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Karmakar S, Madsen AS, Guenther DC, Gibbons BC, Hrdlicka PJ. Recognition of double-stranded DNA using energetically activated duplexes with interstrand zippers of 1-, 2- or 4-pyrenyl-functionalized O2'-alkylated RNA monomers. Org Biomol Chem 2014; 12:7758-73. [PMID: 25144705 PMCID: PMC4167914 DOI: 10.1039/c4ob01183j] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Despite advances with triplex-forming oligonucleotides, peptide nucleic acids, polyamides and--more recently--engineered proteins, there remains an urgent need for synthetic ligands that enable specific recognition of double-stranded (ds) DNA to accelerate studies aiming at detecting, regulating and modifying genes. Invaders, i.e., energetically activated DNA duplexes with interstrand zipper arrangements of intercalator-functionalized nucleotides, are emerging as an attractive approach toward this goal. Here, we characterize and compare Invaders based on 1-, 2- and 4-pyrenyl-functionalized O2'-alkylated uridine monomers X-Z by means of thermal denaturation experiments, optical spectroscopy, force-field simulations and recognition experiments using DNA hairpins as model targets. We demonstrate that Invaders with +1 interstrand zippers of X or Y monomers efficiently recognize mixed-sequence DNA hairpins with single nucleotide fidelity. Intercalator-mediated unwinding and activation of the double-stranded probe, coupled with extraordinary stabilization of probe-target duplexes (ΔT(m)/modification up to +14.0 °C), provides the driving force for dsDNA recognition. In contrast, Z-modified Invaders show much lower dsDNA recognition efficiency. Thus, even very conservative changes in the chemical makeup of the intercalator-functionalized nucleotides used to activate Invader duplexes, affects dsDNA-recognition efficiency of the probes, which highlights the importance of systematic structure-property studies. The insight from this study will guide future design of Invaders for applications in molecular biology and nucleic acid diagnostics.
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Affiliation(s)
- Saswata Karmakar
- Department of Chemistry, University of Idaho, Moscow, ID 83844, USA.
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Nickels BE, Dove SL. NanoRNAs: a class of small RNAs that can prime transcription initiation in bacteria. J Mol Biol 2011; 412:772-81. [PMID: 21704045 DOI: 10.1016/j.jmb.2011.06.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Revised: 06/08/2011] [Accepted: 06/09/2011] [Indexed: 01/12/2023]
Abstract
It has been widely assumed that all transcription in cells occur using NTPs only (i.e., de novo). However, it has been known for several decades that both prokaryotic and eukaryotic RNA polymerases can utilize small (2 to ∼5 nt) RNAs to prime transcription initiation in vitro, raising the possibility that small RNAs might also prime transcription initiation in vivo. A new study by Goldman et al. has now provided the first evidence that priming with so-called "nanoRNAs" (i.e., 2 to ∼5 nt RNAs) can, in fact, occur in vivo. Furthermore, this study provides evidence that altering the extent of nanoRNA-mediated priming of transcription initiation can profoundly influence global gene expression. In this perspective, we summarize the findings of Goldman et al. and discuss the prospect that nanoRNA-mediated priming of transcription initiation represents an underappreciated aspect of gene expression in vivo.
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Affiliation(s)
- Bryce E Nickels
- Department of Genetics and Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA.
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Hernández-Gil J, Ferrer Llusar S, Maldonado CR, Mareque-Rivas JC. Synergy between quantum dots and 1,10-phenanthroline-copper(II) complex towards cleaving DNA. Chem Commun (Camb) 2011; 47:2955-7. [PMID: 21240449 DOI: 10.1039/c0cc04163g] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We have found that the DNA cleaving activity of quantum dots and 1,10-phenanthroline-Cu(II) complex is significantly enhanced when they are combined.
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Affiliation(s)
- Javier Hernández-Gil
- Departament de Química Inorgànica, Facultat de Farmàcia, Universitat de València, 46100-Burjassot, Valencia, Spain
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Hansen ME, Bentin T, Nielsen PE. High-affinity triplex targeting of double stranded DNA using chemically modified peptide nucleic acid oligomers. Nucleic Acids Res 2009; 37:4498-507. [PMID: 19474349 PMCID: PMC2715256 DOI: 10.1093/nar/gkp437] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
While sequence-selective dsDNA targeting by triplex forming oligonucleotides has been studied extensively, only very little is known about the properties of PNA–dsDNA triplexes—mainly due to the competing invasion process. Here we show that when appropriately modified using pseudoisocytosine substitution, in combination with (oligo)lysine or 9-aminoacridine conjugation, homopyrimidine PNA oligomers bind complementary dsDNA targets via triplex formation with (sub)nanomolar affinities (at pH 7.2, 150 mM Na+). Binding affinity can be modulated more than 1000-fold by changes in pH, PNA oligomer length, PNA net charge and/or by substitution of pseudoisocytosine for cytosine, and conjugation of the DNA intercalator 9-aminoacridine. Furthermore, 9-aminoacridine conjugation also strongly enhanced triplex invasion. Specificity for the fully matched target versus one containing single centrally located mismatches was more than 150-fold. Together the data support the use of homopyrimidine PNAs as efficient and sequence selective tools in triplex targeting strategies under physiological relevant conditions.
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Affiliation(s)
- Mads E Hansen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen 2200-N, Denmark
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Oxidative nuclease activity of ferromagnetically coupled μ-hydroxo-μ-propionato copper(II) complexes [Cu3(L)2(μ-OH)2(μ-propionato)2] (L=N-(pyrid-2-ylmethyl)R-sulfonamidato, R=benzene, toluene, naphthalene). J Inorg Biochem 2009; 103:243-55. [DOI: 10.1016/j.jinorgbio.2008.10.015] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2008] [Revised: 10/13/2008] [Accepted: 10/15/2008] [Indexed: 11/20/2022]
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Beane R, Gabillet S, Montaillier C, Arar K, Corey DR. Recognition of chromosomal DNA inside cells by locked nucleic acids. Biochemistry 2009; 47:13147-9. [PMID: 19053275 DOI: 10.1021/bi801930p] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Sequence-selective recognition of DNA inside cells by oligonucleotides would provide valuable insights into cellular processes and new leads for therapeutics. Recent work, however, has shown that noncoding RNA transcripts overlap chromosomal DNA. These RNAs provide alternate targets for oligonucleotides designed to bind promoter DNA, potentially overturning previous assumptions about mechanism. Here, we show that antigene locked nucleic acids (agLNAs) reduce RNA levels of targeted genes, block RNA polymerase and transcription factor association at gene promoters, and bind to chromosomal DNA. These data suggest that the mechanism of LNAs involves recognition of chromosomal DNA and that LNAs are bona fide antigene molecules.
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Affiliation(s)
- Randall Beane
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Road, Dallas, Texas 75390-9041, USA
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Beane RL, Ram R, Gabillet S, Arar K, Monia BP, Corey DR. Inhibiting gene expression with locked nucleic acids (LNAs) that target chromosomal DNA. Biochemistry 2007; 46:7572-80. [PMID: 17536839 PMCID: PMC2527755 DOI: 10.1021/bi700227g] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Oligonucleotides containing locked nucleic acid bases (LNAs) have increased affinity for complementary DNA sequences. We hypothesized that enhanced affinity might allow LNAs to recognize chromosomal DNA inside human cells and inhibit gene expression. To test this hypothesis, we synthesized antigene LNAs (agLNAs) complementary to sequences within the promoters of progesterone receptor (PR) and androgen receptor (AR). We observed inhibition of AR and PR expression by agLNAs but not by analogous oligomers containing 2'-methoxyethyl bases or noncomplementary LNAs. Inhibition was dose dependent and exhibited IC50 values of <10 nM. Efficient inhibition depended on the length of the agLNA, the location of LNA bases, the number of LNA substitutions, and the location of the target sequence within the targeted promoter. LNAs targeting sequences at or near transcription start sites yielded better inhibition than LNAs targeting transcription factor binding sites or an inverted repeat. These results demonstrate that agLNAs can recognize chromosomal target sequences and efficiently block gene expression. agLNAs could be used for gene silencing, as cellular probes for chromosome structure, and therapeutic applications.
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Affiliation(s)
- Randall L. Beane
- The Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Road, Dallas, TX, 75390-9041
| | - Rosalyn Ram
- The Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Road, Dallas, TX, 75390-9041
| | - Sylvie Gabillet
- SIGMA-Proligo Genopole Campus 1 5, rue Desbruères, 91030 Evry Cedex, France
| | - Khalil Arar
- SIGMA-Proligo Genopole Campus 1 5, rue Desbruères, 91030 Evry Cedex, France
| | | | - David R. Corey
- The Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Road, Dallas, TX, 75390-9041
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Ali MM, Nagatsugi F, Sasaki S, Nakahara R, Maeda M. Application of 2-amino-6-vinylpurine as an efficient agent for conjugation of oligonucleotides. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2006; 25:159-69. [PMID: 16541959 DOI: 10.1080/15257770500446873] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Attempts have been made to conjugate a variety of molecules with oligonucleotides to achieve useful functions. In this study, we have established a new efficient method for post-synthetic conjugation of oligonucleotides with the use of the 2-amino-6-vinylpurine nucleoside. Amino nucleophiles form the corresponding conjugates under acidic conditions, whereas thiol nucleophiles reacted efficiently under alkaline conditions. Thus, glutathione and HS-Cys-(Arg)8 without protecting groups were efficiently conjugated to the 2-amino-6-vinylpurine-bearing ODN under alkaline conditions. The use of 2-amino-6-vinylpurine as an agent for conjugation is advantageous in that it is stable during the reaction and may be applied to conjugation of ODNs with multiple functional molecules.
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Affiliation(s)
- Md Monsur Ali
- Graduate School of Pharmaceutical Sciences, Kyushu University, Higashi-ku, Fukuoka, Japan
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Filichev VV, Vester B, Hansen LH, Pedersen EB. Easily denaturing nucleic acids derived from intercalating nucleic acids: thermal stability studies, dual duplex invasion and inhibition of transcription start. Nucleic Acids Res 2005; 33:7129-37. [PMID: 16377781 PMCID: PMC1322271 DOI: 10.1093/nar/gki1019] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The bulged insertions of (R)-1-O-(pyren-1-ylmethyl)glycerol (monomer P) in two complementary 8mer DNA strands (intercalating nucleic acids) opposite to each other resulted in the formation of an easily denaturing duplex, which had lower thermal stability (21.0 degrees C) than the wild-type double-stranded DNA (dsDNA, 26.0 degrees C), but both modified oligodeoxynucleotides had increased binding affinity toward complementary single-stranded DNA (ssDNA) (41.5 and 39.0 degrees C). Zipping of pyrene moieties in an easily denaturing duplex gave formation of a strong excimer band at 480 nm upon excitation at 343 nm in the steady-state fluorescence spectra. The excimer band disappeared upon addition of a similar short dsDNA, but remained when adding a 128mer dsDNA containing the same sequence. When P was inserted into 2'-OMe-RNA strands, the duplex with zipping P was found to be more stable (42.0 degrees C) than duplexes with the complementary ssDNAs (31.5 and 19.5 degrees C). The excimer band observed in the ds2'-OMe-RNA with zipping P had marginal changes upon addition of both 8 and 128mer dsDNA. Synthesized oligonucleotides were tested in a transcriptional inhibition assay for targeting of the open complex formed by Escherichia coli RNA polymerase with the lac UV-5 promoter using the above mentioned 128mer dsDNA. Inhibition of transcription was observed for 8mer DNAs possessing pyrene intercalators and designed to target both template and non-template DNA strands within the open complex. The observed inhibition was partly a result of unspecific binding of the modified DNAs to the RNA polymerase. Furthermore, the addition of 8mer DNA with three bulged insertions of P designed to be complementary to the template strand at the +36 to +43 position downstream of the transcription start resulted in a specific halt of transcription producing a truncated RNA transcript. This is to our knowledge the first report of an RNA elongation stop mediated by a small DNA sequence possessing intercalators. The insertions of P opposite to each other in ds2'-OMe-RNA showed inhibition efficiency of 96% compared with 25% for unmodified ds2'-OMe-RNA.
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Affiliation(s)
- Vyacheslav V Filichev
- Department of Chemistry, Nucleic Acid Center, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark.
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Filichev VV, Vester B, Hansen LH, Abdel Aal MT, Babu BR, Wengel J, Pedersen EB. Enhanced inhibition of transcription start by targeting with 2'-OMe pentaribonucleotides comprising locked nucleic acids and intercalating nucleic acids. Chembiochem 2005; 6:1181-4. [PMID: 15912554 DOI: 10.1002/cbic.200400457] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Vyacheslav V Filichev
- Nucleic Acid Center, Department of Chemistry, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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Hwang JT, Baltasar FE, Cole DL, Sigman DS, Chen CHB, Greenberg MM. Transcription inhibition using modified pentanucleotides. Bioorg Med Chem 2003; 11:2321-8. [PMID: 12713844 DOI: 10.1016/s0968-0896(03)00071-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Inhibition of gene expression was recently achieved by targeting the transcriptionally competent open complex using relatively short, pentameric modified oligonucleotides at approximately 60 microM. Corroborative affinity cleavage experiments using the copper complex of a phenanthroline conjugate provided the impetus to synthesize additional analogues containing substituents at the 2'-position of uridine in a derivative of 5'-GUGGA (-4 to +1), with the purpose of inhibiting transcription at lower concentrations. Conjugates of 5'-GUGGA modified at the 2'-position of uridine were convergently synthesized using a recently reported method. Seven analogues based upon the 5'-GUGGA scaffold were tested for their ability to inhibit transcription of the lac UV-5 operon. The conjugate containing a tethered pyrene showed 70% inhibition at 20 microM, and modest inhibition at as low as 5 microM. This is a significant improvement over previously tested pentanucleotides and provides direction for the preparation of a next generation of inhibitors.
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Affiliation(s)
- Jae-Taeg Hwang
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
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Connors WH, Narayanan S, Kryatova OP, Richert C. Synthesis of oligonucleotides with a 2'-cap at the 3'-terminus via reversed phosphoramidites. Org Lett 2003; 5:247-50. [PMID: 12556163 DOI: 10.1021/ol020212w] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[reaction: see text] A method is presented for the synthesis of single compounds or small combinatorial libraries of oligonucleotides with 2'-acylamido-2'-deoxyuridine residues at the 3'-terminus. Selection experiments identified the residue of anthraquinone-2-carboxylic acid as a "molecular cap" that increases the UV melting point of the duplex (5'-ACGCGU-3')(2) by up to 28 degrees C compared to the unmodified control duplex.
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Affiliation(s)
- William H Connors
- Department of Chemistry, University of Constance, 78457 Konstanz, Germany
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