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Liu J, Ingale SA, Seela F. Guanine and 8-Azaguanine in Anomeric DNA Hybrid Base Pairs: Stability, Fluorescence Sensing, and Efficient Mismatch Discrimination with α-d-Nucleosides. Bioconjug Chem 2018; 29:2265-2277. [PMID: 29771499 DOI: 10.1021/acs.bioconjchem.8b00261] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The α-anomers of 8-aza-2'-deoxyguanosine (αGd*) and 2'-deoxyguanosine (αGd) were site-specifically incorporated in 12-mer duplexes opposite to the four canonical DNA constituents dA, dG, dT, and dC. Oligodeoxyribonucleotides containing αGd* display significant fluorescence at slightly elevated pH (8.0). Oligodeoxyribonucleotides incorporating β-anomeric 8-aza-2'-deoxyguanosine (Gd*) and canonical dG were studied for comparison. For αGd* synthesis, an efficient purification of anomeric 8-azaguanine nucleosides was developed on the basis of protected intermediates, and a new αGd* phosphoramidite was prepared. Differences were observed for sugar conformations ( N vs S) and p Ka values of anomeric nucleosides. Duplex stability and mismatch discrimination were studied employing UV-dependent melting and fluorescence quenching. A gradual fluorescence change takes place in duplex DNA when the α-nucleoside αGd* was positioned opposite to the four canonical β-nucleosides. The strongest fluorescence decrease appeared in duplexes incorporating αGd*-Cd base pair matches. Decreasing fluorescence corresponds to increasing Tm values. For mismatch discrimination, the α-anomers αGd* and αGd are more efficient than the corresponding β-nucleosides. Duplexes with single "purine-purine" αGd*-αGd* or αGd-αGd base pairs are significantly more stable than those displaying β-d configuration. CD spectra indicate that single mutations by α-anomeric nucleosides do not affect the global structure of B-DNA.
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Affiliation(s)
- Jiang Liu
- Laboratory of Bioorganic Chemistry and Chemical Biology , Center for Nanotechnology , Heisenbergstrasse 11 , 48149 Münster , Germany.,State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, and Department of Oral Medicine of West China Hospital of Stomatology , Sichuan University , Chengdu , 610041 Sichuan , P. R. China.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien , Universität Osnabrück , Barbarastrasse 7 , 49069 Osnabrück , Germany
| | - Sachin A Ingale
- Laboratory of Bioorganic Chemistry and Chemical Biology , Center for Nanotechnology , Heisenbergstrasse 11 , 48149 Münster , Germany.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien , Universität Osnabrück , Barbarastrasse 7 , 49069 Osnabrück , Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology , Center for Nanotechnology , Heisenbergstrasse 11 , 48149 Münster , Germany.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien , Universität Osnabrück , Barbarastrasse 7 , 49069 Osnabrück , Germany
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2
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Guo X, Leonard P, Ingale SA, Liu J, Mei H, Sieg M, Seela F. 5-Aza-7-deaza-2'-deoxyguanosine and 2'-Deoxycytidine Form Programmable Silver-Mediated Base Pairs with Metal Ions in the Core of the DNA Double Helix. Chemistry 2018; 24:8883-8892. [PMID: 29573347 DOI: 10.1002/chem.201801273] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Indexed: 02/05/2023]
Abstract
5-Aza-7-deaza-2'-deoxyguanosine (dZ) forms a silver-mediated base pair with dC. The metal ion pair represents a mimic of the H-bonded Watson-Crick dG-dC pair. The modified nucleoside displays a similar shape as the parent 2'-deoxyguanosine from which it can be constructed by transposition of nitrogen-7 to the bridgehead position-5. It lacks the major groove binding site as the positional change moves the dG- acceptor position from nitrogen-7 to nitrogen-1. As a shape mimic of dG, it fits nicely in the DNA double helix. The purine-pyrimidine dZ-dC hetero pair shows a relationship to the pyrimidine-pyrimidine dC-dC homo base pair. The dZ-dC pair forms a mismatch in the absence of silver ions and matches after addition of metal ions. Base-pair formation was verified on self-complementary 6-mer duplexes and 12-mer DNA with random composition by UV-dependent Tm measurements. Modified silver-mediated and hydrogen-bonded canonical base pairs can coexist. The dZ-Ag+ -dC base pair is slightly less stable than the dG-dC pair, shows sequence dependence, and consumes one or two silver ions. These properties make the dZ-Ag+ -dC pair suitable for programmable incorporation of silver ions in DNA which cannot be achieved by canonical base pairs. If the silver ion content is higher than the total number of base pairs the duplexes turn into very stable structures in which all base pairs are considered to be in the silver-mediated pairing mode.
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Affiliation(s)
- Xiurong Guo
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany
| | - Sachin A Ingale
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069, Osnabrück, Germany
| | - Jiang Liu
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany.,State Key Laboratory of Oral Diseases and National Clinical, Research Center for Oral Diseases and Department of Oral Medicine, of West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, P.R. China
| | - Hui Mei
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany
| | - Martha Sieg
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069, Osnabrück, Germany
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3
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Abstract
The formation of canonical base pairs through Watson-Crick hydrogen bonding sits at the heart of the genetic apparatus. The specificity of the base pairing of adenine with thymine/uracil and guanine with cytosine preserves accurate information for the biochemical blueprint and replicates the instructions necessary for carrying out biological function. The chemical evolution question of how these five canonical nucleobases were selected over various other possibilities remains intriguing. Since these and alternative nucleobases would have been available for chemical evolution, the reasons for the emergence of this system appear to be primarily functional. While investigating the base-pairing properties of structural nucleic acid analogs, we encountered a relationship between the pK(a) of a series of nonstandard (and canonical) nucleobases and the pH of the aqueous medium. This relationship appeared to correspond with the propensity of these molecules to self-assemble via Watson-Crick-type base-pairing interactions. A simple correlation of the "magnitude of the difference between the pK(a) and pH" (pK(a)-pH correlation) enables a general prediction of which types of heterocyclic recognition elements form hydrogen-bonded base pairs in aqueous media. Using the pK(a)-pH relationship, we can rationalize why nature chose the canonical nucleobases in terms of hydrophobic and hydrophilic interactions, and further extrapolate its significance within the context of chemical evolution. The connection between the physicochemical properties of bioorganic compounds and the interactions with their aqueous environment directly affects structure and function, at both a molecular and a supramolecular level. A general structure-function pattern emerges in biomolecules and biopolymers in aqueous media near neutral pH. A pK(a) - pH < 2 generally prompts catalytic functions, central to metabolism, but a difference in pK(a) - pH > 2 seems to result in the emergence of structure, central to replication. While this general trend is observed throughout extant biology, it could have also been an important factor in chemical evolution.
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Affiliation(s)
- Ramanarayanan Krishnamurthy
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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4
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Ming X, Ding P, Leonard P, Budow S, Seela F. Parallel-stranded DNA: Enhancing duplex stability by the ‘G-clamp’ and a pyrrolo-dC derivative. Org Biomol Chem 2012; 10:1861-9. [DOI: 10.1039/c2ob06606h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Seela F, Ingale SA. "Double click" reaction on 7-deazaguanine DNA: synthesis and excimer fluorescence of nucleosides and oligonucleotides with branched side chains decorated with proximal pyrenes. J Org Chem 2010; 75:284-95. [PMID: 20000692 DOI: 10.1021/jo902300e] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The 7-tripropargylamine-7-deaza-2'-deoxyguanosine (2) containing two terminal triple bonds in the side chain was synthesized by the Sonogashira cross-coupling reaction from the corresponding 7-iodo nucleoside 1b. This was protected at the 2-amino group with an iso-butyryl residue, affording the protected intermediate 5. Then, compound 5 was converted to the 5'-O-DMT derivative 6, which on phosphitylation afforded the phosphoramidite 7. This was employed in solid-phase synthesis of a series of oligonucleotides. T(m) measurements demonstrate that a covalently attached tripropargylamine side chain increases duplex stability. Both terminal triple bonds of nucleoside 2 and corresponding oligonucleotides were functionalized by the Cu(I)-mediated 1,3-dipolar cycloaddition "double click reaction" with 1-azidomethyl pyrene 3, decorating the side chain with two proximal pyrenes. While the monomeric tripropargylamine nucleoside with two proximal pyrenes (4) shows strong excimer fluorescence, the ss-oligonucleotide containing 4 does not. This was also observed for ds-oligonucleotides when the complementary strand was unmodified. However, duplex DNA bearing pyrene residues in both strands exhibits strong excimer fluorescence when each strand contains two pyrene residues linked to the tripropargylamine moiety. This pyrene-pyrene interstrand interaction occurs when the pyrene modification sites of the duplex are separated by two base pairs which bring the fluorescent dyes in a proximal position. Molecular modeling indicates that only two out of four pyrene residues are interacting forming the exciplex while the other two do not communicate.
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Affiliation(s)
- Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.
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Lahoud G, Timoshchuk V, Lebedev A, Arar K, Hou YM, Gamper H. Properties of pseudo-complementary DNA substituted with weakly pairing analogs of guanine or cytosine. Nucleic Acids Res 2008; 36:6999-7008. [PMID: 18987000 PMCID: PMC2602760 DOI: 10.1093/nar/gkn797] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A straightforward enzymatic protocol for converting regular DNA into pseudo-complementary DNA could improve the performance of oligonucleotide microarrays by generating readily hybridizable structure-free targets. Here we screened several highly destabilizing analogs of G and C for one that could be used with 2-aminoadenine (nA) and 2-thiothymine (sT) to generate structure-free DNA that is fully accessible to complementary probes. The analogs, which included bioactive bases such as 6-thioguanine (sG), 5-nitrocytosine (NitroC), 2-pyrimidinone (P; the free base of zebularine) and 6-methylfuranopyrimidinone (MefP), were prepared as dNTPs and evaluated as substrates for T7 and Phi29 DNA polymerases that lacked editor function. Pairing properties of the analogs were characterized by solution hybridization assays using modified oligonucleotides or primer extension products. P and MeP did not support robust primer extension whereas sG and NitroC did. In hybridization assays, however, sG lacked discrimination and NitroC paired too strongly to C. The dNTPs of two other base analogs, 7-nitro-7-deazahypoxanthine (NitrocH) and 2-thiocytosine (sC), exhibited the greatest promise. Either analog could be used with nA and sT to generate DNA that was nearly structure-free. Hybridization of probes to these modified DNAs will require the development of base analogs that pair strongly to NitrocH or sC.
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Affiliation(s)
- Georges Lahoud
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
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7
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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Affiliation(s)
- Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.
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Lahoud G, Timoshchuk V, Lebedev A, de Vega M, Salas M, Arar K, Hou YM, Gamper H. Enzymatic synthesis of structure-free DNA with pseudo-complementary properties. Nucleic Acids Res 2008; 36:3409-19. [PMID: 18448471 PMCID: PMC2425472 DOI: 10.1093/nar/gkn209] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Long single-stranded DNAs and RNAs possess considerable secondary structure under conditions that support stable hybrid formation with oligonucleotides. Consequently, different oligomeric probes can hybridize to the same target with efficiencies that vary by several orders of magnitude. The ability to enzymatically generate structure-free single-stranded copies of any nucleic acid without impairing Watson–Crick base pairing to short probes would eliminate this problem and significantly improve the performance of many oligonucleotide-based applications. Synthetic nucleic acids that exhibit these properties are defined as pseudo-complementary. Previously, we described a pseudo-complementary A-T couple consisting of 2-aminoadenine (nA) and 2-thiothymine (sT) bases. The nA-sT couple is a mismatch even though nA-T and A-sT are stable base pairs. Here we show that 7-alkyl-7-deazaguanine and N4-alkylcytosine (where alkyl = methyl or ethyl) can be used in conjunction with nA and sT to render DNA largely structure-free and pseudo-complementary. The deoxynucleoside triphosphates (dNTPs) of these bases are incorporated into DNA by selected mesophilic and thermophilic DNA polymerases and the resulting primer extension products hybridize with good specificity and stability to oligonucleotide probes composed of the standard bases. Further optimization and characterization of the synthesis and properties of pseudo-complementary DNA should lead to an ideal target for use with oligonucleotide probes that are <25 nt in length.
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Affiliation(s)
- Georges Lahoud
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
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9
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Seela F, Driller H. 7-Deaza-2′-Deoxy-O6-Methylguanosine: Selective N2-Formylation Via a Formamidine, Phosphoramidite Synthesis and Properties of Oligonucleotides. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328318908054154] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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10
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Jain ML, Bruice TC. Solid-phase synthesis of positively charged deoxynucleic guanidine (DNG) oligonucleotide incorporating 7-deazaguanine bases. Bioorg Med Chem 2006; 14:7333-46. [PMID: 16945544 DOI: 10.1016/j.bmc.2006.05.074] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2006] [Revised: 05/31/2006] [Accepted: 05/31/2006] [Indexed: 10/24/2022]
Abstract
DNG nucleotides represent a positively charged DNA analog in which the negatively charged phosphodiester linkages of DNA are replaced by positively charged guanidinium linkages. We report herein the synthesis of 3'-end, middle, and 5'-end monomers required for the synthesis of a DNG sequence in which the natural guanine base is replaced by 7-deazaguanine (c(7)G). 7-Deazaguanine nucleobase was chosen because of their unique glycoside bond stability and their ability to prevent G-quartet formation. A facile and high yield two-step synthesis of xylo-7-deazaguanine 7, a key intermediate for introducing 3'-amino functionality, is carried out under Mitsunobu conditions. Subsequently, the 3'-Fmoc-protected thiourea monomers 13 and 19 were prepared from 7 via their corresponding 3'-amino-7-deazaguanines 11 and 18, respectively. The smooth coupling of these thiourea monomers with monomethoxytrityl (MMTr)-protected 3'-end monomer 25, prepared from 5, occurred on solid phase in 3'-->5' direction. The resultant trimeric HO-c(7)Ggc(7)Ggc(7)G-OH (1) has been designed to be included into DNA using standard DNA synthesis technology. The combination of C-c(7)G base pairing and electrostatic association of phosphodiester and guanidinium backbone allows the small synthesized DNG trimer 1 to form 1:1 complex with DNA-C pentamer.
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Affiliation(s)
- Moti L Jain
- Department of Chemistry and Biochemistry, University Of California, Santa Barbara, 93106, USA
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11
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Li H, Peng X, Leonard P, Seela F. Binding of actinomycin C1 (D) and actinomin to base-modified oligonucleotide duplexes with parallel chain orientation. Bioorg Med Chem 2006; 14:4089-100. [PMID: 16500105 DOI: 10.1016/j.bmc.2006.02.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2005] [Revised: 02/01/2006] [Accepted: 02/03/2006] [Indexed: 11/29/2022]
Abstract
The binding of actinomycin D (C1, 1) and its analog actinomin (2) was studied on base-modified oligonucleotide duplexes with parallel chain orientation (ps) and with anti-parallel chains (aps) for comparison. Actinomycin D binds not only to aps duplexes containing guanine-cytosine base pairs but also to those incorporating modified bases such as 7-deazaguanine or its 6-deoxo derivative. For this, novel phosphoramidites were prepared. The new building block of 7-deaza-2'-deoxyguanosine is significantly more stable than the one currently used and allows normal oxidation conditions during solid-phase oligonucleotide synthesis. Actinomycin binds weakly to ps duplexes containing guanine-isocytosine base pairs but not to ps-DNA incorporating pairs of isoguanine-cytosine residues. On the contrary, the actinomycin D analog actinomin, which contains positively charged side chains instead of the chiral peptide rings, is strongly bound to both ps- and aps-DNA. Guanines, isoguanine, as well as other 7-deaza derivatives are accepted as nucleobases. Apparently, the pentapeptide lacton rings of actinomycin do not fit nicely into the groove of ps-DNA thereby reducing the binding strength of the antibiotic while the groove size of ps-DNA does not affect actinomin binding notably.
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Affiliation(s)
- Hong Li
- Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie, Universität Osnabrück, Barbarastrasse 7, 49069 Osnabrück, Germany
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12
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Abstract
The propensity of RNA to fold into higher-order structures poses a major barrier to the use of short probes (<15 nucleotides) by preventing their accessibility. Introduction of the pseudo-complementary bases 2-aminoadenine (nA) and 2-thiouracil (sU) and the destabilizing base 7-deazaguanine (cG) into RNA provides a partial solution to this problem. While complementary in hydrogen bonding groups, nA and sU cannot form a stable base pair due to steric hindrance, and are thus pseudo-complementary. Each, however, recognizes the regular T/U and A complements, allowing pairing with oligonucleotides. Short pseudo-complementary RNAs can be prepared by in vitro transcription. Relative to standard transcripts, the modified transcripts possess reduced secondary structure and increased accessibility to short (8-mer) probes in the locked nucleic acid (LNA) configuration. They also hybridize to complementary probes with increased specificity and thermostability. Practical application of this strategy to oligonucleotide-based hybridization assays will require engineering of RNA polymerase for more efficient utilization of pseudo-complementary nucleoside triphosphates.
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Affiliation(s)
- Howard B Gamper
- Department of Biochemistry and Molecular Pharmacology, Room 222BLSB, Thomas Jefferson University, 233 South 10th Street, Philadelphia, Pennsylvania, 19107, USA.
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Rosemeyer H, Kaiser K, Seela F, Zabel V, Saenger W. Spontane Öffnung des Pyrimidinringes in Pyrrolo[2,3-d]pyrimidinen nach intramolekularer Acylierung. Helv Chim Acta 2004. [DOI: 10.1002/hlca.19850680226] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Seela F, Debelak H. The C(8)-(2'-deoxy-beta-D-ribofuranoside) of 7-deazaguanine: synthesis and base pairing of oligonucleotides with unusually linked nucleobases. J Org Chem 2002; 66:3303-12. [PMID: 11348111 DOI: 10.1021/jo001498q] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The 7-deazaguanine (2-aminopyrrolo[2,3-d]pyrimidin-4-one) C(8)-(2'-deoxy-beta-D-ribofuranoside) (6b), which possesses an unusual glycosylation site, was synthesized and incorporated in oligonucleotides. The oligonucleotides were prepared by solid-phase synthesis using phosphoramidite chemistry and were hybridized to form duplex DNA. Compound 6b is able to form base pairs with 2'-deoxy-5-methylisocytidine (m(5)isoC(d)) in oligonucleotide duplexes with antiparallel chain orientation and with dC in parallel duplex DNA. Thus, the C(8)-nucleoside 6b shows a similar base recognition as 2'-deoxyisoguanosine but not as 2'-deoxyguanosine. This indicates that the nucleic acid recognition not only depends on the donor-acceptor pattern of the nucleobase but is influenced by the glycosylation site. Base pairs of compound 6b formed with canonical and modified nucleosides are proposed.
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Affiliation(s)
- F Seela
- Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie, Universität Osnabrück, Barbarastr. 7, D-49069 Osnabrück, Germany.
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Seela F, Debelak H. 8-aza-7-deazaadenine and 7-deazaguanine: synthesis and properties of nucleosides and oligonucleotides with nucleobases linked at position-8. Nucleosides Nucleotides Nucleic Acids 2001; 20:577-85. [PMID: 11563075 DOI: 10.1081/ncn-100002334] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The 8-aza-7-deazaadenine (pyrazolo[3,4-d]pyrimidin-4-amine) N8-(2'-deoxyribonucleoside) (2) and the 7-deazaguanine (pyrrolo[3,4-d]pyrimidine-2-amin-(3H)-4-one) C8-(2'-deoxyribonucleoside) (4) were synthesized and incorporated in oligonucleotides employing phosphoramidite chemistry. Oligonucleotides carrying compound 2 are able to form base pairs with the four canonical DNA constituents without significant structural discrimination. The nucleoside 4 was obtained from the corresponding ribonucleoside by deoxygenation. Oligonucleotides containing compound 4 showed similar base pairing properties as those with 2'-deoxyisoguanosine.
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Affiliation(s)
- F Seela
- Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie, Universität Osnabrück, Barbarastr. 7, D-49069 Osnabrück, Germany
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17
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Abstract
Modification of the heterocyclic moiety of oligonucleotides has led to the discovery of potent antisense compounds. This review describes the physicochemical factors that are responsible for duplex stabilization through base modification. A summary is given of the different heterocyclic modifications that can be used to beneficially influence this duplex stability. The biologic activity of base-modified oligonucleotides is described, and the different factors that are important for obtaining in vivo antisense activity with heterocyclic-modified oligonucleotides are summarized.
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Affiliation(s)
- P Herdewijn
- Rega Institute for Medical Research, K.U. Leuven, Laboratory for Medicinal Chemistry, Belgium
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18
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Seela F, Mittelbach C. 7-Deaza-2′-deoxyinosine: A Stable Nucleoside with the Ambiguous Base Pairing Properties of 2′-Deoxyinosine. ACTA ACUST UNITED AC 1999. [DOI: 10.1080/15257779908043087] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Seela F, Melenewski A. 5-Aza-7-deaza-2′-deoxyguanosine: Oligonucleotide Duplexes with Novel Base Pairs, Parallel Chain Orientation and Protonation Sites in the Core of a Double Helix. European J Org Chem 1999. [DOI: 10.1002/(sici)1099-0690(199902)1999:2<485::aid-ejoc485>3.0.co;2-j] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Ramzaeva N, Seela F. 7-Substituted 7-Deaza-2?-deoxyguanosines: Regioselective Halogenation of Pyrrolo[2,3-d]pyrimidine Nucleosides. Helv Chim Acta 1995. [DOI: 10.1002/hlca.19950780505] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Grein T, Lampe S, Mersmann K, Rosemeyer H, Thomas H, Seela F. 3-deaza- and 7-deazapurines: duplex stability of oligonucleotides containing modified adenine or guanine bases. Bioorg Med Chem Lett 1994; 4:971-6. [DOI: 10.1016/s0960-894x(01)80665-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Seela F, Mersmann K. 7-Deazaguanosine: Synthesis of an oligorbonucleotide building block and disaggregation of the U-G-G-G-G-U G4 structure by the modified base. Helv Chim Acta 1993. [DOI: 10.1002/hlca.19930760404] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Seela F, Driller H. Alternating d(G-C)3 and d(C-G)3 hexanucleotides containing 7-deaza-2'-deoxyguanosine or 8-aza-7-deaza-2'-deoxyguanosine in place of dG. Nucleic Acids Res 1989; 17:901-10. [PMID: 2922275 PMCID: PMC331711 DOI: 10.1093/nar/17.3.901] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The synthesis of alternating hexamers (8-13) derived from d(C-G)3 or d(G-C)3 but containing c7z8Gd (2) or c7Gd (3) instead of dG is described employing phosphoramidite-chemistry. Apart from the isobutyryl group the dimethylaminomethylene residue was used for the nucleobase-protection of 3. The methyl- and the cyanoethyl-phosphoramidites of 3 (5a-c) were synthesized. They were employed together with those of c7G or c7z8Gd in automated oligonucleotide synthesis. Tm-values as well as thermodynamic data of the oligomers 9, 10, 12, and 13 indicated that duplexes were destabilized if c7Gd replaced dG, whereas c7z8Gd stabilized the duplex structure. In contrast to d(C-G)3 which underwent salt-dependent B-Z transition, CD-spectra of oligomers containing c7Gd or c7z8Gd in place of dG showed retained B-conformation.
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Affiliation(s)
- F Seela
- Laboratorium für Organische and Bioorganische Chemie, Universität Osnabrück, FRG
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Chollet A, Kawashima E. DNA containing the base analogue 2-aminoadenine: preparation, use as hybridization probes and cleavage by restriction endonucleases. Nucleic Acids Res 1988; 16:305-17. [PMID: 2829119 PMCID: PMC334628 DOI: 10.1093/nar/16.1.305] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The base analogue 2-aminoadenine (2,6-diaminopurine, D) has been introduced at selected positions into synthetic oligodeoxyribonucleotides and DNA by the combined use of chemical and enzymatic methods. 2-aminoadenine substitution for adenine introduces changes in the minor groove of DNA and creates an additional hydrogen bond in the Watson-Crick base pair with thymine. Oligonucleotide hybridization probes containing 2-aminoadenine showed increased selectivity and hybridization strength during DNA-DNA hybridization to phage or genomic target DNA. Properties of the base analogue with respect to DNA modifying enzymes were examined. 2-aminoadenine was used to probe minor groove determinants during the treatment of DNA by 12 restriction endonucleases. Inhibition of cleavage was found for several restriction enzymes.
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Affiliation(s)
- A Chollet
- Department of Chemistry, Biogen SA, Geneva, Switzerland
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Seela F, Steker H, Driller H, Bindig U. 2-Amino-2′-desoxytubercidin und verwandte Pyrrolo[2,3-d]pyrimidinyl-2′-desoxyribofuranoside. ACTA ACUST UNITED AC 1987. [DOI: 10.1002/jlac.198719870104] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Seela F, Driller H. Palindromic oligonucleotides containing 7-deaza-2'-deoxyguanosine: solid-phase synthesis of d[(p)GG*AATTCC] octamers and recognition by the endodeoxyribonuclease EcoRI. Nucleic Acids Res 1986; 14:2319-32. [PMID: 3008089 PMCID: PMC339660 DOI: 10.1093/nar/14.5.2319] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Octadeoxynucleotides with the sequence d[(p)GG*AATTCC] have been prepared by solid-phase synthesis employing regular and base-modified phosphoramidites. These oligomers which contain an isosterically altered recognition sequence of the endodeoxyribonuclease Eco RI form duplexes under appropriate salt conditions. Since G* can represent 7-deaza-2'-deoxyguanosine the oligomers were used as probes to study their cleavage by the endodeoxyribonuclease Eco RI. The enzymatic hydrolysis of the modified octamer was strongly decreased compared to the regular DNA-fragment. This shows that guanine N-7 located at the cleavage site is important for the recognition process by the enzyme. The residual enzymatic activity is discussed on the basis of reduced specificity towards the recognition fragment. The fact that this cleavage occurs already under regular conditions indicates that the process described here bases on an intrinsic property of the oligomer and is different from the star activity.
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Seela F, Kaiser K. Phosphoramidites of base-modified 2'-deoxyinosine isosteres and solid-phase synthesis of d(GCI*CGC) oligomers containing an ambiguous base. Nucleic Acids Res 1986; 14:1825-44. [PMID: 3951998 PMCID: PMC339576 DOI: 10.1093/nar/14.4.1825] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Novel phosphoramidites (1,2) of appropriately protected 2'-deoxyinosine isosteres (I*) such as allopurinol 2'-deoxyribofuranoside (4a) and 7-deaza-2'-deoxyinosine (4b) have been synthesized. They were employed together with the phosphoramidite of 2'-deoxyinosine in solid-phase synthesis of d(GCI*CGC) hexamers (12a-d). From thermodynamic data of these alternating hexamers it was shown that allopurinol 2'-deoxyribofuranoside destabilizes such duplexes less strongly than 2'-deoxyinosine. Additionally, the phosphoramidite of 7-deaza-2'-deoxyinosine (2) exhibits an extraordinary stability of the N-glycosylic bond. Since the new phosphoramidites are structurally related to 2'-deoxyinosine, they can be used in the construction of hybridization probes containing an ambiguous base.
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Herdering W, Kehne A, Seela F. Phosphoramidites of Chiral (Rp)-and (Sp)-Configurated d(T[P-18O]-A): Synthesis, Configurational Assignment, and Use as Dimer Blocks in Oligonucleotide Synthesis. Helv Chim Acta 1985. [DOI: 10.1002/hlca.19850680805] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Pon RT, Damha MJ, Ogilvie KK. Modification of guanine bases by nucleoside phosphoramidite reagents during the solid phase synthesis of oligonucleotides. Nucleic Acids Res 1985; 13:6447-65. [PMID: 4059050 PMCID: PMC321970 DOI: 10.1093/nar/13.18.6447] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Nucleoside 3'-phosphoramidite and chlorophosphite reagents have been found to react with the lactam function of guanine. This reaction caused unsatisfactory results when oligodeoxyribonucleotides containing a large number of guanine bases were prepared in an automated solid phase synthesizer. The guanine modification is unstable, and leads to depurination and chain cleavage. This side reaction can be eliminated by protecting the O6-position. A new O6-p-nitrophenylethyldeoxyguanosine phosphoramidite derivative, 8, was used to prepare sequences containing up to 24 guanine bases with greatly improved results. A hexatriacontanucleotide, d(CGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCA), was also prepared using O6-protected deoxyguanosine nucleosides.
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Seela F, Steker H. Facile Synthesis of 2?-Deoxyribofuranosides of Allopurinol and 4-Amino-1H-pyrazolo[3,4-d]pyrimidinevia Phase-Transfer Glycosylation. Helv Chim Acta 1985. [DOI: 10.1002/hlca.19850680305] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Seela F, Kehne A. 2'-Desoxytubercidin: synthese des o-3'-phosphoramidites und kondensation zu 2'-desoxytubercidylyl(3' → 5')-2'-desoxytubercidin. Tetrahedron 1985. [DOI: 10.1016/s0040-4020(01)96795-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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