1
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Zhang A, Kondhare D, Leonard P, Seela F. 5-Aza-7-deazaguanine-Isoguanine and Guanine-Isoguanine Base Pairs in Watson-Crick DNA: The Impact of Purine Tracts, Clickable Dendritic Side Chains, and Pyrene Adducts. Chemistry 2021; 27:7453-7466. [PMID: 33443814 PMCID: PMC8251886 DOI: 10.1002/chem.202005199] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Indexed: 12/19/2022]
Abstract
The Watson-Crick coding system depends on the molecular recognition of complementary purine and pyrimidine bases. Now, the construction of hybrid DNAs with Watson-Crick and purine-purine base pairs decorated with dendritic side chains was performed. Oligonucleotides with single and multiple incorporations of 5-aza-7-deaza-2'-deoxyguanosine, its tripropargylamine derivative, and 2'-deoxyisoguanosine were synthesized. Duplex stability decreased if single modified purine-purine base pairs were inserted, but increased if pyrene residues were introduced by click chemistry. A growing number of consecutive 5-aza-7-deazaguanine-isoguanine base pairs led to strong stepwise duplex stabilization, a phenomenon not observed for the guanine-isoguanine base pair. Spacious residues are well accommodated in the large groove of purine-purine DNA tracts. Changes to the global helical structure monitored by circular dichroism spectroscopy show the impact of functionalization to the global double-helix structure. This study explores new areas of molecular recognition realized by purine base pairs that are complementary in hydrogen bonding, but not in size, relative to canonical pairs.
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Affiliation(s)
- Aigui Zhang
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, University of Münster, Heisenbergstrasse 11, 48149, Münster, Germany
| | - Dasharath Kondhare
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, University of Münster, Heisenbergstrasse 11, 48149, Münster, Germany
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, University of Münster, Heisenbergstrasse 11, 48149, Münster, Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, University of Münster, 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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Raguraman P, Wang T, Ma L, Jørgensen PT, Wengel J, Veedu RN. Alpha-l-Locked Nucleic Acid-Modified Antisense Oligonucleotides Induce Efficient Splice Modulation In Vitro. Int J Mol Sci 2020; 21:ijms21072434. [PMID: 32244535 PMCID: PMC7177859 DOI: 10.3390/ijms21072434] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/27/2020] [Accepted: 03/29/2020] [Indexed: 01/04/2023] Open
Abstract
Alpha-l-Locked nucleic acid (α-l-LNA) is a stereoisomeric analogue of locked nucleic acid (LNA), which possesses excellent biophysical properties and also exhibits high target binding affinity to complementary oligonucleotide sequences and resistance to nuclease degradations. Therefore, α-l-LNA nucleotides could be utilised to develop stable antisense oligonucleotides (AO), which can be truncated without compromising the integrity and efficacy of the AO. In this study, we explored the potential of α-l-LNA nucleotides-modified antisense oligonucleotides to modulate splicing by inducing Dmd exon-23 skipping in mdx mouse myoblasts in vitro. For this purpose, we have synthesised and systematically evaluated the efficacy of α-l-LNA-modified 2'-O-methyl phosphorothioate (2'-OMePS) AOs of three different sizes including 20mer, 18mer and 16mer AOs in parallel to fully-modified 2'-OMePS control AOs. Our results demonstrated that the 18mer and 16mer truncated AO variants showed slightly better exon-skipping efficacy when compared with the fully-23 modified 2'-OMePS control AOs, in addition to showing low cytotoxicity. As there was no previous report on using α-l-LNA-modified AOs in splice modulation, we firmly believe that this initial study could be beneficial to further explore and expand the scope of α-l-LNA-modified AO therapeutic molecules.
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Affiliation(s)
- Prithi Raguraman
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth 6150 Australia; (P.R.); (T.W.)
- Perron Institute for Neurological and translational Science, Perth 6005, Australia
| | - Tao Wang
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth 6150 Australia; (P.R.); (T.W.)
- Perron Institute for Neurological and translational Science, Perth 6005, Australia
| | - Lixia Ma
- School of Statistics, Henan University of Economics and Law, Zhengzhou 450001, China;
| | - Per Trolle Jørgensen
- Nucleic Acid Center, Department of Physics and Chemistry and Pharmacy, University of Southern Denmark, M 5230 Odense, Denmark; (P.T.J.); (J.W.)
| | - Jesper Wengel
- Nucleic Acid Center, Department of Physics and Chemistry and Pharmacy, University of Southern Denmark, M 5230 Odense, Denmark; (P.T.J.); (J.W.)
| | - Rakesh N. Veedu
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth 6150 Australia; (P.R.); (T.W.)
- Perron Institute for Neurological and translational Science, Perth 6005, Australia
- Nucleic Acid Center, Department of Physics and Chemistry and Pharmacy, University of Southern Denmark, M 5230 Odense, Denmark; (P.T.J.); (J.W.)
- Correspondence:
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3
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Winiger CB, Langenegger SM, Calzaferri G, Häner R. Formation of Two Homo-chromophoric H-Aggregates in DNA-Assembled Alternating Dye Stacks. Angew Chem Int Ed Engl 2015; 54:3643-7. [DOI: 10.1002/anie.201410041] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 11/18/2014] [Indexed: 12/21/2022]
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4
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Winiger CB, Langenegger SM, Calzaferri G, Häner R. Formation of Two Homo-chromophoric H-Aggregates in DNA-Assembled Alternating Dye Stacks. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201410041] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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5
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Andersen NK, Anderson BA, Wengel J, Hrdlicka PJ. Synthesis and characterization of oligodeoxyribonucleotides modified with 2'-amino-α-L-LNA adenine monomers: high-affinity targeting of single-stranded DNA. J Org Chem 2013; 78:12690-702. [PMID: 24304240 DOI: 10.1021/jo4022937] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The development of conformationally restricted nucleotide building blocks continues to attract considerable interest because of their successful use within antisense, antigene, and other gene-targeting strategies. Locked nucleic acid (LNA) and its diastereomer α-L-LNA are two interesting examples thereof. Oligonucleotides modified with these units display greatly increased affinity toward nucleic acid targets, improved binding specificity, and enhanced enzymatic stability relative to unmodified strands. Here we present the synthesis and biophysical characterization of oligodeoxyribonucleotides (ONs) modified with 2'-amino-α-L-LNA adenine monomers W-Z. The synthesis of the target phosphoramidites 1-4 is initiated from pentafuranose 5, which upon Vorbrüggen glycosylation, O2'-deacylation, O2'-activation and C2'-azide introduction yields nucleoside 8. A one-pot tandem Staudinger/intramolecular nucleophilic substitution converts 8 into 2'-amino-α-L-LNA adenine intermediate 9, which after a series of nontrivial protecting-group manipulations affords key intermediate 15. Subsequent chemoselective N2'-functionalization and O3'-phosphitylation give targets 1-4 in ~1-3% overall yield over 11 steps from 5. ONs modified with pyrene-functionalized 2'-amino-α-L-LNA adenine monomers X-Z display greatly increased affinity toward DNA targets (ΔTm/modification up to +14 °C). Results from absorption and fluorescence spectroscopy suggest that the duplex stabilization is a result of pyrene intercalation. These characteristics render N2'-pyrene-functionalized 2'-amino-α-L-LNAs of considerable interest for DNA-targeting applications.
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Affiliation(s)
- Nicolai K Andersen
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , 5230 Odense, Denmark
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6
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Markova LI, Malinovskii VL, Patsenker LD, Häner R. J- vs. H-type assembly: pentamethine cyanine (Cy5) as a near-IR chiroptical reporter. Chem Commun (Camb) 2013; 49:5298-300. [PMID: 23636273 DOI: 10.1039/c3cc42103a] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The DNA-enabled dimerization of pentamethine cyanine (Cy5) dyes was studied by optical methods. The value of cyanine as a chiroptical reporter using a monomer-to-dimer switch is demonstrated. The specific shape of the CD signal and its high intensity are a result of J-type assembly.
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Affiliation(s)
- Larysa I Markova
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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7
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Hanessian S, Schroeder BR, Merner BL, Chen B, Swayze EE, Seth PP. Synthesis of cis- and trans-α-l-[4.3.0]bicyclo-DNA monomers for antisense technology: methods for the diastereoselective formation of bicyclic nucleosides. J Org Chem 2013; 78:9051-63. [PMID: 23937280 DOI: 10.1021/jo401166q] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Two α-L-ribo-configured bicyclic nucleic acid modifications, represented by analogues 12 and 13, which are epimeric at C3' and C5' have been synthesized using a carbohydrate-based approach to build the bicyclic core structure. An intramolecular L-proline-mediated aldol reaction was employed to generate the cis-configured ring junction of analogue 12 and represents a rare application of this venerable organocatalytic reaction to a carbohydrate system. In the case of analogue 13, where a trans-ring junction was desired, an intermolecular diastereoselective Grignard reaction followed by ring-closing metathesis was used. In order to set the desired stereochemistry at the C5' positions of both nucleoside targets, a study of diastereoselective Lewis acid mediated allylation reactions on a common bicyclic aldehyde precursor was carried out. Analogue 12 was incorporated in oligonucleotide sequences, and thermal denaturation experiments indicate that it is destabilizing when paired with complementary DNA and RNA. However, this construct shows a significant improvement in nuclease stability relative to a DNA oligonucleotide.
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Affiliation(s)
- Stephen Hanessian
- Department of Chemistry, Université de Montréal , Montréal, Québec H3C 3J7, Canada
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8
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Seth PP, Jazayeri A, Yu J, Allerson CR, Bhat B, Swayze EE. Structure Activity Relationships of α-L-LNA Modified Phosphorothioate Gapmer Antisense Oligonucleotides in Animals. MOLECULAR THERAPY. NUCLEIC ACIDS 2012; 1:e47. [PMID: 23344239 PMCID: PMC3499693 DOI: 10.1038/mtna.2012.34] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We report the structure activity relationships of short 14-mer phosphorothioate gapmer antisense oligonucleotides (ASOs) modified with α-L-locked nucleic acid (LNA) and related modifications targeting phosphatase and tensin homologue (PTEN) messenger RNA in mice. α-L-LNA represents the α-anomer of enantio-LNA and modified oligonucleotides show LNA like binding affinity for complementary RNA. In contrast to sequence matched LNA gapmer ASOs which showed elevations in plasma alanine aminotransferase (ALT) levels indicative of hepatotoxicity, gapmer ASOs modified with α-L-LNA and related analogs in the flanks showed potent downregulation of PTEN messenger RNA in liver tissue without producing elevations in plasma ALT levels. However, the α-L-LNA ASO showed a moderate dose-dependent increase in liver and spleen weights suggesting a higher propensity for immune stimulation. Interestingly, replacing α-L-LNA nucleotides in the 3′- and 5′-flanks with R-5′-Me-α-L-LNA but not R-6′-Me- or 3′-Me-α-L-LNA nucleotides, reversed the drug induced increase in organ weights. Examination of structural models of dinucleotide units suggested that the 5′-Me group increases steric bulk in close proximity to the phosphorothioate backbone or produces subtle changes in the backbone conformation which could interfere with recognition of the ASO by putative immune receptors. Our data suggests that introducing steric bulk at the 5′-position of the sugar-phosphate backbone could be a general strategy to mitigate the immunostimulatory profile of oligonucleotide drugs. In a clinical setting, proinflammatory effects manifest themselves as injection site reactions and flu-like symptoms. Thus, a mitigation of these effects could increase patient comfort and compliance when treated with ASOs.
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9
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Takada T, Otsuka Y, Nakamura M, Yamana K. Molecular Arrangement and Assembly Guided by Hydrophobic Cavities inside DNA. Chemistry 2012; 18:9300-4. [DOI: 10.1002/chem.201201469] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2012] [Indexed: 11/07/2022]
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10
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Affiliation(s)
- Yin Nah Teo
- Department of Chemistry, Stanford University, California 94305, United States
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11
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Sau SP, Hrdlicka PJ. C2'-pyrene-functionalized triazole-linked DNA: universal DNA/RNA hybridization probes. J Org Chem 2012; 77:5-16. [PMID: 22087648 PMCID: PMC3253902 DOI: 10.1021/jo201845z] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Development of universal hybridization probes, that is, oligonucleotides displaying identical affinity toward matched and mismatched DNA/RNA targets, has been a longstanding goal due to potential applications as degenerate PCR primers and microarray probes. The classic approach toward this end has been the use of "universal bases" that either are based on hydrogen-bonding purine derivatives or aromatic base analogues without hydrogen-bonding capabilities. However, development of probes that result in truly universal hybridization without compromising duplex thermostability has proven challenging. Here we have used the "click reaction" to synthesize four C2'-pyrene-functionalized triazole-linked 2'-deoxyuridine phosphoramidites. We demonstrate that oligodeoxyribonucleotides modified with the corresponding monomers display (a) minimally decreased thermal affinity toward DNA/RNA complements relative to reference strands, (b) highly robust universal hybridization characteristics (average differences in thermal denaturation temperatures of matched vs mismatched duplexes involving monomer W are <1.7 °C), and (c) exceptional affinity toward DNA targets containing abasic sites opposite of the modification site (ΔT(m) up to +25 °C). The latter observation, along with results from absorption and fluorescence spectroscopy, suggests that the pyrene moiety is intercalating into the duplex whereby the opposing nucleotide is pushed into an extrahelical position. These properties render C2'-pyrene-functionalized triazole-linked DNA as promising universal hybridization probes for applications in nucleic acid chemistry and biotechnology.
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Affiliation(s)
- Sujay P. Sau
- Department of Chemistry, University of Idaho, Moscow, ID-83844, USA
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12
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Ingale SA, Pujari SS, Sirivolu VR, Ding P, Xiong H, Mei H, Seela F. 7-Deazapurine and 8-aza-7-deazapurine nucleoside and oligonucleotide pyrene "click" conjugates: synthesis, nucleobase controlled fluorescence quenching, and duplex stability. J Org Chem 2011; 77:188-99. [PMID: 22129276 DOI: 10.1021/jo202103q] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
7-Deazapurine and 8-aza-7-deazapurine nucleosides related to dA and dG bearing 7-octadiynyl or 7-tripropargylamine side chains as well as corresponding oligonucleotides were synthesized. "Click" conjugation with 1-azidomethyl pyrene (10) resulted in fluorescent derivatives. Octadiynyl conjugates show only monomer fluorescence, while the proximal alignment of pyrene residues in the tripropargylamine derivatives causes excimer emission. 8-Aza-7-deazapurine pyrene "click" conjugates exhibit fluorescence emission much higher than that of 7-deazapurine derivatives. They are quenched by intramolecular charge transfer between the nucleobase and the dye. Oligonucleotide single strands decorated with two "double clicked" pyrenes show weak or no excimer fluorescence. However, when duplexes carry proximal pyrenes in complementary strands, strong excimer fluorescence is observed. A single replacement of a canonical nucleoside by a pyrene conjugate stabilizes the duplex substantially, most likely by stacking interactions: 6-12 °C for duplexes with a modified "adenine" base and 2-6 °C for a modified "guanine" base. The favorable photophysical properties of 8-aza-7-deazapurine pyrene conjugates improve the utility of pyrene fluorescence reporters in oligonucleotide sensing as these nucleoside conjugates are not affected by nucleobase induced quenching.
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Affiliation(s)
- Sachin A Ingale
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology , Heisenbergstraße 11, 48149 Münster, Germany
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13
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Østergaard ME, Hrdlicka PJ. Pyrene-functionalized oligonucleotides and locked nucleic acids (LNAs): tools for fundamental research, diagnostics, and nanotechnology. Chem Soc Rev 2011; 40:5771-88. [PMID: 21487621 PMCID: PMC3644995 DOI: 10.1039/c1cs15014f] [Citation(s) in RCA: 202] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Pyrene-functionalized oligonucleotides (PFOs) are increasingly explored as tools in fundamental research, diagnostics and nanotechnology. Their popularity is linked to the ability of pyrenes to function as polarity-sensitive and quenchable fluorophores, excimer-generating units, aromatic stacking moieties and nucleic acid duplex intercalators. These characteristics have enabled development of PFOs for detection of complementary DNA/RNA targets, discrimination of single nucleotide polymorphisms (SNPs), and generation of π-arrays on nucleic acid scaffolds. This critical review will highlight the physical properties and applications of PFOs that are likely to provide high degree of positional control of the chromophore in nucleic acid complexes. Particular emphasis will be placed on pyrene-functionalized Locked Nucleic Acids (LNAs) since these materials display interesting properties such as fluorescence quantum yields approaching unity and recognition of mixed-sequence double stranded DNA (144 references).
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14
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Seth PP, Allerson CR, Ostergaard ME, Swayze EE. Structural requirements for hybridization at the 5'-position are different in α-l-LNA as compared to β-D-LNA. Bioorg Med Chem Lett 2011; 22:296-9. [PMID: 22153935 DOI: 10.1016/j.bmcl.2011.11.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Revised: 11/02/2011] [Accepted: 11/03/2011] [Indexed: 01/02/2023]
Abstract
The synthesis and biophysical evaluation of R and S-5'-Me-α-l-LNA nucleoside phosphoramidites and modified oligo-2'-deoxyribonucleotides is reported. Synthesis of the nucleoside phosphoramidites was accomplished in multi-gram quantities starting from diacetone glucose. The 5'-methyl group in the S configuration was introduced by reacting the sugar 5'-aldehyde with MeMgBr. Synthesis of the R-5'-Me isomer was accomplished from the S-5'-Me nucleoside by a late stage inversion using Mitsunobu conditions. Evaluation of the modified oligonucleotides in thermal denaturation experiments revealed that R-5'-Me-α-l-LNA showed similar RNA affinity as α-l-LNA while the S-5'-Me analog was less stabilizing. This result is in contrast to the β-d-series where the S-5'-Me isomer showed LNA-like affinity for RNA while the R-5'-Me group completely reversed the stabilization effect on duplex thermostability.
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Affiliation(s)
- Punit P Seth
- Department of Medicinal Chemistry, Isis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA.
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15
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Karmakar S, Anderson BA, Rathje RL, Andersen S, Jensen TB, Nielsen P, Hrdlicka PJ. High-affinity DNA targeting using readily accessible mimics of N2'-functionalized 2'-amino-α-L-LNA. J Org Chem 2011; 76:7119-31. [PMID: 21827174 PMCID: PMC3163049 DOI: 10.1021/jo201095p] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
N2'-Pyrene-functionalized 2'-amino-α-L-LNAs (locked nucleic acids) display extraordinary affinity toward complementary DNA targets due to favorable preorganization of the pyrene moieties for hybridization-induced intercalation. Unfortunately, the synthesis of these monomers is challenging (~20 steps, <3% overall yield), which has precluded full characterization of DNA-targeting applications based on these materials. Access to more readily accessible functional mimics would be highly desirable. Here we describe short synthetic routes to a series of O2'-intercalator-functionalized uridine and N2'-intercalator-functionalized 2'-N-methyl-2'-aminouridine monomers and demonstrate, via thermal denaturation, UV-vis absorption and fluorescence spectroscopy experiments, that several of them mimic the DNA-hybridization properties of N2'-pyrene-functionalized 2'-amino-α-L-LNAs. For example, oligodeoxyribonucleotides (ONs) modified with 2'-O-(coronen-1-yl)methyluridine monomer Z, 2'-O-(pyren-1-yl)methyluridine monomer Y, or 2'-N-(pyren-1-ylmethyl)-2'-N-methylaminouridine monomer Q display prominent increases in thermal affinity toward complementary DNA relative to reference strands (average ΔT(m)/mod up to +12 °C), pronounced DNA-selectivity, and higher target specificity than 2'-amino-α-L-LNA benchmark probes. In contrast, ONs modified with 2'-O-(2-napthyl)uridine monomer W, 2'-O-(pyren-1-yl)uridine monomer X or 2'-N-(pyren-1-ylcarbonyl)-2'-N-methylaminouridine monomer S display very low affinity toward DNA targets. This demonstrates that even conservative alterations in linker chemistry, linker length, and surface area of the appended intercalators have marked impact on DNA-hybridization characteristics. Straightforward access to high-affinity building blocks such as Q, Y, and Z is likely to accelerate their use in DNA-targeting applications within nucleic acid based diagnostics, therapeutics, and material science.
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16
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Seth PP, Allerson CA, Østergaard ME, Swayze EE. Synthesis and biophysical evaluation of 3'-Me-α-L-LNA - Substitution in the minor groove of α-L-LNA duplexes. Bioorg Med Chem Lett 2011; 21:4690-4. [PMID: 21778053 DOI: 10.1016/j.bmcl.2011.06.104] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Revised: 06/22/2011] [Accepted: 06/24/2011] [Indexed: 10/18/2022]
Abstract
The synthesis and biophysical evaluation of 3'-Me-α-L-LNA is reported. The synthesis of the nucleoside building block phosphoramidite was accomplished starting from diacetone glucose. The 3'-Me group was introduced in the desired configuration by hydride mediated opening of an exocyclic epoxide. Inversion of the 2'-hydroxyl group was achieved by means of an oxidation/reduction sequence followed by cyclization onto a 5'-leaving group to assemble the [2.2.1] ring system. Biophysical evaluation of 3'-Me-α-L-LNA modified oligonucleotides showed good duplex thermal stabilizing properties which were similar to α-L-LNA. Mismatch discrimination experiments revealed that 3'-Me-α-L-LNA possess slightly enhanced discrimination properties for the GU wobble base-pair as compared to related nucleic acid analogs.
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Affiliation(s)
- Punit P Seth
- Department of Medicinal Chemistry, Isis Pharmaceuticals, 1891 Rutherford Road, Carlsbad, CA 92008, United States.
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17
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Østergaard ME, Kumar P, Baral B, Guenther DC, Anderson BA, Ytreberg FM, Deobald L, Paszczynski AJ, Sharma PK, Hrdlicka PJ. C5-functionalized DNA, LNA, and α-L-LNA: positional control of polarity-sensitive fluorophores leads to improved SNP-typing. Chemistry 2011; 17:3157-65. [PMID: 21328492 DOI: 10.1002/chem.201002109] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Revised: 11/16/2010] [Indexed: 12/17/2022]
Abstract
Single nucleotide polymorphisms (SNPs) are important markers in disease genetics and pharmacogenomic studies. Oligodeoxyribonucleotides (ONs) modified with 5-[3-(1-pyrenecarboxamido)propynyl]-2'-deoxyuridine monomer X enable detection of SNPs at non-stringent conditions due to differential fluorescence emission of matched versus mismatched nucleic acid duplexes. Herein, the thermal denaturation and optical spectroscopic characteristics of monomer X are compared to the corresponding locked nucleic acid (LNA) and α-L-LNA monomers Y and Z. ONs modified with monomers Y or Z result in a) larger increases in fluorescence intensity upon hybridization to complementary DNA, b) formation of more brightly fluorescent duplexes due to markedly larger fluorescence emission quantum yields (Φ(F)=0.44-0.80) and pyrene extinction coefficients, and c) improved optical discrimination of SNPs in DNA targets. Optical spectroscopy studies suggest that the nucleobase moieties of monomers X-Z adopt anti and syn conformations upon hybridization with matched and mismatched targets, respectively. The polarity-sensitive 1-pyrenecarboxamido fluorophore is, thereby, either positioned in the polar major groove or in the hydrophobic duplex core close to quenching nucleobases. Calculations suggest that the bicyclic skeletons of LNA and α-L-LNA monomers Y and Z influence the glycosidic torsional angle profile leading to altered positional control and photophysical properties of the C5-fluorophore.
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Affiliation(s)
- Michael E Østergaard
- Department of Chemistry, University of Idaho, P.O. Box 442343, Moscow, ID 83844-2343, USA
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18
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Seth PP, Yu J, Allerson CR, Berdeja A, Swayze EE. Synthesis and biophysical characterization of R-6'-Me-α-L-LNA modified oligonucleotides. Bioorg Med Chem Lett 2010; 21:1122-5. [PMID: 21256012 DOI: 10.1016/j.bmcl.2010.12.119] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Revised: 12/22/2010] [Accepted: 12/23/2010] [Indexed: 12/28/2022]
Abstract
The synthesis and biophysical properties of R-6'-Me-α-L-LNA, which has a methyl group in the (R) configuration on the 2',4'-bridging substituent of α-L-LNA, is reported. The synthesis of the uracil nucleobase phosphoramidite was efficiently accomplished in 14 steps and 8 chromatographic purifications starting from a known sugar intermediate. Biophysical evaluation revealed that substitution along the edge of the major groove does not impair the high affinity duplex forming ability of α-L-LNA modified oligonucleotides.
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Affiliation(s)
- Punit P Seth
- Department of Medicinal Chemistry, Isis Pharmaceuticals, 1891 Rutherford Road, Carlsbad, CA 92008, USA.
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19
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Østergaard ME, Cheguru P, Papasani MR, Hill RA, Hrdlicka PJ. Glowing Locked Nucleic Acids: Brightly Fluorescent Probes for Detection of Nucleic Acids in Cells. J Am Chem Soc 2010; 132:14221-8. [DOI: 10.1021/ja1057295] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Michael E. Østergaard
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, Department of Animal Veterinary Science, University of Idaho, Moscow, Idaho 83844-2330, and Biological Applications of Nanotechnology (BANTech) Center, University of Idaho, Moscow, Idaho 83844
| | - Pallavi Cheguru
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, Department of Animal Veterinary Science, University of Idaho, Moscow, Idaho 83844-2330, and Biological Applications of Nanotechnology (BANTech) Center, University of Idaho, Moscow, Idaho 83844
| | - Madhusudhan R. Papasani
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, Department of Animal Veterinary Science, University of Idaho, Moscow, Idaho 83844-2330, and Biological Applications of Nanotechnology (BANTech) Center, University of Idaho, Moscow, Idaho 83844
| | - Rodney A. Hill
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, Department of Animal Veterinary Science, University of Idaho, Moscow, Idaho 83844-2330, and Biological Applications of Nanotechnology (BANTech) Center, University of Idaho, Moscow, Idaho 83844
| | - Patrick J. Hrdlicka
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, Department of Animal Veterinary Science, University of Idaho, Moscow, Idaho 83844-2330, and Biological Applications of Nanotechnology (BANTech) Center, University of Idaho, Moscow, Idaho 83844
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20
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Østergaard ME, Guenther DC, Kumar P, Baral B, Deobald L, Paszczynski AJ, Sharma PK, Hrdlicka PJ. Pyrene-functionalized triazole-linked 2'-deoxyuridines-probes for discrimination of single nucleotide polymorphisms (SNPs). Chem Commun (Camb) 2010; 46:4929-31. [PMID: 20526503 DOI: 10.1039/c0cc01133a] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Oligonucleotides modified with pyrene-functionalized triazole-linked 2'-deoxyuridines display remarkable hybridization-induced increases in fluorescence emission and enable efficient fluorescent discrimination of SNPs via G-specific quenching.
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21
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Gondela A, Kumar TS, Walczak K, Wengel J. Synthesis and biophysical properties of oligodeoxynucleotides containing 2'-deoxy-5-(4-nitro-1H-imidazol-1-yl)-beta-D-uridine and 2'-deoxy-5-(1,3-dioxo-1H-benzo[de]isoquinolin-2(3H)-yl)-beta-D-uridine monomers. Chem Biodivers 2010; 7:350-62. [PMID: 20151382 DOI: 10.1002/cbdv.200900195] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Detection of single-nucleotide polymorphisms (SNPs) of biologically relevant DNA and RNA samples remain a scientific and practical challenge. We have synthesized phosphoramidite building blocks and oligodeoxynucleotide probes containing novel 2'-deoxyuridine monomers modified by 5-(4-nitro-1H-imidazol-1-yl; (monomer X) or 2'-deoxy-5-(1,3-dioxo-1H-benzo[de]isoquinolin-2(3H)-yl; monomer Y) substituents. The effects of monomers X and Y on duplex thermal stability, and their capability towards discrimination of single-base mismatches were furthermore studied. Encouraging results were obtained with respect to thermal mismatch discrimination using oligodeoxynucleotides containing monomer X and fluorescence-based discrimination using oligodeoxynucleotides containing monomer Y.
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Affiliation(s)
- Andrzej Gondela
- Department of Organic Chemistry, Biochemistry and Biotechnology, Selisian University of Technology, Krzywoustego 4, PL-44-100 Gliwice
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22
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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] [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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23
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Sau SP, Kumar TS, Hrdlicka PJ. Invader LNA: efficient targeting of short double stranded DNA. Org Biomol Chem 2010; 8:2028-36. [PMID: 20401378 DOI: 10.1039/b923465a] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Despite progress with triplex-forming oligonucleotides or helix-invading peptide nucleic acids (PNAs), there remains a need for probes facilitating sequence-unrestricted targeting of double stranded DNA (dsDNA) at physiologically relevant conditions. Invader LNA probes, i.e., DNA duplexes with "+1 interstrand zipper arrangements" of intercalator-functionalized 2'-amino-alpha-l-LNA monomers, are demonstrated herein to recognize short mixed sequence dsDNA targets. This approach, like pseudo-complementary PNA (pcPNA), relies on relative differences in stability between probe duplexes and the corresponding probe:target duplexes for generation of a favourable thermodynamic gradient. Unlike pcPNA, Invader LNA probes take advantage of the "nearest neighbour exclusion principle", i.e., intercalating units of Invader LNA monomers are poorly accommodated in probe duplexes but extraordinarily well tolerated in probe-target duplexes (DeltaT(m)/modification up to +11.5 degrees C). Recognition of isosequential dsDNA-targets occurs: a) at experimental temperatures much lower than the thermal denaturation temperatures (T(m)'s) of Invader LNAs or dsDNA-targets, b) at a wide range of ionic strengths, and c) with good mismatch discrimination. Recognition of dsDNA is monitored in real-time using inherent pyrene-pyrene excimer signals of Invader LNA probes, which provides insights into reaction kinetics and enables rational design of probes. These properties render Invader LNAs as promising probes for biomedical applications entailing sequence-unrestricted recognition of dsDNA.
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Affiliation(s)
- Sujay P Sau
- Department of Chemistry, University of Idaho, Moscow, ID 83844-2343, USA
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Schwartz E, Le Gac S, Cornelissen JJLM, Nolte RJM, Rowan AE. Macromolecular multi-chromophoric scaffolding. Chem Soc Rev 2010; 39:1576-99. [DOI: 10.1039/b922160c] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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25
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Malinovskii VL, Wenger D, Häner R. Nucleic acid-guided assembly of aromatic chromophores. Chem Soc Rev 2009; 39:410-22. [PMID: 20111767 DOI: 10.1039/b910030j] [Citation(s) in RCA: 225] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The rational formation of aromatic chromophore arrays is an intriguing challenge since ordered collectives of chromophores possess properties that are largely different from those of the individual molecules. Therefore, nucleic acids are increasingly used as scaffolds for the construction of multi-chromophore arrays. This tutorial review provides an introduction to the field of nucleic acid-guided chromophore assemblies for non-specialists and a reference point for those familiar with the area by highlighting the recent developments and describing some of the spectroscopic methods used for the study of oligonucleotide-chromophore conjugates.
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Affiliation(s)
- Vladimir L Malinovskii
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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26
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Ueno Y, Komatsuzaki S, Takasu K, Kawai S, Kitamura Y, Kitade Y. Synthesis and Properties of Oligonucleotides Containing Novel Fluorescent Biaryl Units. European J Org Chem 2009. [DOI: 10.1002/ejoc.200900567] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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27
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Rigoli JW, Østergaard ME, Canady KM, Guenther DC, Hrdlicka PJ. Selective deacylation of peracylated ribonucleosides. Tetrahedron Lett 2009. [DOI: 10.1016/j.tetlet.2009.01.147] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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28
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Kumar TS, Ostergaard ME, Sharma PK, Nielsen P, Wengel J, Hrdlicka PJ. Parallel RNA-strand recognition by 2'-amino-beta-L-LNA. Bioorg Med Chem Lett 2009; 19:2396-9. [PMID: 19356930 DOI: 10.1016/j.bmcl.2009.03.079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2009] [Revised: 03/18/2009] [Accepted: 03/20/2009] [Indexed: 10/21/2022]
Abstract
A short synthetic route to the first beta-l-ribo configured locked nucleic acid (LNA), that is, 2'-amino-beta-l-LNA thymine phosphoramidite 6, has been developed from bicyclic nucleoside 1. Incorporation of 2'-amino-beta-l-LNA thymine monomers into alpha-DNA strands results in probes forming stable duplexes with complementary RNA in parallel orientation.
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Affiliation(s)
- T Santhosh Kumar
- Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, DK-5230 Odense M, Denmark
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Wagenknecht HA. Helicale Anordnung von Porphyrinen entlang der DNA: auf dem Weg zu DNA-Nanoarchitekturen. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200900327] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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30
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Wagenknecht HA. Helical Arrangement of Porphyrins along DNA: Towards Photoactive DNA-Based Nanoarchitectures. Angew Chem Int Ed Engl 2009; 48:2838-41. [DOI: 10.1002/anie.200900327] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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31
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Kumar TS, Madsen AS, Østergaard ME, Sau SP, Wengel J, Hrdlicka PJ. Functionalized 2'-amino-alpha-L-LNA: directed positioning of intercalators for DNA targeting. J Org Chem 2009; 74:1070-81. [PMID: 19108636 PMCID: PMC2853939 DOI: 10.1021/jo802037v] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Chemically modified oligonucleotides are increasingly applied in nucleic acid based therapeutics and diagnostics. LNA (locked nucleic acid) and its diastereomer alpha-L-LNA are two promising examples thereof that exhibit increased thermal and enzymatic stability. Herein, the synthesis, biophysical characterization, and molecular modeling of N2'-functionalized 2'-amino-alpha-L-LNA is described. Chemoselective N2'-functionalization of protected amino alcohol 1 followed by phosphitylation afforded a structurally varied set of target phosphoramidites, which were incorporated into oligodeoxyribonucleotides. Incorporation of pyrene-functionalized building blocks such as 2'-N-(pyren-1-yl)carbonyl-2'-amino-alpha-L-LNA (monomer X) led to extraordinary increases in thermal affinity of up to +19.5 degrees C per modification against DNA targets in particular. In contrast, incorporation of building blocks with small nonaromatic N2'-functionalities such as 2'-N-acetyl-2'-amino-alpha-L-LNA (monomer V) had detrimental effects on thermal affinity toward DNA/RNA complements with decreases of as much as -16.5 degrees C per modification. Extensive thermal DNA selectivity, favorable entropic contributions upon duplex formation, hybridization-induced bathochromic shifts of pyrene absorption maxima and increases in circular dichroism signal intensity, and molecular modeling studies suggest that pyrene-functionalized 2'-amino-alpha-L-LNA monomers W-Y having short linkers between the bicyclic skeleton and the pyrene moiety allow high-affinity hybridization with DNA complements and precise positioning of intercalators in nucleic acid duplexes. This rigorous positional control has been utilized for the development of probes for emerging therapeutic and diagnostic applications focusing on DNA targeting.
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Affiliation(s)
- T Santhosh Kumar
- Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, DK-5230 Odense M, Denmark
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32
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Santhosh Kumar T, Kumar P, Sharma PK, Hrdlicka PJ. Optimized synthesis of LNA uracil nucleosides. Tetrahedron Lett 2008. [DOI: 10.1016/j.tetlet.2008.09.165] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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