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Evich M, Spring-Connell AM, Germann MW. Impact of modified ribose sugars on nucleic acid conformation and function. HETEROCYCL COMMUN 2017. [DOI: 10.1515/hc-2017-0056] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
AbstractThe modification of the ribofuranose in nucleic acids is a widespread method of manipulating the activity of nucleic acids. These alterations, however, impact the local conformation and chemical reactivity of the sugar. Changes in the conformation and dynamics of the sugar moiety alter the local and potentially global structure and plasticity of nucleic acids, which in turn contributes to recognition, binding of ligands and enzymatic activity of proteins. This review article introduces the conformational properties of the (deoxy)ribofuranose ring and then explores sugar modifications and how they impact local and global structure and dynamics in nucleic acids.
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Affiliation(s)
- Marina Evich
- Georgia State University, Department of Chemistry, 50 Decatur St. SE, Atlanta, GA 30303, USA
| | | | - Markus W. Germann
- Georgia State University, Department of Chemistry, 50 Decatur St. SE, Atlanta, GA 30303, USA
- Georgia State University, Department of Biology, P.O. 4010, Atlanta, GA 30303, USA
- Georgia State University, Neuroscience Institute, P.O. 5030, Atlanta, GA 30303, USA
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2
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Berezney JP, Saleh OA. Locked nucleic acid oligomers as handles for single molecule manipulation. Nucleic Acids Res 2014; 42:e150. [PMID: 25159617 PMCID: PMC4231729 DOI: 10.1093/nar/gku760] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Single-molecule manipulation (SMM) techniques use applied force, and measured elastic response, to reveal microscopic physical parameters of individual biomolecules and details of biomolecular interactions. A major hurdle in the application of these techniques is the labeling method needed to immobilize biomolecules on solid supports. A simple, minimally-perturbative labeling strategy would significantly broaden the possible applications of SMM experiments, perhaps even allowing the study of native biomolecular structures. To accomplish this, we investigate the use of functionalized locked nucleic acid (LNA) oligomers as biomolecular handles that permit sequence-specific binding and immobilization of DNA. We find these probes form bonds with DNA with high specificity but with varied stability in response to the direction of applied mechanical force: when loaded in a shear orientation, the bound LNA oligomers were measured to be two orders of magnitude more stable than when loaded in a peeling, or unzipping, orientation. Our results show that LNA provides a simple, stable means to functionalize dsDNA for manipulation. We provide design rules that will facilitate their use in future experiments.
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Affiliation(s)
- John P Berezney
- Materials Department, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Omar A Saleh
- Materials Department, University of California, Santa Barbara, Santa Barbara, CA 93106, USA Biomolecular Science and Engineering Program, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
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3
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Kumar P, Baral B, Anderson BA, Guenther DC, Østergaard ME, Sharma PK, Hrdlicka PJ. C5-alkynyl-functionalized α-L-LNA: synthesis, thermal denaturation experiments and enzymatic stability. J Org Chem 2014; 79:5062-73. [PMID: 24797769 PMCID: PMC4049248 DOI: 10.1021/jo5006153] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Indexed: 12/23/2022]
Abstract
Major efforts are currently being devoted to improving the binding affinity, target specificity, and enzymatic stability of oligonucleotides used for nucleic acid targeting applications in molecular biology, biotechnology, and medicinal chemistry. One of the most popular strategies toward this end has been to introduce additional modifications to the sugar ring of affinity-inducing conformationally restricted nucleotide building blocks such as locked nucleic acid (LNA). In the preceding article in this issue, we introduced a different strategy toward this end, i.e., C5-functionalization of LNA uridines. In the present article, we extend this strategy to α-L-LNA: i.e., one of the most interesting diastereomers of LNA. α-L-LNA uridine monomers that are conjugated to small C5-alkynyl substituents induce significant improvements in target affinity, binding specificity, and enzymatic stability relative to conventional α-L-LNA. The results from the back-to-back articles therefore suggest that C5-functionalization of pyrimidines is a general and synthetically straightforward approach to modulate biophysical properties of oligonucleotides modified with LNA or other conformationally restricted monomers.
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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
| | - 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
| | - Michael E. Østergaard
- 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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4
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Wey MT, Lyu PC, Kan LS. Thermodynamic and Kinetic Studies of a Stable Imperfect DNA Triplex by Spectroscopic and Calorimetric Methods. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.201000072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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5
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Affiliation(s)
- Yuhao Du
- College of Chemistry and Molecular Sciences; Wuhan University; Hubei; Wuhan; 430072; P. R. China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences; Wuhan University; Hubei; Wuhan; 430072; P. R. China
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6
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Grove TZ, Regan L, Cortajarena AL. Nanostructured functional films from engineered repeat proteins. J R Soc Interface 2013; 10:20130051. [PMID: 23594813 DOI: 10.1098/rsif.2013.0051] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Fundamental advances in biotechnology, medicine, environment, electronics and energy require methods for precise control of spatial organization at the nanoscale. Assemblies that rely on highly specific biomolecular interactions are an attractive approach to form materials that display novel and useful properties. Here, we report on assembly of films from the designed, rod-shaped, superhelical, consensus tetratricopeptide repeat protein (CTPR). We have designed three peptide-binding sites into the 18 repeat CTPR to allow for further specific and non-covalent functionalization of films through binding of fluorescein labelled peptides. The fluorescence signal from the peptide ligand bound to the protein in the solid film is anisotropic, demonstrating that CTPR films can impose order on otherwise isotropic moieties. Circular dichroism measurements show that the individual protein molecules retain their secondary structure in the film, and X-ray scattering, birefringence and atomic force microscopy experiments confirm macroscopic alignment of CTPR molecules within the film. This work opens the door to the generation of innovative biomaterials with tailored structure and function.
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Affiliation(s)
- Tijana Z Grove
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
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7
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Martić S, Kraatz HB. Chemical biology toolkit for exploring protein kinase catalyzed phosphorylation reactions. Chem Sci 2013. [DOI: 10.1039/c2sc20846f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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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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Kim J, Yoon S, Yoo JK, Kim J, Kim H, Kang K. Highly Laminated Electrospun ZnO Nanofibrous Film on the Transparent Conducting Oxide for Photovoltaic Device. J ELECTROCHEM SCI TE 2012. [DOI: 10.5229/jecst.2012.3.2.68] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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11
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Coppock MB, Williams ME. Nucleic Acid Mimetics. Supramol Chem 2012. [DOI: 10.1002/9780470661345.smc169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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12
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D'Alonzo D, Guaragna A, Palumbo G. Exploring the role of chirality in nucleic acid recognition. Chem Biodivers 2012; 8:373-413. [PMID: 21404424 DOI: 10.1002/cbdv.201000303] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The study of the base-pairing properties of nucleic acids with sugar moieties in the backbone belonging to the L-series (β-L-DNA, β-L-RNA, and their analogs) are reviewed. The major structural factors underlying the formation of stable heterochiral complexes obtained by incorporation of modified nucleotides into natural duplexes, or by hybridization between homochiral strands of opposite sense of chirality are highlighted. In addition, the perspective use of L-nucleic acids as candidates for various therapeutic applications, or as tools for both synthetic biology and etiology-oriented investigations on the structure and stereochemistry of natural nucleic acids is discussed.
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Affiliation(s)
- Daniele D'Alonzo
- Dipartimento di Chimica Organica e Biochimica, Università di Napoli Federico II, Complesso Universitario Monte Sant'Angelo, via Cinthia, 4, I-80126 Napoli.
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13
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Abstract
In contrast to B-DNA that has a right-handed double helical structure with Watson-Crick base pairing under the ordinary physiological conditions, repetitive DNA sequences under certain conditions have the potential to fold into non-B DNA structures such as hairpin, triplex, cruciform, left-handed Z-form, tetraplex, A-motif, etc. Since the non-B DNA-forming sequences induce the genetic instability and consequently can cause human diseases, the molecular mechanism for their genetic instability has been extensively investigated. On the contrary, non-B DNA can be widely used for application in biotechnology because many DNA breakage hotspots are mapped in or near the sequences that have the potential to adopt non-B DNA structures. In addition, they are regarded as a fascinating material for the nanotechnology using non-B DNAs because they do not produce any toxic byproducts and are robust enough for the repetitive working cycle. This being the case, an understanding on the mechanism and dynamics of their structural changes is important. In this critical review, we describe the latest studies on the conformational dynamics of non-B DNAs, with a focus on G-quadruplex, i-motif, Z-DNA, A-motif, hairpin and triplex (189 references).
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Affiliation(s)
- Jungkweon Choi
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Ibaraki, Osaka 567-0047, Japan
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14
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Bhattacharyya J, Maiti S, Muhuri S, Nakano SI, Miyoshi D, Sugimoto N. Effect of locked nucleic acid modifications on the thermal stability of noncanonical DNA structure. Biochemistry 2011; 50:7414-25. [PMID: 21774551 DOI: 10.1021/bi200477g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We studied the kinetic and thermodynamic effects of locked nucleic acid (LNA) modifications on parallel and antiparallel DNA duplexes. The LNA modifications were introduced at cytosine bases of the pyrimidine strand. Kinetic parameters evaluated from melting and annealing curves showed that the association and dissociation rate constants for the formation of the LNA-modified parallel duplex at 25.0 °C were 3 orders of magnitude larger and 6 orders of magnitude smaller, respectively, than that of the unmodified parallel duplex. The activation energy evaluated from the temperature-dependent rate constants was largely altered by the LNA modifications, suggesting that the LNA modifications affected a prenucleation event in the folding process. Moreover, thermodynamic parameters showed that the extent of stabilization by the LNA modification for parallel duplexes (3.6 kcal mol(-1) per one modification) was much more significant than that of antiparallel duplexes (1.6 kcal mol(-1)). This large stabilization was due to the decrease in ΔH° that was more favorable than the decrease in TΔS°. These quantitative parameters demonstrated that LNA modification specifically stabilized the noncanonical parallel duplex. On the basis of these observations, we succeeded to stabilize the parallel duplex by LNA modification at the physiological pH. These results can be useful in the rational design of functional molecules such as more effective antisense and antigene strands, more sensitive strands for detection of target DNA and RNA strands, and molecular switches responding to solution pH.
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Affiliation(s)
- Jhimli Bhattacharyya
- FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
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15
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Kolevzon N, Yavin E. Site-Specific DNA Photocleavage and Photomodulation by Oligonucleotide Conjugates. Oligonucleotides 2010; 20:263-75. [DOI: 10.1089/oli.2010.0247] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Netanel Kolevzon
- The School of Pharmacy, The Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Eylon Yavin
- The School of Pharmacy, The Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
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16
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Arslan P, Jyo A, Ihara T. Reversible circularization of an anthracene-modified DNA conjugate through bimolecular triplex formation and its analytical application. Org Biomol Chem 2010; 8:4843-8. [PMID: 20734012 DOI: 10.1039/c0ob00282h] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We prepared an oligodeoxyribonucleotide conjugate (5-3ant(2)18) carrying two anthracenes, each of which was tethered to both ends of the conjugate through hexamethylene linker chains. The conjugate has a mirror repeat of two heptamer sequences, such that it forms a bimolecular triplex with the single stranded target, forming a two-fold U-shaped conformation. The conformation of the conjugate in its triplex structure could be frozen instantaneously by circularization through photodimerization of the anthracenes. Compared with the duplex formation of linear probes with relevant sequences, bimolecular triplex formation of 5-3ant(2)18 shows a unique feature in its target recognition; it binds the target tightly, yet still retains high sequence selectivity. Circularization of 5-3ant(2)18 by UV photoirradiation was verified as the probe reaction for a DNA assay. The probe reaction could be performed in a few seconds over a wide range of temperatures, at least between 0 and 25 °C. In addition, the reaction could be regarded as a reversible method for the preparation of circular DNA that shows higher affinity for the target.
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Affiliation(s)
- Pelin Arslan
- Department of Applied Chemistry and Biochemistry, Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami, Kumamoto 860-8555, Japan
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17
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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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18
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Alvira M, Eritja R. Triplex-stabilizing properties of parallel clamps carrying LNA derivatives at the Hoogsteen strand. Chem Biodivers 2010; 7:376-82. [PMID: 20151386 DOI: 10.1002/cbdv.200900230] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
DNA Parallel clamps with a polypurine strand linked to a polypyrimidine Hoogsteen strand containing locked nucleic acids bind their corresponding polypyrimidine targets with high affinity.
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Affiliation(s)
- Margarita Alvira
- Institute for Research in Biomedicine, IQAC-CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Edifici Helix, Baldiri Reixac 15, ES-08028 Barcelona, Spain
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19
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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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20
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Sau SP, Kumar P, Anderson BA, Østergaard ME, Deobald L, Paszczynski A, Sharma PK, Hrdlicka PJ. Optimized DNA-targeting using triplex forming C5-alkynyl functionalized LNA. Chem Commun (Camb) 2009:6756-8. [PMID: 19885469 DOI: 10.1039/b917312a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Triplex forming oligonucleotides (TFOs) modified with C5-alkynyl functionalized LNA (locked nucleic acid) monomers display extraordinary thermal affinity toward double stranded DNA targets, excellent discrimination of Hoogsteen-mismatched targets, and high stability against 3?-exonucleases.
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Affiliation(s)
- Sujay P Sau
- Dept. of Chemistry, Univ. of Idaho, ID-83844, USA
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21
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Ihara T, Ishii T, Araki N, Wilson AW, Jyo A. Silver Ion Unusually Stabilizes the Structure of a Parallel-Motif DNA Triplex. J Am Chem Soc 2009; 131:3826-7. [DOI: 10.1021/ja809702n] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Toshihiro Ihara
- Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami, Kumamoto 860-8555, Japan, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Kumamoto 860-8556, Japan, and PRESTO, Japan Science and Technology Agency, San-bancho Building, 3-5 Sanbancho, Chiyodaku, Tokyo 332-0012, Japan
| | - Tatsuaki Ishii
- Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami, Kumamoto 860-8555, Japan, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Kumamoto 860-8556, Japan, and PRESTO, Japan Science and Technology Agency, San-bancho Building, 3-5 Sanbancho, Chiyodaku, Tokyo 332-0012, Japan
| | - Norie Araki
- Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami, Kumamoto 860-8555, Japan, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Kumamoto 860-8556, Japan, and PRESTO, Japan Science and Technology Agency, San-bancho Building, 3-5 Sanbancho, Chiyodaku, Tokyo 332-0012, Japan
| | - Anthony W. Wilson
- Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami, Kumamoto 860-8555, Japan, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Kumamoto 860-8556, Japan, and PRESTO, Japan Science and Technology Agency, San-bancho Building, 3-5 Sanbancho, Chiyodaku, Tokyo 332-0012, Japan
| | - Akinori Jyo
- Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami, Kumamoto 860-8555, Japan, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Kumamoto 860-8556, Japan, and PRESTO, Japan Science and Technology Agency, San-bancho Building, 3-5 Sanbancho, Chiyodaku, Tokyo 332-0012, Japan
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Kumar TS, Madsen AS, Østergaard ME, Sau SP, Wengel J, Hrdlicka PJ. Functionalized 2'-amino-alpha-L-LNA: directed positioning of intercalators for DNA targeting. J Org Chem 2009; 74:1070-81. [PMID: 19108636 PMCID: PMC2853939 DOI: 10.1021/jo802037v] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Chemically modified oligonucleotides are increasingly applied in nucleic acid based therapeutics and diagnostics. LNA (locked nucleic acid) and its diastereomer alpha-L-LNA are two promising examples thereof that exhibit increased thermal and enzymatic stability. Herein, the synthesis, biophysical characterization, and molecular modeling of N2'-functionalized 2'-amino-alpha-L-LNA is described. Chemoselective N2'-functionalization of protected amino alcohol 1 followed by phosphitylation afforded a structurally varied set of target phosphoramidites, which were incorporated into oligodeoxyribonucleotides. Incorporation of pyrene-functionalized building blocks such as 2'-N-(pyren-1-yl)carbonyl-2'-amino-alpha-L-LNA (monomer X) led to extraordinary increases in thermal affinity of up to +19.5 degrees C per modification against DNA targets in particular. In contrast, incorporation of building blocks with small nonaromatic N2'-functionalities such as 2'-N-acetyl-2'-amino-alpha-L-LNA (monomer V) had detrimental effects on thermal affinity toward DNA/RNA complements with decreases of as much as -16.5 degrees C per modification. Extensive thermal DNA selectivity, favorable entropic contributions upon duplex formation, hybridization-induced bathochromic shifts of pyrene absorption maxima and increases in circular dichroism signal intensity, and molecular modeling studies suggest that pyrene-functionalized 2'-amino-alpha-L-LNA monomers W-Y having short linkers between the bicyclic skeleton and the pyrene moiety allow high-affinity hybridization with DNA complements and precise positioning of intercalators in nucleic acid duplexes. This rigorous positional control has been utilized for the development of probes for emerging therapeutic and diagnostic applications focusing on DNA targeting.
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Affiliation(s)
- T Santhosh Kumar
- Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, DK-5230 Odense M, Denmark
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Kumar N, Patowary A, Sivasubbu S, Petersen M, Maiti S. Silencing c-MYC expression by targeting quadruplex in P1 promoter using locked nucleic acid trap. Biochemistry 2009; 47:13179-88. [PMID: 19053274 DOI: 10.1021/bi801064j] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The nuclease hypersensitive element of P1 promoter in c-MYC gene harbors a potential of unusual structure called quadruplex, which is involved in molecular recognition and function. This Hoogsteen bonded structure is in dynamic equilibrium with the usual Watson-Crick duplex structure, and these competing secondary structures undergo interconversion for execution of their respective biological roles. Herein, we investigate the sensitivity of the c-MYC quadruplex-duplex equilibrium by employing a locked nucleic acid (LNA) modified complementary strand as a pharmacological agent. Our biophysical experiments indicate that the c-MYC quadruplex under physiological conditions is stable and dominates the quadruplex-WC duplex equilibrium in both sodium and potassium buffers. This equilibrium is perturbed upon introducing the LNA modified complementary strand, which demonstrates efficient invasion of stable c-MYC quadruplex and duplex formation in contrast to the unmodified complementary strand. Our data indicate that LNA modifications confer increased thermodynamic stability to the duplex and thus favor the predominance of the duplex population over that of the quadruplex. Further, we demonstrate that this perturbation of equilibrium by a pharmacological agent results in altered gene expression. Our in vivo experiment performed using the LNA modified complementary strand suggests the influence of the quadruplex-duplex structural switch in the modulation of gene expression. We believe that this exploratory approach utilizing the selectivity and specificity of Watson-Crick base pairing of LNA bases would allow the modulation of quadruplex regulated gene expression.
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Affiliation(s)
- Niti Kumar
- Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110007, India
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Van Daele I, Bomholt N, Filichev VV, Van Calenbergh S, Pedersen EB. Triplex formation by pyrene-labelled probes for nucleic acid detection in fluorescence assays. Chembiochem 2008; 9:791-801. [PMID: 18327861 DOI: 10.1002/cbic.200700533] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Triplex-forming homopyrimidine oligonucleotides containing insertions of a 2'-5' uridine linkage featuring a pyrene moiety at the 3'-position exhibit strong fluorescence enhancement upon binding to double-stranded DNA through Hoogsteen base pairing. It is shown that perfect matching of the new modification to the base pair in the duplex is a prerequisite for strong fluorescence, thus offering the potential to detect single mutations in purine stretches of duplex DNA. The increase in the fluorescence signal was dependent on the thermal stability of the parallel triplex, so a reduction in the pH from 6.0 to 5.0 resulted in an increase in thermal stability from 25.0 to 55.0 degrees C and in an increase in the fluorescence quantum yield (Phi(F)) from 0.061 to 0.179, while the probe alone was fluorescently silent (Phi(F)=0.001-0.004). To achieve higher triplex stability, five nucleobases in a 14-mer sequence were substituted with alpha-L-LNA monomers, which provided a triplex with a T(m) of 49.5 degrees C and a Phi(F) of 0.158 at pH 6.0. Under similar conditions, a Watson-Crick-type duplex formed with the latter probe showed lower fluorescence intensity (Phi(F)=0.081) than for the triplex.
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Affiliation(s)
- Ineke Van Daele
- Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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Koch T, Rosenbohm C, Hansen HF, Hansen B, Marie Straarup E, Kauppinen S. Locked Nucleic Acid: Properties and Therapeutic Aspects. THERAPEUTIC OLIGONUCLEOTIDES 2008. [DOI: 10.1039/9781847558275-00103] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Troels Koch
- Santaris Pharma A/S Bøge Allé 3 DK-2970 Hørsholm Denmark
| | | | | | - Bo Hansen
- Santaris Pharma A/S Bøge Allé 3 DK-2970 Hørsholm Denmark
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Kaur H, Babu BR, Maiti S. Perspectives on chemistry and therapeutic applications of Locked Nucleic Acid (LNA). Chem Rev 2007; 107:4672-97. [PMID: 17944519 DOI: 10.1021/cr050266u] [Citation(s) in RCA: 232] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Harleen Kaur
- Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007, India
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27
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Abstract
The synthesis of modified nucleic acids has been the subject of much study ever since the structure of DNA was elucidated by Watson and Crick at Cambridge and Wilkins and Franklin at King's College over half a century ago. This review describes recent developments in the synthesis and application of these artificial nucleic acids, predominantly the phosphoramidites which allow for easy inclusion into oligonucleotides, and is divided into three separate sections. Firstly, modifications to the base portion will be discussed followed secondly by modifications to the sugar portion. Finally, changes in the type of nucleic acid linker will be discussed in the third section. Peptide Nucleic Acids (PNAs) are not discussed in this review as they represent a separate and large area of nucleic acid mimics.
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Affiliation(s)
- Alexander J A Cobb
- School of Pharmacy, University of Reading, Whiteknights, Reading, Berks RG6 6AD, UK.
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Højland T, Kumar S, Babu BR, Umemoto T, Albaek N, Sharma PK, Nielsen P, Wengel J. LNA (locked nucleic acid) and analogs as triplex-forming oligonucleotides. Org Biomol Chem 2007; 5:2375-9. [PMID: 17637956 DOI: 10.1039/b706101c] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The triplex-forming abilities of some conformationally restricted nucleotide analogs are disclosed and compared herein. 2'-Amino-LNA monomers proved to be less stabilising to triplexes than LNA monomers when incorporated into a triplex-forming third strand. N2'-functionalisation of 2'-amino-LNA monomers with a glycyl unit induced the formation of exceptionally stable triplexes. Nucleotide analogs containing a C2',C3'-oxymethylene linker (E-type furanose conformation) or a C2',C4'-propylene linker (N-type furanose conformation) had no significant effect on triplex stability proving that conformational restriction per se is insufficient to stabilise triplexes.
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Affiliation(s)
- Torben Højland
- Nucleic Acid Center, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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Rahman SMA, Seki S, Obika S, Haitani S, Miyashita K, Imanishi T. Highly Stable Pyrimidine-Motif Triplex Formation at Physiological pH Values by a Bridged Nucleic Acid Analogue. Angew Chem Int Ed Engl 2007; 46:4306-9. [PMID: 17469090 DOI: 10.1002/anie.200604857] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- S M Abdur Rahman
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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30
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Rahman S, Seki S, Obika S, Haitani S, Miyashita K, Imanishi T. Highly Stable Pyrimidine-Motif Triplex Formation at Physiological pH Values by a Bridged Nucleic Acid Analogue. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200604857] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Madsen AS, Hrdlicka PJ, Kumar TS, Wengel J. Synthesis, nucleic acid hybridization properties and molecular modelling studies of conformationally restricted 3'-O,4'-C-methylene-linked alpha-L-ribonucleotides. Carbohydr Res 2006; 341:1398-407. [PMID: 16709404 DOI: 10.1016/j.carres.2006.04.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2006] [Revised: 04/07/2006] [Accepted: 04/08/2006] [Indexed: 01/09/2023]
Abstract
Nucleotides with conformationally restricted carbohydrate rings such as locked nucleic acid (LNA), alpha-L-LNA or 2',5'-linked 3'-O,4'-C-methyleribonucleotides exhibit significant potential as building blocks for antigene and antisense strategies. 2',5'-Linked alpha-L-ribo configured monomer X (termed alpha-L-ONA) was designed as a potential structural mimic of alpha-L-LNA. The corresponding phosphoramidite building block of monomer X was obtained in five steps (10% overall yield) from the easily obtainable thymine derivative 1. Incorporation of monomer X into oligodeoxyribonucleotides (ONs) results in dramatically decreased thermal stabilities with DNA/RNA complements (DeltaTm/mod=-11.5 to -17.0 degrees C) compared to unmodified reference ONs. Less pronounced decreases (DeltaTm/mod=-4.5 to -8.5 degrees C) are observed when monomer X is incorporated into triplex forming ONs and targeted against double-stranded DNA (parallel orientation, pyrimidine motif). This biophysical data, together with modelling studies, suggest that 2',5'-linked alpha-L-ONA is a poor structural mimic of alpha-L-LNA.
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Affiliation(s)
- Andreas S Madsen
- Nucleic Acid Center, Department of Chemistry, University of Southern Denmark, DK-5230 Odense M, Denmark
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