151
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Berezney JP, Saleh OA. Locked nucleic acid oligomers as handles for single molecule manipulation. Nucleic Acids Res 2014; 42:e150. [PMID: 25159617 PMCID: PMC4231729 DOI: 10.1093/nar/gku760] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Single-molecule manipulation (SMM) techniques use applied force, and measured elastic response, to reveal microscopic physical parameters of individual biomolecules and details of biomolecular interactions. A major hurdle in the application of these techniques is the labeling method needed to immobilize biomolecules on solid supports. A simple, minimally-perturbative labeling strategy would significantly broaden the possible applications of SMM experiments, perhaps even allowing the study of native biomolecular structures. To accomplish this, we investigate the use of functionalized locked nucleic acid (LNA) oligomers as biomolecular handles that permit sequence-specific binding and immobilization of DNA. We find these probes form bonds with DNA with high specificity but with varied stability in response to the direction of applied mechanical force: when loaded in a shear orientation, the bound LNA oligomers were measured to be two orders of magnitude more stable than when loaded in a peeling, or unzipping, orientation. Our results show that LNA provides a simple, stable means to functionalize dsDNA for manipulation. We provide design rules that will facilitate their use in future experiments.
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Affiliation(s)
- John P Berezney
- Materials Department, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Omar A Saleh
- Materials Department, University of California, Santa Barbara, Santa Barbara, CA 93106, USA Biomolecular Science and Engineering Program, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
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152
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Therapeutic potential of siRNA and DNAzymes in cancer. Tumour Biol 2014; 35:9505-21. [PMID: 25149153 DOI: 10.1007/s13277-014-2477-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 08/07/2014] [Indexed: 02/07/2023] Open
Abstract
Cancer is characterized by uncontrolled cell growth, invasion, and metastasis and possess threat to humans worldwide. The scientific community is facing numerous challenges despite several efforts to cure cancer. Though a number of studies were done earlier, the molecular mechanism of cancer progression is not completely understood. Currently available treatments like surgery resection, adjuvant chemotherapy, and radiotherapy are not completely effective in curing all the cancers. Recent advances in the antisense technology provide a powerful tool to investigate various cancer pathways and target them. Small interfering RNAs (siRNAs) could be effective in downregulating the cancer-associated genes, but their in vivo delivery is the main obstacle. DNA enzymes (DNAzymes) have great potential in the treatment of cancer due to high selectivity and significant catalytic efficiency. In this review, we are focusing on antisense molecules such as siRNA and DNAzymes in cancer therapeutics development. This review also describes the challenges and approaches to overcome obstacles involved in using siRNA and DNAzymes in the treatment of cancers.
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153
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Poongavanam V, Madala PK, Højland T, Veedu RN. Computational investigation of locked nucleic acid (LNA) nucleotides in the active sites of DNA polymerases by molecular docking simulations. PLoS One 2014; 9:e102126. [PMID: 25036012 PMCID: PMC4103837 DOI: 10.1371/journal.pone.0102126] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 06/16/2014] [Indexed: 01/07/2023] Open
Abstract
Aptamers constitute a potential class of therapeutic molecules typically selected from a large pool of oligonucleotides against a specific target. With a scope of developing unique shorter aptamers with very high biostability and affinity, locked nucleic acid (LNA) nucleotides have been investigated as a substrate for various polymerases. Various reports showed that some thermophilic B-family DNA polymerases, particularly KOD and Phusion DNA polymerases, accepted LNA-nucleoside 5'-triphosphates as substrates. In this study, we investigated the docking of LNA nucleotides in the active sites of RB69 and KOD DNA polymerases by molecular docking simulations. The study revealed that the incoming LNA-TTP is bound in the active site of the RB69 and KOD DNA polymerases in a manner similar to that seen in the case of dTTP, and with LNA structure, there is no other option than the locked C3'-endo conformation which in fact helps better orienting within the active site.
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Affiliation(s)
- Vasanthanathan Poongavanam
- Nucleic Acid Center and Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
| | - Praveen K. Madala
- Institute of Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Torben Højland
- Nucleic Acid Center and Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
| | - Rakesh N. Veedu
- Nucleic Acid Center and Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- * E-mail:
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154
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Kauppinen S, Vester B, Wengel J. Locked nucleic acid (LNA): High affinity targeting of RNA for diagnostics and therapeutics. DRUG DISCOVERY TODAY. TECHNOLOGIES 2014; 2:287-90. [PMID: 24981949 PMCID: PMC7105916 DOI: 10.1016/j.ddtec.2005.08.012] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Locked nucleic acid (LNA) is a nucleic acid analogue containing one or more LNA nucleotide monomers with a bicyclic furanose unit locked in an RNA mimicking sugar conformation. This conformational restriction results in unprecedented hybridization affinity towards complementary single stranded RNA and thus, makes LNA uniquely suited for mimicking RNA structures and sequence specific targeting of RNA in vitro or in vivo. The focus of this paper is on LNA-antisense, LNA-modified siRNA (siLNA), and detection and analysis of microRNAs by LNA-modified oligonucleotide probes. Steve Gullans – RxGen, Inc., New Haven, CT, USA Robert Zivin – Johnson and Johnson, New Brunswick, NJ, USA
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Affiliation(s)
- Sakari Kauppinen
- Wilhelm Johannsen Centre for Functional Genome Research, Institute of Medical Biochemistry and Genetics, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Birte Vester
- Nucleic Acid Center, Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Jesper Wengel
- Nucleic Acid Center, Department of Chemistry, University of Southern Denmark, DK-5230 Odense M, Denmark.
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155
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Yuan L, Tian T, Chen Y, Zhang Z, Zhou X. An L-DNA G-quadruplex: application for peroxidase DNAzyme. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2014; 32:589-98. [PMID: 24138498 DOI: 10.1080/15257770.2013.838260] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
L-DNA is the mirror-image form of natural D-DNA. We demonstrate that one left-handed G-rich sequence can form an L-DNA intramolecular G-quadruplex. Further investigation revealed that a DNAzyme formed by an L-nucleotide G-quadruplex exhibited peroxidase catalytic efficiency. The enhancement of the color change of the oxygenation product ABTS(•-) caused by L-nucleotide G-quadruplex formation could be clearly observed with naked eyes. This research provides a new concept for the application of the L-DNA peroxidase DNAzyme complex in nuclease-containing biological systems.
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Affiliation(s)
- Libo Yuan
- a College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education , Wuhan University , Wuhan , Hubei , P. R. China
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156
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Suresh G, Priyakumar UD. Atomistic investigation of the effect of incremental modification of deoxyribose sugars by locked nucleic acid (β-D-LNA and α-L-LNA) moieties on the structures and thermodynamics of DNA-RNA hybrid duplexes. J Phys Chem B 2014; 118:5853-63. [PMID: 24845216 DOI: 10.1021/jp5014779] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Chemically modified oligonucleotides offer many possibilities in utilizing their special features for a vast number of applications in nucleic acid based therapies and synthetic molecular biology. Locked nucleic acid analogues (α-/β-LNA) are modifications having an extra ring of 2'-O,4'-C-methylene group in the furanose sugar. LNA strands have been shown to exhibit high binding affinity toward RNA and DNA strands, and the resultant duplexes show significantly high melting temperatures. In the present study, molecular dynamics (MD) simulations were performed on DNA-RNA hybrid duplexes by systematically modifying their deoxyribose sugars with locked nucleic acid analogues. Several geometrical and energetic analyses were performed using principal component (PCA) analysis and binding free energy methods to understand the consequence of incorporated isomeric LNA modifications on the structure, dynamics, and stability of DNA-RNA hybrid duplex. The β-modification systematically changes the conformation of the DNA-RNA hybrid duplex whereas drastic changes are observed for α-modification. The fully modified duplexes have distinct properties compared to partial and unmodified duplexes, and the partly modified duplexes have properties intermediate to full strand and unmodified duplexes. The distribution of BI versus BII populations suggests that backbone rearrangement is minimal for β-LNA modification in order to accommodate it in duplexes whereas extensive backbone rearrangement is necessary in order to incorporate α-LNA modification which subsequently alters the energetic and structural properties of the duplexes. The simulation results also suggest that the alteration of DNA-RNA hybrid properties depends on the position of modification and the gap between the modifications.
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Affiliation(s)
- Gorle Suresh
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology , Hyderabad 500 032, India
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157
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Oligonucleotide-based therapy for neurodegenerative diseases. Brain Res 2014; 1584:116-28. [PMID: 24727531 DOI: 10.1016/j.brainres.2014.04.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 04/04/2014] [Accepted: 04/05/2014] [Indexed: 12/12/2022]
Abstract
Molecular genetics insight into the pathogenesis of several neurodegenerative diseases, such as Alzheimer׳s disease, Parkinson׳s disease, Huntington׳s disease and amyotrophic lateral sclerosis, encourages direct interference with the activity of neurotoxic genes or the molecular activation of neuroprotective pathways. Oligonucleotide-based therapies are recently emerging as an efficient strategy for drug development and these can be employed as new treatments of neurodegenerative states. Here we review advances in this field in recent years which suggest an encouraging assessment that oligonucleotide technologies for targeting of RNAs will enable the development of new therapies and will contribute to preservation of brain integrity.
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158
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Zhang L, Zhou L, Tian J, Li X. Hetero-ring-expansion design for purine analogs: A theoretical study on the structural, electronic, and excited-state properties. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.02.033] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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159
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Abstract
MicroRNAs (miRNAs) are emerging as key control molecules in the regulation of gene expression, and their role in heart disease is becoming increasingly evident. Given the critical role of Ca
2+
handling and signaling proteins in the maintenance of cardiac function, the targeting of such proteins by miRNAs would be expected to have important consequences. miRNAs have indeed been shown to control the expression of genes encoding important Ca
2+
handling and signaling proteins, and are themselves regulated by Ca
2+
-dependent processes. Ca
2+
-related miRNAs have been found to be significant pathophysiological contributors in conditions like myocardial ischemic injury, cardiac hypertrophy, heart failure, ventricular arrhythmogenesis, and atrial fibrillation. This review is a comprehensive analysis of the present knowledge concerning miRNA regulation of Ca
2+
handling processes, the participation of Ca
2+
-regulating miRNAs in the evolution of heart disease, the mutual relationship between Ca
2+
signaling and miRNAs in the control of cardiac function, and the potential value of miRNA-control of Ca
2+
handling as a therapeutic target.
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Affiliation(s)
- Masahide Harada
- From the Department of Medicine and Research Center, Montreal Heart Institute and Université de Montréal, Montreal, Quebec, Canada (M.H., X.L., S.N.); Department of Cardiology, Hamamatsu Medical Center, Hamamatsu, Japan (M.H.); Cardiovascular Research Institute and Department of Pharmacology, Harbin Medical University, Harbin, People’s Republic of China (X.L.; B.Y.); Department of Cardiology, Nagoya University Graduate School of Medicine, Nagoya, Japan (T.M.); and Institute of Pharmacology, Faculty
| | - Xiaobin Luo
- From the Department of Medicine and Research Center, Montreal Heart Institute and Université de Montréal, Montreal, Quebec, Canada (M.H., X.L., S.N.); Department of Cardiology, Hamamatsu Medical Center, Hamamatsu, Japan (M.H.); Cardiovascular Research Institute and Department of Pharmacology, Harbin Medical University, Harbin, People’s Republic of China (X.L.; B.Y.); Department of Cardiology, Nagoya University Graduate School of Medicine, Nagoya, Japan (T.M.); and Institute of Pharmacology, Faculty
| | - Toyoaki Murohara
- From the Department of Medicine and Research Center, Montreal Heart Institute and Université de Montréal, Montreal, Quebec, Canada (M.H., X.L., S.N.); Department of Cardiology, Hamamatsu Medical Center, Hamamatsu, Japan (M.H.); Cardiovascular Research Institute and Department of Pharmacology, Harbin Medical University, Harbin, People’s Republic of China (X.L.; B.Y.); Department of Cardiology, Nagoya University Graduate School of Medicine, Nagoya, Japan (T.M.); and Institute of Pharmacology, Faculty
| | - Baofeng Yang
- From the Department of Medicine and Research Center, Montreal Heart Institute and Université de Montréal, Montreal, Quebec, Canada (M.H., X.L., S.N.); Department of Cardiology, Hamamatsu Medical Center, Hamamatsu, Japan (M.H.); Cardiovascular Research Institute and Department of Pharmacology, Harbin Medical University, Harbin, People’s Republic of China (X.L.; B.Y.); Department of Cardiology, Nagoya University Graduate School of Medicine, Nagoya, Japan (T.M.); and Institute of Pharmacology, Faculty
| | - Dobromir Dobrev
- From the Department of Medicine and Research Center, Montreal Heart Institute and Université de Montréal, Montreal, Quebec, Canada (M.H., X.L., S.N.); Department of Cardiology, Hamamatsu Medical Center, Hamamatsu, Japan (M.H.); Cardiovascular Research Institute and Department of Pharmacology, Harbin Medical University, Harbin, People’s Republic of China (X.L.; B.Y.); Department of Cardiology, Nagoya University Graduate School of Medicine, Nagoya, Japan (T.M.); and Institute of Pharmacology, Faculty
| | - Stanley Nattel
- From the Department of Medicine and Research Center, Montreal Heart Institute and Université de Montréal, Montreal, Quebec, Canada (M.H., X.L., S.N.); Department of Cardiology, Hamamatsu Medical Center, Hamamatsu, Japan (M.H.); Cardiovascular Research Institute and Department of Pharmacology, Harbin Medical University, Harbin, People’s Republic of China (X.L.; B.Y.); Department of Cardiology, Nagoya University Graduate School of Medicine, Nagoya, Japan (T.M.); and Institute of Pharmacology, Faculty
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160
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Song SJ, Ito K, Ala U, Kats L, Webster K, Sun SM, Jongen-Lavrencic M, Manova-Todorova K, Teruya-Feldstein J, Avigan DE, Delwel R, Pandolfi PP. The oncogenic microRNA miR-22 targets the TET2 tumor suppressor to promote hematopoietic stem cell self-renewal and transformation. Cell Stem Cell 2014; 13:87-101. [PMID: 23827711 DOI: 10.1016/j.stem.2013.06.003] [Citation(s) in RCA: 258] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Revised: 03/07/2013] [Accepted: 06/11/2013] [Indexed: 12/21/2022]
Abstract
MicroRNAs are frequently deregulated in cancer. Here we show that miR-22 is upregulated in myelodysplastic syndrome (MDS) and leukemia and its aberrant expression correlates with poor survival. To explore its role in hematopoietic stem cell function and malignancy, we generated transgenic mice conditionally expressing miR-22 in the hematopoietic compartment. These mice displayed reduced levels of global 5-hydroxymethylcytosine (5-hmC) and increased hematopoietic stem cell self-renewal accompanied by defective differentiation. Conversely, miR-22 inhibition blocked proliferation in both mouse and human leukemic cells. Over time, miR-22 transgenic mice developed MDS and hematological malignancies. We also identify TET2 as a key target of miR-22 in this context. Ectopic expression of TET2 suppressed the miR-22-induced phenotypes. Downregulation of TET2 protein also correlated with poor clinical outcomes and miR-22 overexpression in MDS patients. Our results therefore identify miR-22 as a potent proto-oncogene and suggest that aberrations in the miR-22/TET2 regulatory network are common in hematopoietic malignancies.
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Affiliation(s)
- Su Jung Song
- Cancer Genetics Program, Beth Israel Deaconess Cancer Center, Harvard Medical School, Boston, MA 02215, USA
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161
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Plowright AT, Engkvist O, Gill A, Knerr L, Wang QD. Heart regeneration: opportunities and challenges for drug discovery with novel chemical and therapeutic methods or agents. Angew Chem Int Ed Engl 2014; 53:4056-75. [PMID: 24470316 DOI: 10.1002/anie.201307034] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Indexed: 12/11/2022]
Abstract
Following a heart attack, more than a billion cardiac muscle cells (cardiomyocytes) can be killed, leading to heart failure and sudden death. Much research in this area is now focused on the regeneration of heart tissue through differentiation of stem cells, proliferation of existing cardiomyocytes and cardiac progenitor cells, and reprogramming of fibroblasts into cardiomyocytes. Different chemical modalities (i.e. methods or agents), ranging from small molecules and RNA approaches (including both microRNA and anti-microRNA) to modified peptides and proteins, are showing potential to meet this medical need. In this Review, we outline the recent advances in these areas and describe both the modality and progress, including novel screening strategies to identify hits, and the upcoming challenges and opportunities to develop these hits into pharmaceuticals, at which chemistry plays a key role.
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Affiliation(s)
- Alleyn T Plowright
- Department of Medicinal Chemistry, Cardiovascular and Metabolic Diseases Innovative Medicines, AstraZeneca, Pepparedsleden 1, Mölndal, 43183 (Sweden).
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162
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Plowright AT, Engkvist O, Gill A, Knerr L, Wang QD. Herzregeneration: Chancen und Aufgaben für die Wirkstoff-Forschung mit neuartigen chemischen und therapeutischen Methoden oder Agentien. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201307034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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163
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Picelli S, Faridani OR, Björklund AK, Winberg G, Sagasser S, Sandberg R. Full-length RNA-seq from single cells using Smart-seq2. Nat Protoc 2014; 9:171-81. [PMID: 24385147 DOI: 10.1038/nprot.2014.006] [Citation(s) in RCA: 2533] [Impact Index Per Article: 253.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Emerging methods for the accurate quantification of gene expression in individual cells hold promise for revealing the extent, function and origins of cell-to-cell variability. Different high-throughput methods for single-cell RNA-seq have been introduced that vary in coverage, sensitivity and multiplexing ability. We recently introduced Smart-seq for transcriptome analysis from single cells, and we subsequently optimized the method for improved sensitivity, accuracy and full-length coverage across transcripts. Here we present a detailed protocol for Smart-seq2 that allows the generation of full-length cDNA and sequencing libraries by using standard reagents. The entire protocol takes ∼2 d from cell picking to having a final library ready for sequencing; sequencing will require an additional 1-3 d depending on the strategy and sequencer. The current limitations are the lack of strand specificity and the inability to detect nonpolyadenylated (polyA(-)) RNA.
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Affiliation(s)
| | | | - Asa K Björklund
- 1] Ludwig Institute for Cancer Research, Stockholm, Sweden. [2] Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Gösta Winberg
- 1] Ludwig Institute for Cancer Research, Stockholm, Sweden. [2] Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Sven Sagasser
- 1] Ludwig Institute for Cancer Research, Stockholm, Sweden. [2] Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Rickard Sandberg
- 1] Ludwig Institute for Cancer Research, Stockholm, Sweden. [2] Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
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164
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Wu H, Kong L, Zhou S, Cui W, Xu F, Luo M, Li X, Tan Y, Miao L. The role of microRNAs in diabetic nephropathy. J Diabetes Res 2014; 2014:920134. [PMID: 25258717 PMCID: PMC4165734 DOI: 10.1155/2014/920134] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Accepted: 07/29/2014] [Indexed: 01/27/2023] Open
Abstract
Diabetic nephropathy (DN), as one of the chronic complications of diabetes, is the major cause of end-stage renal disease. However, the pathogenesis of this disease is not fully understood. In recent years, research on microRNAs (miRNAs) has become a hotspot because of their critical role in regulating posttranscriptional levels of protein-coding genes that may serve as key pathogenic factors in diseases. Several miRNAs were found to participate in the pathogenesis of DN, while others showed renal protective effects. Therefore, targeting miRNAs that are involved in DN may have a good prospect in the treatment of the disease. The aim of this review is to summarize DN-related miRNAs and provide potential targets for diagnostic strategies and therapeutic intervention.
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Affiliation(s)
- Hao Wu
- Department of Nephrology, The Second Hospital of Jilin University, 218 Ziqiang Street, Changchun 130041, China
- Chinese-American Research Institute for Diabetic Complications at Wenzhou Medical University, Wenzhou 325035, China
- Kosair Children's Hospital Research Institute, Department of Pediatrics, University of Louisville, Louisville, KY 40202, USA
| | - Lili Kong
- Department of Nephrology, The Second Hospital of Jilin University, 218 Ziqiang Street, Changchun 130041, China
- Kosair Children's Hospital Research Institute, Department of Pediatrics, University of Louisville, Louisville, KY 40202, USA
| | - Shanshan Zhou
- Kosair Children's Hospital Research Institute, Department of Pediatrics, University of Louisville, Louisville, KY 40202, USA
- Cardiovascular Center, The First Hospital of Jilin University, Changchun 130021, China
| | - Wenpeng Cui
- Department of Nephrology, The Second Hospital of Jilin University, 218 Ziqiang Street, Changchun 130041, China
| | - Feng Xu
- Department of Nephrology, The Second Hospital of Jilin University, 218 Ziqiang Street, Changchun 130041, China
| | - Manyu Luo
- Department of Nephrology, The Second Hospital of Jilin University, 218 Ziqiang Street, Changchun 130041, China
- Kosair Children's Hospital Research Institute, Department of Pediatrics, University of Louisville, Louisville, KY 40202, USA
| | - Xiangqi Li
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Shanghai 200031, China
| | - Yi Tan
- Chinese-American Research Institute for Diabetic Complications at Wenzhou Medical University, Wenzhou 325035, China
- Kosair Children's Hospital Research Institute, Department of Pediatrics, University of Louisville, Louisville, KY 40202, USA
- *Yi Tan: and
| | - Lining Miao
- Department of Nephrology, The Second Hospital of Jilin University, 218 Ziqiang Street, Changchun 130041, China
- *Lining Miao:
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165
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Li Z, Lech CJ, Phan AT. Sugar-modified G-quadruplexes: effects of LNA-, 2'F-RNA- and 2'F-ANA-guanosine chemistries on G-quadruplex structure and stability. Nucleic Acids Res 2013; 42:4068-79. [PMID: 24371274 PMCID: PMC3973314 DOI: 10.1093/nar/gkt1312] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
G-quadruplex-forming oligonucleotides containing modified nucleotide chemistries have demonstrated promising pharmaceutical potential. In this work, we systematically investigate the effects of sugar-modified guanosines on the structure and stability of a (4+0) parallel and a (3+1) hybrid G-quadruplex using over 60 modified sequences containing a single-position substitution of 2′-O-4′-C-methylene-guanosine (LNAG), 2′-deoxy-2′-fluoro-riboguanosine (FG) or 2′-deoxy-2′-fluoro-arabinoguanosine (FANAG). Our results are summarized in two parts: (I) Generally, LNAG substitutions into ‘anti’ position guanines within a guanine-tetrad lead to a more stable G-quadruplex, while substitutions into ‘syn’ positions disrupt the native G-quadruplex conformation. However, some interesting exceptions to this trend are observed. We discover that a LNAG modification upstream of a short propeller loop hinders G-quadruplex formation. (II) A single substitution of either FG or FANAG into a ‘syn’ position is powerful enough to perturb the (3+1) G-quadruplex. Substitution of either FG or FANAG into any ‘anti’ position is well tolerated in the two G-quadruplex scaffolds. FANAG substitutions to ‘anti’ positions are better tolerated than their FG counterparts. In both scaffolds, FANAG substitutions to the central tetrad layer are observed to be the most stabilizing. The observations reported herein on the effects of LNAG, FG and FANAG modifications on G-quadruplex structure and stability will enable the future design of pharmaceutically relevant oligonucleotides.
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Affiliation(s)
- Zhe Li
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371
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166
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Fernandes SA, Douglas AGL, Varela MA, Wood MJA, Aoki Y. Oligonucleotide-Based Therapy for FTD/ALS Caused by the C9orf72 Repeat Expansion: A Perspective. J Nucleic Acids 2013; 2013:208245. [PMID: 24349764 PMCID: PMC3855979 DOI: 10.1155/2013/208245] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 09/19/2013] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive and lethal disease of motor neuron degeneration, leading to paralysis of voluntary muscles and death by respiratory failure within five years of onset. Frontotemporal dementia (FTD) is characterised by degeneration of frontal and temporal lobes, leading to changes in personality, behaviour, and language, culminating in death within 5-10 years. Both of these diseases form a clinical, pathological, and genetic continuum of diseases, and this link has become clearer recently with the discovery of a hexanucleotide repeat expansion in the C9orf72 gene that causes the FTD/ALS spectrum, that is, c9FTD/ALS. Two basic mechanisms have been proposed as being potentially responsible for c9FTD/ALS: loss-of-function of the protein encoded by this gene (associated with aberrant DNA methylation) and gain of function through the formation of RNA foci or protein aggregates. These diseases currently lack any cure or effective treatment. Antisense oligonucleotides (ASOs) are modified nucleic acids that are able to silence targeted mRNAs or perform splice modulation, and the fact that they have proved efficient in repeat expansion diseases including myotonic dystrophy type 1 makes them ideal candidates for c9FTD/ALS therapy. Here, we discuss potential mechanisms and challenges for developing oligonucleotide-based therapy for c9FTD/ALS.
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Affiliation(s)
- Stephanie A. Fernandes
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
- Institute of Biosciences, University of Sao Paulo, Rua do Matao, 05508-090 Sao Paulo, SP, Brazil
| | - Andrew G. L. Douglas
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
| | - Miguel A. Varela
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
| | - Matthew J. A. Wood
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
| | - Yoshitsugu Aoki
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
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167
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Ruiz-Mirazo K, Briones C, de la Escosura A. Prebiotic Systems Chemistry: New Perspectives for the Origins of Life. Chem Rev 2013; 114:285-366. [DOI: 10.1021/cr2004844] [Citation(s) in RCA: 563] [Impact Index Per Article: 51.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kepa Ruiz-Mirazo
- Biophysics
Unit (CSIC-UPV/EHU), Leioa, and Department of Logic and Philosophy
of Science, University of the Basque Country, Avenida de Tolosa 70, 20080 Donostia−San Sebastián, Spain
| | - Carlos Briones
- Department
of Molecular Evolution, Centro de Astrobiología (CSIC−INTA, associated to the NASA Astrobiology Institute), Carretera de Ajalvir, Km 4, 28850 Torrejón de Ardoz, Madrid, Spain
| | - Andrés de la Escosura
- Organic
Chemistry Department, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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168
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Shigdar S, Macdonald J, O'Connor M, Wang T, Xiang D, Al.Shamaileh H, Qiao L, Wei M, Zhou SF, Zhu Y, Kong L, Bhattacharya S, Li C, Duan W. Aptamers as theranostic agents: modifications, serum stability and functionalisation. SENSORS 2013; 13:13624-37. [PMID: 24152925 PMCID: PMC3859083 DOI: 10.3390/s131013624] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 09/24/2013] [Accepted: 09/27/2013] [Indexed: 02/07/2023]
Abstract
Aptamers, and the selection process known as Systematic Evolution of Ligands by Exponential Enrichment (SELEX) used to generate them, were first described more than twenty years ago. Since then, there have been numerous modifications to the selection procedures. This review discusses the use of modified bases as a means of enhancing serum stability and producing effective therapeutic tools, as well as functionalising these nucleic acids to be used as potential diagnostic agents.
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Affiliation(s)
- Sarah Shigdar
- School of Medicine, Deakin University, Pigdons Road, Waurn Ponds, Victoria 3217, Australia; E-Mails: (J.M.); (M.O.); (T.W.); (D.X.); (H.A.)
- Authors to whom correspondence should be addressed; E-Mails: (S.S.); (W.D.)
| | - Joanna Macdonald
- School of Medicine, Deakin University, Pigdons Road, Waurn Ponds, Victoria 3217, Australia; E-Mails: (J.M.); (M.O.); (T.W.); (D.X.); (H.A.)
| | - Michael O'Connor
- School of Medicine, Deakin University, Pigdons Road, Waurn Ponds, Victoria 3217, Australia; E-Mails: (J.M.); (M.O.); (T.W.); (D.X.); (H.A.)
| | - Tao Wang
- School of Medicine, Deakin University, Pigdons Road, Waurn Ponds, Victoria 3217, Australia; E-Mails: (J.M.); (M.O.); (T.W.); (D.X.); (H.A.)
| | - Dongxi Xiang
- School of Medicine, Deakin University, Pigdons Road, Waurn Ponds, Victoria 3217, Australia; E-Mails: (J.M.); (M.O.); (T.W.); (D.X.); (H.A.)
| | - Hadi Al.Shamaileh
- School of Medicine, Deakin University, Pigdons Road, Waurn Ponds, Victoria 3217, Australia; E-Mails: (J.M.); (M.O.); (T.W.); (D.X.); (H.A.)
| | - Liang Qiao
- Storr Liver Unit, at the Westmead Millennium Institute, The University of Sydney at the Westmead Hospital, Westmead NSW 2145, Australia; E-Mail:
| | - Ming Wei
- School of Medical Science and Griffith Health Institute, Griffith University, Gold Coast Campus, Southport 4222, Australia; E-Mail:
| | - Shu-Feng Zhou
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL 33612, USA; E-Mail:
| | - Yimin Zhu
- Suzhou Key Laboratory of Nanobiomedicine, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, Jiangsu 215123, China; E-Mail:
| | - Lingxue Kong
- Institute for Frontier Materials, Deakin University, Waurn Ponds, Victoria 3217, Australia; E-Mail:
| | - Santanu Bhattacharya
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560 012, India; E-Mail:
| | - ChunGuang Li
- Centre for Complimentary Medicine Research, National Institute of Complementary Medicine, University of Western Sydney, Campbelltown Campus, Penrith, NSW 2751, Australia; E-Mail:
| | - Wei Duan
- School of Medicine, Deakin University, Pigdons Road, Waurn Ponds, Victoria 3217, Australia; E-Mails: (J.M.); (M.O.); (T.W.); (D.X.); (H.A.)
- Authors to whom correspondence should be addressed; E-Mails: (S.S.); (W.D.)
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169
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Zhu J, Fu H, Wu Y, Zheng X. Function of lncRNAs and approaches to lncRNA-protein interactions. SCIENCE CHINA-LIFE SCIENCES 2013; 56:876-85. [PMID: 24091684 DOI: 10.1007/s11427-013-4553-6] [Citation(s) in RCA: 254] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Accepted: 09/05/2013] [Indexed: 01/10/2023]
Abstract
Long non-coding RNAs (lncRNAs), which represent a new frontier in molecular biology, play important roles in regulating gene expression at epigenetic, transcriptional and post-transcriptional levels. More and more lncRNAs have been found to play important roles in normal cell physiological activities, and participate in the development of varieties of tumors and other diseases. Previously, we have only been able to determine the function of lncRNAs through multiple mechanisms, including genetic imprinting, chromatin remodeling, splicing regulation, mRNA decay, and translational regulation. Application of technological advances to research into the function of lncRNAs is extremely important. The major tools for exploring lncRNAs include microarrays, RNA sequencing (RNA-seq), Northern blotting, real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR), fluorescence in situ hybridization (FISH), RNA interference (RNAi), RNA-binding protein immunoprecipitation (RIP), chromatin isolation by RNA purification (ChIRP), crosslinking-immunopurification (CLIP), and bioinformatic prediction. In this review, we highlight the functions of lncRNAs, and advanced methods to research lncRNA-protein interactions.
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Affiliation(s)
- Juanjuan Zhu
- Institute of Radiation Medicine, Academy of Military Medical Sciences, Beijing, 100850, China
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170
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Chen R, D'Alessandro M, Lee C. miRNAs are required for generating a time delay critical for the circadian oscillator. Curr Biol 2013; 23:1959-68. [PMID: 24094851 DOI: 10.1016/j.cub.2013.08.005] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 02/04/2013] [Accepted: 08/02/2013] [Indexed: 10/26/2022]
Abstract
BACKGROUND Circadian clocks coordinate an organism's activities and regulate metabolic homeostasis in relation to daily environmental changes, most notably light/dark cycles. As in other organisms, the timekeeping mechanism in mammals depends on a self-sustaining transcriptional negative feedback loop with a built-in time delay in feedback inhibition. Although the time delay is essential for generating a slow, self-sustaining negative feedback loop with a period close to 24 hr, the exact mechanisms underlying the time delay are not known. RESULTS Here, we show that RNAi mediated by microRNAs (miRNAs) is an essential mechanism in generating the time delay. In Dicer-deficient (and thus miRNA-deficient) cells and mice, circadian rhythms were dramatically shortened (by ∼2 hr), although the rhythms remained robust. The period shortening was caused by faster PER1 and PER2 translation in the Dicer-deficient cells. We also identified three specific miRNAs that regulate Per expression and showed that knockdown of these miRNAs in wild-type cells also shortened the circadian period. CONCLUSIONS Consistent with the canonical function of miRNAs as translational modulators of target genes and their widespread roles in cell physiology, circadian rhythms are also modulated by miRNA-mediated RNAi acting on posttranscriptional regulation of key clock genes. Our present study definitively shows that RNAi is an important modulator of circadian rhythms by controlling the pace of PER synthesis and presents a novel layer of regulation for the clock.
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Affiliation(s)
- Rongmin Chen
- Department of Biomedical Sciences, Neuroscience Program, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL 32306, USA
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171
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A quencher-free molecular beacon design based on pyrene excimer fluorescence using pyrene-labeled UNA (unlocked nucleic acid). Bioorg Med Chem 2013; 21:6186-90. [DOI: 10.1016/j.bmc.2013.04.062] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 04/08/2013] [Accepted: 04/16/2013] [Indexed: 11/18/2022]
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172
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Picelli S, Björklund ÅK, Faridani OR, Sagasser S, Winberg G, Sandberg R. Smart-seq2 for sensitive full-length transcriptome profiling in single cells. Nat Methods 2013; 10:1096-8. [PMID: 24056875 DOI: 10.1038/nmeth.2639] [Citation(s) in RCA: 1540] [Impact Index Per Article: 140.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 07/17/2013] [Indexed: 12/25/2022]
Abstract
Single-cell gene expression analyses hold promise for characterizing cellular heterogeneity, but current methods compromise on either the coverage, the sensitivity or the throughput. Here, we introduce Smart-seq2 with improved reverse transcription, template switching and preamplification to increase both yield and length of cDNA libraries generated from individual cells. Smart-seq2 transcriptome libraries have improved detection, coverage, bias and accuracy compared to Smart-seq libraries and are generated with off-the-shelf reagents at lower cost.
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173
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Migawa MT, Prakash TP, Vasquez G, Seth PP, Swayze EE. Synthesis and biophysical properties of constrained D-altritol nucleic acids (cANA). Org Lett 2013; 15:4316-9. [PMID: 23937264 DOI: 10.1021/ol401730d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The first synthesis of constrained altritol nucleic acids (cANA) containing antisense oligonucleotides (ASOs) was carried out to ascertain how conformationally restricting the D-altritol backbone-containing ASO (Me-ANA) would affect their ability to form duplexes with RNA. It was found that the thermal stability was reduced (cANA/RNA -1.1 °C/modification) compared to DNA/RNA, suggesting the constrained system results in a small destabilizing perturbation in the duplex structure.
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Affiliation(s)
- Michael T Migawa
- Department of Medicinal Chemistry, Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, California 92010, USA.
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174
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Antisense therapy in neurology. J Pers Med 2013; 3:144-76. [PMID: 25562650 PMCID: PMC4251390 DOI: 10.3390/jpm3030144] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 07/26/2013] [Accepted: 07/29/2013] [Indexed: 12/12/2022] Open
Abstract
Antisense therapy is an approach to fighting diseases using short DNA-like molecules called antisense oligonucleotides. Recently, antisense therapy has emerged as an exciting and promising strategy for the treatment of various neurodegenerative and neuromuscular disorders. Previous and ongoing pre-clinical and clinical trials have provided encouraging early results. Spinal muscular atrophy (SMA), Huntington’s disease (HD), amyotrophic lateral sclerosis (ALS), Duchenne muscular dystrophy (DMD), Fukuyama congenital muscular dystrophy (FCMD), dysferlinopathy (including limb-girdle muscular dystrophy 2B; LGMD2B, Miyoshi myopathy; MM, and distal myopathy with anterior tibial onset; DMAT), and myotonic dystrophy (DM) are all reported to be promising targets for antisense therapy. This paper focuses on the current progress of antisense therapies in neurology.
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175
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De A, Souchelnytskyi S, van den Berg A, Carlen ET. Peptide nucleic acid (PNA)-DNA duplexes: comparison of hybridization affinity between vertically and horizontally tethered PNA probes. ACS APPLIED MATERIALS & INTERFACES 2013; 5:4607-4612. [PMID: 23668364 DOI: 10.1021/am4011429] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
We compare the PNA-DNA duplex hybridization characteristics of vertically tethered and new horizontally tethered PNA probes on solid surfaces. The horizontal 15-mer PNA probe has been synthesized with linker molecules attached at three locations (γ-points) positioned along the PNA backbone that provides covalent attachment of the probe with the backbone aligned parallel to the surface, which is important for DNA hybridization assays that use electric field effect sensors for detection. A radioactive labeled assay and real-time surface plasmon resonance (SPR) biosensor are used to assess the probe surface density, nonspecific binding, and DNA hybridization affinity, respectively, of the new PNA probe configuration. The estimated equilibrium dissociation constants of the horizontally tethered duplex and the vertically tethered duplex are of the same order of magnitude (KD ≈ 5 nM), which indicates a sufficient hybridization affinity for many electronic biosensors that benefit from the horizontal alignment, which minimizes the effects of counterion screening.
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177
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Amodio N, Di Martino MT, Neri A, Tagliaferri P, Tassone P. Non-coding RNA: a novel opportunity for the personalized treatment of multiple myeloma. Expert Opin Biol Ther 2013; 13 Suppl 1:S125-37. [PMID: 23692413 DOI: 10.1517/14712598.2013.796356] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
INTRODUCTION Increasing evidence indicates that non-coding RNAs (ncRNAs) are aberrantly expressed and/or functionally deregulated in hematological malignancies, including multiple myeloma. Harnessing these abnormalities by either replacing or inhibiting ncRNAs is emerging as novel therapeutic option. AREAS COVERED We review the recent remarkable advancement in the understanding of the biological functions of human ncRNAs in multiple myeloma, including the biogenesis, the mechanisms of expression, the relevance as biomarkers, and mostly, the therapeutic potential. Special emphasis is given to microRNAs, the best characterized class of ncRNAs. EXPERT OPINION An improved understanding of the role of ncRNAs in multiple myeloma would provide valuable information about key cancer-promoting pathways and might be highly useful for diagnostic and prognostic assessments. This knowledge might also lead to advancement in the management of multiple myeloma through the development of novel personalized ncRNA-based therapies.
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Affiliation(s)
- Nicola Amodio
- Magna Graecia University and T. Campanella Cancer Center, Department of Experimental and Clinical Medicine, Medical Oncology Unit, Viale Europa, 88100 Catanzaro, Italy
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178
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C3'-endo-puckered pyrrolidine containing PNA has favorable geometry for RNA binding: novel ethano locked PNA (ethano-PNA). Bioorg Med Chem 2013; 21:4092-101. [PMID: 23743441 DOI: 10.1016/j.bmc.2013.05.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Revised: 05/08/2013] [Accepted: 05/09/2013] [Indexed: 11/22/2022]
Abstract
A novel peptide nucleic acid (PNA) analogue is designed with a constraint in the aminoethyl segment of the aegPNA backbone so that the dihedral angle β is restricted within 60-80°, compatible to form PNA:RNA duplexes. The designed monomer is further functionalized with positively charged amino-/guanidino-groups. The appropriately protected monomers were synthesized and incorporated into aegPNA oligomers at predetermined positions and their binding abilities with cDNA and RNA were investigated. A single incorporation of the modified PNA monomer into a 12-mer PNA sequence resulted in stronger binding with complementary RNA over cDNA. No significant changes in the CD signatures of the derived duplexes of modified PNA with complementary RNA were observed.
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179
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Tomaselli S, Panera N, Gallo A, Alisi A. Circulating miRNA profiling to identify biomarkers of dysmetabolism. Biomark Med 2013; 6:729-42. [PMID: 23227838 DOI: 10.2217/bmm.12.91] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
During the last two decades, numerous efforts have been made to identify reliable and predictive noninvasive biomarkers to detect the early signs of metabolic disorders due to deregulation of lipid and glucose homeostasis. Several studies demonstrate that miRNAs--small noncoding RNAs involved in the regulation of gene expression--may play crucial roles in the control of metabolism. Alterations of miRNA levels often occur in metabolic disorders, both in specific tissues and plasma. Therefore, it is conceivable that the analysis of circulating miRNA profiles may improve not only the knowledge of miRNA-mediated mechanisms and effects in metabolism, but may also offer an alternative diagnostic tool. In the first part of this review we provide an overview of miRNA biogenesis and regulation, and experimental approaches for studying their expression levels. Afterwards, we discuss recent data regarding altered intracellular and circulating miRNAs associated with specific metabolic disorders.
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Affiliation(s)
- Sara Tomaselli
- RNA-Editing Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
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180
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Wang Q, Chen L, Long Y, Tian H, Wu J. Molecular beacons of xeno-nucleic acid for detecting nucleic acid. Theranostics 2013; 3:395-408. [PMID: 23781286 PMCID: PMC3677410 DOI: 10.7150/thno.5935] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 04/10/2013] [Indexed: 12/24/2022] Open
Abstract
Molecular beacons (MBs) of DNA and RNA have aroused increasing interest because they allow a continuous readout, excellent spatial and temporal resolution to observe in real time. This kind of dual-labeled oligonucleotide probes can differentiate between bound and unbound DNA/RNA in homogenous hybridization with a high signal-to-background ratio in living cells. This review briefly summarizes the different unnatural sugar backbones of oligonucleotides combined with fluorophores that have been employed to sense DNA/RNA. With different probes, we epitomize the fundamental understanding of driving forces and these recognition processes. Moreover, we will introduce a few novel and attractive emerging applications and discuss their advantages and disadvantages. We also highlight several perspective probes in the application of cancer therapeutics.
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181
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Suresh G, Priyakumar UD. Structures, dynamics, and stabilities of fully modified locked nucleic acid (β-D-LNA and α-L-LNA) duplexes in comparison to pure DNA and RNA duplexes. J Phys Chem B 2013; 117:5556-64. [PMID: 23617391 DOI: 10.1021/jp4016068] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Locked nucleic acid (LNA) is a chemical modification which introduces a -O-CH2- linkage in the furanose sugar of nucleic acids and blocks its conformation in a particular state. Two types of modifications, namely, 2'-O,4'-C-methylene-β-D-ribofuranose (β-D-LNA) and 2'-O,4'-C-methylene-α-L-ribofuranose (α-L-LNA), have been shown to yield RNA and DNA duplex-like structures, respectively. LNA modifications lead to increased melting temperatures of DNA and RNA duplexes, and have been suggested as potential therapeutic agents in antisense therapy. In this study, molecular dynamics (MD) simulations were performed on fully modified LNA duplexes and pure DNA and RNA duplexes sharing a similar sequence to investigate their structure, stabilities, and solvation properties. Both LNA duplexes undergo unwinding of the helical structure compared to the pure DNA and RNA duplexes. Though the α-LNA substituent has been proposed to mimic deoxyribose sugar in its conformational properties, the fully modified duplex was found to exhibit unique structural and dynamic properties with respect to the other three nucleic acid structures. Free energy calculations accurately capture the enhanced stabilization of the LNA duplex structures compared to DNA and RNA molecules as observed in experiments. π-stacking interaction between bases from complementary strands is shown to be one of the contributors to enhanced stabilization upon LNA substitution. A combination of two factors, namely, nature of the -O-CH2- linkage in the LNAs vs their absence in the pure duplexes and similar conformations of the sugar rings in DNA and α-LNA vs the other two, is suggested to contribute to the stark differences among the four duplexes studied here in terms of their structural, dynamic, and energetic properties.
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Affiliation(s)
- Gorle Suresh
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, India
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182
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Zhang L, Ren T, Tian J, Yang X, Zhou L, Li X. Excited State Properties of Naphtho-Homologated xxDNA Bases and Effect of Methanol Solution, Deoxyribose, and Base Pairing. J Phys Chem B 2013; 117:3983-92. [DOI: 10.1021/jp3123242] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Laibin Zhang
- School of
Physics and Engineering, Qufu Normal University, Qufu, 273165, P. R. China
| | - Tingqi Ren
- School of
Physics and Engineering, Qufu Normal University, Qufu, 273165, P. R. China
| | - Jianxiang Tian
- School of
Physics and Engineering, Qufu Normal University, Qufu, 273165, P. R. China
| | - Xiuqin Yang
- School of
Physics and Engineering, Qufu Normal University, Qufu, 273165, P. R. China
- State Key Laboratory of Crystal Materials, Shandong University, Jinan, 250100, P. R. China
| | - Liuzhu Zhou
- School of
Physics and Engineering, Qufu Normal University, Qufu, 273165, P. R. China
| | - Xiaoming Li
- School of
Physics and Engineering, Qufu Normal University, Qufu, 273165, P. R. China
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183
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Natural antisense transcript-targeted regulation of inducible nitric oxide synthase mRNA levels. Nitric Oxide 2013; 30:9-16. [DOI: 10.1016/j.niox.2013.01.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 12/26/2012] [Accepted: 01/14/2013] [Indexed: 12/27/2022]
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184
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Cao L, Xi Z. Fast thiol–maleamic methyl ester addition for facile covalent cross-linking of oligonucleotides. Tetrahedron Lett 2013. [DOI: 10.1016/j.tetlet.2013.01.112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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185
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Simonatto M, Barozzi I, Natoli G. Non-coding transcription at cis-regulatory elements: computational and experimental approaches. Methods 2013; 63:66-75. [PMID: 23542771 DOI: 10.1016/j.ymeth.2013.03.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 03/18/2013] [Accepted: 03/20/2013] [Indexed: 12/17/2022] Open
Abstract
Mammalian genomes are pervasively transcribed, generating mostly RNAs with no coding potential that display different size, structure and interspecies sequence conservation. A prominent contribution to the ncRNA pool comes from the transcription of cis-regulatory elements, namely promoters, enhancers and locus control regions. While this phenomenon has been extensively documented, possible roles of such ncRNAs in gene regulation are still unclear. Addressing this issue will require experimental strategies dealing with the low abundance of enhancer-templated ncRNAs and aimed at specifically dissecting the relative role of transcription per se vs. RNA products. In this review, we first focus on the identification and characterization of cis-regulatory elements, highlighting the differences between emerging classes of ncRNAs associated to specific chromatin signatures. We then discuss current experimental strategies to dissect the function of nc transcription and computational approaches to the analysis and classification of regulatory sequences identified in next-generation sequencing experiments.
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Affiliation(s)
- Marta Simonatto
- Department of Experimental Oncology, European Institute of Oncology (IEO), Via Adamello 16, 20139 Milan, Italy.
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186
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Abstract
This review summarizes the results of structural studies carried out with analogs of G-quadruplexes built from natural nucleotides. Several dozens of base-, sugar-, and phosphate derivatives of the biological building blocks have been incorporated into more than 50 potentially quadruplex forming DNA and RNA oligonucleotides and the stability and folding topology of the resultant intramolecular, bimolecular and tetramolecular architectures characterized. The TG4T, TG5T, the 15 nucleotide-long thrombin binding aptamer, and the human telomere repeat AG3(TTAG3)3 sequences were modified in most cases, and four guanine analogs can be noted as being particularly useful in structural studies. These are the fluorescent 2-aminopurine, the 8-bromo-, and 8-methylguanines, and the hypoxanthine. The latter three analogs stabilize a given fold in a mixture of structures making possible accurate structural determinations by circular dichroism and nuclear magnetic resonance measurements.
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Affiliation(s)
- Janos Sagi
- a Rimstone Laboratory , RLI, 29 Lancaster Way, Cheshire , CT , 06410 , USA
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187
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Martin JA, Parekh P, Kim Y, Morey TE, Sefah K, Gravenstein N, Dennis DM, Tan W. Selection of an aptamer antidote to the anticoagulant drug bivalirudin. PLoS One 2013; 8:e57341. [PMID: 23483901 PMCID: PMC3590194 DOI: 10.1371/journal.pone.0057341] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Accepted: 01/21/2013] [Indexed: 11/18/2022] Open
Abstract
Adverse drug reactions, including severe patient bleeding, may occur following the administration of anticoagulant drugs. Bivalirudin is a synthetic anticoagulant drug sometimes employed as a substitute for heparin, a commonly used anticoagulant that can cause a condition called heparin-induced thrombocytopenia (HIT). Although bivalrudin has the advantage of not causing HIT, a major concern is lack of an antidote for this drug. In contrast, medical professionals can quickly reverse the effects of heparin using protamine. This report details the selection of an aptamer to bivalirudin that functions as an antidote in buffer. This was accomplished by immobilizing the drug on a monolithic column to partition binding sequences from nonbinding sequences using a low-pressure chromatography system and salt gradient elution. The elution profile of binding sequences was compared to that of a blank column (no drug), and fractions with a chromatographic difference were analyzed via real-time PCR (polymerase chain reaction) and used for further selection. Sequences were identified by 454 sequencing and demonstrated low micromolar dissociation constants through fluorescence anisotropy after only two rounds of selection. One aptamer, JPB5, displayed a dose-dependent reduction of the clotting time in buffer, with a 20 µM aptamer achieving a nearly complete antidote effect. This work is expected to result in a superior safety profile for bivalirudin, resulting in enhanced patient care.
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Affiliation(s)
- Jennifer A. Martin
- Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center and Center for Research at the Bio/nano Interface, University of Florida, Gainesville, Florida, United States of America
| | - Parag Parekh
- Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center and Center for Research at the Bio/nano Interface, University of Florida, Gainesville, Florida, United States of America
| | - Youngmi Kim
- Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center and Center for Research at the Bio/nano Interface, University of Florida, Gainesville, Florida, United States of America
| | - Timothy E. Morey
- Department of Anesthesiology and Pharmacology, University of Florida, Gainesville, Florida, United States of America
| | - Kwame Sefah
- Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center and Center for Research at the Bio/nano Interface, University of Florida, Gainesville, Florida, United States of America
| | - Nikolaus Gravenstein
- Department of Anesthesiology and Pharmacology, University of Florida, Gainesville, Florida, United States of America
| | - Donn M. Dennis
- Department of Anesthesiology and Pharmacology, University of Florida, Gainesville, Florida, United States of America
| | - Weihong Tan
- Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center and Center for Research at the Bio/nano Interface, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
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188
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Gene silencing by chemically modified siRNAs. N Biotechnol 2013; 30:302-7. [DOI: 10.1016/j.nbt.2012.07.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 07/09/2012] [Accepted: 07/10/2012] [Indexed: 12/11/2022]
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189
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Sharma P, Lait LA, Wetmore SD. yDNA versus yyDNA pyrimidines: computational analysis of the effects of unidirectional ring expansion on the preferred sugar-base orientation, hydrogen-bonding interactions and stacking abilities. Phys Chem Chem Phys 2013; 15:2435-48. [PMID: 23303174 DOI: 10.1039/c2cp43910g] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The properties of natural, y- and yy-pyrimidines are compared using computational (B3LYP, MP2) methods. Ring expansion upon incorporation of benzene or naphthalene into the natural pyrimidines affects the preferred orientation of the base about the glycosidic bond in the corresponding nucleoside to a similar extent. Specifically, although the natural pyrimidines preferentially adopt the anti orientation with respect to the 2'-deoxyribose moiety, the expanded analogues will likely display (anti/syn) conformational heterogeneity, which may lead to alternate hydrogen-bonding modes in double-stranded duplexes. Nevertheless, the A:T Watson-Crick hydrogen-bond strengths do not significantly change upon base expansion, while the G:C interaction energy is slightly strengthened upon incorporation of either expanded pyrimidine. The largest effect of base expansion occurs in the stacking energies. Specifically, the maximum (most negative) stacking energies in isolated dimers formed by aligning the nucleobase centers of mass can be increased up to 45% by inclusion of a single y-pyrimidine and up to 55% by consideration of a yy-pyrimidine. Similar increases in the stacking interactions are found when a simplified duplex model composed of two stacked (hydrogen-bonded) base pairs is considered, where both the intrastrand and interstrand stacking interactions can be increased and the effects are more pronounced for the yy-pyrimidines. Moreover, the total stability (sum of all hydrogen-bonding and stacking interactions) is greater for duplexes containing expanded yy-pyrimidines compared to y-pyrimidines, which is mainly due to enhanced stacking interactions. Thus, our calculations suggest that multiple unidirectional increases in the size of the nucleobase spacer can continuously enhance the stability of expanded duplexes.
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Affiliation(s)
- Purshotam Sharma
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
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190
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Leu K, Kervio E, Obermayer B, Turk-MacLeod RM, Yuan C, Luevano JM, Chen E, Gerland U, Richert C, Chen IA. Cascade of reduced speed and accuracy after errors in enzyme-free copying of nucleic acid sequences. J Am Chem Soc 2013; 135:354-66. [PMID: 23259600 PMCID: PMC3557965 DOI: 10.1021/ja3095558] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nonenzymatic, template-directed synthesis of nucleic acids is a paradigm for self-replicating systems. The evolutionary dynamics of such systems depend on several factors, including the mutation rates, relative replication rates, and sequence characteristics of mutant sequences. We measured the kinetics of correct and incorrect monomer insertion downstream of a primer-template mismatch (mutation), using a range of backbone structures (RNA, DNA, and LNA templates and RNA and DNA primers) and two types of 5'-activated nucleotides (oxyazabenzotriazolides and imidazolides, i.e., nucleoside 5'-phosphorimidazolides). Our study indicated that for all systems studied, an initial mismatch was likely to be followed by another error (54-75% of the time), and extension after a single mismatch was generally 10-100 times slower than extension without errors. If the mismatch was followed by a matched base pair, the extension rate recovered to nearly normal levels. On the basis of these data, we simulated nucleic acid replication in silico, which indicated that a primer suffering an initial error would lag behind properly extended counterparts due to a cascade of subsequent errors and kinetic stalling, with the typical mutational event consisting of several consecutive errors. Our study also included different sequence contexts, which suggest the presence of cooperativity among monomers affecting both absolute rate (by up to 2 orders of magnitude) and fidelity. The results suggest that molecular evolution in enzyme-free replication systems would be characterized by large "leaps" through sequence space rather than isolated point mutations, perhaps enabling rapid exploration of diverse sequences. The findings may also be useful for designing self-replicating systems combining high fidelity with evolvability.
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Affiliation(s)
- Kevin Leu
- FAS Center for Systems Biology, Harvard University, Cambridge, MA, USA
| | - Eric Kervio
- Institute for Organic Chemistry, University of Stuttgart, Stuttgart, Germany
| | | | | | - Caterina Yuan
- FAS Center for Systems Biology, Harvard University, Cambridge, MA, USA
| | | | - Eric Chen
- FAS Center for Systems Biology, Harvard University, Cambridge, MA, USA
| | - Ulrich Gerland
- Physics Department and Center for Nanoscience, University of Munich, Munich, Germany
| | - Clemens Richert
- Institute for Organic Chemistry, University of Stuttgart, Stuttgart, Germany
| | - Irene A. Chen
- FAS Center for Systems Biology, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
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191
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Ulrich S, Dumy P, Boturyn D, Renaudet O. Engineering of biomolecules for sensing and imaging applications. J Drug Deliv Sci Technol 2013. [DOI: 10.1016/s1773-2247(13)50001-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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192
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Lau PS, Li Y. Exploration of structure-switching in the design of aptamer biosensors. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2013; 140:69-92. [PMID: 23851586 DOI: 10.1007/10_2013_223] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The process of "structure-switching" enables biomolecular switches to function as effective biosensing tools. Biomolecular switches can be activated or inactivated by binding to a specific target that triggers a precise conformational change in the biomolecules involved. Although many examples of aptamer-based biomolecular switches can be found in nature, substantial effort has been made in the last decade to engineer structure-switching aptamer sensors by coupling aptamers to a signal transduction method to generate a readout signal upon target binding to the aptamer domain. This chapter focuses on the progress of research on engineered structure-switching aptamer sensors. We begin by discussing the origin of the structure-switching aptamer design, highlight the key developments of structure-switching DNA aptamers for fluorescence-, electrochemistry-, and colorimetry-based detection, and introduce our recent efforts in exploring RNA aptamers to create structure-switching molecular sensors.
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Affiliation(s)
- Pui Sai Lau
- Department of Biochemistry and Biomedical Sciences, Department of Chemistry and Chemical Biology, and Michael D. DeGroote Infectious Disease Research Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
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193
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Abstract
Synthetic small interfering RNAs (siRNAs) have revolutionized functional genomics in mammalian cell cultures due to their reliability, efficiency, and ease of use. This success, however, has not fully translated into siRNA applications in vivo and in siRNA therapeutics where initial optimism has been dampened by a lack of efficient delivery strategies and reports of siRNA off-target effects and immunogenicity. Encouragingly, most aspects of siRNA behavior can be addressed by careful engineering of siRNAs incorporating beneficial chemical modifications into discrete nucleotide positions during siRNA synthesis. Here, we review the literature (Subheadings 1 -3) and provide a quick guide (Subheading 4) to how the performance of siRNA can be improved by chemical modification to suit specific applications in vitro and in vivo.
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Affiliation(s)
- Jesper B Bramsen
- Department of Molecular Biology and Genetics, Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, Aarhus, Denmark.
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194
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Siciliano V, Garzilli I, Fracassi C, Criscuolo S, Ventre S, di Bernardo D. MiRNAs confer phenotypic robustness to gene networks by suppressing biological noise. Nat Commun 2013; 4:2364. [PMID: 24077216 PMCID: PMC3836244 DOI: 10.1038/ncomms3364] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 07/26/2013] [Indexed: 01/23/2023] Open
Abstract
miRNAs are small non-coding RNAs able to modulate target gene expression. It has been postulated that miRNAs confer robustness to biological processes, but clear experimental evidence is still missing. Here, using a synthetic biological approach, we demonstrate that microRNAs provide phenotypic robustness to transcriptional regulatory networks by buffering fluctuations in protein levels. We construct a network motif in mammalian cells exhibiting a 'toggle-switch' phenotype in which two alternative protein expression levels define its ON and OFF states. The motif consists of an inducible transcription factor that self-regulates its own transcription and that of a miRNA against the transcription factor itself. We confirm, using mathematical modelling and experimental approaches, that the microRNA confers robustness to the toggle-switch by enabling the cell to maintain and transmit its state. When absent, a dramatic increase in protein noise level occurs, causing the cell to randomly switch between the two states.
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Affiliation(s)
- Velia Siciliano
- Telethon Institute of Genetics and Medicine (TIGEM), Via P. Castellino 111, 80131, Naples, Italy
| | - Immacolata Garzilli
- Telethon Institute of Genetics and Medicine (TIGEM), Via P. Castellino 111, 80131, Naples, Italy
| | - Chiara Fracassi
- Telethon Institute of Genetics and Medicine (TIGEM), Via P. Castellino 111, 80131, Naples, Italy
| | - Stefania Criscuolo
- Telethon Institute of Genetics and Medicine (TIGEM), Via P. Castellino 111, 80131, Naples, Italy
| | - Simona Ventre
- Telethon Institute of Genetics and Medicine (TIGEM), Via P. Castellino 111, 80131, Naples, Italy
| | - Diego di Bernardo
- Telethon Institute of Genetics and Medicine (TIGEM), Via P. Castellino 111, 80131, Naples, Italy
- Dept. of Electrical Engineering and Information Technology, University of Naples FEDERICO II, Via Claudio 21, 80125
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195
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Abstract
MicroRNAs (miRNAs) have been uncovered as important posttranscriptional regulators of nearly every biological process in the cell. Furthermore, mounting evidence implies that miRNAs play key roles in the pathogenesis of cancer and that many miRNAs can function either as oncogenes or tumor suppressors. Thus, miRNAs have rapidly emerged as promising targets for the development of novel anticancer therapeutics. The development of miRNA-based cancer therapeutics relies on restoring the activity of tumor suppressor miRNAs using double-stranded miRNA mimics or inhibition of oncogenic miRNAs using single-stranded antisense oligonucleotides, termed antimiRs. In the present review, we focus on recent advancements in the discovery and development of miRNA-based cancer therapeutics using these 2 approaches. In addition, we summarize selected studies, in which modulation of miRNA activity in preclinical cancer models in vivo has demonstrated promising therapeutic potential.
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196
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Liu Y, Döring J, Hurek T. Bias in topoisomerase (TOPO)-cloning of multitemplate PCR products using locked nucleic acid (LNA)-substituted primers. J Microbiol Methods 2012; 91:483-6. [PMID: 23064262 DOI: 10.1016/j.mimet.2012.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 10/05/2012] [Accepted: 10/06/2012] [Indexed: 11/15/2022]
Abstract
Locked nucleic acid (LNA) modifications help to improve nucleic acid recognition in molecular biology applications. We report that LNA-substituted primers in PCR reactions may cause considerable cloning bias when the widely used topoisomerase-based ligation is used for cloning of multitemplate PCR products.
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Affiliation(s)
- Yuan Liu
- University of Bremen, Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), 28359 Bremen, Germany
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197
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Bramsen JB, Kjems J. Development of Therapeutic-Grade Small Interfering RNAs by Chemical Engineering. Front Genet 2012; 3:154. [PMID: 22934103 PMCID: PMC3422727 DOI: 10.3389/fgene.2012.00154] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 07/31/2012] [Indexed: 12/25/2022] Open
Abstract
Recent successes in clinical trials have provided important proof of concept that small interfering RNAs (siRNAs) indeed constitute a new promising class of therapeutics. Although great efforts are still needed to ensure efficient means of delivery in vivo, the siRNA molecule itself has been successfully engineered by chemical modification to meet initial challenges regarding specificity, stability, and immunogenicity. To date, a great wealth of siRNA architectures and types of chemical modification are available for promoting safe siRNA-mediated gene silencing in vivo and, consequently, the choice of design and modification types can be challenging to individual experimenters. Here we review the literature and devise how to improve siRNA performance by structural design and specific chemical modification to ensure potent and specific gene silencing without unwarranted side-effects and hereby complement the ongoing efforts to improve cell targeting and delivery by other carrier molecules.
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Affiliation(s)
- Jesper B Bramsen
- Interdisciplinary Nanoscience Center, Department of Molecular Biology and Genetics, Aarhus University Aarhus C, Denmark
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198
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Kimura Y, Hanami T, Tanaka Y, de Hoon MJL, Soma T, Harbers M, Lezhava A, Hayashizaki Y, Usui K. Effect of thiazole orange doubly labeled thymidine on DNA duplex formation. Biochemistry 2012; 51:6056-67. [PMID: 22765348 DOI: 10.1021/bi300293d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Nucleic acid oligonucleotides are widely used in hybridization experiments for specific detection of complementary nucleic acid sequences. For design and application of oligonucleotides, an understanding of their thermodynamic properties is essential. Recently, exciton-controlled hybridization-sensitive fluorescent oligonucleotides (ECHOs) were developed as uniquely labeled DNA oligomers containing commonly one thymidine having two covalently linked thiazole orange dye moieties. The fluorescent signal of an ECHO is strictly hybridization-controlled, where the dye moieties have to intercalate into double-stranded DNA for signal generation. Here we analyzed the hybridization thermodynamics of ECHO/DNA duplexes, and thermodynamic parameters were obtained from melting curves of 64 ECHO/DNA duplexes measured by ultraviolet absorbance and fluorescence. Both methods demonstrated a substantial increase in duplex stability (ΔΔG°(37) ~ -2.6 ± 0.7 kcal mol(-1)) compared to that of DNA/DNA duplexes of the same sequence. With the exception of T·G mismatches, this increased stability was mostly unaffected by other mismatches in the position opposite the labeled nucleotide. A nearest neighbor model was constructed for predicting thermodynamic parameters for duplex stability. Evaluation of the nearest neighbor parameters by cross validation tests showed higher predictive reliability for the fluorescence-based than the absorbance-based parameters. Using our experimental data, a tool for predicting the thermodynamics of formation of ECHO/DNA duplexes was developed that is freely available at http://genome.gsc.riken.jp/echo/thermodynamics/. It provides reliable thermodynamic data for using the unique features of ECHOs in fluorescence-based experiments.
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Affiliation(s)
- Yasumasa Kimura
- RIKEN Omics Science Center (OSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Yokohama, Kanagawa 230-0045, Japan.
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199
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Applications of peptide nucleic acids (PNAs) and locked nucleic acids (LNAs) in biosensor development. Anal Bioanal Chem 2012; 402:3071-89. [PMID: 22297860 DOI: 10.1007/s00216-012-5742-z] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Accepted: 01/12/2012] [Indexed: 01/06/2023]
Abstract
Nucleic acid biosensors have a growing number of applications in genetics and biomedicine. This contribution is a critical review of the current state of the art concerning the use of nucleic acid analogues, in particular peptide nucleic acids (PNA) and locked nucleic acids (LNA), for the development of high-performance affinity biosensors. Both PNA and LNA have outstanding affinity for natural nucleic acids, and the destabilizing effect of base mismatches in PNA- or LNA-containing heterodimers is much higher than in double-stranded DNA or RNA. Therefore, PNA- and LNA-based biosensors have unprecedented sensitivity and specificity, with special applicability in DNA genotyping. Herein, the most relevant PNA- and LNA-based biosensors are presented, and their advantages and their current limitations are discussed. Some of the reviewed technology, while promising, still needs to bridge the gap between experimental status and the harder reality of biotechnological or biomedical applications.
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200
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Rudnicki A, Avraham KB. microRNAs: the art of silencing in the ear. EMBO Mol Med 2012; 4:849-59. [PMID: 22745034 PMCID: PMC3491818 DOI: 10.1002/emmm.201100922] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Revised: 05/15/2012] [Accepted: 05/24/2012] [Indexed: 11/11/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression through the RNA interference (RNAi) pathway and by inhibition of mRNA translation. miRNAs first made their appearance in the auditory and vestibular systems in 2005, with the discovery of a triad of hair cell-specific miRNAs later found to be involved in both human and mouse deafness. Since then, miRNAs have been implicated in other medical conditions related to these systems, such as cholesteatomas, vestibular schwannomas and otitis media. Due to the limitations in studying miRNAs and their targets derived from human inner ears, animal models are vital in this field of research. Therefore their role in inner ear development and function has been demonstrated by studies in zebrafish and mice. Transcriptomic and proteomic approaches have been undertaken to identify miRNAs and their targets. Finally, it has been suggested that miRNAs may be used in the future in regeneration of inner ear hair cells and ultimately play a role in therapeutics.
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Affiliation(s)
- Anya Rudnicki
- Sackler Faculty of Medicine, Department of Human Molecular Genetics and Biochemistry, Tel Aviv University, Israel
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