1
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Verma V, Maity J, Maikhuri VK, Sharma R, Ganguly HK, Prasad AK. Double-headed nucleosides: Synthesis and applications. Beilstein J Org Chem 2021; 17:1392-1439. [PMID: 34194579 PMCID: PMC8204177 DOI: 10.3762/bjoc.17.98] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 05/27/2021] [Indexed: 12/19/2022] Open
Abstract
Double-headed nucleoside monomers have immense applications for studying secondary nucleic acid structures. They are also well-known as antimicrobial agents. This review article accounts for the synthetic methodologies and the biological applications of double-headed nucleosides.
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Affiliation(s)
- Vineet Verma
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi-110 007, India
| | - Jyotirmoy Maity
- Department of Chemistry, St. Stephen’s College, University of Delhi, Delhi-110 007, India
| | - Vipin K Maikhuri
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi-110 007, India
| | - Ritika Sharma
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi-110 007, India
| | - Himal K Ganguly
- Department of Biophysics, Bose Institute, P1/12 CIT Scheme VIIM, Kolkata-700 054, India
| | - Ashok K Prasad
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi-110 007, India
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2
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Stendevad J, Hornum M, Wüstner D, Kongsted J. Photophysical investigation of two emissive nucleosides exhibiting gigantic stokes shifts. Photochem Photobiol Sci 2019; 18:1858-1865. [DOI: 10.1039/c9pp00172g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present discovery of two highly emissive nucleoside analogs with gigantic Stokes shifts and use in silico methods for rationalizing their striking fluorescent properties.
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Affiliation(s)
- Julie Stendevad
- Department of Physics
- Chemistry and Pharmacy
- University of Southern Denmark
- DK-5230 Odense M
- Denmark
| | - Mick Hornum
- Department of Physics
- Chemistry and Pharmacy
- University of Southern Denmark
- DK-5230 Odense M
- Denmark
| | - Daniel Wüstner
- Department of Biochemistry and Molecular Biology
- University of Southern Denmark
- DK-5230 Odense M
- Denmark
| | - Jacob Kongsted
- Department of Physics
- Chemistry and Pharmacy
- University of Southern Denmark
- DK-5230 Odense M
- Denmark
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3
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He Z, Chen Y, Wang Y, Wang J, Mo J, Fu B, Wang Z, Du Y, Zhou X. A rapidly photo-activatable light-up fluorescent nucleoside and its application in DNA base variation sensing. Chem Commun (Camb) 2018; 52:8545-8. [PMID: 27315545 DOI: 10.1039/c6cc03098j] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A new DNA building block (d(Tet)U) bearing a tetrazole and allyloxy group at N-phenyl ring linked through an aminopropynyl linker to the 5-position of 2'-deoxyuridine was synthesized. The modified DNA can be lit up via a photoinduced intramolecular tetrazole-alkene cycloaddition reaction, but quenched when the fully-matched double strand is formed. This conspicuous difference in fluorescence could open a door for DNA single nucleotide polymorphism (SNP) typing.
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Affiliation(s)
- Zhiyong He
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan, Hubei 430072, P. R. China.
| | - Yuqi Chen
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan, Hubei 430072, P. R. China.
| | - Yafen Wang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan, Hubei 430072, P. R. China.
| | - Jiaqi Wang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan, Hubei 430072, P. R. China.
| | - Jing Mo
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan, Hubei 430072, P. R. China.
| | - Boshi Fu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan, Hubei 430072, P. R. China.
| | - Zijing Wang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan, Hubei 430072, P. R. China.
| | - Yuhao Du
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan, Hubei 430072, P. R. China.
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan, Hubei 430072, P. R. China.
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4
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Hong SW, Hwang GT. Photophysical Study of 2-Fluorenyl-1,2,3-Triazole-labeled 2′-Deoxyuridine and Its Oligonucleotide. B KOREAN CHEM SOC 2017. [DOI: 10.1002/bkcs.11349] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Seung Woo Hong
- Department of Chemistry; Kyungpook National University; Daegu 41566 Republic of Korea
| | - Gil Tae Hwang
- Department of Chemistry; Kyungpook National University; Daegu 41566 Republic of Korea
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5
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Krasheninina OA, Novopashina DS, Apartsin EK, Venyaminova AG. Recent Advances in Nucleic Acid Targeting Probes and Supramolecular Constructs Based on Pyrene-Modified Oligonucleotides. Molecules 2017; 22:E2108. [PMID: 29189716 PMCID: PMC6150046 DOI: 10.3390/molecules22122108] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 11/28/2017] [Accepted: 11/28/2017] [Indexed: 12/17/2022] Open
Abstract
In this review, we summarize the recent advances in the use of pyrene-modified oligonucleotides as a platform for functional nucleic acid-based constructs. Pyrene is of special interest for the development of nucleic acid-based tools due to its unique fluorescent properties (sensitivity of fluorescence to the microenvironment, ability to form excimers and exciplexes, long fluorescence lifetime, high quantum yield), ability to intercalate into the nucleic acid duplex, to act as a π-π-stacking (including anchoring) moiety, and others. These properties of pyrene have been used to construct novel sensitive fluorescent probes for the sequence-specific detection of nucleic acids and the discrimination of single nucleotide polymorphisms (SNPs), aptamer-based biosensors, agents for binding of double-stranded DNAs, and building blocks for supramolecular complexes. Special attention is paid to the influence of the design of pyrene-modified oligonucleotides on their properties, i.e., the structure-function relationships. The perspectives for the applications of pyrene-modified oligonucleotides in biomolecular studies, diagnostics, and nanotechnology are discussed.
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Affiliation(s)
- Olga A Krasheninina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
| | - Darya S Novopashina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
| | - Evgeny K Apartsin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
| | - Alya G Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
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6
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Piras L, Avitabile C, D'Andrea LD, Saviano M, Romanelli A. Detection of oligonucleotides by PNA-peptide conjugates recognizing the biarsenical fluorescein complex FlAsH-EDT 2. Biochem Biophys Res Commun 2017; 493:126-131. [PMID: 28919425 DOI: 10.1016/j.bbrc.2017.09.064] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 09/13/2017] [Indexed: 12/31/2022]
Abstract
We report the application of the arsenical complex FlAsH-EDT2 for the identification of oligonucleotide sequences. We designed PNA sequences conjugated to either a tetracysteine motif and to split tetracysteine sequences, that are recognized by FlAsH. The effect of conjugation of the PNA to the tetracysteine peptide and RNA hybridization on the fluorescence of the arsenical complex has been investigated. The reconstitution of the tetracysteine motif, starting from 15-mer PNAs conjugated to split tetracysteine sequences and hybridized to a complementary oligonucleotide was also explored.
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Affiliation(s)
- Linda Piras
- Institute of Crystallography (IC), CNR, Via Amendola 122/O, 70126, Bari, Italy
| | - Concetta Avitabile
- Institute of Biostructures and Bioimaging (IBB), CNR, via Mezzocannone 16, 80134, Napoli, Italy
| | - Luca Domenico D'Andrea
- Institute of Biostructures and Bioimaging (IBB), CNR, via Mezzocannone 16, 80134, Napoli, Italy
| | - Michele Saviano
- Institute of Crystallography (IC), CNR, Via Amendola 122/O, 70126, Bari, Italy
| | - Alessandra Romanelli
- Department of Pharmacy, University of Naples "Federico II", via Mezzocannone 16, 80134, Napoli, Italy.
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7
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Imincan G, Pei F, Yu L, Jin H, Zhang L, Yang X, Zhang L, Tang X. Microenvironmental Effect of 2'-O-(1-Pyrenylmethyl)uridine Modified Fluorescent Oligonucleotide Probes on Sensitive and Selective Detection of Target RNA. Anal Chem 2016; 88:4448-55. [PMID: 27021236 DOI: 10.1021/acs.analchem.6b00227] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
2'-O-(1-Pyrenylmethyl)uridine modified oligoribonucleotides provide highly sensitive pyrene fluorescent probes for detecting specific nucleotide mutation of RNA targets. To develop more stable and cost-effective oligonucleotide probes, we investigated the local microenvironmental effects of nearby nucleobases on pyrene fluorescence in duplexes of RNAs and 2'-O-(1-pyrenylmethyl)uridine modified oligonucleotides. By incorporation of deoxyribonucleotides, ribonucleotides, 2'-MeO-nucleotides and 2'-F-nucleotides at both sides of 2'-O-(1-pyrenylmethyl)uridine (U(p)) in oligodeoxynucleotide probes, we synthesized a series of pyrene modified oligonucleotide probes. Their pyrene fluorescence emission spectra indicated that only two proximal nucleotides have a substantial effect on the pyrene fluorescence properties of these oligonucleotide probes hybridized with target RNA with an order of fluorescence sensitivity of 2'-F-nucleotides > 2'-MeO-nucleotides > ribonucleotides ≫ deoxyribonucleotides. While based on circular dichroism spectra, overall helix conformations (either A- or B-form) of the duplexes have marginal effects on the sensitivity of the probes. Instead, the local substitution reflected the propensity of the nucleotide sugar ring to adopt North type conformation and, accordingly, shifted their helix geometry toward a more A-type like conformation in local microenvironments. Thus, higher enhancement of pyrene fluorescence emission favored local A-type helix structures and more polar and hydrophobic environments (F > MeO > OH at 2' substitution) of duplex minor grooves of probes with the target RNA. Further dynamic simulation revealed that local microenvironmental effect of 2'-F-nucleotides or ribonucleotides was enough for pyrene moiety to move out of nucleobases to the minor groove of duplexes; in addition, 2'-F-nucleotide had less effect on π-stack of pyrene-modified uridine with upstream and downstream nucleobases. The present oligonucleotide probes successfully distinguished target RNA from single-mutated RNA analyte during an in vitro assay of RNA synthesis.
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Affiliation(s)
- Gülnur Imincan
- State Key Laboratory of Natural and Biomimetic Drugs, the School of Pharmaceutical Sciences, Peking University , Beijing, 100191, China
| | - Fen Pei
- State Key Laboratory of Natural and Biomimetic Drugs, the School of Pharmaceutical Sciences, Peking University , Beijing, 100191, China
| | - Lijia Yu
- State Key Laboratory of Natural and Biomimetic Drugs, the School of Pharmaceutical Sciences, Peking University , Beijing, 100191, China
| | - Hongwei Jin
- State Key Laboratory of Natural and Biomimetic Drugs, the School of Pharmaceutical Sciences, Peking University , Beijing, 100191, China
| | - Liangren Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, the School of Pharmaceutical Sciences, Peking University , Beijing, 100191, China
| | - Xiaoda Yang
- State Key Laboratory of Natural and Biomimetic Drugs, the School of Pharmaceutical Sciences, Peking University , Beijing, 100191, China
| | - Lihe Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, the School of Pharmaceutical Sciences, Peking University , Beijing, 100191, China
| | - XinJing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, the School of Pharmaceutical Sciences, Peking University , Beijing, 100191, China
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8
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Gavey EL, Pilkington M. Employing Schiff-base macrocycles to probe the effect of ligand field on the relaxation dynamics of a family of DyIII SMMs. Polyhedron 2016. [DOI: 10.1016/j.poly.2015.11.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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9
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Li P, He H, Wang Z, Feng M, Jin H, Wu Y, Zhang L, Zhang L, Tang X. Sensitive Detection of Single-Nucleotide Mutation in the BRAF Mutation Site (V600E) of Human Melanoma Using Phosphate-Pyrene-Labeled DNA Probes. Anal Chem 2015; 88:883-9. [PMID: 26652624 DOI: 10.1021/acs.analchem.5b03523] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A series of novel nucleotide phosphoramidites were rationally designed and synthesized and were then site-specifically incorporated in DNA oligonucleotide probes with pyrene-modified phosphate. These oligodeoxynucleotide (ODN) probes almost have no inherent fluorescence emission with pyrene modification at 3' phosphate of corresponding nucleotides as a result of the photoinduced electron-transfer quenching effect of nucleobases (thymidine ∼ cytidine > guanosine ≫ adenosine). However, strong fluorescence emission was observed only with the perfectly matched duplex for the probes with pyrene modified at 3' phosphate of thymidine and cytidine. These rationally designed ODN probes successfully worked as "turn on" fluorescence oligonucleotide sensors for single-nucleotide polymorphism (SNP) and were used for detecting a single BRAF mutation site (V600E) of human melanoma.
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Affiliation(s)
- Pengfei Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, People's Republic of China
| | - Hongyan He
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, People's Republic of China
| | - Zhixuan Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, People's Republic of China
| | - Mengke Feng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, People's Republic of China
| | - Hongwei Jin
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, People's Republic of China
| | - Yun Wu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, People's Republic of China
| | - Liangren Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, People's Republic of China
| | - Lihe Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, People's Republic of China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, People's Republic of China.,State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University , Nanjing, Jiangsu 210093, People's Republic of China.,Center for Noncoding RNA Medicine, Peking University Health Center , Beijing 100191, People's Republic of China
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10
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Kaura M, Hrdlicka PJ. Locked nucleic acid (LNA) induced effect on the hybridization and fluorescence properties of oligodeoxyribonucleotides modified with nucleobase-functionalized DNA monomers. Org Biomol Chem 2015; 13:7236-47. [PMID: 26055658 DOI: 10.1039/c5ob00860c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
LNA and nucleobase-modified DNA monomers are two types of building blocks that are used extensively in oligonucleotide chemistry. However, there are only very few reports in which these two monomer families are used alongside each other. In the present study we set out to characterize the biophysical properties of oligodeoxyribonucleotides in which C5-modified 2'-deoxyuridine or C8-modified 2'-deoxyadenosine monomers are flanked by LNA nucleotides. We hypothesized that the LNA monomers would alter the sugar rings of the modified DNA monomers toward more RNA-like North-type conformations for maximal DNA/RNA affinity and specificity. Indeed, the incorporation of LNA monomers almost invariably results in increased target affinity and specificity relative to the corresponding LNA-free ONs, but the magnitude of the stabilization varies greatly. Introduction of LNA nucleotides as direct neighbors into C5-pyrene-functionalized pyrimidine DNA monomers yields oligonucleotide probes with more desirable photophysical properties as compared to the corresponding LNA-free probes, including more intense fluorescence emission upon target binding and improved discrimination of single nucleotide polymorphisms (SNPs). These hybrid oligonucleotides are therefore promising probes for diagnostic applications.
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Affiliation(s)
- Mamta Kaura
- Department of Chemistry, University of Idaho, Moscow, ID 83844-2343, USA.
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11
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Krasheninina OA, Novopashina DS, Lomzov AA, Venyaminova AG. 2'-Bispyrene-modified 2'-O-methyl RNA probes as useful tools for the detection of RNA: synthesis, fluorescent properties, and duplex stability. Chembiochem 2014; 15:1939-46. [PMID: 25044697 DOI: 10.1002/cbic.201402105] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Indexed: 01/01/2023]
Abstract
The synthesis and properties two series of new 2'-O-methyl RNA probes, each containing a single insertion of a 2'-bispyrenylmethylphosphorodiamidate derivative of a nucleotide (U, C, A, and G), are described. As demonstrated by UV melting studies, the probes form stable complexes with model RNAs and DNAs. Significant increases (up to 21-fold) in pyrene excimer fluorescence intensity were observed upon binding of most of the probes with complementary RNAs, but not with DNAs. The fluorescence spectra are independent of the nature of the modified nucleotides. The nucleotides on the 5'-side of the modified nucleotide have no effect on the fluorescence spectra, whereas the natures of the two nucleotides on the 3'-side are important: CC, CG, and UC dinucleotide units on the 3'-side of the modified nucleotide provide the maximum increases in excimer fluorescence intensity. This study suggests that these 2'-bispyrene-labeled 2'-O-methyl RNA probes might be useful tools for detection of RNAs.
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Affiliation(s)
- Olga A Krasheninina
- Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentiev Avenue, Novosibirsk, 630090 (Russia); Novosibirsk State University, 2 Pirogov St., Novosibirsk, 630090 (Russia).
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12
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Kaura M, Kumar P, Hrdlicka PJ. Synthesis, hybridization characteristics, and fluorescence properties of oligonucleotides modified with nucleobase-functionalized locked nucleic acid adenosine and cytidine monomers. J Org Chem 2014; 79:6256-68. [PMID: 24933409 DOI: 10.1021/jo500994c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Conformationally restricted nucleotides such as locked nucleic acid (LNA) are very popular as affinity-, specificity-, and stability-enhancing modifications in oligonucleotide chemistry to produce probes for nucleic acid targeting applications in molecular biology, biotechnology, and medicinal chemistry. Considerable efforts have been devoted in recent years to optimize the biophysical properties of LNA through additional modification of the sugar skeleton. We recently introduced C5-functionalization of LNA uridines as an alternative and synthetically more straightforward approach to improve the biophysical properties of LNA. In the present work, we set out to test the generality of this concept by studying the characteristics of oligonucleotides modified with four different C5-functionalized LNA cytidine and C8-functionalized LNA adenosine monomers. The results strongly suggest that C5-functionalization of LNA pyrimidines is indeed a viable approach for improving the binding affinity, target specificity, and/or enzymatic stability of LNA-modified ONs, whereas C8-functionalization of LNA adenosines is detrimental to binding affinity and specificity. These insights will impact the future design of conformationally restricted nucleotides for nucleic acid targeting applications.
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Affiliation(s)
- Mamta Kaura
- Department of Chemistry, University of Idaho , Moscow, Idaho 83844-2343, United States
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13
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Kumar P, Østergaard ME, Baral B, Anderson BA, Guenther DC, Kaura M, Raible DJ, Sharma PK, Hrdlicka PJ. Synthesis and biophysical properties of C5-functionalized LNA (locked nucleic acid). J Org Chem 2014; 79:5047-61. [PMID: 24825249 PMCID: PMC4049237 DOI: 10.1021/jo500614a] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Indexed: 01/07/2023]
Abstract
Oligonucleotides modified with conformationally restricted nucleotides such as locked nucleic acid (LNA) monomers are used extensively in molecular biology and medicinal chemistry to modulate gene expression at the RNA level. Major efforts have been devoted to the design of LNA derivatives that induce even higher binding affinity and specificity, greater enzymatic stability, and more desirable pharmacokinetic profiles. Most of this work has focused on modifications of LNA's oxymethylene bridge. Here, we describe an alternative approach for modulation of the properties of LNA: i.e., through functionalization of LNA nucleobases. Twelve structurally diverse C5-functionalized LNA uridine (U) phosphoramidites were synthesized and incorporated into oligodeoxyribonucleotides (ONs), which were then characterized with respect to thermal denaturation, enzymatic stability, and fluorescence properties. ONs modified with monomers that are conjugated to small alkynes display significantly improved target affinity, binding specificity, and protection against 3'-exonucleases relative to regular LNA. In contrast, ONs modified with monomers that are conjugated to bulky hydrophobic alkynes display lower target affinity yet much greater 3'-exonuclease resistance. ONs modified with C5-fluorophore-functionalized LNA-U monomers enable fluorescent discrimination of targets with single nucleotide polymorphisms (SNPs). In concert, these properties render C5-functionalized LNA as a promising class of building blocks for RNA-targeting applications and nucleic acid diagnostics.
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Affiliation(s)
- Pawan Kumar
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
- Department of Chemistry, Kurukshetra University, Kurukshetra 136119, India
| | - Michael E. Østergaard
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
| | - Bharat Baral
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
| | - Brooke A. Anderson
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
| | - Dale C. Guenther
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
| | - Mamta Kaura
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
| | - Daniel J. Raible
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
| | - Pawan K. Sharma
- Department of Chemistry, Kurukshetra University, Kurukshetra 136119, India
| | - Patrick J. Hrdlicka
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
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14
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Kumar P, Hornum M, Nielsen LJ, Enderlin G, Andersen NK, Len C, Hervé G, Sartori G, Nielsen P. High-affinity RNA targeting by oligonucleotides displaying aromatic stacking and amino groups in the major groove. Comparison of triazoles and phenyl substituents. J Org Chem 2014; 79:2854-63. [PMID: 24611639 DOI: 10.1021/jo4025896] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Three 5-modified 2'-deoxyuridine nucleosides were synthesized and incorporated into oligonucleotides and compared with the previously published 5-(1-phenyl-1,2,3-triazol-4-yl)-2'-deoxyuridine monomer W. The introduction of an aminomethyl group on the phenyl group led to monomer X, which was found to thermally stabilize a 9-mer DNA:RNA duplex, presumably through the partial neutralization of the negative charge of the backbone. By also taking advantage of the stacking interactions in the major groove of two or more of the monomer X, an extremely high thermal stability was obtained. A regioisomer of the phenyltriazole substituent, that is the 5-(4-phenyl-1,2,3-triazol-1-yl)-2'-deoxyuridine monomer Y, was found to destabilize the DNA:RNA duplex significantly, but stacking in the major groove compensated for this when two to four monomers were incorporated consecutively. Finally, the 5-phenyl-2'-deoxyuridine monomer Z was incorporated for comparison, and it was found to give a more neutral influence on duplex stability indicating less efficient stacking interactions. The duplexes were investigated by CD spectroscopy and MD simulations.
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Affiliation(s)
- Pawan Kumar
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , 5230 Odense M, Denmark
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15
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Nucleoside and oligonucleotide pyrene conjugates with 1,2,3-triazolyl or ethynyl linkers: synthesis, duplex stability, and fluorescence changes generated by the DNA-dye connector. Tetrahedron 2014. [DOI: 10.1016/j.tet.2013.11.048] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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16
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Boonlua C, Ditmangklo B, Reenabthue N, Suparpprom C, Poomsuk N, Siriwong K, Vilaivan T. Pyrene-labeled pyrrolidinyl peptide nucleic acid as a hybridization-responsive DNA probe: comparison between internal and terminal labeling. RSC Adv 2014. [DOI: 10.1039/c3ra47997h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Internally pyrene-labeled pyrrolidinyl PNA yields much larger fluorescence increase than terminally labeled PNA upon hybridization with complementary DNA.
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Affiliation(s)
- Chalothorn Boonlua
- Organic Synthesis Research Unit
- Department of Chemistry
- Faculty of Science
- Chulalongkorn University
- Bangkok 10330, Thailand
| | - Boonsong Ditmangklo
- Organic Synthesis Research Unit
- Department of Chemistry
- Faculty of Science
- Chulalongkorn University
- Bangkok 10330, Thailand
| | - Nisanath Reenabthue
- Department of Chemistry
- Faculty of Science
- Naresuan University
- Phitsanulok 65000, Thailand
| | - Chaturong Suparpprom
- Department of Chemistry
- Faculty of Science
- Naresuan University
- Phitsanulok 65000, Thailand
| | - Nattawee Poomsuk
- Materials Chemistry Research Unit
- Department of Chemistry
- Faculty of Science
- Khon Kaen University
- Khon Kaen 40002, Thailand
| | - Khatcharin Siriwong
- Materials Chemistry Research Unit
- Department of Chemistry
- Faculty of Science
- Khon Kaen University
- Khon Kaen 40002, Thailand
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit
- Department of Chemistry
- Faculty of Science
- Chulalongkorn University
- Bangkok 10330, Thailand
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17
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Kaura M, Kumar P, Hrdlicka PJ. Synthesis and hybridization properties of oligonucleotides modified with 5-(1-aryl-1,2,3-triazol-4-yl)-2'-deoxyuridines. Org Biomol Chem 2013; 10:8575-8. [PMID: 23042241 DOI: 10.1039/c2ob26717a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Oligonucleotides modified with consecutive incorporations of 5-(1-aryl-1,2,3-triazol-4-yl)-2'-deoxyuridine monomers display strong thermal affinity and binding specificity toward RNA targets, due to formation of chromophore arrays in the major groove.
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Affiliation(s)
- Mamta Kaura
- Department of Chemistry, University of Idaho, PO Box 442343, Moscow, ID 83844-2343, USA
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18
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Zhang R, Yang L, Zhao M, Dong J, Dong H, Wen Y, Zhan X, Yang H, Wang G. Synthesis and fluorescence study of a pyrene-functionalized poly(4-vinylpyridine) quaternary ammonium for detection of DNA hybridization. POLYMER 2013. [DOI: 10.1016/j.polymer.2012.12.080] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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19
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Zhao M, Yang L, Zhang R, Dong J, Dong H, Wen Y, Zhan X, Wang G, Lu Y, Wang G. Detection of DNA hybridization by a pyrene-labeled polyelectrolyte prepared by ATRP. POLYMER 2013. [DOI: 10.1016/j.polymer.2012.11.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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20
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Karmakar S, Hrdlicka PJ. DNA strands with alternating incorporations of LNA and 2'- O-(pyren-1-yl)methyluridine: SNP-discriminating RNA detection probes. Chem Sci 2013; 4:3447-3454. [PMID: 23930202 DOI: 10.1039/c3sc50726b] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Detection of nucleic acids using fluorophore-modified oligonucleotides forms the basis of many important applications in molecular biology, genetics and medical diagnostics. Here we demonstrate that DNA strands with central segments of alternating locked nucleic acid (LNA) and 2'-O-(pyren-1-yl)methyluridine monomers display very large and highly mismatch-sensitive increases in fluorescence emission upon RNA hybridization, whereas corresponding "LNA-free" controls do not. Absorbance spectra strongly suggest that LNA-induced conformational tuning of flanking 2'-O-(pyren-1-yl)methyluridine monomers places the reporter group in the minor groove upon RNA binding, whereby pyrene-nucleobase interactions leading to quenching of fluorescence are minimized. Accordingly, these easy-to-synthesize probes are promising SNP-discriminating RNA detection probes.
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Affiliation(s)
- Saswata Karmakar
- University of Idaho, Department of Chemistry, Moscow, ID 83844-2343, USA
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21
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Liang F, Liu YZ, Zhang P. Universal base analogues and their applications in DNA sequencing technology. RSC Adv 2013. [DOI: 10.1039/c3ra41492b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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22
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Yang L, Zhao M, Zhang R, Dong J, Zhang T, Zhan X, Wang G. Synthesis and Fluorescence Study of a Quaternized Copolymer Containing Pyrene for DNA-Hybridization Detection. Chemphyschem 2012; 13:4099-104. [DOI: 10.1002/cphc.201200765] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Indexed: 12/27/2022]
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23
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Efthymiou T, Gong W, Desaulniers JP. Chemical architecture and applications of nucleic acid derivatives containing 1,2,3-triazole functionalities synthesized via click chemistry. Molecules 2012; 17:12665-703. [PMID: 23103533 PMCID: PMC6268694 DOI: 10.3390/molecules171112665] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 10/19/2012] [Accepted: 10/19/2012] [Indexed: 11/16/2022] Open
Abstract
There is considerable attention directed at chemically modifying nucleic acids with robust functional groups in order to alter their properties. Since the breakthrough of copper-assisted azide-alkyne cycloadditions (CuAAC), there have been several reports describing the synthesis and properties of novel triazole-modified nucleic acid derivatives for potential downstream DNA- and RNA-based applications. This review will focus on highlighting representative novel nucleic acid molecular structures that have been synthesized via the “click” azide-alkyne cycloaddition. Many of these derivatives show compatibility for various applications that involve enzymatic transformation, nucleic acid hybridization, molecular tagging and purification, and gene silencing. The details of these applications are discussed. In conclusion, the future of nucleic acid analogues functionalized with triazoles is promising.
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Affiliation(s)
| | | | - Jean-Paul Desaulniers
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe St N, Oshawa, ON L1H 7K4, Canada
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24
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Kumar P, Shaikh KI, Jørgensen AS, Kumar S, Nielsen P. Three pyrene-modified nucleotides: synthesis and effects in secondary nucleic acid structures. J Org Chem 2012; 77:9562-73. [PMID: 23039223 DOI: 10.1021/jo301571s] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Synthesis of three pyrene-modified nucleosides was accomplished using the CuAAC reaction. Hereby, pyrene is attached either to the 5'-position of thymidine or to the 2'-position of 2'-deoxyuridine through triazolemethylene linkers, or to the 2'-position of 2'-deoxyuridine through a more rigid triazole linker. The three nucleosides were incorporated into oligonucleotides, and these were combined in different duplexes and other secondary structures, which were analyzed by thermal stability and fluorescence studies. The three monomers were found to have different impacts on the nucleic acid complexes. Hence, pyrene attached to the 5'-position shows a tendency for intercalation into the duplex as indicated by a general decrease in fluorescence intensity followed by an increase in duplex thermal stability. Pyrene attached to the 2'-position through a rigid triazole linker also shows a tendency for intercalation but with decrease in duplex stability, whereas the pyrene attached to the 2'-position through a triazolemethylene linker is primarily situated in the minor groove as indicated by an increase in fluorescence but here in most cases leading to increase in duplex stability. All three pyrene nucleotides lead to thermal stabilization of bulged duplexes and three-way junctions. In some cases when two pyrenes were introduced into the core of these complexes, the formation or disappearance of a fluorescence excimer band can be used to indicate the hybridization process. Hereby these oligonucleotides can act as specific recognition probes.
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Affiliation(s)
- Pawan Kumar
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark
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25
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Cho HY, Woo SK, Hwang GT. Synthesis and photophysical study of 2'-deoxyuridines labeled with fluorene derivatives. Molecules 2012; 17:12061-71. [PMID: 23085656 PMCID: PMC6268453 DOI: 10.3390/molecules171012061] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 10/03/2012] [Accepted: 10/10/2012] [Indexed: 12/17/2022] Open
Abstract
We examined microenvironment-sensitive fluorescent 2′-deoxyuridines labeled with fluorene derivatives that exhibited solvent-dependent photophysical properties. The high sensitivity of the fluorescence shift and the nucleoside intensity dependence on solvent polarity provided information useful for estimating the polarity of the environment surrounding the fluorescent nucleoside.
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Affiliation(s)
- Hyun Yi Cho
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, Daegu 702-701, Korea;
| | - Sang Keun Woo
- Molecular Imaging Research Center, Korea Institute of Radiological and Medical Sciences, 75 Nowon-gil, Seoul 139-706, Korea
- Authors to whom correspondence should be addressed; (S.K.W.); (G.T.H.); Tel.: +82-2-970-1659 (S.K.W.); Fax: +82-2-970-1341 (S.K.W.); Tel.: +82-53-950-5331 (G.T.H.); Fax: +82-53-950-6330 (G.T.H.)
| | - Gil Tae Hwang
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, Daegu 702-701, Korea;
- Authors to whom correspondence should be addressed; (S.K.W.); (G.T.H.); Tel.: +82-2-970-1659 (S.K.W.); Fax: +82-2-970-1341 (S.K.W.); Tel.: +82-53-950-5331 (G.T.H.); Fax: +82-53-950-6330 (G.T.H.)
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26
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Clicked polycyclic aromatic hydrocarbon as a hybridization-responsive fluorescent artificial nucleobase in pyrrolidinyl peptide nucleic acids. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.03.062] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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27
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Loakes D. Nucleotides and nucleic acids; oligo- and polynucleotides. ORGANOPHOSPHORUS CHEMISTRY 2012. [DOI: 10.1039/9781849734875-00169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- David Loakes
- Medical Research Council Laboratory of Molecular Biology, Hills Road Cambridge CB2 2QH UK
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28
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Heaney F. Nitrile Oxide/Alkyne Cycloadditions - A Credible Platform for Synthesis of Bioinspired Molecules by Metal-Free Molecular Clicking. European J Org Chem 2012. [DOI: 10.1002/ejoc.201101823] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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29
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Karlsen KK, Pasternak A, Jensen TB, Wengel J. Pyrene-Modified Unlocked Nucleic Acids: Synthesis, Thermodynamic Studies, and Fluorescent Properties. Chembiochem 2012; 13:590-601. [DOI: 10.1002/cbic.201100689] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Indexed: 01/09/2023]
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30
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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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31
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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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32
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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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33
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Freeman C, Ni Cheallaigh A, Heaney F. Conjugation at the oligonucleotide level based on isoxazole phosphoramidites generated by click chemistry. Tetrahedron 2011. [DOI: 10.1016/j.tet.2011.06.096] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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34
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Andersen NK, Døssing H, Jensen F, Vester B, Nielsen P. Duplex and triplex formation of mixed pyrimidine oligonucleotides with stacking of phenyl-triazole moieties in the major groove. J Org Chem 2011; 76:6177-87. [PMID: 21692520 DOI: 10.1021/jo200919y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
5-(1-Phenyl-1,2,3-triazol-4-yl)-2'-deoxycytidine was synthesized from a modified CuAAC protocol and incorporated into mixed pyrimidine oligonucleotide sequences together with the corresponding 5-(1-phenyl-1,2,3-triazol-4-yl)-2'-deoxyuridine. With consecutive incorporations of the two modified nucleosides, improved duplex formation with a complementary RNA and improved triplex formation with a complementary DNA duplex were observed. The improvement is due to π-π stacking of the phenyl-triazole moieties in the major groove. The strongest stacking and most pronounced positive influence on thermal stability was found in between the uridine analogues or with the cytidine analogue placed in the 3' direction to the uridine analogue. Modeling indicated a different orientation of the phenyl-triazole moieties in the major groove to account for the difference between the two nucleotides. The modified oligonucleotides were all found to be significantly stabilized toward nucleolytic degration.
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Affiliation(s)
- Nicolai Krog Andersen
- Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, 5230 Odense M, Denmark
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35
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Mori K, Kodama T, Baba T, Obika S. Bridged nucleic acid conjugates at 6'-thiol: synthesis, hybridization properties and nuclease resistances. Org Biomol Chem 2011; 9:5272-9. [PMID: 21643564 DOI: 10.1039/c1ob05469d] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The bridged nucleic acid (BNA) containing a thiol at the 6'-position in the bridged structure was synthesized from the disulfide-type BNA and conjugated with various functional molecules via the thioether or the disulfide linkage post-synthetically and efficiently in solution phase. The disulfide-linked conjugate was cleaved under reductive conditions derived from glutathione and an oligonucleotide bearing a free thiol was released smoothly. Conjugated functional molecules had great effects on duplex stability with the DNA complement. In contrast, the molecules little influenced the stability with the RNA complement. Moreover, the oligonucleotides with functional groups at the 6'-position had as high or higher resistances against 3'-exonuclease than phosphorothioate oligonucleotide (S-oligo).
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Affiliation(s)
- Kazuto Mori
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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36
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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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37
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Østergaard ME, Maity J, Babu BR, Wengel J, Hrdlicka PJ. Novel insights into the use of Glowing LNA as nucleic acid detection probes--influence of labeling density and nucleobases. Bioorg Med Chem Lett 2010; 20:7265-8. [PMID: 21071224 DOI: 10.1016/j.bmcl.2010.10.089] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2010] [Revised: 10/15/2010] [Accepted: 10/18/2010] [Indexed: 10/18/2022]
Abstract
Appropriately designed 2'-N-(pyren-1-yl)carbonyl-2'-amino-LNA (locked nucleic acid) display large increases in fluorescence intensity and remarkably high quantum yields upon hybridization with nucleic acid targets. Thermal denaturation and fluorescence spectroscopy studies on ONs modified with known thymine monomer X and novel 5-methylcytosine monomer Y provide new insights into the design principles and mechanism of these Glowing LNA nucleic acid detection probes.
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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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