1
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Géci I, Fatthalla MI, Heintz M, Jørgensen PT, Pedersen EB. Hoogsteen triplexes stabilized through ethynyl-linked pyrene-indole synthesized by high-temperature Sonogashira coupling. Org Biomol Chem 2022; 20:8873-8884. [PMID: 36102841 DOI: 10.1039/d2ob01466a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The low binding affinity of unmodified triplex-forming oligonucleotides (TFO) is the main drawback to their promising utilization in gene therapy. In the present study, we have synthesized DNA intercalator 5-(pyren-1-ylethynyl)indole Y, known as twisted intercalating nucleic acid (TINA), by a Cu-mediated Sonogashira palladium-catalyzed coupling reaction of 1-ethynylpyrene with 5-iodoindole at a high temperature under anaerobic conditions. Coupling with indole C-5 was far more preferable in obtaining stable TINA-indole than enamine site C-3, as neither hydration of the triple bond to ketones nor competitive Glaser-type homocoupling of acetylenes was observed. The insertion of the new TINA monomer Y as a bulge in the middle or at the 5'-end of the oligodeoxynucleotide sequence via a flexible butane-1,2-diol linker showed extraordinary binding potential, resulting in excellent thermal stabilization of Hoogsteen-type triplex- and duplex-deoxyribonucleic acid (DNA) structures which was detected by thermal denaturation studies and supported by circular dichroism (CD). Molecular dynamics AMBER* revealed the lowest energy conformation in which a pyrenyl residue of the TINA monomer Y stacks in the dsDNA part, while an indolyl unit intercalates between the nucleobases of the TFO pattern. Overall the torsionally rigid conjugated TINA system with a decent twisting of 15.1° around acetylene is confirmed here as a requirement for the best fit inside the intercalation site of the triplex, resulting in high TFO-dsDNA affinity.
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Affiliation(s)
- Imrich Géci
- Department of Medical and Clinical Biophysics, Faculty of Medicine, P. J. Šafárik University in Košice, Trieda SNP 1, 04011 Košice, Slovakia. .,Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark
| | - Maha I Fatthalla
- Department of Chemistry, Faculty of Science, Helwan University, 11795 Ain Helwan, Cairo, Egypt.,Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark.,Universite Paris-Sud, CNRS, Faculte de Pharmacie, 5 rue J.-B. Clement, Chatenay-Malabry, 92296 France
| | - Maike Heintz
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark
| | - Per T Jørgensen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark
| | - Erik B Pedersen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark
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2
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Appukutti N, Serpell CJ. High definition polyphosphoesters: between nucleic acids and plastics. Polym Chem 2018. [DOI: 10.1039/c8py00251g] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Nucleic acids and synthetic polyphosphoester materials have been distinct fields – this review shows how these areas now comprise a continuum.
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3
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Krasheninina OA, Novopashina DS, Apartsin EK, Venyaminova AG. Recent Advances in Nucleic Acid Targeting Probes and Supramolecular Constructs Based on Pyrene-Modified Oligonucleotides. Molecules 2017; 22:E2108. [PMID: 29189716 PMCID: PMC6150046 DOI: 10.3390/molecules22122108] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 11/28/2017] [Accepted: 11/28/2017] [Indexed: 12/17/2022] Open
Abstract
In this review, we summarize the recent advances in the use of pyrene-modified oligonucleotides as a platform for functional nucleic acid-based constructs. Pyrene is of special interest for the development of nucleic acid-based tools due to its unique fluorescent properties (sensitivity of fluorescence to the microenvironment, ability to form excimers and exciplexes, long fluorescence lifetime, high quantum yield), ability to intercalate into the nucleic acid duplex, to act as a π-π-stacking (including anchoring) moiety, and others. These properties of pyrene have been used to construct novel sensitive fluorescent probes for the sequence-specific detection of nucleic acids and the discrimination of single nucleotide polymorphisms (SNPs), aptamer-based biosensors, agents for binding of double-stranded DNAs, and building blocks for supramolecular complexes. Special attention is paid to the influence of the design of pyrene-modified oligonucleotides on their properties, i.e., the structure-function relationships. The perspectives for the applications of pyrene-modified oligonucleotides in biomolecular studies, diagnostics, and nanotechnology are discussed.
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Affiliation(s)
- Olga A Krasheninina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
| | - Darya S Novopashina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
| | - Evgeny K Apartsin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
| | - Alya G Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
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Astakhova K, Golovin AV, Prokhorenko IA, Ustinov AV, Stepanova IA, Zatsepin TS, Korshun VA. Design of 2′-phenylethynylpyrene excimer forming DNA/RNA probes for homogeneous SNP detection: The attachment manner matters. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.04.045] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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5
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Hartono Y, Pabon-Martinez YV, Uyar A, Wengel J, Lundin KE, Zain R, Smith CIE, Nilsson L, Villa A. Role of Pseudoisocytidine Tautomerization in Triplex-Forming Oligonucleotides: In Silico and in Vitro Studies. ACS OMEGA 2017; 2:2165-2177. [PMID: 30023656 PMCID: PMC6044803 DOI: 10.1021/acsomega.7b00347] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 05/02/2017] [Indexed: 06/08/2023]
Abstract
Pseudoisocytidine (ΨC) is a synthetic cytidine analogue that can target DNA duplex to form parallel triplex at neutral pH. Pseudoisocytidine has mainly two tautomers, of which only one is favorable for triplex formation. In this study, we investigated the effect of sequence on ΨC tautomerization using λ-dynamics simulation, which takes into account transitions between states. We also performed in vitro binding experiments with sequences containing ΨC and furthermore characterized the structure of the formed triplex using molecular dynamics simulation. We found that the neighboring methylated or protonated cytidine promotes the formation of the favorable tautomer, whereas the neighboring thymine or locked nucleic acid has a poor effect, and consecutive ΨC has a negative influence. The deleterious effect of consecutive ΨC in a triplex formation was confirmed using in vitro binding experiments. Our findings contribute to improving the design of ΨC-containing triplex-forming oligonucleotides directed to target G-rich DNA sequences.
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Affiliation(s)
- Yossa
Dwi Hartono
- Department
of Biosciences and Nutrition, Karolinska
Institutet, SE-141 83 Huddinge, Sweden
- Division
of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Y. Vladimir Pabon-Martinez
- Department
of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86 Huddinge, Sweden
| | - Arzu Uyar
- Department
of Biosciences and Nutrition, Karolinska
Institutet, SE-141 83 Huddinge, Sweden
| | - Jesper Wengel
- Department
of Physics, Chemistry and Pharmacy, Nucleic Acid Center, University of Southern Denmark, 5230 Odense M, Denmark
| | - Karin E. Lundin
- Department
of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86 Huddinge, Sweden
| | - Rula Zain
- Department
of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86 Huddinge, Sweden
- Department
of Clinical Genetics, Centre for Rare Diseases, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - C. I. Edvard Smith
- Department
of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86 Huddinge, Sweden
| | - Lennart Nilsson
- Department
of Biosciences and Nutrition, Karolinska
Institutet, SE-141 83 Huddinge, Sweden
| | - Alessandra Villa
- Department
of Biosciences and Nutrition, Karolinska
Institutet, SE-141 83 Huddinge, Sweden
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6
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Aparin IO, Farzan VM, Veselova OA, Chistov AA, Podkolzin AT, Ustinov AV, Shipulin GA, Formanovsky AA, Korshun VA, Zatsepin TS. 1-Phenylethynylpyrene (PEPy) as a novel blue-emitting dye for qPCR assay. Analyst 2016; 141:1331-8. [PMID: 26738806 DOI: 10.1039/c5an01767j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
An alkyl azide derivative of 1-phenylethynylpyrene (PEPy) dye was prepared and used in the functionalization of oligonucleotides via click chemistry. Spectral and photo-physical properties of the PEPy-modified oligonucleotides as a single strand, and in perfect or mismatched duplexes, have been studied. A series of PEPy-Dabcyl fluorogenic TaqMan probes were synthesized and tested in qPCR. PEPy proved to be a superior substitute for AMCA as a short wavelength fluorescent dye for qPCR probes. PEPy probes were shown to significantly reduce Cq (a fractional PCR cycle used for quantification) vs. AMCA labeled probes, thus improving on the reliability of detection. Moreover, a larger increase of fluorescence during amplification was observed in the case of PEPy probes that makes this dye very suitable for an end-point PCR technique. This study broadens the panel of fluorescent dyes suitable for the use in probes for quantitative real-time PCR.
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Affiliation(s)
- Ilya O Aparin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia.
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7
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Podbevšek P, Plavec J. KRAS promoter oligonucleotide with decoy activity dimerizes into a unique topology consisting of two G-quadruplex units. Nucleic Acids Res 2015; 44:917-25. [PMID: 26656490 PMCID: PMC4737153 DOI: 10.1093/nar/gkv1359] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 11/23/2015] [Indexed: 12/31/2022] Open
Abstract
Mutations of the KRAS proto-oncogene are associated with several tumor types, which is why it is being considered as a target for anti-cancer drug development. The human KRAS promoter contains a nuclease hypersensitive element (NHE), which can bind to nuclear proteins and is believed to form G-quadruplex structures. Previous studies showed that a 32-nt oligonucleotide (32R-3n) mimicking the KRAS NHE can reduce gene transcription by sequestering MAZ, a crucial transcription factor. Here we show that 32R-3n has to dimerize in order to fold into a G-quadruplex structure. Individual 5′- and 3′-end G-quadruplex units are formed and both feature a symmetric head-to-head topology with edge-type loops. The MAZ binding sequence is located within the 3′-end unit. Nuclear magnetic resonance data complemented by CD and UV spectra show that nucleotides of the MAZ binding G-rich motif are dynamic and could be available for sequence or structure based recognition. Both stable G-quadruplex structures could protect 5′- and 3′-ends of 32R-3n and enhance its anti-cancer activity. Single stranded genomic KRAS NHE including nucleotides flanking the 32R-3n sequence could favor a different monomeric fold, which remains unknown.
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Affiliation(s)
- Peter Podbevšek
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia EN-FIST Centre of Excellence, Trg OF 13, SI-1000 Ljubljana, Slovenia
| | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia EN-FIST Centre of Excellence, Trg OF 13, SI-1000 Ljubljana, Slovenia Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
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8
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Mutsamwira S, Ainscough EW, Partridge AC, Derrick PJ, Filichev VV. DNA-Based Assemblies for Photochemical Upconversion. J Phys Chem B 2015; 119:14045-52. [DOI: 10.1021/acs.jpcb.5b07489] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Saymore Mutsamwira
- Institute
of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand
| | - Eric W. Ainscough
- Institute
of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand
| | - Ashton C. Partridge
- Institute
of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand
- Department
of Physics and School of Engineering, The University of Auckland, 20 Symonds Street, Auckland 1010, New Zealand
| | - Peter J. Derrick
- Institute
of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand
- Department
of Physics and School of Engineering, The University of Auckland, 20 Symonds Street, Auckland 1010, New Zealand
| | - Vyacheslav V. Filichev
- Institute
of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand
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9
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El-Sayed AA, Pedersen EB, Khaireldin NA. Studying the influence of the pyrene intercalator TINA on the stability of DNA i-motifs. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2014; 31:872-9. [PMID: 23215550 DOI: 10.1080/15257770.2012.742199] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Certain cytosine-rich (C-rich) DNA sequences can fold into secondary structures as four-stranded i-motifs with hemiprotonated base pairs. Here we synthesized C-rich TINA-intercalating oligonucleotides by inserting a nonnucleotide pyrene moiety between two C-rich regions. The stability of their i-motif structures was studied by using UV melting temperature measurements and circular dichroism spectra at different pH values under noncrowding and crowding conditions (20% poly(ethylene glycol)). When TINA ((R)-3-((4-(1-pyrenylethynyl)benzyl)oxy) propane-1,2-diol) is inserted, the oligonucleotides could form an i-motif at a higher pH than observed for the corresponding wildtype oligonucleotide.
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Affiliation(s)
- Ahmed A El-Sayed
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
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10
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Doluca O, Hale TK, Edwards PJB, González C, Filichev VV. Assembly Dependent Fluorescence Enhancing Nucleic Acids in Sequence-Specific Detection of Double-Stranded DNA. Chempluschem 2013; 79:58-66. [PMID: 31986766 DOI: 10.1002/cplu.201300310] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 10/29/2013] [Indexed: 12/19/2022]
Abstract
In this study the position of the thiazole orange derivative in triplex-forming oligonucleotides (TFOs) is varied and the fluorescence of the resulting complexes with DNA duplexes, single-stranded DNAs and RNAs are evaluated. Under similar conditions single attachment of the TO-dye to 2'-O-propargyl nucleotides in the TFOs (assembly dependent fluorescence enhancing nucleic acids, AFENA) led to probes with low fluorescent intensity in the single-stranded state with fluorescence quantum yield (ΦF ) of 0.9 %-1.5 %. Significant increase in fluorescence intensity was detected after formation of DNA triplexes (ΦF =23.5 %-34.9 %). Under similar conditions, Watson-Crick-type duplexes formed by the probes with single stranded (ss) RNA and ssDNA showed lower fluorescence intensities. Bugle insertions of twisted intercalating nucleic acid (TINA) monomers were shown to improve the fluorescent characteristics of GT/GA-containing antiparallel AFENA-TFOs. Self-aggregation of TFOs caused by guanosines was eliminated by TINA insertion which also promoted DNA triplex formation at pH 7.2. Importantly these AFENA-TINA-TFOs can bind to the duplex in the presence of complementary RNA at 37 °C.
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Affiliation(s)
- Osman Doluca
- College of Sciences, Institute of Fundamental Sciences, Massey University, Private Bag 11-222, 4442 Palmerston North (New Zealand), Fax: (+64) 6-3505682.,International Burch University, Francuske Revolucije, 71210 Sarajevo (Bosnia and Herzegovina)
| | - Tracy K Hale
- College of Sciences, Institute of Fundamental Sciences, Massey University, Private Bag 11-222, 4442 Palmerston North (New Zealand), Fax: (+64) 6-3505682
| | - Patrick J B Edwards
- College of Sciences, Institute of Fundamental Sciences, Massey University, Private Bag 11-222, 4442 Palmerston North (New Zealand), Fax: (+64) 6-3505682
| | - Carlos González
- Instituto de Química Física Rocasalano, CSIC, Serrano 119, 28006 Madrid (Spain)
| | - Vyacheslav V Filichev
- College of Sciences, Institute of Fundamental Sciences, Massey University, Private Bag 11-222, 4442 Palmerston North (New Zealand), Fax: (+64) 6-3505682
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11
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Osman AMA, Pedersen EB, Bergman J. Synthesis of a new intercalating nucleic acid 6H-INDOLO[2,3-b] quinoxaline oligonucleotides to improve thermal stability of Hoogsteen-type triplexes. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2013; 32:98-108. [PMID: 23448144 DOI: 10.1080/15257770.2013.765013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
A new intercalating nucleic acid monomer X was obtained in high yield starting from alkylation of 4-iodophenol with (S)-(+)-2-(2,2-dimethyl-1,3-dioxolan-4-yl)ethanol under Mitsunobu conditions followed by hydrolysis with 80% aqueous acetic acid to give a diol which was coupled under Sonogashira conditions with trimethylsilylacetylene (TMSA) to achieve the TMS protected (S)-4-(4-((trimethylsilyl)ethynyl)phenoxy)butane-1,2-diol. Tetrabutylammonium flouride was used to remove the silyl protecting group to obtain (S)-4-(4-ethynylphenoxy)butane-1,2-diol which was coupled under Sonogashira conditions with 2-(9-bromo-6H-indolo[2,3-b]quinoxalin-6-yl)-N,N-dimethylethanamine to achieve (S)-4-(4-((6-(2-(dimethylamino)ethyl)-6H-indolo[2,3-b]quinoxalin-9-yl)ethynyl)phenoxy)butane-1,2-diol. This compound was tritylated with 4,4'-dimethoxytrityl chloride followed by treatment with 2-cyanoethyltetraisopropylphosphordiamidite in the presence of N,N'-diisopropyl ammonium tetrazolide to afford the corresponding phosphoramidite. This phosphoramidite was used to insert the monomer X into an oligonucleotide which was used for thermal denaturation studies of a corresponding parallel triplex.
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Affiliation(s)
- Amany M A Osman
- Department of Physics, Nucleic Acid Center, University of Southern Denmark, Odense, Denmark
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Cogoi S, Zorzet S, Rapozzi V, Géci I, Pedersen EB, Xodo LE. MAZ-binding G4-decoy with locked nucleic acid and twisted intercalating nucleic acid modifications suppresses KRAS in pancreatic cancer cells and delays tumor growth in mice. Nucleic Acids Res 2013; 41:4049-64. [PMID: 23471001 PMCID: PMC3627599 DOI: 10.1093/nar/gkt127] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
KRAS mutations are primary genetic lesions leading to pancreatic cancer. The promoter of human KRAS contains a nuclease-hypersensitive element (NHE) that can fold in G4-DNA structures binding to nuclear proteins, including MAZ (myc-associated zinc-finger). Here, we report that MAZ activates KRAS transcription. To knockdown oncogenic KRAS in pancreatic cancer cells, we designed oligonucleotides that mimic one of the G-quadruplexes formed by NHE (G4-decoys). To increase their nuclease resistance, two locked nucleic acid (LNA) modifications were introduced at the 3'-end, whereas to enhance the folding and stability, two polycyclic aromatic hydrocarbon units (TINA or AMANY) were inserted internally, to cap the quadruplex. The most active G4-decoy (2998), which had two para-TINAs, strongly suppressed KRAS expression in Panc-1 cells. It also repressed their metabolic activity (IC50 = 520 nM), and it inhibited cell growth and colony formation by activating apoptosis. We finally injected 2998 and control oligonucleotides 5153, 5154 (2 nmol/mouse) intratumorally in SCID mice bearing a Panc-1 xenograft. After three treatments, 2998 reduced tumor xenograft growth by 64% compared with control and increased the Kaplan-Meier median survival time by 70%. Together, our data show that MAZ-specific G4-decoys mimicking a KRAS quadruplex are promising for pancreatic cancer therapy.
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Affiliation(s)
- Susanna Cogoi
- Department of Medical and Biological Sciences, School of Medicine, P.le Kolbe 4, 33100 Udine, Italy
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13
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Fatthalla MI, Elkholy YM, Abbas NS, Mandour AH, Jørgensen PT, Bomholt N, Pedersen EB. Conjugation of a 3-(1H-phenanthro[9,10-d]imidazol-2-yl)-1H-indole intercalator to a triplex oligonucleotide and to a three-way junction. Bioorg Med Chem 2011; 20:207-14. [PMID: 22154560 DOI: 10.1016/j.bmc.2011.11.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Revised: 11/02/2011] [Accepted: 11/07/2011] [Indexed: 11/29/2022]
Abstract
A new intercalating nucleic acid monomer M comprising a 4-(1-indole)-butane-1,2-diol moiety was synthesized via a classical alkylation reaction of indole-3-carboxaldehyde followed by a condensation reaction with phenanthrene-9,10-dione in the presence of ammonium acetate to form a phenanthroimidazole moiety linked to the indole ring. Insertion of the new intercalator as a bulge into a Triplex Forming Oligonucleotide resulted in good thermal stability of the corresponding Hoogsteen-type triplexes. Molecular modeling supports the possible intercalating ability of M. Hybridisation properties of DNA/DNA and RNA/DNA three-way junctions (TWJ) with M in the branching point were also evaluated by their thermal stability at pH 7. DNA/DNA TWJ showed increase in thermal stability compared to wild type oligonucleotides whereas this was not the case for RNA/DNA TWJ.
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Affiliation(s)
- Maha I Fatthalla
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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14
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Doluca O, Boutorine AS, Filichev VV. Triplex-Forming Twisted Intercalating Nucleic Acids (TINAs): Design Rules, Stabilization of Antiparallel DNA Triplexes and Inhibition of G-Quartet-Dependent Self-Association. Chembiochem 2011; 12:2365-74. [DOI: 10.1002/cbic.201100354] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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15
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Gaber HM, Moussa TAM. Regioselective synthesis and antimicrobial studies of novel bridgehead nitrogen heterocycles containing the thienopyrimidinone skeleton. ACTA ACUST UNITED AC 2011. [DOI: 10.5155/eurjchem.2.2.251-259.380] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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16
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Gaber HM, Bagley MC, Sherif SM, Abdul-Raouf UM. Promising antimicrobial agents: Synthetic approaches to novel tricyclic and tetracyclic pyrimidinones with antimicrobial properties. J Heterocycl Chem 2010. [DOI: 10.1002/jhet.446] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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17
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Gaber HM, Bagley MC, Sherif SM. Antimicrobial investigations on synthetic p-tolylazo derivatives of thienopyrimidinone based on an ortho funtionalized thiophene nucleus. ACTA ACUST UNITED AC 2010. [DOI: 10.5155/eurjchem.1.2.115-123.56] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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18
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Schneider UV, Mikkelsen ND, Jøhnk N, Okkels LM, Westh H, Lisby G. Optimal design of parallel triplex forming oligonucleotides containing Twisted Intercalating Nucleic Acids--TINA. Nucleic Acids Res 2010; 38:4394-403. [PMID: 20338879 PMCID: PMC2910062 DOI: 10.1093/nar/gkq188] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Twisted intercalating nucleic acid (TINA) is a novel intercalator and stabilizer of Hoogsteen type parallel triplex formations (PT). Specific design rules for position of TINA in triplex forming oligonucleotides (TFOs) have not previously been presented. We describe a complete collection of easy and robust design rules based upon more than 2500 melting points (Tm) determined by FRET. To increase the sensitivity of PT, multiple TINAs should be placed with at least 3 nt in-between or preferable one TINA for each half helixturn and/or whole helixturn. We find that ΔTm of base mismatches on PT is remarkably high (between 7.4 and 15.2°C) compared to antiparallel duplexes (between 3.8 and 9.4°C). The specificity of PT by ΔTm increases when shorter TFOs and higher pH are chosen. To increase ΔTms, base mismatches should be placed in the center of the TFO and when feasible, A, C or T to G base mismatches should be avoided. Base mismatches can be neutralized by intercalation of a TINA on each side of the base mismatch and masked by a TINA intercalating direct 3′ (preferable) or 5′ of it. We predict that TINA stabilized PT will improve the sensitivity and specificity of DNA based clinical diagnostic assays.
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Affiliation(s)
- Uffe V Schneider
- QuantiBact Inc, Department of Clinical Microbiology, Hvidovre Hospital, Kettegaards Alle 30, 2650 Hvidovre, Denmark.
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Cogoi S, Paramasivam M, Filichev V, Géci I, Pedersen EB, Xodo LE. Identification of a new G-quadruplex motif in the KRAS promoter and design of pyrene-modified G4-decoys with antiproliferative activity in pancreatic cancer cells. J Med Chem 2009; 52:564-8. [PMID: 19099510 DOI: 10.1021/jm800874t] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A new quadruplex motif located in the promoter of the human KRAS gene, within a nuclease hypersensitive element (NHE), has been characterized. Oligonucleotides mimicking this quadruplex are found to compete with a DNA-protein complex between NHE and a nuclear extract from pancreatic cancer cells. When modified with (R)-1-O-[4-1-(1-pyrenylethynyl) phenylmethyl]glycerol insertions (TINA), the quadruplex oligonucleotides showed a dramatic increase of the T(m) (deltaT(m) from 22 to 32 degrees C) and a strong antiproliferative effects in Panc-1 cells.
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Affiliation(s)
- Susanna Cogoi
- Department of Biomedical Science and Technology, School of Medicine, P.le Kolbe 4, 33100 Udine, Italy
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Using an aryl phenanthroimidazole moiety as a conjugated flexible intercalator to improve the hybridization efficiency of a triplex-forming oligonucleotide. Bioorg Med Chem 2008; 16:9937-47. [PMID: 18977149 DOI: 10.1016/j.bmc.2008.10.037] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2008] [Revised: 10/03/2008] [Accepted: 10/12/2008] [Indexed: 11/23/2022]
Abstract
When inserting 2-phenyl or 2-naphth-1-yl-phenanthroimidazole intercalators (X and Y, respectively) as bulges into triplex-forming oligonucleotides, both intercalators show extraordinary high thermal stability of the corresponding Hoogsteen-type triplexes and Hoogsteen-type parallel duplexes with high discrimination to Hoogsteen mismatches. Molecular modeling shows that the phenyl or the naphthyl ring stacks with the nucleobases in the TFO, while the phenanthroimidazol moiety stacks with the base pairs of the dsDNA. DNA-strands containing the intercalator X show higher thermal triplex stability than DNA-strands containing the intercalator Y. The difference can be explained by a lower degree of planarity of the intercalator in the case of naphthyl. It was also observed that triplex stability was considerably reduced when the intercalators X or Y was replaced by 2-(naphthlen-1-yl)imidazole. This confirms intercalation as the important factor for triplex stabilization and it rules out an alternative complexation of protonated imidazole with two phosphate groups. The intercalating nucleic acid monomers X and Y were obtained via a condensation reaction of 9,10-phenanthrenequinone (4) with (S)-4-(2-(2,2-dimethyl-1,3-dioxolan-4-yl)ethoxy)benzaldehyde (3a) or (S)-4-(2-(2,2-dimethyl-1,3-dioxolan-4-yl)ethoxy)-1-naphthaldehyde (3b), respectively, in the presence of acetic acid and ammonium acetate. The required monomers for DNA synthesis using amidite chemistry were obtained by standard deprotection of the hydroxy groups followed by 4,4'-dimethoxytritylation and phosphitylation.
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Paramasivam M, Cogoi S, Filichev VV, Bomholt N, Pedersen EB, Xodo LE. Purine twisted-intercalating nucleic acids: a new class of anti-gene molecules resistant to potassium-induced aggregation. Nucleic Acids Res 2008; 36:3494-507. [PMID: 18456705 PMCID: PMC2425464 DOI: 10.1093/nar/gkn242] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Sequence-specific targeting of genomic DNA by triplex-forming oligonucleotides (TFOs) is a promising strategy to modulate in vivo gene expression. Triplex formation involving G-rich oligonucleotides as third strand is, however, strongly inhibited by potassium-induced TFO self-association into G-quartet structures. We report here that G-rich TFOs with bulge insertions of (R)-1-O-[4-(1-pyrenylethynyl)-phenylmethyl] glycerol (called twisted intercalating nucleic acids, TINA) show a much lower tendency to aggregate in potassium than wild-type analogues do. We designed purine-motif TINA–TFOs for binding to a regulatory polypurine-polypyrimidine (pur/pyr) motif present in the promoter of the KRAS proto-oncogene. The binding of TINA–TFOs to the KRAS target has been analysed by electrophoresis mobility shift assays and DNase I footprinting experiments. We discovered that in the presence of potassium the wild-type TFOs did not bind to the KRAS target, differently from the TINA analogues, whose binding was observed up to 140 mM KCl. The designed TINA–TFOs were found to abrogate the formation of a DNA–protein complex at the pur/pyr site and to down-regulate the transcription of CAT driven by the murine KRAS promoter. Molecular modelling of the DNA/TINA–TFO triplexes are also reported. This study provides a new and promising approach to create TFOs to target in vivo the genome.
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Globisch D, Bomholt N, Filichev V, Pedersen E. Stability ofHoogsteen-Type Triplexes – Electrostatic Attraction between Duplex Backbone and Triplex-Forming Oligonucleotide (TFO) Using an Intercalating Conjugate. Helv Chim Acta 2008. [DOI: 10.1002/hlca.200890082] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Bomholt N, Osman AMA, Pedersen EB. High physiological thermal triplex stability optimization of twisted intercalating nucleic acids (TINA). Org Biomol Chem 2008; 6:3714-22. [DOI: 10.1039/b808564a] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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