman Cancer Center, McIntyre Medical Sciences Building, McGill University, Montreal, QC, Canada H3G 1Y6 and Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Anna Kalota
- Department of Chemistry, McGill University, Montréal, QC, Canada H3A 2K6, Department of Biochemistry and Goodman Cancer Center, McGill University, Montreal, QC, Canada H3A 1A3, Department of Biochemistry and Goodman Cancer Center, McIntyre Medical Sciences Building, McGill University, Montreal, QC, Canada H3G 1Y6 and Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Veenu Aishwarya
- Department of Chemistry, McGill University, Montréal, QC, Canada H3A 2K6, Department of Biochemistry and Goodman Cancer Center, McGill University, Montreal, QC, Canada H3A 1A3, Department of Biochemistry and Goodman Cancer Center, McIntyre Medical Sciences Building, McGill University, Montreal, QC, Canada H3G 1Y6 and Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Jerry Pelletier
- Department of Chemistry, McGill University, Montréal, QC, Canada H3A 2K6, Department of Biochemistry and Goodman Cancer Center, McGill University, Montreal, QC, Canada H3A 1A3, Department of Biochemistry and Goodman Cancer Center, McIntyre Medical Sciences Building, McGill University, Montreal, QC, Canada H3G 1Y6 and Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Alan M. Gewirtz
- Department of Chemistry, McGill University, Montréal, QC, Canada H3A 2K6, Department of Biochemistry and Goodman Cancer Center, McGill University, Montreal, QC, Canada H3A 1A3, Department of Biochemistry and Goodman Cancer Center, McIntyre Medical Sciences Building, McGill University, Montreal, QC, Canada H3G 1Y6 and Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Nahum Sonenberg
- Department of Chemistry, McGill University, Montréal, QC, Canada H3A 2K6, Department of Biochemistry and Goodman Cancer Center, McGill University, Montreal, QC, Canada H3A 1A3, Department of Biochemistry and Goodman Cancer Center, McIntyre Medical Sciences Building, McGill University, Montreal, QC, Canada H3G 1Y6 and Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Masad J. Damha
- Department of Chemistry, McGill University, Montréal, QC, Canada H3A 2K6, Department of Biochemistry and Goodman Cancer Center, McGill University, Montreal, QC, Canada H3A 1A3, Department of Biochemistry and Goodman Cancer Center, McIntyre Medical Sciences Building, McGill University, Montreal, QC, Canada H3G 1Y6 and Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| |
Collapse
|
39
|
Abstract
The ability to manipulate the RNA interference (RNAi) machinery to specifically silence the expression of target genes could be a powerful therapeutic strategy. Since the discovery that RNAi can be triggered in mammalian cells by short double-stranded RNAs (small interfering RNA, siRNA), there has been a tremendous push by researchers, from academia to big pharma, to move siRNAs into clinical application. The challenges facing siRNA therapeutics are significant. The inherent properties of siRNAs (polyanionic, vulnerable to nuclease cleavage) make clinical application difficult due to poor cellular uptake and rapid clearance. Side effects of siRNAs have also proven to be a further complication. Fortunately, numerous chemical modification strategies have been identified that allow many of these obstacles to be overcome. This unit will present an overview of (1) the chemical modifications available to the nucleic acid chemist for modifying siRNAs, (2) the application of chemical modifications to address specific therapeutic obstacles, and (3) the factors that must be considered when assessing the activity of modified siRNAs.
Collapse
|
40
|
Watts JK, Martín-Pintado N, Gómez-Pinto I, Schwartzentruber J, Portella G, Orozco M, González C, Damha MJ. Differential stability of 2'F-ANA*RNA and ANA*RNA hybrid duplexes: roles of structure, pseudohydrogen bonding, hydration, ion uptake and flexibility. Nucleic Acids Res 2010; 38:2498-511. [PMID: 20071751 PMCID: PMC2853132 DOI: 10.1093/nar/gkp1225] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Hybrids of RNA with arabinonucleic acids 2′F-ANA and ANA have very similar structures but strikingly different thermal stabilities. We now present a thorough study combining NMR and other biophysical methods together with state-of-the-art theoretical calculations on a fully modified 10-mer hybrid duplex. Comparison between the solution structure of 2′F-ANA•RNA and ANA•RNA hybrids indicates that the increased binding affinity of 2′F-ANA is related to several subtle differences, most importantly a favorable pseudohydrogen bond (2′F–purine H8) which contrasts with unfavorable 2′-OH–nucleobase steric interactions in the case of ANA. While both 2′F-ANA and ANA strands maintained conformations in the southern/eastern sugar pucker range, the 2′F-ANA strand’s structure was more compatible with the A-like structure of a hybrid duplex. No dramatic differences are found in terms of relative hydration for the two hybrids, but the ANA•RNA duplex showed lower uptake of counterions than its 2′F-ANA•RNA counterpart. Finally, while the two hybrid duplexes are of similar rigidities, 2′F-ANA single strands may be more suitably preorganized for duplex formation. Thus the dramatically increased stability of 2′F-ANA•RNA and ANA•RNA duplexes is caused by differences in at least four areas, of which structure and pseudohydrogen bonding are the most important.
Collapse
Affiliation(s)
- Jonathan K Watts
- Department of Chemistry, McGill University, Montreal, QC H3A 2K6, Canada
| | | | | | | | | | | | | | | |
Collapse
|
41
|
Rodionova T, Komarov V, Lipkowski J, Kuratieva N. The structure of the ionic clathrate hydrate of tetrabutylammonium valerate (C4H9)4NC4H9CO2·39.8H2O. NEW J CHEM 2010. [DOI: 10.1039/b9nj00530g] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
42
|
Egli M, Pallan PS. Crystallographic studies of chemically modified nucleic acids: a backward glance. Chem Biodivers 2010; 7:60-89. [PMID: 20087997 PMCID: PMC2905155 DOI: 10.1002/cbdv.200900177] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Chemically modified nucleic acids (CNAs) are widely explored as antisense oligonucleotide or small interfering RNA (siRNA) candidates for therapeutic applications. CNAs are also of interest in diagnostics, high-throughput genomics and target validation, nanotechnology and as model systems in investigations directed at a better understanding of the etiology of nucleic acid structure, as well as the physicochemical and pairing properties of DNA and RNA, and for probing protein-nucleic acid interactions. In this article, we review research conducted in our laboratory over the past two decades with a focus on crystal-structure analyses of CNAs and artificial pairing systems. We highlight key insights into issues ranging from conformational distortions as a consequence of modification to the modulation of pairing strength, and RNA affinity by stereoelectronic effects and hydration. Although crystal structures have only been determined for a subset of the large number of modifications that were synthesized and analyzed in the oligonucleotide context to date, they have yielded guiding principles for the design of new analogs with tailor-made properties, including pairing specificity, nuclease resistance, and cellular uptake. And, perhaps less obviously, crystallographic studies of CNAs and synthetic pairing systems have shed light on fundamental aspects of DNA and RNA structure and function that would not have been disclosed by investigations solely focused on the natural nucleic acids.
Collapse
Affiliation(s)
- Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232-0146, USA.
| | | |
Collapse
|
43
|
Williams AA, Darwanto A, Theruvathu JA, Burdzy A, Neidigh JW, Sowers LC. Impact of sugar pucker on base pair and mispair stability. Biochemistry 2009; 48:11994-2004. [PMID: 19899814 PMCID: PMC2814217 DOI: 10.1021/bi9014133] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The selection of nucleoside triphosphates by a polymerase is controlled by several energetic and structural features, including base pairing geometry as well as sugar structure and conformation. Whereas base pairing has been considered exhaustively, substantially less is known about the role of sugar modifications for both nucleotide incorporation and primer extension. In this study, we synthesized oligonucleotides containing 2'-fluoro-modified nucleosides with constrained sugar pucker in an internucleotide position and, for the first time, at a primer 3'-end. The thermodynamic stability of these duplexes was examined. The nucleoside 2'-deoxy-2'-fluoroarabinofuranosyluracil [U(2'F(ara))] favors the 2'-endo conformation (DNA-like), while 2'-deoxy-2'-fluororibofuranosyluracil [U(2'F(ribo))] favors the 3'-endo conformation (RNA-like). Oligonucleotides containing U(2'F(ara)) have slightly higher melting temperatures (T(m)) than those containing U(2'F(ribo)) when located in internucleotide positions or at the 3'-end and when correctly paired with adenine or mispaired with guanine. However, both modifications decrease the magnitude of DeltaH degrees and DeltaS degrees for duplex formation in all sequence contexts. In examining the thermodynamic properties for this set of oligonucleotides, we find entropy-enthalpy compensation is apparent. Our thermodynamic findings led to a series of experiments with DNA ligase that reveal, contrary to expectation based upon observed T(m) values, that the duplex containing the U(2'F(ribo)) analogue is more easily ligated. The 2'-fluoro-2'-deoxynucleosides examined here are valuable probes of the impact of sugar constraint and are also members of an important class of antitumor and antiviral agents. The data reported here may facilitate an understanding of the biological properties of these agents, as well as the contribution of sugar conformation to replication fidelity.
Collapse
Affiliation(s)
- Adides A. Williams
- Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, California 92350
| | - Agus Darwanto
- Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, California 92350
| | - Jacob A. Theruvathu
- Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, California 92350
| | - Artur Burdzy
- Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, California 92350
| | - Jonathan W. Neidigh
- Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, California 92350
| | - Lawrence C. Sowers
- Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, California 92350
| |
Collapse
|
44
|
Maiti A, Morgan MT, Drohat AC. Role of two strictly conserved residues in nucleotide flipping and N-glycosylic bond cleavage by human thymine DNA glycosylase. J Biol Chem 2009; 284:36680-36688. [PMID: 19880517 DOI: 10.1074/jbc.m109.062356] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Thymine DNA glycosylase (TDG) promotes genomic integrity by excising thymine from mutagenic G.T mismatches arising by deamination of 5-methylcytosine, and follow-on base excision repair enzymes restore a G.C pair. TDG cleaves the N-glycosylic bond of dT and some other nucleotides, including 5-substituted 2'-deoxyuridine analogs, once they have been flipped from the helix into its active site. We examined the role of two strictly conserved residues; Asn(140), implicated in the chemical step, and Arg(275), implicated in nucleotide flipping. The N140A variant binds substrate DNA with the same tight affinity as wild-type TDG, but it has no detectable base excision activity for a G.T substrate, and its excision rate is vastly diminished (by approximately 10(4.4)-fold) for G.U, G.FU, and G.BrU substrates. Thus, Asn(140) does not contribute substantially to substrate binding but is essential for the chemical step, where it stabilizes the transition state by approximately 6 kcal/mol (compared with 11.6 kcal/mol stabilization provided by TDG overall). Our recent crystal structure revealed that Arg(275) penetrates the DNA minor groove, filling the void created by nucleotide flipping. We found that the R275A and R275L substitutions weaken substrate binding and substantially decrease the base excision rate for G.T and G.BrU substrates. Our results indicate that Arg(275) promotes and/or stabilizes nucleotide flipping, a role that is most important for target nucleotides that are relatively large (dT and bromodeoxyuridine) and/or have a stable N-glycosylic bond (dT). Arg(275) does not contribute substantially to the binding of TDG to abasic DNA product, and it cannot account for the slow product release exhibited by TDG.
Collapse
Affiliation(s)
- Atanu Maiti
- Department of Biochemistry and Molecular Biology, Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Michael T Morgan
- Department of Biochemistry and Molecular Biology, Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Alexander C Drohat
- Department of Biochemistry and Molecular Biology, Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland 21201.
| |
Collapse
|
45
|
Varghese MK, Thomas R, Unnikrishnan NV, Sudarsanakumar C. Molecular dynamics simulations of xDNA. Biopolymers 2009; 91:351-60. [DOI: 10.1002/bip.21137] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
46
|
Pallan PS, Prakash TP, Li F, Eoff RL, Manoharan M, Egli M. A conformational transition in the structure of a 2'-thiomethyl-modified DNA visualized at high resolution. Chem Commun (Camb) 2009:2017-9. [PMID: 19333476 PMCID: PMC2909737 DOI: 10.1039/b822781k] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Crystal structures of A-form and B-form DNA duplexes containing 2'-S-methyl-uridines reveal that the modified residues adopt a RNA-like C3'-endo pucker, illustrating that the replacement of electronegative oxygen at the 2'-carbon of RNA by sulfur does not appear to fundamentally alter the conformational preference of the sugar in the oligonucleotide context and sterics trump stereoelectronics.
Collapse
Affiliation(s)
- Pradeep S. Pallan
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, Fax: (+) 1-615-322-7122
| | - Thazha P. Prakash
- Department of Medicinal Chemistry, ISIS Pharmaceuticals Inc., Carlsbad, California 92008
| | - Feng Li
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, Fax: (+) 1-615-322-7122
| | - Robert L. Eoff
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, Fax: (+) 1-615-322-7122
| | - Muthiah Manoharan
- Department of Drug Discovery, Alnylam Pharmaceuticals Inc., Cambridge, Massachusetts 02142
| | - Martin Egli
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, Fax: (+) 1-615-322-7122
| |
Collapse
|
47
|
Bowman BR, Lee S, Wang S, Verdine GL. Structure of the E. coli DNA glycosylase AlkA bound to the ends of duplex DNA: a system for the structure determination of lesion-containing DNA. Structure 2008; 16:1166-74. [PMID: 18682218 DOI: 10.1016/j.str.2008.04.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2008] [Revised: 04/23/2008] [Accepted: 04/30/2008] [Indexed: 10/21/2022]
Abstract
The constant attack on DNA by endogenous and exogenous agents gives rise to nucleobase modifications that cause mutations, which can lead to cancer. Visualizing the effects of these lesions on the structure of duplex DNA is key to understanding their biologic consequences. The most definitive method of obtaining such structures, X-ray crystallography, is troublesome to employ owing to the difficulty of obtaining diffraction-quality crystals of DNA. Here, we present a crystallization system that uses a protein, the DNA glycosylase AlkA, as a scaffold to mediate the crystallization of lesion-containing duplex DNA. We demonstrate the use of this system to facilitate the rapid structure determination of DNA containing the lesion 8-oxoguanine in several different sequence contexts, and also deoxyinosine and 1,N(6)-ethenoadenine, each stabilized as the corresponding 2'-flouro analog. The structures of 8-oxoguanine provide a correct atomic-level view of this important endogenous lesion in DNA.
Collapse
Affiliation(s)
- Brian R Bowman
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | | | | | | |
Collapse
|
48
|
Peng CG, Damha MJ. Probing DNA polymerase activity with stereoisomeric 2′-fluoro-β-D-arabinose (2′F-araNTPs) and 2′-fluoro-β-D-ribose (2′F-rNTPs) nucleoside 5′-triphosphates. CAN J CHEM 2008. [DOI: 10.1139/v08-089] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
2′-Deoxy-2′-fluoro-β-D-ribonucleosides (2′F-rN) and 2′-deoxy-2′-fluoro-β-D-arabinonucleosides (2′F-araN) differ solely in the stereochemistry at the 2′-carbon of the furanose sugar ring. 2′F-rN 5′-triphosphates (2′F-rNTPs) are among the most commonly used sugar-modified nucleoside 5′-triphosphates (NTPs) for in vitro selection; however, the epimeric 2′F-araN 5′-triphosphates (2′F-araNTPs) have only recently been applied to polymerase-directed biosynthesis [C.G. Peng and M.J. Damha. J. Am. Chem. Soc. 129, 5310 (2007)]. The present study describes primer extension assays that compare, for the first time, the incorporation efficiency of the two isomeric NTPs, namely, 2′F-araNTPs or 2′F-rNTPs, by four DNA polymerases [Deep Vent (exo-), 9°Nm, HIV-1 RT, and MMLV-RT]. Under the conditions used, incorporation of 2′F-araTTP proceeded more efficiently relative to 2′F-rUTP, while the incorporation of 2′F-araCTP is comparable or slightly less efficient than that observed with 2′F-rCTP. Interestingly, these preferences were observed for all four of the DNA polymerases tested. Unexpected differences in NTP incorporation were observed for 2′F-rCTP vs. rCTP. Despite their seemingly similar conformation, they behaved striking differently in the in vitro polymerization assays. 2′F-rCTP is a much better substrate than the native counterpart (rCTP), an observation first made with human DNA polymerases [F.C. Richardson, R.D. Kuchta, A. Mazurkiewicz, K.A. Richardson. Biochem. Pharmacol. 59, 1045 (2000)]. In contrast, 2′F-rUTP behaved like rUTP, providing poor yield of full-length products. Taken together, this indicates that 2′F-rCTP is very unusual with regard to enzyme/substrate recognition; an observation that can be exploited for the production of DNA oligomers enriched with both ribose and arabinose modifications. These findings are timely given the significant interest and growing need to develop chemically modified oligonucleotides for therapeutic and diagnostic research. By examining the structure-activity relationship (SAR) of the ribose and arabinose sugar, this study furthers our understanding of how the nature of the 2′ substituent (e.g., α vs. β; F vs. OH) and the heterocyclic base affect NTP selection (specificity) by DNA polymerases.Key words: 2′F-rNTPs, 2′F-araNTPs, DNA polymerases, biosynthesis, modified nucleoside triphosphates.
Collapse
|
49
|
Lee S, Bowman BR, Ueno Y, Wang S, Verdine GL. Synthesis and structure of duplex DNA containing the genotoxic nucleobase lesion N7-methylguanine. J Am Chem Soc 2008; 130:11570-1. [PMID: 18686953 DOI: 10.1021/ja8025328] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The predominant product of aberrant DNA methylation is the genotoxic lesion N7-methyl-2'-deoxyguanosine (m7dG). M7dG is recognized and excised by lesion-specific DNA glycosylases, namely AlkA in E. coli and Aag in humans. Structural studies of m7dG recognition and catalysis by these enzymes have been hampered due to a lack of efficient means by which to incorporate the chemically labile m7dG moiety site-specifically into DNA on a preparative scale. Here we report a solution to this problem. We stabilized the lesion toward acid-catalyzed and glycosylase-catalyzed depurination by 2'-fluorination and toward base-catalyzed degradation using mild, nonaqueous conditions in the DNA deprotection reaction. Duplex DNA containing 2'-fluoro-m7dG (Fm7dG) cocrystallized with AlkA as a host-guest complex in which the lesion-containing segment of DNA was nearly devoid of protein contacts, thus enabling the first direct visualization of the N7-methylguanine lesion nucleobase in DNA. The structure reveals that the base-pairing mode of Fm7dG:C is nearly identical to that of G:C, and Fm7dG does not induce any apparent structural disturbance of the duplex structure. These observations suggest that AlkA and Aag must perform a structurally invasive interrogation of DNA in order to detect the presence of intrahelical m7dG lesions.
Collapse
Affiliation(s)
- Seongmin Lee
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | | | | | | | | |
Collapse
|
50
|
Seela F, Xu K. DNA with stable fluorinated dA and dG substitutes: syntheses, base pairing and 19F-NMR spectra of 7-fluoro-7-deaza-2'-deoxyadenosine and 7-fluoro-7-deaza-2'-deoxyguanosine. Org Biomol Chem 2008; 6:3552-60. [PMID: 19082156 DOI: 10.1039/b806145a] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Fluorinated DNA containing stable fluorine substituents in the "purine" base were synthesized for the first time. For this, the phosphoramidites of 7-fluoro-7-deaza-2'-deoxyadenosine and 7-fluoro-7-deaza-2'-deoxyguanosine were prepared and oligonucleotides were synthesized. The 7-fluoro substitution leads to increased duplex stability and more selective base pairing compared to the non-functionalized 7-deazapurine oligonucleotides. (19)F NMR spectra of fluorinated nucleosides, single stranded oligonucleotides and DNA duplex show only a single signal for one fluorine modification. The NMR sensitive (19)F spin or the positron emitting (18)F isotope make these compounds applicable for DNA detection or imaging in vitro and in vivo.
Collapse
Affiliation(s)
- Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.
| | | |
Collapse
|