1
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Filho MS, Massi L, Millet A, Michel D, Moussa W, Ronco C, Benhida R. Energy-resolved mass spectrometry to investigate nucleobase triplexes – a study applied to triplex-forming artificial nucleobases. NEW J CHEM 2022. [DOI: 10.1039/d2nj00665k] [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
This paper discloses the use of an energy-resolved mass spectrometric-based approach to assess the stabilities of base triplexes encompassing artificial nucleobases by using variable energy collision-induced dissociation.
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Affiliation(s)
- Mauro Safir Filho
- Institut de Chimie de Nice CNRS UMR7272, Université Côte d’Azur, 28 Avenue Valrose 06108 Nice, France
| | - Lionel Massi
- Institut de Chimie de Nice CNRS UMR7272, Université Côte d’Azur, 28 Avenue Valrose 06108 Nice, France
| | - Antoine Millet
- Institut de Chimie de Nice CNRS UMR7272, Université Côte d’Azur, 28 Avenue Valrose 06108 Nice, France
| | - Dylan Michel
- Institut de Chimie de Nice CNRS UMR7272, Université Côte d’Azur, 28 Avenue Valrose 06108 Nice, France
| | - Wafa Moussa
- Institut de Chimie de Nice CNRS UMR7272, Université Côte d’Azur, 28 Avenue Valrose 06108 Nice, France
| | - Cyril Ronco
- Institut de Chimie de Nice CNRS UMR7272, Université Côte d’Azur, 28 Avenue Valrose 06108 Nice, France
| | - Rachid Benhida
- Institut de Chimie de Nice CNRS UMR7272, Université Côte d’Azur, 28 Avenue Valrose 06108 Nice, France
- Mohamed VI Polytechnic University, UM6P, 43150, Ben Guerir, Morocco
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2
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Lohani N, Rajeswari MR. Antigene and Antiproliferative Effects of Triplex-Forming Oligonucleotide (TFO) Targeted on hmgb1 Gene in Human Hepatoma Cells. Anticancer Agents Med Chem 2021; 20:1943-1955. [PMID: 32560618 DOI: 10.2174/1871520620666200619170438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 03/30/2020] [Accepted: 04/12/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND The high mobility group box 1 (hmgb1) is one of the frequently over-expressed genes whose aberrant expression is reported in a number of human cancers. Various strategies are underway to inhibit hmgb1 expression in cancer cells having considerable therapeutic value. OBJECTIVE The present work involves selective transcriptional inhibition of the hmgb1 gene using selective DNA triplex structure-based gene technology. Here, the promoter region of the hmgb1 gene at position (-183 to -165) from the transcription start site as a target was selected using bioinformatic tools. METHODS The DNA triplex formation by the DNA of the target gene and TFO was confirmed using UV absorption spectroscopy, Circular Dichroism, and Isothermal Calorimetry. RESULTS Treatment of HepG2 cell with specific Triplex-forming Oligonucleotide significantly downregulated HMGB1 expression level at mRNA and protein levels by 50%, while the classical anticancer drugs, actinomycin/ adriamycin as positive controls showed 65% and the combination of TFO and drug decreased by 70%. The anti-proliferative effects of TFO correlated well with the fact of accumulation of cells in the Go phase and apoptotic cell death. Further, the binding of anti-cancer drugs to hmgb1 is stronger in DNA triplex state as compared to hmgb1 alone, suggesting the combination therapy as a better option. CONCLUSION Therefore, the ability of hmgb1 targeted triplex-forming oligonucleotide in combination with triplex selective anticancer drug holds promise in the treatment of malignancies associated with hmgb1 overexpression. The result obtained may open up new vistas to provide a basis for the rational drug design and searching for high-affinity ligands with a high triplex selectivity.
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Affiliation(s)
- Neelam Lohani
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Moganty R Rajeswari
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
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3
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Liczner C, Duke K, Juneau G, Egli M, Wilds CJ. Beyond ribose and phosphate: Selected nucleic acid modifications for structure-function investigations and therapeutic applications. Beilstein J Org Chem 2021; 17:908-931. [PMID: 33981365 PMCID: PMC8093555 DOI: 10.3762/bjoc.17.76] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/14/2021] [Indexed: 12/16/2022] Open
Abstract
Over the past 25 years, the acceleration of achievements in the development of oligonucleotide-based therapeutics has resulted in numerous new drugs making it to the market for the treatment of various diseases. Oligonucleotides with alterations to their scaffold, prepared with modified nucleosides and solid-phase synthesis, have yielded molecules with interesting biophysical properties that bind to their targets and are tolerated by the cellular machinery to elicit a therapeutic outcome. Structural techniques, such as crystallography, have provided insights to rationalize numerous properties including binding affinity, nuclease stability, and trends observed in the gene silencing. In this review, we discuss the chemistry, biophysical, and structural properties of a number of chemically modified oligonucleotides that have been explored for gene silencing.
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Affiliation(s)
- Christopher Liczner
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Kieran Duke
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Gabrielle Juneau
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Martin Egli
- Department of Biochemistry, Vanderbilt Institute of Chemical Biology, and Center for Structural Biology, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Christopher J Wilds
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
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4
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Li N, Wang J, Ma K, Liang L, Mi L, Huang W, Ma X, Wang Z, Zheng W, Xu L, Chen JH, Yu Z. The dynamics of forming a triplex in an artificial telomere inferred by DNA mechanics. Nucleic Acids Res 2019; 47:e86. [PMID: 31114915 PMCID: PMC6735771 DOI: 10.1093/nar/gkz464] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 05/06/2019] [Accepted: 05/15/2019] [Indexed: 11/21/2022] Open
Abstract
A telomere carrying repetitive sequences ends with a single-stranded overhang. The G-rich overhang could fold back and bind in the major groove of its upstream duplex, forming an antiparallel triplex structure. The telomeric triplex has been proposed to function in protecting chromosome ends. However, we lack strategies to mechanically probe the dynamics of a telomeric triplex. Here, we show that the topological dynamics of a telomeric triplex involves 3' overhang binding at the ds/ssDNA junction inferred by DNA mechanics. Assisted by click chemistry and branched polymerase chain reaction, we developed a rescue-rope-strategy for mechanically manipulating an artificial telomeric DNA with a free end. Using single-molecule magnetic tweezers, we identified a rarely forming (5%) telomeric triplex which pauses at an intermediate state upon unzipping the Watson-Crick paired duplex. Our findings revealed that a mechanically stable triplex formed in a telomeric DNA can resist a force of 20 pN for a few seconds in a physiological buffer. We also demonstrated that the rescue-rope-strategy assisted mechanical manipulation can directly rupture the interactions between the third strand and its targeting duplex in a DNA triplex. Our single-molecule rescue-rope-strategy will serve as a general tool to investigate telomere dynamics and further develop triplex-based biotechnologies.
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Affiliation(s)
- Ning Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| | - Junli Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| | - Kangkang Ma
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| | - Lin Liang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| | - Lipei Mi
- State Key Laboratory of Precision Measuring Technology and Instruments, Tianjin University, Tianjin 300072, China
| | - Wei Huang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| | - Xiaofeng Ma
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| | - Zeyu Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| | - Wei Zheng
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| | - Linyan Xu
- State Key Laboratory of Precision Measuring Technology and Instruments, Tianjin University, Tianjin 300072, China
| | - Jun-Hu Chen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Center for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai 200025, China
| | - Zhongbo Yu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
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5
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Fujimoto K, Sasago S, Mihara J, Nakamura S. DNA Photo-cross-linking Using Pyranocarbazole and Visible Light. Org Lett 2018; 20:2802-2805. [DOI: 10.1021/acs.orglett.8b00593] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Kenzo Fujimoto
- Department of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, Asahidai 1-1, Nomi, Ishikawa, 923-1292, Japan
| | - Shinobu Sasago
- Department of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, Asahidai 1-1, Nomi, Ishikawa, 923-1292, Japan
| | - Junichi Mihara
- Department of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, Asahidai 1-1, Nomi, Ishikawa, 923-1292, Japan
| | - Shigetaka Nakamura
- Department of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, Asahidai 1-1, Nomi, Ishikawa, 923-1292, Japan
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6
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Rathnam C, Chueng STD, Yang L, Lee KB. Advanced Gene Manipulation Methods for Stem Cell Theranostics. Theranostics 2017; 7:2775-2793. [PMID: 28824715 PMCID: PMC5562215 DOI: 10.7150/thno.19443] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 04/18/2017] [Indexed: 12/20/2022] Open
Abstract
In the field of tissue engineering, autologous cell sources are ideal to prevent adverse immune responses; however, stable and reliable cell sources are limited. To acquire more reliable cell sources, the harvesting and differentiation of stem cells from patients is becoming more and more common. To this end, the need to control the fate of these stem cells before transplantation for therapeutic purposes is urgent. Since transcription factors orchestrate all of the gene activities inside of a cell, researchers have developed engineered and synthetic transcription factors to precisely control the fate of stem cells allowing for safer and more effective cell sources. Engineered transcription factors, mutant fusion proteins of naturally occurring proteins, comprise the three main domains of natural transcription factors including DNA binding domains, transcriptional activation domains, and a linker domain. Several key advancements of engineered zinc finger proteins, transcriptional activator-like effectors, and deficient cas9 proteins have revolutionized the field of engineered transcription factors allowing for precise control of gene regulation. Synthetic transcription factors are chemically made transcription factor mimics that use small molecule based moieties to replicate the main functions of natural transcription factors. These include hairpin polyamides, triple helix forming oligonucleotides, and nanoparticle-based methods. Synthetic transcription factors allow for non-viral delivery and greater spatiotemporal control of gene expression. The developments in engineered and synthetic transcription factors have lowered the risk of tumorigenicity and improved differentiation capability of stem cells, as well as facilitated many key discoveries in the fields of cancer and stem cell biology, thus providing a stepping stone to advance regenerative medicine in the clinic for cell replacement therapies.
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7
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Nakamura S, Kawabata H, Fujimoto K. Sequence-Specific DNA Photosplitting of Crosslinked DNAs Containing the 3-Cyanovinylcarbazole Nucleoside by Using DNA Strand Displacement. Chembiochem 2016; 17:1499-503. [PMID: 27357523 DOI: 10.1002/cbic.201600236] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Indexed: 12/30/2022]
Abstract
An oligodeoxynucleotide (ODN) containing the ultrafast reversible 3-cyanovinylcarbazole ((CNV) K) photo-crosslinker was photo-crosslinked to a complementary strand upon exposure to 366 nm irradiation and photosplit by use of 312 nm irradiation. In this paper we report that the photoreaction of (CNV) K on irradiation at 366 nm involves a photostationary state and that its reaction can be controlled by temperature. Guided by this new insight, we proposed and have now demonstrated previously unknown photosplitting of (CNV) K aided by DNA strand displacement as an alternative to heating. The photo-crosslinked double-stranded DNA (dsDNA) underwent >80 % photosplitting aided by DNA strand displacement on irradiation at 366 nm without heating. In this photosplitting based on DNA strand displacement, the relative thermal stability of the invader strand with respect to the template strands plays an important role, and an invader strand/template strand system that is more stable than the passenger strand/template strand system induces photosplitting without heating. This new strand-displacement-aided photosplitting occurred in a sequence-specific manner through irradiation at 366 nm in the presence of an invader strand.
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Affiliation(s)
- Shigetaka Nakamura
- School of Materials Science, Japan Advanced Institute Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa, Japan
| | - Hayato Kawabata
- School of Materials Science, Japan Advanced Institute Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa, Japan
| | - Kenzo Fujimoto
- School of Materials Science, Japan Advanced Institute Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa, Japan.
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8
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Nakamura S, Kawabata H, Muramatsu H, Fujimoto K. Effect of 5-Substitution of Uracil Base in DNA Photocrosslinking Using 3-Cyanovinylcarbazole. CHEM LETT 2016. [DOI: 10.1246/cl.160382] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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9
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Vasilyeva SV, Filichev VV, Boutorine AS. Application of Cu(I)-catalyzed azide-alkyne cycloaddition for the design and synthesis of sequence specific probes targeting double-stranded DNA. Beilstein J Org Chem 2016; 12:1348-60. [PMID: 27559384 PMCID: PMC4979877 DOI: 10.3762/bjoc.12.128] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 06/08/2016] [Indexed: 12/27/2022] Open
Abstract
Efficient protocols based on Cu(I)-catalyzed azide-alkyne cycloaddition were developed for the synthesis of conjugates of pyrrole-imidazole polyamide minor groove binders (MGB) with fluorophores and with triplex-forming oligonucleotides (TFOs). Diverse bifunctional linkers were synthesized and used for the insertion of terminal azides or alkynes into TFOs and MGBs. The formation of stable triple helices by TFO-MGB conjugates was evaluated by gel-shift experiments. The presence of MGB in these conjugates did not affect the binding parameters (affinity and triplex stability) of the parent TFOs.
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Affiliation(s)
- Svetlana V Vasilyeva
- Institute of Chemical Biology & Fundamental Medicine, SB of RAS, pr. Lavrent’eva 8, 630090 Novosibirsk, Russia
| | - Vyacheslav V Filichev
- Institute of Fundamental Sciences, Massey University, Private Bag 11-222, 4442 Palmerston North, New Zealand
| | - Alexandre S Boutorine
- Structure and Instability of Genomes, Sorbonne Universités, Muséum National d'Histoire Naturelle, INSERM U 1154, CNRS UMR 7196, 57 rue Cuvier, C.P. 26, 75231 Paris cedex 05, France
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10
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Geinguenaud F, Guenin E, Lalatonne Y, Motte L. Vectorization of Nucleic Acids for Therapeutic Approach: Tutorial Review. ACS Chem Biol 2016; 11:1180-91. [PMID: 26950048 DOI: 10.1021/acschembio.5b01053] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Oligonucleotides present a high therapeutic potential for a wide variety of diseases. However, their clinical development is limited by their degradation by nucleases and their poor blood circulation time. Depending on the administration mode and the cellular target, these macromolecules will have to cross the vascular endothelium, to diffuse through the extracellular matrix, to be transported through the cell membrane, and finally to reach the cytoplasm. To overcome these physiological barriers, many strategies have been developed. Here, we review different methods of DNA vectorization, discuss limitations and advantages of the various vectors, and provide new perspectives for future development.
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Affiliation(s)
- Frederic Geinguenaud
- Laboratoire CSPBAT,
CNRS UMR 7244, UFR SMBH, Université Paris 13, Sorbonne Paris Cité, F-93017 Bobigny, France
| | - Erwann Guenin
- Inserm, U1148,
Laboratory for Vascular Translational Science, UFR SMBH, Université Paris 13, Sorbonne Paris Cité, F-93017 Bobigny, France
| | - Yoann Lalatonne
- Inserm, U1148,
Laboratory for Vascular Translational Science, UFR SMBH, Université Paris 13, Sorbonne Paris Cité, F-93017 Bobigny, France
- Service
de Médecine Nucléaire, Hôpital Avicenne Assistance Publique-Hôpitaux de Paris 93009 Bobigny France
| | - Laurence Motte
- Inserm, U1148,
Laboratory for Vascular Translational Science, UFR SMBH, Université Paris 13, Sorbonne Paris Cité, F-93017 Bobigny, France
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11
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Lohani N, Rajeswari MR. Preferential binding of anticancer drugs to triplex DNA compared to duplex DNA: a spectroscopic and calorimetric study. RSC Adv 2016. [DOI: 10.1039/c6ra03514k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Binding study of adriamycin and actinomycin to triplex DNA formed on the promoter region of hmgb1 gene using spectroscopic and calorimetric technique.
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Affiliation(s)
- Neelam Lohani
- Department of Biochemistry
- All India Institute of Medical Sciences
- New Delhi
- India
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12
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Le Grice SFJ. Targeting the HIV RNA genome: high-hanging fruit only needs a longer ladder. Curr Top Microbiol Immunol 2015; 389:147-69. [PMID: 25735922 PMCID: PMC7120518 DOI: 10.1007/82_2015_434] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Small molecules targeting the enzymes responsible for human immunodeficiency virus (HIV) maturation, DNA synthesis and its subsequent chromosomal integration as ribonucleotide-free double-stranded DNA remain the mainstay of combination antiretroviral therapy. For infected individuals harboring drug-susceptible virus, this approach has afforded complete or near-complete viral suppression. However, in the absence of a curative strategy, the predictable emergence of drug-resistant variants requires continued development of improved antiviral strategies, inherent to which is the necessity of identifying novel targets. Regulatory elements that mediate transcription, translation, nucleocytoplasmic transport, dimerization, packaging and reverse transcription of the (+) strand RNA genome should now be considered viable targets for small molecule, peptide- and oligonucleotide-based therapeutics. Where target specificity and cellular penetration and toxicity have been the primary obstacle to successful “macromolecule therapeutics”, this chapter summarizes (a) novel approaches targeting RNA motifs whose three-dimensional structure is critical for biological function and consequently may be less prone to resistance-conferring mutations and (b) improved methods for delivery.
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Affiliation(s)
- Stuart F J Le Grice
- RT Biochemistry Section, Basic Research Laboratory, National Cancer Institute, Frederick, MD, 21702, USA,
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13
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In vitro antiviral activity of circular triple helix forming oligonucleotide RNA towards Feline Infectious Peritonitis virus replication. BIOMED RESEARCH INTERNATIONAL 2014; 2014:654712. [PMID: 24707494 PMCID: PMC3950953 DOI: 10.1155/2014/654712] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 01/02/2014] [Accepted: 01/14/2014] [Indexed: 02/06/2023]
Abstract
Feline Infectious Peritonitis (FIP) is a severe fatal immune-augmented disease in cat population. It is caused by FIP virus (FIPV), a virulent mutant strain of Feline Enteric Coronavirus (FECV). Current treatments and prophylactics are not effective. The in vitro antiviral properties of five circular Triple-Helix Forming Oligonucleotide (TFO) RNAs (TFO1 to TFO5), which target the different regions of virulent feline coronavirus (FCoV) strain FIPV WSU 79-1146 genome, were tested in FIPV-infected Crandell-Rees Feline Kidney (CRFK) cells. RT-qPCR results showed that the circular TFO RNAs, except TFO2, inhibit FIPV replication, where the viral genome copy numbers decreased significantly by 5-fold log10 from 1014 in the virus-inoculated cells to 109 in the circular TFO RNAs-transfected cells. Furthermore, the binding of the circular TFO RNA with the targeted viral genome segment was also confirmed using electrophoretic mobility shift assay. The strength of binding kinetics between the TFO RNAs and their target regions was demonstrated by NanoITC assay. In conclusion, the circular TFOs have the potential to be further developed as antiviral agents against FIPV infection.
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14
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Kusano S, Haruyama T, Ishiyama S, Hagihara S, Nagatsugi F. Development of the crosslinking reactions to RNA triggered by oxidation. Chem Commun (Camb) 2014; 50:3951-4. [DOI: 10.1039/c3cc49463b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In this paper, we have reported a novel oxidation triggered crosslinking nucleobase ATVP (1) and demonstrated that the oxidized form ASVP (2) showed a very fast and selective crosslinking reaction to cytosine in RNA.
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Affiliation(s)
- Shuhei Kusano
- Institute of Multidisciplinary Research for Advanced Materials
- Tohoku University
- Sendai-shi, Japan
| | - Takuya Haruyama
- Institute of Multidisciplinary Research for Advanced Materials
- Tohoku University
- Sendai-shi, Japan
| | - Shogo Ishiyama
- Institute of Multidisciplinary Research for Advanced Materials
- Tohoku University
- Sendai-shi, Japan
| | - Shinya Hagihara
- Institute of Transformative Bio-Molecules (WPI-ITbM)
- Nagoya University
- Nagoya, Japan
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials
- Tohoku University
- Sendai-shi, Japan
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15
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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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16
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Fujimoto K, Yamada A, Yoshimura Y, Tsukaguchi T, Sakamoto T. Details of the Ultrafast DNA Photo-Cross-Linking Reaction of 3-Cyanovinylcarbazole Nucleoside: Cis–Trans Isomeric Effect and the Application for SNP-Based Genotyping. J Am Chem Soc 2013; 135:16161-7. [DOI: 10.1021/ja406965f] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
| | | | | | - Tadashi Tsukaguchi
- Faculty
of Bioresources and Environmental Sciences, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa 921-8836, Japan
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17
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Novopashina DS, Siniakov AN, Riabinin VA, Perrouault L, Giovannangeli C, Venyaminova AG, Butorin AS. [Oligo(2'-O-Methylribonucleotides) and their derivatives: IV. Conjugates of oligo(2'-O-methylribonucleotides) with minor groove binders and intercalators: synthesis, properties and application]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2013; 39:159-74. [PMID: 23964516 DOI: 10.1134/s1068162013010081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Conjugates of pyrimidine triplex forming 3'-protected oligo(2'-O-methylribonucleotides) with minor groove binders (MGB) and triplex specific intercalator benzoindoloquinoline (BIQ) at 5'-terminus were synthesized. The conjugates formed stable complexes with target dsDNA by simultaneous binding both in its minor and major grooves and BIQ intercalation. The dissociation constants and thermal stability of the conjugate complexes with model dsDNA corresponding to polypurine tract (PPT) of genes nef and pol from HIV proviral genome were determined. Conjugation of oligo(2'-O-methylribonucleotides) with MGB and intercalator increased the stability of the triple complexes with dsDNA at pH 7.2 and 37 degrees C. Intercalator introduction accelerates the process of complex formation. Dose-dependent arrest of the in vitro transcription was demonstrated when a 780 b.p. DNA fragment containing the polypurine tract was transcribed under the control of T7 promoter in the presence of different concentrations of conjugates of oligo(2'-O-methylribonucleotides) containing MGB and BIQ intercalator.
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Doluca O, Withers JM, Filichev VV. Molecular engineering of guanine-rich sequences: Z-DNA, DNA triplexes, and G-quadruplexes. Chem Rev 2013; 113:3044-83. [PMID: 23391174 DOI: 10.1021/cr300225q] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Osman Doluca
- Institute of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, New Zealand
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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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20
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Won YW, Lim KS, Kim YH. Intracellular organelle-targeted non-viral gene delivery systems. J Control Release 2011; 152:99-109. [PMID: 21255626 DOI: 10.1016/j.jconrel.2011.01.013] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Revised: 12/30/2010] [Accepted: 01/07/2011] [Indexed: 10/18/2022]
Abstract
Gene therapy is a rapidly growing approach for the treatment of various diseases. To achieve successful gene therapy, a gene delivery system is necessary to overcome several barriers in the extracellular and intracellular spaces. Polymers, peptides, liposomes and nanoparticles developed as gene carriers have achieved efficient cellular uptake of genes. Among these carriers, cationic polymers and peptides have been further developed as intracellular organelle-targeted delivery systems. The cytoplasm, nucleus and mitochondria have been considered primary targets for gene delivery using targeting moieties or environment-responsive materials. In this review, we explore recently developed non-viral gene carriers based on reducible systems specialized to target the cytoplasm, nucleus and mitochondria.
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Affiliation(s)
- Young-Wook Won
- Department of Bioengineering, Institute for Bioengineering and Biopharmaceutical Research, and Institute of Aging Society, Hanyang University, 17 Haengdang-dong, Seongdong-gu, Seoul 133-791, Republic of Korea
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21
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Patterson A, Caprio F, Vallée-Bélisle A, Moscone D, Plaxco KW, Palleschi G, Ricci F. Using triplex-forming oligonucleotide probes for the reagentless, electrochemical detection of double-stranded DNA. Anal Chem 2010; 82:9109-15. [PMID: 20936782 PMCID: PMC3134121 DOI: 10.1021/ac1024528] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report a reagentless, electrochemical sensor for the detection of double-stranded DNA targets that employs triplex-forming oligonucleotides (TFOs) as its recognition element. These sensors are based on redox-tagged TFO probes strongly chemisorbed onto an interrogating gold electrode. Upon the addition of the relevant double-stranded DNA target, the probe forms a rigid triplex structure via reverse Hoogsteen base pairing in the major groove. The formation of the triplex impedes contact between the probe's redox moiety and the interrogating electrode, thus signaling the presence of the target. We first demonstrated the proof of principle of this approach by using a well-characterized 22-base polypurine TFO sequence that readily detects a synthetic, double-stranded DNA target. We then confirmed the generalizability of our platform with a second probe, a 19-base polypyrimidine TFO sequence that targets a polypurine tract (PPT) sequence conserved in all HIV-1 strains. Both sensors rapidly and specifically detect their double-stranded DNA targets at concentrations as low as ~10 nM and are selective enough to be employed directly in complex sample matrices such as blood serum. Moreover, to demonstrate real-world applicability of this new sensor platform, we have successfully detected unpurified, double-stranded PCR amplicons containing the relevant conserved HIV-1 sequence.
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22
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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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Krishnan R, Oh DH. Structural determinants of photoreactivity of triplex forming oligonucleotides conjugated to psoralens. J Nucleic Acids 2010; 2010. [PMID: 20725628 PMCID: PMC2915845 DOI: 10.4061/2010/523498] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2010] [Accepted: 06/03/2010] [Indexed: 11/23/2022] Open
Abstract
Triplex-forming oligonucleotides (TFOs) with both DNA and 2′-O-methyl RNA backbones can direct psoralen photoadducts to specific DNA sequences. However, the functional consequences of these differing structures on psoralen photoreactivity are unknown. We designed TFO sequences with DNA and 2′-O-methyl RNA backbones conjugated to psoralen by 2-carbon linkers and examined their ability to bind and target damage to model DNA duplexes corresponding to sequences within the human HPRT gene. While TFO binding affinity was not dramatically affected by the type of backbone, psoralen photoreactivity was completely abrogated by the 2′-O-methyl RNA backbone. Photoreactivity was restored when the psoralen was conjugated to the RNA TFO via a 6-carbon linker. In contrast to the B-form DNA of triplexes formed by DNA TFOs, the CD spectra of triplexes formed with 2′-O-methyl RNA TFOs exhibited features of A-form DNA. These results indicate that 2′-O-methyl RNA TFOs induce a partial B-to-A transition in their target DNA sequences which may impair the photoreactivity of a conjugated psoralen and suggest that optimal design of TFOs to target DNA damage may require a balance between binding ability and drug reactivity.
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Affiliation(s)
- Rajagopal Krishnan
- Department of Dermatology, University of California at San Francisco, San Francisco, CA 94121, USA
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24
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Gryaznov SM. Oligonucleotide n3'-->p5' phosphoramidates and thio-phoshoramidates as potential therapeutic agents. Chem Biodivers 2010; 7:477-93. [PMID: 20232321 DOI: 10.1002/cbdv.200900187] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Nucleic acids analogues, i.e., oligonucleotide N3'-->P5' phosphoramidates and N3'-->P5' thio-phosphoramidates, containing 3'-amino-3'-deoxy nucleosides with various 2'-substituents were synthesized and extensively studied. These compounds resist nuclease hydrolysis and form stable duplexes with complementary native phosphodiester DNA and, particularly, RNA strands. An increase in duplexes' melting temperature, DeltaT(m), relative to their phosphodiester counterparts, reaches 2.2-4.0 degrees per modified nucleoside. 2'-OH- (RNA-like), 2'-O-Me-, and 2'-ribo-F-nucleoside substitutions result in the highest degree of duplex stabilization. Moreover, under close to physiological salt and pH conditions, the 2'-deoxy- and 2'-fluoro-phosphoramidate compounds form extremely stable triple-stranded complexes with either single- or double-stranded phosphodiester DNA oligonucleotides. Melting temperature, T(m), of these triplexes exceeds T(m) values for the isosequential phosphodiester counterparts by up to 35 degrees . 2'-Deoxy-N3'-->P5' phosphoramidates adopt RNA-like C3'-endo or N-type nucleoside sugar-ring conformations and hence can be used as stable RNA mimetics. Duplexes formed by 2'-deoxy phosphoramidates with complementary RNA strands are not substrates for RNase H-mediated cleavage in vitro. Oligonucleotide phosphoramidates and especially thio-phosphoramidates conjugated with lipid groups are cell-permeable and demonstrate high biological target specific activity in vitro. In vivo, these compounds show good bioavailability and efficient biodistribution to all major organs, while exerting acceptable toxicity at therapeutically relevant doses. Short oligonucleotide N3'-->P5' thio-phosphoramidate conjugated to 5'-palmitoyl group, designated as GRN163L (Imetelstat), was recently introduced as a potent human telomerase inhibitor. GRN163L is not an antisense agent; it is a direct competitive inhibitor of human telomerase, which directly binds to the active site of the enzyme and thus inhibits its activity. This compound is currently in multiple Phase-I and Phase-I/II clinical trials as potential broad-spectrum anticancer agent.
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Affiliation(s)
- Sergei M Gryaznov
- Geron Corporation, 230 Constitution Drive, Menlo Park, CA 94025, USA.
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Watts JK, Yu D, Charisse K, Montaillier C, Potier P, Manoharan M, Corey DR. Effect of chemical modifications on modulation of gene expression by duplex antigene RNAs that are complementary to non-coding transcripts at gene promoters. Nucleic Acids Res 2010; 38:5242-59. [PMID: 20403811 PMCID: PMC2926613 DOI: 10.1093/nar/gkq258] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Antigene RNAs (agRNAs) are small RNA duplexes that target non-coding transcripts rather than mRNA and specifically suppress or activate gene expression in a sequence-dependent manner. For many applications in vivo, it is likely that agRNAs will require chemical modification. We have synthesized agRNAs that contain different classes of chemical modification and have tested their ability to modulate expression of the human progesterone receptor gene. We find that both silencing and activating agRNAs can retain activity after modification. Both guide and passenger strands can be modified and functional agRNAs can contain 2'F-RNA, 2'OMe-RNA, and locked nucleic acid substitutions, or combinations of multiple modifications. The mechanism of agRNA activity appears to be maintained after chemical modification: both native and modified agRNAs modulate recruitment of RNA polymerase II, have the same effect on promoter-derived antisense transcripts, and must be double-stranded. These data demonstrate that agRNA activity is compatible with a wide range of chemical modifications and may facilitate in vivo applications.
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Affiliation(s)
- Jonathan K Watts
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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26
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Pavlova AS, Vorob'ev PE, Zarytova VF. [Direct site-specific cleavage of double-stranded DNA by conjugates of bleomycin A5 with triplex-forming oligonucleotide]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2009; 35:215-25. [PMID: 19537173 DOI: 10.1134/s1068162009020083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Monofunctional conjugates of 15-mer triplex-forming oligonucleotide (TFO) with covalently attached bleomycin A5 residue at the 5'-end (Blm-p15) were synthesized. Bifunctional conjugates of TFO containing, in addition to Blm, the residues of intercalator 6-chloro-2-methoxy-9-aminoacridine (Acr) or (N-(2-hydroxyethyl)phenazinium (Phn) were obtained for the first time. The Acr and Phn residues were attached to the 3'-phosphate group of TFO through L1 and L2 linkers, respectively, resulting in the compounds Blm-p15pL1-Acr and Blm-p15pL2-Phn. The values of dissociation constants of the corresponding triplexes were evaluated using the gel retardation method. The Acr residue in Blm-p15pL1-Acr was shown to enhance the stability of the formed triplex by one order of magnitude. It was demonstrated that all synthesized conjugates are capable of specifically and nonspecifically damaging a target DNA, forming direct breaks and alkaline-labile sites. The extent of the specific cleavage of the target DNA was 15% in the case of a fivefold excess of the conjugates over the DNA duplex. The site-specific triplex-mediated cleavage of a target DNA was shown for the first time to occur predominantly (> 90%) with the formation of the direct breaks of both DNA strands. The results show the availability of bleomycin-containing oligonucleotides as antigene compounds.
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27
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Torigoe H, Maruyama A, Obika S, Imanishi T, Katayama T. Synergistic stabilization of nucleic acid assembly by 2'-O,4'-C-methylene-bridged nucleic acid modification and additions of comb-type cationic copolymers. Biochemistry 2009; 48:3545-53. [PMID: 19170613 DOI: 10.1021/bi801795z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Stabilization of nucleic acid assemblies, such as duplex and triplex, is quite important for their wide variety of potential applications. Various stabilization methods, including molecular designs of chemically modified nucleotides and hybrid stabilizers, and combinations of different stabilization methods have been developed to increase stability of nucleic acid assemblies. However, combinations of two stabilizing methods have not always yielded desired synergistic effects. In the present study, to propose a strategy for selection of a rational combination of stabilizing methods, we demonstrate synergistic stabilization of triplex by 2'-O,4'-C-methylene-bridged nucleic acid (2',4'-BNA) modification of triplex-forming oligonucleotide and addition of poly(l-lysine)-graft-dextran copolymer [poly(l-lysine) grafted with hydrophilic dextran side chains]. Each of these methods increased the binding constant for triplex formation by nearly 2 orders of magnitude. However, their kinetic contributions were quite distinct. The copolymer increased the association rate constant, whereas the 2',4'-BNA modification decreased the dissociation rate constant for triplex stabilization. The combination of both stabilizing methods increased the binding constant by nearly 4 orders of magnitude. Kinetic analyses revealed that the successful synergistic stabilization resulted from kinetic complementarity between increased association rate constants by the copolymer and decreased dissociation rate constants by the 2',4'-BNA modification. The stabilizing effect of one stabilization method did not alter that of the other stabilization method. We propose that kinetic analyses of each stabilizing effect permit selection of a rational combination of stabilizing methods for successful synergy in stabilizing nucleic acid assemblies.
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Affiliation(s)
- Hidetaka Torigoe
- Department of Applied Chemistry, Faculty of Science, Tokyo UniVersity of Science, 1-3 Kagurazaka,Shinjuku-ku, Tokyo 162-8601, Japan.
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28
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Waldeck W, Pipkorn R, Korn B, Mueller G, Schick M, Tóth K, Wiessler M, Didinger B, Braun K. Transporter molecules influence the gene expression in HeLa cells. Int J Med Sci 2009; 6:18-27. [PMID: 19214198 PMCID: PMC2610340 DOI: 10.7150/ijms.6.18] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2008] [Accepted: 12/16/2008] [Indexed: 12/13/2022] Open
Abstract
Progresses in biology and pharmacology led to highly specific bioactive substances, but their poor bioavailability at the site of action is a result of their physico-chemical properties. Various design approaches for transport carrier molecules facilitating the cellular entry of bioactive substances could help to reach their molecular target in cells and tissues. The transfer efficacy and the subsequent pharmacological effects of the cargo molecules are well investigated, but the investigations of effects of the carrier molecules themselves on the target cells or tissues remain necessary. A special attention should be paid to the differential gene expression, particularly in the interpretation of the data achieved by highly specific active pharmaceutical products. After application of transmembrane transport peptides, particularly the pAnt and also the HIV-1 Tat, cells respond with a conspicuous altered gene expression of at least three genes. The PKN1 gene was induced and two genes (ZCD1 and BSG) were slightly repressed. The genes and the chromosomes are described, the moderate differential gene expression graphed, and the ontology is listed.
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Affiliation(s)
- Waldemar Waldeck
- German Cancer Research Center, Division of Biophysics of Macromolecules, INF 580, D-69120 Heidelberg, Germany
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29
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Duca M, Vekhoff P, Oussedik K, Halby L, Arimondo PB. The triple helix: 50 years later, the outcome. Nucleic Acids Res 2008; 36:5123-38. [PMID: 18676453 PMCID: PMC2532714 DOI: 10.1093/nar/gkn493] [Citation(s) in RCA: 265] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Triplex-forming oligonucleotides constitute an interesting DNA sequence-specific tool that can be used to target cleaving or cross-linking agents, transcription factors or nucleases to a chosen site on the DNA. They are not only used as biotechnological tools but also to induce modifications on DNA with the aim to control gene expression, such as by site-directed mutagenesis or DNA recombination. Here, we report the state of art of the triplex-based anti-gene strategy 50 years after the discovery of such a structure, and we show the importance of the actual applications and the main challenges that we still have ahead of us.
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Affiliation(s)
- Maria Duca
- LCMBA CNRS UMR6001, University of Nice-Sophia Antipolis, Parc Valrose, 06108 NICE Cedex 2, France
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30
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Fearon KL, Nelson JS. Synthesis and purification of oligonucleotide N3'-->P5' phosphoramidates and their phosphodiester and phosphorothioate chimeras. ACTA ACUST UNITED AC 2008; Chapter 4:Unit 4.7. [PMID: 18428854 DOI: 10.1002/0471142700.nc0407s03] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This unit describes the synthesis and purification of oligonucleotide N3'-->P5' phosphoramidates, wherein each 3'-oxygen is replaced by a 3'-amine in the 2'-deoxyribose ring. The synthesis of required monomers and application of the method to preparation of phosphodiester- and phosphorothioate-containing chimera of phosphoramidate is also reported.
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Affiliation(s)
- K L Fearon
- Lynx Therapeutics, Hayward, California, USA
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31
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Thuong NT, Asseline U. Modification of the 5' terminus of oligonucleotides for attachment of reporter and conjugate groups. ACTA ACUST UNITED AC 2008; Chapter 4:Unit 4.2. [PMID: 18428849 DOI: 10.1002/0471142700.nc0402s00] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Reporter and conjugate groups can be added directly to the 5' terminus of oligonucleotides by appropriate modification. Conjugate groups can be used to increase the affinity of complementary strands, induce irreversible modification of target sequences, or enable sequences to recognize and permeate target cell membranes. This overview discusses the 5' modifications that can be used and strategies for the covalent attachment of ligands to the modified oligonucleotides. Step-by-step protocols for attachment of conjugate groups are given elsewhere in the series.
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Affiliation(s)
- N T Thuong
- Centre de Biophysique Moléculaire, CNRS, Orléans, France
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32
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Simon P, Cannata F, Concordet JP, Giovannangeli C. Targeting DNA with triplex-forming oligonucleotides to modify gene sequence. Biochimie 2008; 90:1109-16. [PMID: 18460344 DOI: 10.1016/j.biochi.2008.04.004] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2007] [Accepted: 04/14/2008] [Indexed: 12/19/2022]
Abstract
Molecules that interact with DNA in a sequence-specific manner are attractive tools for manipulating gene sequence and expression. For example, triplex-forming oligonucleotides (TFOs), which bind to oligopyrimidine.oligopurine sequences via Hoogsteen hydrogen bonds, have been used to inhibit gene expression at the DNA level as well as to induce targeted mutagenesis in model systems. Recent advances in using oligonucleotides and analogs to target DNA in a sequence-specific manner will be discussed. In particular, chemical modification of TFOs has been used to improve binding to chromosomal target sequences in living cells. Various oligonucleotide analogs have also been found to expand the range of sequences amenable to manipulation, including so-called "Zorro" locked nucleic acids (LNAs) and pseudo-complementary peptide nucleic acids (pcPNAs). Finally, we will examine the potential of TFOs for directing targeted gene sequence modification and propose that synthetic nucleases, based on conjugation of sequence-specific DNA ligands to DNA damaging molecules, are a promising alternative to protein-based endonucleases for targeted gene sequence modification.
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Affiliation(s)
- Philippe Simon
- Laboratoire de Biophysique, Muséum National d'Histoire Naturelle, USM 503, 43 rue Cuvier, 75005 Paris, France
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33
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Ye Z, Houssein HSH, Mahato RI. Bioconjugation of oligonucleotides for treating liver fibrosis. Oligonucleotides 2008; 17:349-404. [PMID: 18154454 DOI: 10.1089/oli.2007.0097] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Liver fibrosis results from chronic liver injury due to hepatitis B and C, excessive alcohol ingestion, and metal ion overload. Fibrosis culminates in cirrhosis and results in liver failure. Therefore, a potent antifibrotic therapy is urgently needed to reverse scarring and eliminate progression to cirrhosis. Although activated hepatic stellate cells (HSCs) remain the principle cell type responsible for liver fibrosis, perivascular fibroblasts of portal and central veins as well as periductular fibroblasts are other sources of fibrogenic cells. This review will critically discuss various treatment strategies for liver fibrosis, including prevention of liver injury, reduction of inflammation, inhibition of HSC activation, degradation of scar matrix, and inhibition of aberrant collagen synthesis. Oligonucleotides (ODNs) are short, single-stranded nucleic acids, which disrupt expression of target protein by binding to complementary mRNA or forming triplex with genomic DNA. Triplex forming oligonucleotides (TFOs) provide an attractive strategy for treating liver fibrosis. A series of TFOs have been developed for inhibiting the transcription of alpha1(I) collagen gene, which opens a new area for antifibrotic drugs. There will be in-depth discussion on the use of TFOs and how different bioconjugation strategies can be utilized for their site-specific delivery to HSCs or hepatocytes for enhanced antifibrotic activities. Various insights developed in individual strategy and the need for multipronged approaches will also be discussed.
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Affiliation(s)
- Zhaoyang Ye
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN 38163, USA
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Jain A, Wang G, Vasquez KM. DNA triple helices: biological consequences and therapeutic potential. Biochimie 2008; 90:1117-30. [PMID: 18331847 DOI: 10.1016/j.biochi.2008.02.011] [Citation(s) in RCA: 191] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2008] [Accepted: 02/08/2008] [Indexed: 01/25/2023]
Abstract
DNA structure is a critical element in determining its function. The DNA molecule is capable of adopting a variety of non-canonical structures, including three-stranded (i.e. triplex) structures, which will be the focus of this review. The ability to selectively modulate the activity of genes is a long-standing goal in molecular medicine. DNA triplex structures, either intermolecular triplexes formed by binding of an exogenously applied oligonucleotide to a target duplex sequence, or naturally occurring intramolecular triplexes (H-DNA) formed at endogenous mirror repeat sequences, present exploitable features that permit site-specific alteration of the genome. These structures can induce transcriptional repression and site-specific mutagenesis or recombination. Triplex-forming oligonucleotides (TFOs) can bind to duplex DNA in a sequence-specific fashion with high affinity, and can be used to direct DNA-modifying agents to selected sequences. H-DNA plays important roles in vivo and is inherently mutagenic and recombinogenic, such that elements of the H-DNA structure may be pharmacologically exploitable. In this review we discuss the biological consequences and therapeutic potential of triple helical DNA structures. We anticipate that the information provided will stimulate further investigations aimed toward improving DNA triplex-related gene targeting strategies for biotechnological and potential clinical applications.
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Affiliation(s)
- Aklank Jain
- Department of Carcinogenesis, University of Texas, M.D. Anderson Cancer Center, Science Park--Research Division, 1808 Park Road 1-C, P.O. Box 389, Smithville, TX 78957, USA
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35
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Halby L, Ryabinin VA, Sinyakov AN, Novopashina DS, Venyaminova AG, Grokhovsky SL, Surovaya AN, Gursky GV, Boutorine AS. Head-to-head bis-hairpin polyamide minor groove binders and their conjugates with triplex-forming oligonucleotides: studies of interaction with target double-stranded DNA. J Biomol Struct Dyn 2007; 25:61-76. [PMID: 17676939 DOI: 10.1080/07391102.2007.10507156] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Two hairpin hexa(N-methylpyrrole)carboxamide DNA minor groove binders (MGB) were linked together via their N-termini in head-to-head orientation. Complex formation between these bis-MGB conjugates and target DNA has been studied using DNase I footprinting, circular dichroism, thermal dissociation, and molecular modeling. DNase I footprint revealed binding of these conjugates to all the sites of 492 b.p. DNA fragment containing (A/T)(n)X(m)(A/T)(p) sequences, where n>3, p>3; m=1,2; X = A,T,G, or C. Binding affinity depended on the sequence context of the target. CD experiments and molecular modeling showed that oligo(N-methylpyrrole)carboxamide moieties in the complex form two short antiparallel hairpins rather than a long parallel head-to-head hairpin. Binding of bis-MGB also stabilized a target duplex thermodynamically. Sequence specificity of bis-MGB/DNA binding was validated using bis-conjugates of sequence-specific hairpin (N-methylpyrrole)/(N-methylimidazole) carboxamides. In order to increase the size of recognition sequence, the conjugates of bis-MGB with triplex-forming oligonucleotides (TFO) were synthesized and compared to TFO conjugated with single MGB hairpin unit. Bis-MGB-oligonucleotide conjugates also bind to two blocks of three and more A.T/T.A pairs similarly to bis-MGB alone, independently of the oligonucleotide moiety, but with lower affinity. However, the role of TFO in DNA recognition was demonstrated for mono-MGB-TFO conjugate where the binding was detected mainly in the area of the target sequence consisting of both MGB and TFO recognition sites. Basing on the molecular modeling, three-dimensional models of both target DNA/bis-MGB and target DNA/TFO-bis-MGB complexes were built, where bis-MGB forms two antiparallel hairpins. According to the second model, one MGB hairpin is in the minor groove of 5'-adjacent A/T sequence next to the triplex-forming region, whereas the other one occupies the minor groove of the TFO binding polypurine tract. All these data together give a key information for the construction of MGB-MGB and MGB-oligonucleotide conjugates possessing high specificity and affinity for the target double-stranded DNA.
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Affiliation(s)
- Ludovic Halby
- Museum National d'Histoire Naturelle, RDDM, USM 0503, 57 rue Cuvier, B.P. 26, Paris Cedex 05, F-75231 France
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Abstract
We have previously demonstrated site-specific delivery of antiparallel phosphorothioate triplex forming oligonucleotide (TFO) specific to -165 to -141 promoter region of alpha1(I) collagen (abbreviated as APS165) to hepatic stellate cells (HSCs) of fibrotic rats after conjugation with mannose 6-phosphate-bovine serum albumin. However, we still need to determine whether there is correlation between transcription inhibition and triplex formation with genomic DNA. In this study, APS165 was modified with psoralen and the extent of triplex formation with alpha1(I) collagen DNA was determined in naked genomic DNA, isolated nuclei of HSC-T6 cells and whole cells by using a simple real-time PCR based method. In this method, a purification step was added to remove unbound APS165, which eliminated the possible artifacts during real-time PCR. Psoralen photoadduct formation was shown to be essential to retain triplex structure under denaturing conditions. On naked genomic DNA, 82.2% of DNA formed triplex and 36.7% of genomic DNA in isolated nuclei at 90 min contained triplex structure. As quantified by real-time PCR, 50% of genomic DNA in living cells at 12 h postincubation contained triplex structures. Furthermore, the triplex formation was dose-dependent with 26.5% and 50% of DNA having triplex structure at concentrations of 1 microM and 5 microM, respectively. Moreover, on a plasmid pCol-CAT220 containing rat alpha1(I) gene promoter (-225 to +113), 75.3% of triplex formation was observed, which was correlated with a 73.6% of transcription inhibition. These findings will further strengthen the therapeutic applications of APS165.
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Affiliation(s)
- Zhaoyang Ye
- Department of Pharmaceutical, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Ramareddy V. Guntaka
- Department of Molecular Sciences, University of Tennessee Health Science Center, Memphis, TN 38163, USA
- * Corresponding authors Ram I. Mahato, Ph.D., 26 S Dunlap Street, Feurt 413, Memphis, TN 38163, USA, Tel: (901) 448-6929, Fax: (901) 448-6092, E-mail: , Http://cop.utmem.edu/rmahato. Ramareddy V. Guntaka, Ph. D., 101 Molecular Science Bldg., Memphis, TN 38163, USA, Tel: (901) 448-8230, Fax: (901) 448-8462, E-mail:
| | - Ram I. Mahato
- Department of Pharmaceutical, University of Tennessee Health Science Center, Memphis, TN 38163, USA
- * Corresponding authors Ram I. Mahato, Ph.D., 26 S Dunlap Street, Feurt 413, Memphis, TN 38163, USA, Tel: (901) 448-6929, Fax: (901) 448-6092, E-mail: , Http://cop.utmem.edu/rmahato. Ramareddy V. Guntaka, Ph. D., 101 Molecular Science Bldg., Memphis, TN 38163, USA, Tel: (901) 448-8230, Fax: (901) 448-8462, E-mail:
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Boutorine AS, Escudé C. Biophysical Analysis of Triple‐Helix Formation. ACTA ACUST UNITED AC 2007; Chapter 7:Unit 7.12. [DOI: 10.1002/0471142700.nc0712s29] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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38
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Oh DH, Hanawalt PC. Binding and Photoreactivity of Psoralen Linked to Triple Helix-Forming Oligonucleotides ¶. Photochem Photobiol 2007. [DOI: 10.1562/0031-8655(2000)0720298bapopl2.0.co2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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39
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Novopashina DS, Sinyakov AN, Ryabinin VA, Venyaminova AG, Halby L, Sun JS, Boutorine AS. Sequence-specific conjugates of oligo(2'-O-methylribonucleotides) and hairpin oligocarboxamide minor-groove binders: design, synthesis, and binding studies with double-stranded DNA. Chem Biodivers 2007; 2:936-52. [PMID: 17193185 DOI: 10.1002/cbdv.200590071] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
New conjugates of triplex-forming pyrimidine oligo(2'-O-methylribonucleotides) with one or two 'head-to-head' hairpin oligo(N-methylpyrrole carboxamide) minor-groove binders (MGBs) attached to the terminal phosphate of the oligonucleotides with a oligo(ethylene glycol) linker were synthesized. It was demonstrated that, under appropriate conditions, the conjugates form stable complexes with double-stranded DNA (dsDNA) similarly to triplex-forming oligo(deoxyribonucleotide) (TFO) conjugates containing 5-methylated cytosines. Kinetic and thermodynamic parameters of the complex formation were evaluated by gel-shift assay and thermal denaturation. Higher melting temperatures (Tm), faster complex formation, and lower dissociation constants (Kd) of the triple helices (6-7 nM) were observed for complexes of MGB-oligo(2'-O-methylribonucleotide) conjugates with the target dsDNA compared to the nonconjugated individual components. Interaction of MGB moieties with the HIV proviral DNA fragment was indicated by UV/VIS absorption changes at 320 nm in the melting curves. The introduction of thymidine via a 3',3'-type 'inverted' phosphodiester linkage at the 3'-end of oligo(2'-O-methylribonucleotide) conjugates (3'-protection) had no strong influence on triplex formation, but slightly affected complex stability. At pH 6.0, when one or two hairpin MGBs were attached to the oligonucleotide, both triplex formation and minor-groove binding played important roles in complex formation. When two 'head-to-head' oligo(N-methylpyrrole) ligands were attached to the same terminal phosphate of the oligonucleotide or the linker, binding was observed at pH >7.5 and at high temperatures (up to 74 degrees). However, under these conditions, binding was retained only by the MGB part of the conjugate.
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Affiliation(s)
- Darya S Novopashina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, pr. Lavrentieva 8, 630090 Novosibirsk, Russia.
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40
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Daunomycin-TFO Conjugates for Downregulation of Gene Expression. Top Curr Chem (Cham) 2007; 283:45-71. [DOI: 10.1007/128_2007_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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41
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Zhu J, Fu H, Jiang Y, Zhao Y. A general and chemoselective synthesis of phosphoramidates through reaction of silylated nucleoside di- and triphosphates with silylated amines containing multifunctional groups. J Org Chem 2006; 71:1722-4. [PMID: 16468833 DOI: 10.1021/jo0521403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An approach to various phosphoramidates has been developed through one-pot chemoselective reaction of nucleoside di- and triphosphates with 3'-amino-3'-deoxythymidine, d-glucosamine, and peptides mediated by trimethylsilyl chloride, and the corresponding conjugates via the linkage of phosphate were obtained. The method could be generally applied for the synthesis of phosphoramidates without any preprotection of polyphosphates and amines containing multifunctional groups.
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Affiliation(s)
- Jigang Zhu
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, PR China
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42
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Brunet E, Corgnali M, Cannata F, Perrouault L, Giovannangeli C. Targeting chromosomal sites with locked nucleic acid-modified triplex-forming oligonucleotides: study of efficiency dependence on DNA nuclear environment. Nucleic Acids Res 2006; 34:4546-53. [PMID: 16951289 PMCID: PMC1636373 DOI: 10.1093/nar/gkl630] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Triplex-forming oligonucleotides (TFOs) are synthetic DNA code-reading molecules that have been demonstrated to function to some extent in chromatin within cell nuclei. Here we have investigated the impact of DNA nuclear environment on the efficiency of TFO binding. For this study we have used locked nucleic acid-containing TFOs (TFO/LNAs) and we report the development of a rapid PCR-based method to quantify triplex formation. We have first compared triplex formation on genes located at different genomic sites and containing the same oligopyrimidine•oligopurine sequence. We have shown that efficient TFO binding is possible on both types of genes, expressed and silent. Then we have further investigated when gene transcription may influence triplex formation in chromatin. We have identified situations where for a given gene, increase of transcriptional activity leads to enhanced TFO binding: this was observed for silent or weakly expressed genes that are not or are only slightly accessible to TFO. Such a transcriptional dependence was observed for integrated and endogenous loci, and chemical and biological activations of transcription. Finally, we provide evidence that TFO binding is sequence-specific as measured on mutated target sequences and that up to 50% of chromosomal targets can be covered by the TFO/LNA in living cells.
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Affiliation(s)
- Erika Brunet
- CNRS, UMR5153Paris, F-75005, France
- Inserm, U565Paris, F-75005, France
- Museum National d'Histoire Naturelle, USM503Paris, F-75005, France
| | - Maddalena Corgnali
- Dipartimento di Scienze e Tecnologie Biomediche, Universita degli Studi di Udine33100 Udine, Italy
| | - Fabio Cannata
- CNRS, UMR5153Paris, F-75005, France
- Inserm, U565Paris, F-75005, France
- Museum National d'Histoire Naturelle, USM503Paris, F-75005, France
| | - Loïc Perrouault
- CNRS, UMR5153Paris, F-75005, France
- Inserm, U565Paris, F-75005, France
- Museum National d'Histoire Naturelle, USM503Paris, F-75005, France
| | - Carine Giovannangeli
- CNRS, UMR5153Paris, F-75005, France
- Inserm, U565Paris, F-75005, France
- Museum National d'Histoire Naturelle, USM503Paris, F-75005, France
- To whom correspondence should be addressed. Tel: +33 1 40793711; Fax: + 33 1 40793705;
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Kan LS, Pasternack L, Wey MT, Tseng YY, Huang DH. The paperclip triplex: understanding the role of apex residues in tight turns. Biophys J 2006; 91:2552-63. [PMID: 16829568 PMCID: PMC1562401 DOI: 10.1529/biophysj.106.084137] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In this study, we investigate the role of the apex nucleotides of the two turns found in the intramolecular "paperclip" type triplex DNA formed by 5'-TCTCTCCTCTCTAGAGAG-3'. Our previously published structure calculations show that residues C7-A18 form a hairpin turn via Watson-Crick basepairing and residues T1-C6 bind into the major groove of the hairpin via Hoogsteen basepairing resulting in a broad turn of the T1-T12 5'-pyrimidine section of the DNA. We find that only the C6C7/G18 apex triad (and not the T12A13/T1 apex triad) is required for intramolecular triplex formation, is base independent, and occurs whether the purine section is located at the 5' or 3' end of the sequence. NMR spectroscopy and molecular dynamics simulations are used to investigate a bimolecular complex (which retains only the C6C7/G18 apex) in which a pyrimidine strand 5'- TCTCTCCTCTCT-3' makes a broad fold stabilized by the purine strand 5'-AGAGAG-3' via Watson Crick pairing to the T8-T12 and Hoogsteen basepairing to T1-T5 of the pyrimidine strand. Interestingly, this investigation shows that this 5'-AGAGAG-3' oligo acts as a new kind of triplex forming oligonucleotide, and adds to the growing number of triplex forming oligonucleotides that may prove useful as therapeutic agents.
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Affiliation(s)
- Lou-sing Kan
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan 11529
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44
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Seela F, Shaikh K, Wiglenda T. pH-Independent Recognition of the dG ⋅ dC Base Pair in Triplex DNA: 9-DeazaguanineN7-(2′-Deoxyribonucleoside) and Halogenated Derivatives Replacing Protonated dC. Helv Chim Acta 2006. [DOI: 10.1002/hlca.200690063] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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45
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Napoli S, Negri U, Arcamone F, Capobianco ML, Carbone GM, Catapano CV. Growth inhibition and apoptosis induced by daunomycin-conjugated triplex-forming oligonucleotides targeting the c-myc gene in prostate cancer cells. Nucleic Acids Res 2006; 34:734-44. [PMID: 16449206 PMCID: PMC1356532 DOI: 10.1093/nar/gkj473] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Covalent attachment of intercalating agents to triplex-forming oligonucleotides (TFOs) is a promising strategy to enhance triplex stability and biological activity. We have explored the possibility to use the anticancer drug daunomycin as triplex stabilizing agent. Daunomycin-conjugated TFOs (dauno-TFOs) bind with high affinity and maintain the sequence-specificity required for targeting individual genes in the human genome. Here, we examined the effects of two dauno-TFOs targeting the c-myc gene on gene expression, cell proliferation and survival. The dauno-TFOs were directed to sequences immediately upstream (dauno-GT11A) and downstream (dauno-GT11B) the major transcriptional start site in the c-myc gene. Both dauno-TFOs were able to down-regulate promoter activity and transcription of the endogenous gene. Myc-targeted dauno-TFOs inhibited growth and induced apoptosis of prostate cancer cells constitutively expressing the gene. Daunomycin-conjugated control oligonucleotides with similar sequences had only minimal effects, confirming that the activity of dauno-TFOs was sequence-specific and triplex-mediated. To test the selectivity of dauno-TFOs, we examined their effects on growth of normal human fibroblasts, which express low levels of c-myc. Despite their ability to inhibit c-myc transcription, both dauno-TFOs failed to inhibit growth of normal fibroblasts at concentrations that inhibited growth of prostate cancer cells. In contrast, daunomycin inhibited equally fibroblasts and prostate cancer cells. Thus, daunomycin per se did not contribute to the antiproliferative activity of dauno-TFOs, although it greatly enhanced their ability to form stable triplexes at the target sites and down-regulate c-myc. Our data indicate that dauno-TFOs are attractive gene-targeting agents for development of new cancer therapeutics.
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Affiliation(s)
| | | | | | | | | | - Carlo V. Catapano
- To whom correspondence should be addressed at Oncology Institute of Southern Switzerland, 6500 Bellinzona, Switzerland. Tel: +41 91 820 0365; Fax: +41 91 820 0397;
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46
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Ghosh MK, Katyal A, Chandra R, Brahmachari V. Targeted activation of transcription in vivo through hairpin-triplex forming oligonucleotide in Saccharomyces cerevisiae. Mol Cell Biochem 2006; 278:147-55. [PMID: 16180100 DOI: 10.1007/s11010-005-7283-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2005] [Accepted: 05/12/2005] [Indexed: 11/24/2022]
Abstract
Triplex forming oligonucleotides (TFO) are known to be potential agents for modifying gene function. In most instances they are utilized for repression of transcription. However hybrid molecules containing cis-acting elements in a duplex DNA in a hairpin form contiguously with the TFO can bind transcription factors in vitro. In the present manuscript we demonstrate that hairpin-TFO can be employed in vivo for targeted activation of gene expression of two genes mapping on chromosome XI of Saccharomyces cerevisiae. The cis-acting GAL4 protein-binding site contained in the hairpin-TFO is targeted in vivo to the 5' upstream sequence of STE6 and CBT1 genes that are transcribed in opposite directions and share a poly(pu/py) sequence that can form triple helical structure. The hairpin-TFO is targeted to this site and promotes the activation of both the genes. These results demonstrate four important aspects relating to activation of gene expression: (i) accessibility of duplex DNA packaged into chromatin to triplex forming sequences in vivo, (ii) the potential use of hairpin-TFO in therapeutics by activation of transcription in vivo, (iii) Sharing of transcription factors between two genes transcribed in opposite directions and (iv) specific activation of genes even when their cognate site is not covalently linked to the gene being activated.
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Affiliation(s)
- Mrinal Kanti Ghosh
- Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, India
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47
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Capobianco ML, De Champdoré M, Arcamone F, Garbesi A, Guianvarc'h D, B Arimondo P. Improved synthesis of daunomycin conjugates with triplex-forming oligonucleotides. The polypurine tract of HIV-1 as a target. Bioorg Med Chem 2005; 13:3209-18. [PMID: 15809156 DOI: 10.1016/j.bmc.2005.02.040] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2004] [Revised: 02/09/2005] [Accepted: 02/18/2005] [Indexed: 11/27/2022]
Abstract
Triple helix-forming oligonucleotides (TFOs) are promising agents for the control of gene expression, as they can selectively bind to a chosen oligopyrimidine.oligopurine region of a gene of interest thus interfering with its expression. The stability of the triplex formed by the TFO and the duplex is often too poor for successful applications of TFOs in vivo and the conjugation of a DNA intercalating moiety to the TFO is a common way to enhance the TFO affinity for its target. In a previous work, we investigated the properties of daunomycin conjugated TFO (dauno-TFO) and found that this class of compounds showed a higher degree of affinity than native oligonucleotides for an oligopyrimidine.oligopurine duplex target and that the presence of the amino sugar increases such stability. Here, we report a significantly improved synthetic procedure for the preparation of the conjugates, based on the protection of the daunosamine moiety by N-trifluoroacetylation. This protecting group is removed as a final step from the conjugation product by mild basic hydrolysis to give the desired dauno-TFO. Compared to the previous synthetic procedure, the improvement is important. The synthesis is now more reproducible and no side products are formed. Moreover, the thus protected daunomycin derivative is very stable, up to at least one year. Two dauno-TFOs, differing by the length of the oligonucleotide moiety, were prepared to target the polypurine tract (PPT) of HIV-1. Triplex formation by these compounds with model duplexes was studied by UV spectroscopy, thermal gradient gel electrophoresis (TGGE) and gel electrophoretic mobility shift. The experimental results demonstrate that dauno-TFOs bind to the PPT of HIV-1 more strongly than the unconjugated TFOs.
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Affiliation(s)
- Massimo L Capobianco
- Istituto di Sintesi Organica e Fotoreattività del Consiglio Nazionale delle Ricerche, Via Gobetti 101, 40129 Bologna, Italy.
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48
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Halby L, Ryabinin VA, Sinyakov AN, Boutorine AS. Functionalized head-to-head hairpin polyamides: Synthesis, double-stranded DNA-binding activity and affinity. Bioorg Med Chem Lett 2005; 15:3720-4. [PMID: 16005219 DOI: 10.1016/j.bmcl.2005.05.106] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2005] [Revised: 05/17/2005] [Accepted: 05/18/2005] [Indexed: 11/23/2022]
Abstract
A series of 4 functionalized head-to-head-linked hairpin oligo(N-methylpyrrole) carboxamides with different linkers have been synthesized. Their ability to bind double-stranded DNA and sequence specificity were compared and the apparent Kd values of their DNA complexes were determined. These compounds, particularly those with iminodiacetic linkers, revealed a high affinity for DNA (Kd = 4.5-4.8 x 10(-9) M) and sequence specific recognition of 9-10 base pairs.
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Affiliation(s)
- Ludovic Halby
- USM 0503-Régulation et Dynamique des Génomes, Muséum National d'Histoire Naturelle, Paris, France
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49
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Ziemba AJ, Zhilina ZV, Krotova-Khan Y, Stankova L, Ebbinghaus SW. Targeting and regulation of the HER-2/neu oncogene promoter with bis-peptide nucleic acids. Oligonucleotides 2005; 15:36-50. [PMID: 15788899 DOI: 10.1089/oli.2005.15.36] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Antigene oligonucleotides have the potential to regulate gene expression through site-specific DNA binding. However, in vivo applications have been hindered by inefficient cellular uptake, degradation, and strand displacement. Peptide nucleic acids (PNAs) address several of these problems, as they are resistant to degradation and bind DNA with high affinity. We designed two cationic pyrimidine bis-PNAs (cpy-PNAs) to target the polypurine tract of the HER-2/neu promoter and compared them to an unmodified phosphodiester triplex-forming oligonucleotide (TFO1) and a TFO-nitrogen mustard conjugate (TFO2). PNA1 contains a + 2 charge and bound two adjacent 9-bp target sequences with high affinity and specificity, but only at low pH. PNA2 contains a +5 charge and bound one 11-bp target with high affinity up to pH 7.4, but with lower specificity. The PNA:DNA:PNA triplex formed by these cpy-bis-PNAs presented a stable barrier to DNA polymerase extension. The cpy-bis-PNAs and the TFO-alkylator conjugate prevented HER-2/neu transcription in a reporter gene assay (TFO2 = PNA1 > PNA2 >> TFO1). Both PNAs and TFOs were effective at binding the target sequence in naked genomic DNA, but only the TFO-alkylator (TFO2) and the more cationic PNA (PNA2) were detected at the endogenous HER-2/neu promoter in permeabilized cells. This work demonstrates the potential for preventing HER-2/neu gene expression with cpy-bis-PNAs in tumor cells.
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50
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Kalish JM, Seidman MM, Weeks DL, Glazer PM. Triplex-induced recombination and repair in the pyrimidine motif. Nucleic Acids Res 2005; 33:3492-502. [PMID: 15961731 PMCID: PMC1151591 DOI: 10.1093/nar/gki659] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Triplex-forming oligonucleotides (TFOs) bind DNA in a sequence-specific manner at polypurine/polypyrimidine sites and mediate targeted genome modification. Triplexes are formed by either pyrimidine TFOs, which bind parallel to the purine strand of the duplex (pyrimidine, parallel motif), or purine TFOs, which bind in an anti-parallel orientation (purine, anti-parallel motif). Both purine and pyrimidine TFOs, when linked to psoralen, have been shown to direct psoralen adduct formation in cells, leading to mutagenesis or recombination. However, only purine TFOs have been shown to mediate genome modification without the need for a targeted DNA-adduct. In this work, we report the ability of a series of pyrimidine TFOs, with selected chemical modifications, to induce repair and recombination in two distinct episomal targets in mammalian cells in the absence of any DNA-reactive conjugate. We find that TFOs containing N3′→P5′ phosphoramidate (amidate), 5-(1-propynyl)-2′-deoxyuridine (pdU), 2′-O-methyl-ribose (2′-O-Me), 2′-O-(2-aminoethyl)-ribose, or 2′-O, 4′-C-methylene bridged or locked nucleic acid (LNA)-modified nucleotides show substantially increased formation of non-covalent triplexes under physiological conditions compared with unmodified DNA TFOs. However, of these modified TFOs, only the amidate and pdU-modified TFOs mediate induced recombination in cells and stimulate repair in cell extracts, at levels comparable to those seen with purine TFOs in similar assays. These results show that amidate and pdU-modified TFOs can be used as reagents to stimulate site-specific gene targeting without the need for conjugation to DNA-reactive molecules. By demonstrating the potential for induced repair and recombination with appropriately modified pyrimidine TFOs, this work expands the options available for triplex-mediated gene targeting.
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Affiliation(s)
- Jennifer M. Kalish
- Department of Therapeutic Radiology, Yale University School of MedicinePO Box 208040, HRT 140, New Haven, CT 06520-8040, USA
- Department of Genetics, Yale University School of MedicinePO Box 208040, HRT 140, New Haven, CT 06520-8040, USA
| | - Michael M. Seidman
- National Institute on Aging, National Institutes of Health5600 Nathan Shock Drive, Baltimore, MD 21224, USA
| | - Daniel L. Weeks
- Department of Biochemistry, University of IowaIowa City, IA 52242, USA
| | - Peter M. Glazer
- Department of Therapeutic Radiology, Yale University School of MedicinePO Box 208040, HRT 140, New Haven, CT 06520-8040, USA
- Department of Genetics, Yale University School of MedicinePO Box 208040, HRT 140, New Haven, CT 06520-8040, USA
- To whom correspondence should be addressed. Tel: +1 203 737 2788; Fax: +1 203 785 6309;
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