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Balasubramaniyam T, Oh KI, Jin HS, Ahn HB, Kim BS, Lee JH. Non-Canonical Helical Structure of Nucleic Acids Containing Base-Modified Nucleotides. Int J Mol Sci 2021; 22:9552. [PMID: 34502459 PMCID: PMC8430589 DOI: 10.3390/ijms22179552] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/27/2021] [Accepted: 08/29/2021] [Indexed: 12/12/2022] Open
Abstract
Chemically modified nucleobases are thought to be important for therapeutic purposes as well as diagnosing genetic diseases and have been widely involved in research fields such as molecular biology and biochemical studies. Many artificially modified nucleobases, such as methyl, halogen, and aryl modifications of purines at the C8 position and pyrimidines at the C5 position, are widely studied for their biological functions. DNA containing these modified nucleobases can form non-canonical helical structures such as Z-DNA, G-quadruplex, i-motif, and triplex. This review summarizes the synthesis of chemically modified nucleotides: (i) methylation, bromination, and arylation of purine at the C8 position and (ii) methylation, bromination, and arylation of pyrimidine at the C5 position. Additionally, we introduce the non-canonical structures of nucleic acids containing these modifications.
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Affiliation(s)
- Thananjeyan Balasubramaniyam
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
- The Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
| | - Kwnag-Im Oh
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
- The Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
| | - Ho-Seong Jin
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
| | - Hye-Bin Ahn
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
| | - Byeong-Seon Kim
- The Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
- Department of Chemistry Education, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
| | - Joon-Hwa Lee
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
- The Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
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2
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Danielsen MB, Wengel J. Cationic oligonucleotide derivatives and conjugates: A favorable approach for enhanced DNA and RNA targeting oligonucleotides. Beilstein J Org Chem 2021; 17:1828-1848. [PMID: 34386102 PMCID: PMC8329367 DOI: 10.3762/bjoc.17.125] [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: 04/06/2021] [Accepted: 07/14/2021] [Indexed: 12/20/2022] Open
Abstract
Antisense oligonucleotides (ASOs) have the ability of binding to endogenous nucleic acid targets, thereby inhibiting the gene expression. Although ASOs have great potential in the treatment of many diseases, the search for favorable toxicity profiles and distribution has been challenging and consequently impeded the widespread use of ASOs as conventional medicine. One strategy that has been employed to optimize the delivery profile of ASOs, is the functionalization of ASOs with cationic amine groups, either by direct conjugation onto the sugar, nucleobase or internucleotide linkage. The introduction of these positively charged groups has improved properties like nuclease resistance, increased binding to the nucleic acid target and improved cell uptake for oligonucleotides (ONs) and ASOs. The modifications highlighted in this review are some of the most prevalent cationic amine groups which have been attached as single modifications onto ONs/ASOs. The review has been separated into three sections, nucleobase, sugar and backbone modifications, highlighting what impact the cationic amine groups have on the ONs/ASOs physiochemical and biological properties. Finally, a concluding section has been added, summarizing the important knowledge from the three chapters, and examining the future design for ASOs.
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Affiliation(s)
- Mathias B Danielsen
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Jesper Wengel
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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3
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Li Y, Liu S, Ling L. Sensitive Fluorescent Sensor for Recognition of HIV-1 dsDNA by Using Glucose Oxidase and Triplex DNA. JOURNAL OF ANALYTICAL METHODS IN CHEMISTRY 2018; 2018:8298365. [PMID: 29805840 PMCID: PMC5901486 DOI: 10.1155/2018/8298365] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 12/05/2017] [Accepted: 12/19/2017] [Indexed: 05/08/2023]
Abstract
A sensitive fluorescent sensor for sequence-specific recognition of double-stranded DNA (dsDNA) was developed on the surface of silver-coated glass slide (SCGS). Oligonucleotide-1 (Oligo-1) was designed to assemble on the surface of SCGS and act as capture DNA, and oligonucleotide-2 (Oligo-2) was designed as signal DNA. Upon addition of target HIV-1 dsDNA (Oligo-3•Oligo-4), signal DNA could bind on the surface of silver-coated glass because of the formation of C•GoC in parallel triplex DNA structure. Biotin-labeled glucose oxidase (biotin-GOx) could bind to signal DNA through the specific interaction of biotin-streptavidin, thereby GOx was attached to the surface of SCGS, which was dependent on the concentration of target HIV-1 dsDNA. GOx could catalyze the oxidation of glucose and yield H2O2, and the HPPA can be oxidized into a fluorescent product in the presence of HRP. Therefore, the concentration of target HIV-1 dsDNA could be estimated with fluorescence intensity. Under the optimum conditions, the fluorescence intensity was proportional to the concentration of target HIV-1 dsDNA over the range of 10 pM to 1000 pM, the detection limit was 3 pM. Moreover, the sensor had good sequence selectivity and practicability and might be applied for the diagnosis of HIV disease in the future.
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Affiliation(s)
- Yubin Li
- College of Chemistry and Environment, Guangdong Ocean University, Zhanjiang 524088, China
| | - Sheng Liu
- College of Chemistry and Environment, Guangdong Ocean University, Zhanjiang 524088, China
| | - Liansheng Ling
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
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4
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Geny S, Moreno PMD, Krzywkowski T, Gissberg O, Andersen NK, Isse AJ, El-Madani AM, Lou C, Pabon YV, Anderson BA, Zaghloul EM, Zain R, Hrdlicka PJ, Jørgensen PT, Nilsson M, Lundin KE, Pedersen EB, Wengel J, Smith CIE. Next-generation bis-locked nucleic acids with stacking linker and 2'-glycylamino-LNA show enhanced DNA invasion into supercoiled duplexes. Nucleic Acids Res 2016; 44:2007-19. [PMID: 26857548 PMCID: PMC4797291 DOI: 10.1093/nar/gkw021] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 01/08/2016] [Indexed: 12/17/2022] Open
Abstract
Targeting and invading double-stranded DNA with synthetic oligonucleotides under physiological conditions remain a challenge. Bis-locked nucleic acids (bisLNAs) are clamp-forming oligonucleotides able to invade into supercoiled DNA via combined Hoogsteen and Watson–Crick binding. To improve the bisLNA design, we investigated its mechanism of binding. Our results suggest that bisLNAs bind via Hoogsteen-arm first, followed by Watson–Crick arm invasion, initiated at the tail. Based on this proposed hybridization mechanism, we designed next-generation bisLNAs with a novel linker able to stack to adjacent nucleobases, a new strategy previously not applied for any type of clamp-constructs. Although the Hoogsteen-arm limits the invasion, upon incorporation of the stacking linker, bisLNA invasion is significantly more efficient than for non-clamp, or nucleotide-linker containing LNA-constructs. Further improvements were obtained by substituting LNA with 2′-glycylamino-LNA, contributing a positive charge. For regular bisLNAs a 14-nt tail significantly enhances invasion. However, when two stacking linkers were incorporated, tail-less bisLNAs were able to efficiently invade. Finally, successful targeting of plasmids inside bacteria clearly demonstrates that strand invasion can take place in a biologically relevant context.
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Affiliation(s)
- Sylvain Geny
- Department of Laboratory Medicine, Karolinska Institutet and Clinical Research Center, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden
| | - Pedro M D Moreno
- Department of Laboratory Medicine, Karolinska Institutet and Clinical Research Center, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden INEB-Instituto de Engenharia Biomedica, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
| | - Tomasz Krzywkowski
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, SE-171 21, Sweden
| | - Olof Gissberg
- Department of Laboratory Medicine, Karolinska Institutet and Clinical Research Center, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden
| | - Nicolai K Andersen
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, Nucleic Acid Centre, University of Southern Denmark, 5230 Odense, Denmark
| | - Abdirisaq J Isse
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, Nucleic Acid Centre, University of Southern Denmark, 5230 Odense, Denmark
| | - Amro M El-Madani
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, Nucleic Acid Centre, University of Southern Denmark, 5230 Odense, Denmark
| | - Chenguang Lou
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, Nucleic Acid Centre, University of Southern Denmark, 5230 Odense, Denmark
| | - Y Vladimir Pabon
- Department of Laboratory Medicine, Karolinska Institutet and Clinical Research Center, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden
| | | | - Eman M Zaghloul
- Department of Laboratory Medicine, Karolinska Institutet and Clinical Research Center, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden
| | - Rula Zain
- Department of Laboratory Medicine, Karolinska Institutet and Clinical Research Center, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden Centre for Rare Diseases, Department of Clinical Genetics, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | | | - Per T Jørgensen
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, Nucleic Acid Centre, University of Southern Denmark, 5230 Odense, Denmark
| | - Mats Nilsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, SE-171 21, Sweden
| | - Karin E Lundin
- Department of Laboratory Medicine, Karolinska Institutet and Clinical Research Center, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden
| | - Erik B Pedersen
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, Nucleic Acid Centre, University of Southern Denmark, 5230 Odense, Denmark
| | - Jesper Wengel
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, Nucleic Acid Centre, University of Southern Denmark, 5230 Odense, Denmark
| | - C I Edvard Smith
- Department of Laboratory Medicine, Karolinska Institutet and Clinical Research Center, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden
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5
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Morihiro K, Hasegawa O, Mori S, Tsunoda S, Obika S. C5-azobenzene-functionalized locked nucleic acid uridine: isomerization properties, hybridization ability, and enzymatic stability. Org Biomol Chem 2016; 13:5209-14. [PMID: 25853508 DOI: 10.1039/c5ob00477b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Oligonucleotides (ONs) modified with a locked nucleic acid (LNA) are widely used in the fields of therapeutics, diagnosis, and nanotechnology. There have been significant efforts towards developing LNA analogues bearing modified bridges to improve their hybridization ability, nuclease resistance, and pharmacokinetic profiles. Moreover, nucleobase modifications of LNA are useful strategies for the functionalization of ONs. Modifications of the C5-position of pyrimidine nucleobases are particularly interesting because they enable predictable positioning of functional groups in the major groove of the duplex. Here we report the synthesis of C5-azobenzene-functionalized LNA uridine (LNA-U(Az)) and properties of LNA-U(Az)-modified ONs, including isomerization properties, hybridization ability, and enzyme stability. LNA-U(Az) in ON is photo-isomerized effectively and reversibly by irradiation at 365 nm (trans to cis) and 450 nm (cis to trans). LNA-U(Az)-modified ONs show RNA-selective hybridization ability despite the large hydrophobic azobenzene moiety extending into the major groove of the duplex. The enzymatic stability of LNA-U(Az)-modified ONs is higher than that of natural and LNA-modified ONs with or without photo-irradiation. Our results indicate that LNA-U(Az) holds promise for RNA targeting and photo-switchable technologies.
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Affiliation(s)
- K Morihiro
- National Institute of Biomedical Innovation (NIBIO), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan.
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6
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Miao X, Guo X, Xiao Z, Ling L. Electrochemical molecular beacon biosensor for sequence-specific recognition of double-stranded DNA. Biosens Bioelectron 2014; 59:54-7. [PMID: 24690562 DOI: 10.1016/j.bios.2014.03.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 02/16/2014] [Accepted: 03/03/2014] [Indexed: 01/03/2023]
Abstract
Direct recognition of double-stranded DNA (dsDNA) was crucial to disease diagnosis and gene therapy, because DNA in its natural state is double stranded. Here, a novel sensor for the sequence-specific recognition of dsDNA was developed based on the structure change of ferrocene (Fc) redox probe modified molecular beacon (MB). For constructing such a sensor, gold nanoparticles (AuNPs) were initially electrochemical-deposited onto glass carbon electrode (GCE) surface to immobilize thiolated MB in their folded states with Au-S bond. Hybridization of MB with target dsDNA induced the formation of parallel triplex DNA and opened the stem-loop structure of it, which resulted in the redox probe (Fc) away from the electrode and triggered the decrease of current signals. Under optimal conditions, dsDNA detection could be realized in the range from 350 pM to 25 nM, with a detection limit of 275 pM. Moreover, the proposed method has good sequence-specificity for target dsDNA compared with single base pair mismatch and two base pairs mismatches.
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Affiliation(s)
- Xiangmin Miao
- School of Life Science, Jiangsu Normal University, Xuzhou 221116, PR China.
| | - Xiaoting Guo
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Zhiyou Xiao
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Liansheng Ling
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, PR China.
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7
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Xiao Z, Guo X, Ling L. Sequence-specific recognition of double-stranded DNA with molecular beacon with the aid of Ag+ under neutral pH environment. Chem Commun (Camb) 2013; 49:3573-5. [DOI: 10.1039/c3cc40333e] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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8
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Lundin KE, Højland T, Hansen BR, Persson R, Bramsen JB, Kjems J, Koch T, Wengel J, Smith CIE. Biological activity and biotechnological aspects of locked nucleic acids. ADVANCES IN GENETICS 2013; 82:47-107. [PMID: 23721720 DOI: 10.1016/b978-0-12-407676-1.00002-0] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Locked nucleic acid (LNA) is one of the most promising new nucleic acid analogues that has been produced under the past two decades. In this chapter, we have tried to cover many of the different areas, where this molecule has been used to improve the function of synthetic oligonucleotides (ONs). The use of LNA in antisense ONs, including gapmers, splice-switching ONs, and siLNA, as well as antigene ONs, is reviewed. Pharmacokinetics as well as pharmacodynamics of LNA ONs and a description of selected compounds in, or close to, clinical testing are described. In addition, new LNA modifications and the adaptation of enzymes for LNA incorporation are reviewed. Such enzymes may become important for the development of stabilized LNA-containing aptamers.
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Affiliation(s)
- Karin E Lundin
- Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, Novum, Huddinge, Stockholm, Sweden.
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9
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Sau SP, Kumar P, Sharma PK, Hrdlicka PJ. Fluorescent intercalator displacement replacement (FIDR) assay: determination of relative thermodynamic and kinetic parameters in triplex formation--a case study using triplex-forming LNAs. Nucleic Acids Res 2012; 40:e162. [PMID: 22855561 PMCID: PMC3505983 DOI: 10.1093/nar/gks729] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Triplex forming oligonucleotides (TFOs) are the most commonly used approach for site-specific targeting of double stranded DNA (dsDNA). Important parameters describing triplex formation include equilibrium binding constants (K(eq)) and association/dissociation rate constants (k(on) and k(off)). The 'fluorescent intercalator displacement replacement' (FIDR) assay is introduced herein as an operationally simple approach toward determination of these parameters for triplexes involving TC-motif TFOs. Briefly described, relative rate constants are determined from fluorescence intensity changes upon: (i) TFO-mediated displacement of pre-intercalated and fluorescent ethidium from dsDNA targets (triplex association) and (ii) Watson-Crick complement-mediated displacement of the TFO and replacement with ethidium (triplex dissociation). The assay is used to characterize triplexes between purine-rich dsDNA targets and TC-motif TFOs modified with six different locked nucleic acid (LNA) monomers, i.e. conventional and C5-alkynyl-functionalized LNA and α-L-LNA pyrimidine monomers. All of the studied monomers increase triplex stability by decreasing the triplex dissociation rate. LNA-modified TFOs form more stable triplexes than α-L-LNA-modified counterparts owing to slower triplex dissociation. Triplexes modified with C5-(3-aminopropyn-1-yl)-LNA-U monomer Z are particularly stable. The study demonstrates that three affinity-enhancing features can be combined into one high-affinity TFO monomer: conformational restriction of the sugar ring, expansion of the pyrimidine π-stacking surface and introduction of an exocyclic amine.
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Affiliation(s)
- Sujay P Sau
- Department of Chemistry, University of Idaho, PO Box 442343, Moscow, ID 83844-2343, USA
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10
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Towards artificial metallonucleases for gene therapy: recent advances and new perspectives. Future Med Chem 2011; 3:1935-66. [DOI: 10.4155/fmc.11.139] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The process of DNA targeting or repair of mutated genes within the cell, induced by specifically positioned double-strand cleavage of DNA near the mutated sequence, can be applied for gene therapy of monogenic diseases. For this purpose, highly specific artificial metallonucleases are developed. They are expected to be important future tools of modern genetics. The present state of art and strategies of research are summarized, including protein engineering and artificial ‘chemical’ nucleases. From the results, we learn about the basic role of the metal ions and the various ligands, and about the DNA binding and cleavage mechanism. The results collected provide useful guidance for engineering highly controlled enzymes for use in gene therapy.
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11
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Miao XM, Xiong C, Wang WW, Ling LS, Shuai XT. Dynamic-light-scattering-based sequence-specific recognition of double-stranded DNA with oligonucleotide-functionalized gold nanoparticles. Chemistry 2011; 17:11230-6. [PMID: 21922555 DOI: 10.1002/chem.201003010] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Revised: 06/21/2011] [Indexed: 11/08/2022]
Abstract
An ultrasensitive and simple dynamic-light-scattering (DLS) assay for the sequence-specific recognition of double-stranded DNA (dsDNA) was developed based on detection of the average diameter change of Au nanoparticle (AuNP) probes modified with oligonucleotides 5'-TTTCTCTTCCTT- CTCTTC-(T)(12)-SH-3' (Oligo 1) and 5'-TTCTTTCTTTTCTTTTTC-(T)(12)- SH-3' (Oligo 2). The target dsDNA was composed of two complementary oligonucleotides: 5'-AAAGAGAAGGAAGAGAAGAAGAAAGAAAAGAAAAAG-3' (Oligo 3) and 3'-TTTCTCTTCCTTCTCTTCTTCTTTCTTTTCTTTTTC-5' (Oligo 4). Hybridization of the two AuNPs-Oligo probes with the target dsDNA induced aggregation of the target dsDNA by forming triplex DNA, which accordingly increased the average diameter. This diameter change could then be detected by DLS. The average diameter was proportional to the target dsDNA concentration over the range from 593 fM to 40 pM, with a detection limit of 593 fM. Moreover, the assay had good sequence specificity for the target dsDNA.
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Affiliation(s)
- Xiang-Min Miao
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China
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12
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Kumar P, Østergaard ME, Hrdlicka PJ. Preparation of C5-functionalized locked nucleic acids (LNAs). CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2011; Chapter 4:Unit 4.43. [PMID: 21400703 DOI: 10.1002/0471142700.nc0443s44] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Relative to conventional locked nucleic acids (LNAs), C5-functionalized LNAs with small entities at the C5-position display markedly higher (1) duplex thermostability with complementary single-stranded DNA/RNA targets, (2) target specificity, and (3) 3'-exonuclease stability. C5-Functionalized LNAs carrying a polarity-sensitive fluorophore enable sensitive and efficient discrimination of single nucleotide polymorphisms (SNPs) under non-stringent conditions. This unit describes protocols for chemical synthesis of an LNA uridine diol and corresponding C5-functionalized LNA uridine phosphoramidites. A procedure for incorporation of C5-functionalized LNA uridine phosphoramidites into oligodeoxyribonucleotides by automated DNA synthesis is also described.
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13
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Wu C, Zhou Y, Miao X, Ling L. A novel fluorescent biosensor for sequence-specific recognition of double-stranded DNA with the platform of graphene oxide. Analyst 2011; 136:2106-10. [PMID: 21442091 DOI: 10.1039/c1an15061h] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A fluorescent biosensor for sequence-specific recognition of double-stranded DNA (dsDNA) was developed based upon the DNA hybridization between dye-labeled single-stranded DNA (ssDNA) and double-stranded DNA. The fluorescence of FAM-labeled single-stranded DNA was quenched when it adsorbed on the surface of graphene oxide (GO). Upon addition of the target dsDNA, a homopyrimidine·homopurine part of dsDNA on the Simian virus 40 (SV40) (4424-4440, gp6), hybridization occurred between the dye-labeled DNA and the target dsDNA, which induced the dye-labeled DNA desorbed from the surface of GO, and turned on the fluorescence of the dye. Under the optimum conditions, the enhanced fluorescence intensity was proportional to the concentration of target dsDNA in the range 40.0-260 nM, and the detection limit was found to be 14.3 nM alongside the good sequence selectivity.
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Affiliation(s)
- Chengke Wu
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou, PR China
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14
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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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15
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Veedu RN, Burri HV, Kumar P, Sharma PK, Hrdlicka PJ, Vester B, Wengel J. Polymerase-directed synthesis of C5-ethynyl locked nucleic acids. Bioorg Med Chem Lett 2010; 20:6565-8. [PMID: 20932755 DOI: 10.1016/j.bmcl.2010.09.044] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Revised: 09/06/2010] [Accepted: 09/08/2010] [Indexed: 11/17/2022]
Abstract
Modified nucleic acids have considerable potential in nanobiotechnology for the development of nanomedicines and new materials. Locked nucleic acid (LNA) is one of the most prominent nucleic acid analogues reported so far and we herein for the first time report the enzymatic incorporation of LNA-U and C5-ethynyl LNA-U nucleotides into oligonucleotides. Phusion High Fidelity and KOD DNA polymerases efficiently incorporated LNA-U and C5-ethynyl LNA-U nucleotides into a DNA strand and T7 RNA polymerase successfully accepted the LNA-U nucleoside 5'-triphosphate as substrate for RNA transcripts.
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Affiliation(s)
- Rakesh N Veedu
- Nucleic Acid Center, Department of Physics & Chemistry, University of Southern Denmark, Campusvej 55, Odense M 5230, Denmark.
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Biton A, Ezra A, Kasparkova J, Brabec V, Yavin E. DNA photocleavage by DNA and DNA-LNA amino acid-dye conjugates. Bioconjug Chem 2010; 21:616-21. [PMID: 20345124 DOI: 10.1021/bc900372h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
DNA photocleavage by triplex forming oligonucleotides (TFO) has potential implications in both biotechnology and medicine. We have synthesized a series of homopurine DNA and DNA/LNA 14-mers to which an amino acid (glycine or l-tryptophan) and a cyanine dye are covalently linked. Two cyanine dyes were examined that include a quinolinium ring linked to a benzothiazolium ring through a monomethine (TO1) or trimethine (TO2) linker. The 14-mer sequence was chosen to target mdm2, a ubiquitin ligase (E3) that regulates p53 by promoting its ubiquitylation and proteosomal degradation. Such inhibition has been previously proposed as a therapeutic approach to target wild-type p53-expressing cancers. To examine whether our TFO conjugates photocleave the mdm2 target, we incubated the various conjugates with the mdm2 plasmid and irradiated the samples with visible light. We show that only the TFO with the complementary sequence and with an intervening l-tryptophan leads to the linearization of the plasmid after a short irradiation time (10 min) exciting the dye (lambda(max)(TO1) = 500 nm and lambda(max)(TO2) = 630 nm) with visible light. Furthermore, the photoreactivity is more pronounced for the LNA/DNA conjugate, an observation that is consistent with improved hybridization to the DNA target. Sequence specificity of the photoreaction is further corroborated on a synthetic 44-mer duplex containing the TFO site. Evidence for a ROS-dependent mechanism is also given and discussed.
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Affiliation(s)
- Adva Biton
- Department of Medicinal Chemistry, The Institute for Drug Research, The School of Pharmacy, The Hebrew University of Jerusalem, Hadassah Ein-Karem, Jerusalem 91120, Israel
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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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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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