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Canalis E, Yu J, Schilling L, Yee SP, Zanotti S. The lateral meningocele syndrome mutation causes marked osteopenia in mice. J Biol Chem 2018; 293:14165-14177. [PMID: 30042232 DOI: 10.1074/jbc.ra118.004242] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 07/11/2018] [Indexed: 12/26/2022] Open
Abstract
Lateral meningocele syndrome (LMS) is a rare genetic disorder characterized by neurological complications and osteoporosis. LMS is associated with mutations in exon 33 of NOTCH3 leading to a truncated protein lacking sequences for NOTCH3 degradation and presumably causing NOTCH3 gain of function. To create a mouse model reproducing human LMS-associated mutations, we utilized CRISPR/Cas9 to introduce a tandem termination codon at bases 6691-6696 (ACCAAG→TAATGA) and verified this mutation (Notch3tm1.1Ecan ) by DNA sequencing of F1 mice. One-month-old male and female heterozygous Notch3tm1.1Ecan mice had cancellous and cortical bone osteopenia but exhibited no obvious neurological alterations, and histopathology of multiple organs revealed no abnormalities. Microcomputed tomography of these mutants revealed a 35-60% decrease in cancellous bone volume associated with a reduction in trabecular number and decreased connectivity. During maturation, cancellous and cortical bones were restored in female but not in male mice, which exhibited cancellous bone osteopenia at 4 months. Cancellous bone histomorphometry revealed increased osteoblast and osteocyte numbers and a modest increase in osteoclast surface and bone formation rate. Notch3tm1.1Ecan calvarial osteoblasts had increased proliferation and increased bone γ-carboxyglutamate protein (Bglap) and TNF superfamily member 11 (Tnfsf11) mRNA levels and lower Tnfrsf11b levels. Tnfsf11 mRNA was increased in osteocyte-rich femora from Notch3tm1.1Ecan mice. Cultures of bone marrow-derived macrophages from Notch3tm1.1Ecan mice revealed increased osteoclast formation, particularly in cocultures with osteoblasts from Notch3tm1.1Ecan mice. In conclusion, the Notch3tm1.1Ecan mutation causes osteopenia despite an increase in osteoblast proliferation and function and is associated with enhanced Tnfsf11 expression in osteoblasts and osteocytes.
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Affiliation(s)
- Ernesto Canalis
- From the Departments of Orthopaedic Surgery, .,Medicine, and.,UConn Musculoskeletal Institute, and
| | - Jungeun Yu
- From the Departments of Orthopaedic Surgery.,UConn Musculoskeletal Institute, and
| | - Lauren Schilling
- From the Departments of Orthopaedic Surgery.,UConn Musculoskeletal Institute, and
| | - Siu-Pok Yee
- Cell Biology.,Center for Mouse Genome Modification, UConn Health, Farmington, Connecticut 06030
| | - Stefano Zanotti
- From the Departments of Orthopaedic Surgery.,Medicine, and.,UConn Musculoskeletal Institute, and
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52
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Sun L, Zhao Q. Direct fluorescence anisotropy approach for aflatoxin B1 detection and affinity binding study by using single tetramethylrhodamine labeled aptamer. Talanta 2018; 189:442-450. [PMID: 30086944 DOI: 10.1016/j.talanta.2018.07.036] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 07/07/2018] [Accepted: 07/11/2018] [Indexed: 12/20/2022]
Abstract
The discovery of aptamers for aflatoxin B1 (AFB1), one of toxic carcinogens, has allowed to develop aptamer-based sensors and assays for aflatoxin. In this work, we reported a direct fluorescence anisotropy (FA) assay for investigation of aptamer-AFB1 binding and detection of AFB1 with the aptamer having single tetramethylrhodamine (TMR) label on a specific site. From a series of labeling sites of a 50-mer aptamer, we screened out the aptamer with TMR labeling at the 26th T, capable of generating good and large FA-decreasing response to AFB1. By using the T26-labeled 50-mer aptamer probe in FA analysis, we determined the affinity and selectivity of aptamer, and identified the crucial region of aptamer and optimum experimental conditions for strong binding. The aptamer could be further truncated to as short as 26 nucleotides in length, and this shorter aptamer possessed a simple stem-loop secondary structure and retained good binding affinity. Nucleotides in the loop region of the aptamer were conserved and important for affinity recognition. We achieved FA detection of AFB1 with a detection limit about 2 nM by using the TMR-labeled aptamer probe. The cross reactivity of aflatoxin B1, aflatoxin B2, aflatoxin M1, aflatoxin M2, aflatoxin G1, and aflatoxin G2 with aptamer were estimated to be 100%, 61%, 23%, 21%, 6.3%, 6.5%, respectively. The aptamer probe presented good selectivity over other mycotoxins and showed potential in complex sample analysis. This study of affinity binding between aptamer and aflatoxins will be helpful for developing other aptamer-based assays and sensors for aflatoxins.
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Affiliation(s)
- Linlin Sun
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiang Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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53
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Taylor EL, Kesavan PM, Wolfe AE, O'Brien PJ. Distinguishing Specific and Nonspecific Complexes of Alkyladenine DNA Glycosylase. Biochemistry 2018; 57:4440-4454. [PMID: 29940097 DOI: 10.1021/acs.biochem.8b00531] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Human alkyladenine DNA glycosylase (AAG) recognizes many alkylated and deaminated purine lesions and excises them to initiate the base excision DNA repair pathway. AAG employs facilitated diffusion to rapidly scan nonspecific sites and locate rare sites of damage. Nonspecific DNA binding interactions are critical to the efficiency of this search for damage, but little is known about the binding footprint or the affinity of AAG for nonspecific sites. We used biochemical and biophysical approaches to characterize the binding of AAG to both undamaged and damaged DNA. Although fluorescence anisotropy is routinely used to study DNA binding, we found unexpected complexities in the data for binding of AAG to DNA. Systematic comparison of different fluorescent labels and different lengths of DNA allowed binding models to be distinguished and demonstrated that AAG can bind with high affinity and high density to nonspecific DNA. Fluorescein-labeled DNA gave the most complex behavior but also showed the greatest potential to distinguish specific and nonspecific binding modes. We suggest a unified model that is expected to apply to many DNA binding proteins that exhibit affinity for nonspecific DNA. Although AAG strongly prefers to excise lesions from duplex DNA, nonspecific binding is comparable for single- and double-stranded nonspecific sites. The electrostatically driven binding of AAG to small DNA sites (∼5 nucleotides of single-stranded and ∼6 base pairs of duplex) facilitates the search for DNA damage in chromosomal DNA, which is bound by nucleosomes and other proteins.
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Affiliation(s)
- Erin L Taylor
- Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Preethi M Kesavan
- Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Abigail E Wolfe
- Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Patrick J O'Brien
- Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
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54
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Real-time Detection and Monitoring of Loop Mediated Amplification (LAMP) Reaction Using Self-quenching and De-quenching Fluorogenic Probes. Sci Rep 2018; 8:5548. [PMID: 29615801 PMCID: PMC5883045 DOI: 10.1038/s41598-018-23930-1] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 03/22/2018] [Indexed: 01/09/2023] Open
Abstract
Loop-mediated isothermal amplification (LAMP) is an isothermal nucleic acid amplification (iNAAT) technique known for its simplicity, sensitivity and speed. Its low-cost feature has resulted in its wide scale application, especially in low resource settings. The major disadvantage of LAMP is its heavy reliance on indirect detection methods like turbidity and non-specific dyes, which often leads to the detection of false positive results. In the present work, we have developed a direct detection approach, whereby a labelled loop probe quenched in its unbound state, fluoresces only when bound to its target (amplicon). Henceforth, referred to as Fluorescence of Loop Primer Upon Self Dequenching-LAMP (FLOS-LAMP), it allows for the sequence-specific detection of LAMP amplicons. The FLOS-LAMP concept was validated for rapid detection of the human pathogen, Varicella-zoster virus, from clinical samples. The FLOS-LAMP had a limit of detection of 500 copies of the target with a clinical sensitivity and specificity of 96.8% and 100%, respectively. The high level of specificity is a major advance and solves one of the main shortcomings of the LAMP technology, i.e. false positives. Self-quenching/de-quenching probes were further used with other LAMP primer sets and different fluorophores, thereby demonstrating its versatility and adaptability.
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55
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Zanotti S, Yu J, Adhikari S, Canalis E. Glucocorticoids inhibit notch target gene expression in osteoblasts. J Cell Biochem 2018; 119:6016-6023. [PMID: 29575203 DOI: 10.1002/jcb.26798] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 02/20/2018] [Indexed: 12/13/2022]
Abstract
Glucocorticoids in excess suppress osteoblast function and cause osteoporosis. We demonstrated that cortisol induces the expression of selected Notch receptors in osteoblasts, revealing a potential mechanism for the skeletal effects of glucocorticoids. However, it remains to be determined whether increased expression of Notch receptors results into enhanced signaling. Following activation of Notch, its intracellular domain (NICD) binds to the DNA-associated protein recombination signal binding protein for immunoglobulin kappa-J region (RBPJ) and induces the expression of target genes such as Hey1, Hey2, and HeyL. To determine whether glucocorticoids modulate Notch signaling in the skeleton, 1 month old wild-type mice were administered prednisolone or placebo and sacrificed after 72 h, and gene expression was analyzed in femoral bone. Prednisolone induced Tsc22d3, a glucocorticoid target gene, and suppressed Hey1 and HeyL expression, which is indicative of inhibited Notch receptor activity or direct Hey downregulation. To determine the mechanisms of Hey suppression, wild-type osteoblast-enriched cells were seeded on the Notch cognate ligand Delta-like (DLL)1 or transfected with constructs expressing the NOTCH1 NICD fragment and exposed to either cortisol or vehicle. Cortisol opposed the induction of mRNA and heterogeneous nuclear RNA for Hey1, Hey2, and HeyL by DLL1, but had no effect on mRNA stability, indicating that glucocorticoids inhibit Hey expression by transcriptional mechanisms. Transactivation studies and electrophoretic mobility shift assays revealed that cortisol did not oppose RBPJ-mediated transcription or RBPJ/DNA interactions, respectively. In conclusion, glucocorticoids suppress expression of Hey1, Hey2, and HeyL in osteoblasts by RBPJ-independent transcriptional mechanisms.
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Affiliation(s)
- Stefano Zanotti
- Department of Orthopaedic Surgery, UConn Health, Farmington, Connecticut.,Department of Medicine, UConn Health, Farmington, Connecticut.,UConn Musculoskeletal Institute, UConn Health, Farmington, Connecticut
| | - Jungeun Yu
- Department of Orthopaedic Surgery, UConn Health, Farmington, Connecticut.,UConn Musculoskeletal Institute, UConn Health, Farmington, Connecticut
| | | | - Ernesto Canalis
- Department of Orthopaedic Surgery, UConn Health, Farmington, Connecticut.,Department of Medicine, UConn Health, Farmington, Connecticut.,UConn Musculoskeletal Institute, UConn Health, Farmington, Connecticut
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56
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Yu J, Zanotti S, Schilling L, Schoenherr C, Economides AN, Sanjay A, Canalis E. Induction of the Hajdu-Cheney Syndrome Mutation in CD19 B Cells in Mice Alters B-Cell Allocation but Not Skeletal Homeostasis. THE AMERICAN JOURNAL OF PATHOLOGY 2018; 188:1430-1446. [PMID: 29545197 DOI: 10.1016/j.ajpath.2018.02.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 02/09/2018] [Accepted: 02/27/2018] [Indexed: 01/19/2023]
Abstract
Mice harboring Notch2 mutations replicating Hajdu-Cheney syndrome (Notch2tm1.1ECan) have osteopenia and exhibit an increase in splenic marginal zone B cells with a decrease in follicular B cells. Whether the altered B-cell allocation is responsible for the osteopenia of Notch2tm1.1ECan mutants is unknown. To determine the effect of NOTCH2 activation in B cells on splenic B-cell allocation and skeletal phenotype, a conditional-by-inversion (COIN) Hajdu-Cheney syndrome allele of Notch2 (Notch2[ΔPEST]COIN) was used. Cre recombination generates a permanent Notch2ΔPEST allele expressing a transcript for which sequences coding for the proline, glutamic acid, serine, and threonine-rich (PEST) domain are replaced by a stop codon. CD19-Cre drivers were backcrossed into Notch2[ΔPEST]COIN/[ΔPEST]COIN to generate CD19-specific Notch2ΔPEST/ΔPEST mutants and control Notch2[ΔPEST]COIN/[ΔPEST]COIN littermates. There was an increase in marginal zone B cells and a decrease in follicular B cells in the spleen of CD19Cre/WT;Notch2ΔPEST/ΔPEST mice, recapitulating the splenic phenotype of Notch2tm1.1ECan mice. The effect was reproduced when the NOTCH1 intracellular domain was induced in CD19-expressing cells (CD19Cre/WT;RosaNotch1/WT mice). However, neither CD19Cre/WT;Notch2ΔPEST/ΔPEST nor CD19Cre/WT;RosaNotch1/WT mice had a skeletal phenotype. Moreover, splenectomies in Notch2tm1.1ECan mice did not reverse their osteopenic phenotype. In conclusion, Notch2 activation in CD19-expressing cells determines B-cell allocation in the spleen but has no skeletal consequences.
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Affiliation(s)
- Jungeun Yu
- Department of Orthopaedic Surgery, UConn Health, Farmington, Connecticut; UConn Musculoskeletal Institute, UConn Health, Farmington, Connecticut
| | - Stefano Zanotti
- Department of Orthopaedic Surgery, UConn Health, Farmington, Connecticut; UConn Musculoskeletal Institute, UConn Health, Farmington, Connecticut; Department of Medicine, UConn Health, Farmington, Connecticut
| | - Lauren Schilling
- UConn Musculoskeletal Institute, UConn Health, Farmington, Connecticut
| | - Chris Schoenherr
- Genome Engineering Technologies, Regeneron Pharmaceuticals, Tarrytown, New York
| | - Aris N Economides
- Genome Engineering Technologies, Regeneron Pharmaceuticals, Tarrytown, New York
| | - Archana Sanjay
- Department of Orthopaedic Surgery, UConn Health, Farmington, Connecticut; UConn Musculoskeletal Institute, UConn Health, Farmington, Connecticut.
| | - Ernesto Canalis
- Department of Orthopaedic Surgery, UConn Health, Farmington, Connecticut; UConn Musculoskeletal Institute, UConn Health, Farmington, Connecticut; Department of Medicine, UConn Health, Farmington, Connecticut.
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57
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Oshima T, Ishiguro K, Suzuki T, Kawahara Y. Quantification of methylation efficiency at a specific N6-methyladenosine position in rRNA by using BNA probes. Chem Commun (Camb) 2018; 54:9627-9630. [DOI: 10.1039/c8cc03713b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Probes containing bridged nucleic acids (BNA) enable us to quantify methylation efficiency at m6A sites in rRNA with high accuracy.
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Affiliation(s)
- Takuya Oshima
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University
- Suita
- Japan
| | - Kensuke Ishiguro
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo
- Bunkyo-ku
- Tokyo 113-8656
- Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo
- Bunkyo-ku
- Tokyo 113-8656
- Japan
| | - Yukio Kawahara
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University
- Suita
- Japan
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58
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Kim HY, Li T, Jung C, Fu R, Cho DY, Park KS, Park HG. Universally applicable, quantitative PCR method utilizing fluorescent nucleobase analogs. RSC Adv 2018; 8:37391-37395. [PMID: 35557795 PMCID: PMC9089284 DOI: 10.1039/c8ra06675b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 10/28/2018] [Indexed: 11/21/2022] Open
Abstract
We herein describe a novel quantitative PCR (qPCR) method, which operates in both signal-off and on manners, by utilizing a unique property of fluorescent nucleobase analogs. The first, signal-off method is developed by designing the primers to contain pyrrolo-dC (PdC), one of the most common fluorescent nucleobase analogs. The specially designed single-stranded primer is extended to form double-stranded DNA during PCR and the fluorescence signal from the PdCs incorporated in the primer is accordingly reduced due to its conformation-dependent fluorescence properties. In addition, the second, signal-on method is devised by designing the primers to contain 5′-overhang sequences complementary to the PdC-incorporated DNA probes. At the initial phase, the PdC-incorporated DNA probes are hybridized to the 5′-overhang sequences of the primer, exhibiting the significantly quenched fluorescence signal, but are detached by either hydrolysis or strand displacement reaction during PCR, leading to the highly enhanced fluorescence signal. This method is more advanced than the first one since it produces signal-on fluorescence response and permits the use of a single PdC-incorporated DNA probe for the detection of multiple target nucleic acids, remarkably decreasing the assay cost. With these novel qPCR methods, we successfully quantified target nucleic acids derived from sexually transmitted disease (STD) pathogens with high accuracy. Importantly, the proposed strategies overcome the major drawbacks in the current SYBR Green and TaqMan probe-based qPCR methods such as low specificity and high assay cost. A novel quantitative PCR (qPCR) method was developed by utilizing a unique property of fluorescent nucleobase analogs (PdCs).![]()
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Affiliation(s)
- Hyo Yong Kim
- Department of Chemical and Biomolecular Engineering (BK21 Program)
- KAIST
- Daejeon 305-701
- Republic of Korea
| | - Taihua Li
- College of Biology and the Environment
- Co-Innovation Centre for Sustainable Forestry in Southern China
- Nanjing Forestry University
- Nanjing
- China
| | - Cheulhee Jung
- Department of Chemical and Biomolecular Engineering (BK21 Program)
- KAIST
- Daejeon 305-701
- Republic of Korea
| | - Rongzhan Fu
- Department of Chemical and Biomolecular Engineering (BK21 Program)
- KAIST
- Daejeon 305-701
- Republic of Korea
| | - Dae-Yeon Cho
- Labgenomics Clinical Research Institute
- Labgenomics Co. Ltd
- Yong-In
- Republic of Korea
| | - Ki Soo Park
- Department of Biological Engineering
- College of Engineering
- Konkuk University
- Seoul 05029
- Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK21 Program)
- KAIST
- Daejeon 305-701
- Republic of Korea
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59
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Wang B, Ren D, You Z, Yalikun Y, Tanaka Y. Ultrasensitive detection of nucleic acids based on dually enhanced fluorescence polarization. Analyst 2018; 143:3560-3569. [DOI: 10.1039/c8an00952j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Increase of the molecular volume and quenching effect induced by AuNP conjugation can both enhance the fluorescence polarization of Alexa488.
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Affiliation(s)
- Bin Wang
- State Key Laboratory of Precision Measurement Technology and Instruments
- Department of Precision Instrument
- Tsinghua University
- Beijing
- China
| | - Dahai Ren
- State Key Laboratory of Precision Measurement Technology and Instruments
- Department of Precision Instrument
- Tsinghua University
- Beijing
- China
| | - Zheng You
- State Key Laboratory of Precision Measurement Technology and Instruments
- Department of Precision Instrument
- Tsinghua University
- Beijing
- China
| | - Yaxiaer Yalikun
- Laboratory for Integrated Biodevice
- Quantitative Biology Center
- Osaka 565-0871
- Japan
| | - Yo Tanaka
- Laboratory for Integrated Biodevice
- Quantitative Biology Center
- Osaka 565-0871
- Japan
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60
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Yu J, Zanotti S, Walia B, Jellison E, Sanjay A, Canalis E. The Hajdu Cheney Mutation Is a Determinant of B-Cell Allocation of the Splenic Marginal Zone. THE AMERICAN JOURNAL OF PATHOLOGY 2017; 188:149-159. [PMID: 29037852 DOI: 10.1016/j.ajpath.2017.09.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/25/2017] [Accepted: 09/21/2017] [Indexed: 12/27/2022]
Abstract
The neurogenic locus notch homolog protein (Notch)-2 receptor is a determinant of B-cell allocation, and gain-of-NOTCH2-function mutations are associated with Hajdu-Cheney syndrome (HCS), a disease presenting with osteoporosis and acro-osteolysis. We generated a mouse model reproducing the HCS mutation (Notch2HCS), and heterozygous global mutant mice displayed gain-of-Notch2 function. In the mutant spleen, the characteristic perifollicular rim marking the marginal zone (MZ), which is the interface between the nonlymphoid red pulp and the lymphoid white pulp, merged with components of the white pulp. As a consequence, the MZ of Notch2HCS mice occupied most of the splenic structure. To explore the mechanisms involved, lymphocyte populations from the bone marrow and spleen were harvested from heterozygous Notch2HCS mice and sex-matched control littermates and analyzed by flow cytometry. Notch2HCS mice had an increase in CD21/35highCD23- splenic MZ B cells of approximately fivefold and a proportional decrease in splenic follicular B cells (CD21/35intCD23+) at 1, 2, and 12 months of age. Western blot analysis revealed that Notch2HCS mutant splenocytes had increased phospho-Akt and phospho-Jun N-terminal kinase, and gene expression analysis of splenic CD19+ B cells demonstrated induction of Hes1 and Hes5 in Notch2HCS mutants. Anti-Notch2 antibodies decreased MZ B cells in control and Notch2HCS mice. In conclusion, Notch2HCS mutant mice have increased mature B cells in the MZ of the spleen.
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Affiliation(s)
- Jungeun Yu
- Department of Orthopaedic Surgery, UConn Musculoskeletal Institute, Farmington, Connecticut
| | - Stefano Zanotti
- Department of Orthopaedic Surgery, UConn Musculoskeletal Institute, Farmington, Connecticut; Department of Medicine, UConn Musculoskeletal Institute, Farmington, Connecticut
| | - Bhavita Walia
- Department of Genetics and Developmental Biology, UConn Health, Farmington, Connecticut
| | - Evan Jellison
- Department of Immunology, UConn Health, Farmington, Connecticut
| | - Archana Sanjay
- Department of Orthopaedic Surgery, UConn Musculoskeletal Institute, Farmington, Connecticut.
| | - Ernesto Canalis
- Department of Orthopaedic Surgery, UConn Musculoskeletal Institute, Farmington, Connecticut; Department of Medicine, UConn Musculoskeletal Institute, Farmington, Connecticut.
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Zanotti S, Canalis E. Parathyroid hormone inhibits Notch signaling in osteoblasts and osteocytes. Bone 2017; 103:159-167. [PMID: 28676438 PMCID: PMC5568480 DOI: 10.1016/j.bone.2017.06.027] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 06/28/2017] [Accepted: 06/30/2017] [Indexed: 10/19/2022]
Abstract
Parathyroid hormone (PTH) and Notch receptors regulate bone formation by governing the function of osteoblastic cells. To determine whether PTH interacts with Notch signaling as a way to control osteoblast function, we tested the effects of PTH on Notch activity in osteoblast- and osteocyte-enriched cultures. Notch signaling was activated in osteoblast-enriched cells from wild-type C57BL/6J mice following exposure to the Notch ligand Delta-like (Dll)1 or by the transient transfection of the Notch intracellular domain (NICD), the transcriptionally active fragment of Notch1. To induce Notch signaling in osteocyte-enriched cultures, a murine model of Notch2 gain-of-function was used. PTH opposed the stimulatory effects of Dll1 on Hey1, Hey2 and HeyL mRNA levels in osteoblast-enriched cells and suppressed the expression of selected Notch target genes in osteocyte-enriched cultures, either under basal conditions or in the context of Notch2 gain-of-function. Induction of Notch signaling in osteocytes did not alter the inhibitory effect of PTH on Sost expression, but reduced the stimulation of Tnfsf11 mRNA levels by PTH. In agreement with these in vitro observations, male mice administered with PTH displayed suppressed Hey1 and HeyL expression in parietal bones. Transactivation experiments with a Notch reporter construct and electrophoretic mobility shift assays in osteoblast-enriched cells suggest that PTH acts by decreasing the capacity of Rbpjκ to bind to DNA. In conclusion, downregulation of Notch in osteoblasts and osteocytes may represent a mechanism contributing to the anabolic effects of PTH in bone.
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Affiliation(s)
- Stefano Zanotti
- Departments of Orthopaedic Surgery and Medicine, UConn Musculoskeletal Institute, UConn Health, Farmington, CT 06030-5456, USA.
| | - Ernesto Canalis
- Departments of Orthopaedic Surgery and Medicine, UConn Musculoskeletal Institute, UConn Health, Farmington, CT 06030-5456, USA
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62
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Jiang S, Hong F, Hu H, Yan H, Liu Y. Understanding the Elementary Steps in DNA Tile-Based Self-Assembly. ACS NANO 2017; 11:9370-9381. [PMID: 28813590 DOI: 10.1021/acsnano.7b04845] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Although many models have been developed to guide the design and implementation of DNA tile-based self-assembly systems with increasing complexity, the fundamental assumptions of the models have not been thoroughly tested. To expand the quantitative understanding of DNA tile-based self-assembly and to test the fundamental assumptions of self-assembly models, we investigated DNA tile attachment to preformed "multi-tile" arrays in real time and obtained the thermodynamic and kinetic parameters of single tile attachment in various sticky end association scenarios. With more sticky ends, tile attachment becomes more thermostable with an approximately linear decrease in the free energy change (more negative). The total binding free energy of sticky ends is partially compromised by a sequence-independent energy penalty when tile attachment forms a constrained configuration: "loop". The minimal loop is a 2 × 2 tetramer (Loop4). The energy penalty of loops of 4, 6, and 8 tiles was analyzed with the independent loop model assuming no interloop tension, which is generalizable to arbitrary tile configurations. More sticky ends also contribute to a faster on-rate under isothermal conditions when nucleation is the rate-limiting step. Incorrect sticky end contributes to neither the thermostability nor the kinetics. The thermodynamic and kinetic parameters of DNA tile attachment elucidated here will contribute to the future improvement and optimization of tile assembly modeling, precise control of experimental conditions, and structural design for error-free self-assembly.
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Affiliation(s)
- Shuoxing Jiang
- Center for Molecular Design and Biomimetics at the Biodesign Institute, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Fan Hong
- Center for Molecular Design and Biomimetics at the Biodesign Institute, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Huiyu Hu
- Center for Molecular Design and Biomimetics at the Biodesign Institute, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Hao Yan
- Center for Molecular Design and Biomimetics at the Biodesign Institute, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Yan Liu
- Center for Molecular Design and Biomimetics at the Biodesign Institute, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
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63
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A novel quantitative PCR mediated by high-fidelity DNA polymerase. Sci Rep 2017; 7:10365. [PMID: 28871131 PMCID: PMC5583327 DOI: 10.1038/s41598-017-10782-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 08/14/2017] [Indexed: 01/19/2023] Open
Abstract
The biggest challenge for accurate diagnosis of viral infectious disease is the high genetic variability of involved viruses, which affects amplification efficiency and results in low sensitivity and narrow spectrum. Here, we developed a new simple qPCR mediated by high-fidelity (HF) DNA polymerase. The new method utilizes an HFman probe and one primer. Fluorescent signal was generated from the 3'-5' hydrolysis of HFman probe by HF DNA polymerase before elongation initiation. Mismatches between probe/primer and template have less influence on the amplification efficiency of the new method. The new qPCR exhibited higher sensitivity and better adaptability to sequence variable templates than the conventional TaqMan probe based-qPCR in quantification of HIV-1 viral load. Further comparison with COBAS TaqMan HIV-1 Test (v2.0) showed a good correlation coefficient (R2 = 0.79) between both methods in quantification of HIV-1 viral load among 21 clinical samples. The characteristics of tolerance to variable templates and one probe-one primer system imply that the probe/primer design for the new method will be easier and more flexible than the conventional method for highly heterogeneous viruses. Therefore, the HF DNA polymerase-mediated qPCR method is a simple, sensitive and promising approach for the development of diagnostics for viral infectious diseases.
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Zanotti S, Yu J, Sanjay A, Schilling L, Schoenherr C, Economides AN, Canalis E. Sustained Notch2 signaling in osteoblasts, but not in osteoclasts, is linked to osteopenia in a mouse model of Hajdu-Cheney syndrome. J Biol Chem 2017; 292:12232-12244. [PMID: 28592489 DOI: 10.1074/jbc.m117.786129] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 06/05/2017] [Indexed: 12/19/2022] Open
Abstract
Individuals with Hajdu-Cheney syndrome (HCS) present with osteoporosis, and HCS is associated with NOTCH2 mutations causing deletions of the proline-, glutamic acid-, serine-, and threonine-rich (PEST) domain that are predicted to enhance NOTCH2 stability and cause gain-of-function. Previously, we demonstrated that mice harboring Notch2 mutations analogous to those in HCS (Notch2HCS) are severely osteopenic because of enhanced bone resorption. We attributed this phenotype to osteoclastic sensitization to the receptor activator of nuclear factor-κB ligand and increased osteoblastic tumor necrosis factor superfamily member 11 (Tnfsf11) expression. Here, to determine the individual contributions of osteoclasts and osteoblasts to HCS osteopenia, we created a conditional-by-inversion (Notch2COIN ) model in which Cre recombination generates a Notch2ΔPEST allele expressing a Notch2 mutant lacking the PEST domain. Germ line Notch2COIN inversion phenocopied the Notch2HCS mutant, validating the model. To activate Notch2 in osteoclasts or osteoblasts, Notch2COIN mice were bred with mice expressing Cre from the Lyz2 or the BGLAP promoter, respectively. These crosses created experimental mice harboring a Notch2ΔPEST allele in Cre-expressing cells and control littermates expressing a wild-type Notch2 transcript. Notch2COIN inversion in Lyz2-expressing cells had no skeletal consequences and did not affect the capacity of bone marrow macrophages to form osteoclasts in vitro In contrast, Notch2COIN inversion in osteoblasts led to generalized osteopenia associated with enhanced bone resorption in the cancellous bone compartment and with suppressed endocortical mineral apposition rate. Accordingly, Notch2 activation in osteoblast-enriched cultures from Notch2COIN mice induced Tnfsf11 expression. In conclusion, introduction of the HCS mutation in osteoblasts, but not in osteoclasts, causes osteopenia.
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Affiliation(s)
- Stefano Zanotti
- Department of Orthopaedic Surgery, UConn Health, Farmington, Connecticut 06030; Department of Medicine, UConn Health, Farmington, Connecticut 06030; UConn Musculoskeletal Institute, UConn Health, Farmington, Connecticut 06030
| | - Jungeun Yu
- Department of Orthopaedic Surgery, UConn Health, Farmington, Connecticut 06030; UConn Musculoskeletal Institute, UConn Health, Farmington, Connecticut 06030
| | - Archana Sanjay
- Department of Orthopaedic Surgery, UConn Health, Farmington, Connecticut 06030; UConn Musculoskeletal Institute, UConn Health, Farmington, Connecticut 06030
| | - Lauren Schilling
- UConn Musculoskeletal Institute, UConn Health, Farmington, Connecticut 06030
| | | | | | - Ernesto Canalis
- Department of Orthopaedic Surgery, UConn Health, Farmington, Connecticut 06030; Department of Medicine, UConn Health, Farmington, Connecticut 06030; UConn Musculoskeletal Institute, UConn Health, Farmington, Connecticut 06030.
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DNA secondary structure formation by DNA shuffling of the conserved domains of the Cry protein of Bacillus thuringiensis. BMC BIOPHYSICS 2017; 10:4. [PMID: 28540040 PMCID: PMC5441083 DOI: 10.1186/s13628-017-0036-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Accepted: 05/11/2017] [Indexed: 12/26/2022]
Abstract
Background The Cry toxins, or δ-endotoxins, are a diverse group of proteins produced by Bacillus thuringiensis. While DNA secondary structures are biologically relevant, it is unknown if such structures are formed in regions encoding conserved domains of Cry toxins under shuffling conditions. We analyzed 5 holotypes that encode Cry toxins and that grouped into 4 clusters according to their phylogenetic closeness. The mean number of DNA secondary structures that formed and the mean Gibbs free energy \documentclass[12pt]{minimal}
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\begin{document}$$ \left(\overline{\varDelta G}\right) $$\end{document}ΔG¯ were determined by an in silico analysis using different experimental DNA shuffling scenarios. In terms of spontaneity, shuffling efficiency was directly proportional to the formation of secondary structures but inversely proportional to ∆G. Results The results showed a shared thermodynamic pattern for each cluster and relationships among sequences that are phylogenetically close at the protein level. The regions of the cry11Aa, Ba and Bb genes that encode domain I showed more spontaneity and thus a greater tendency to form secondary structures (<∆G). In the region of domain III; this tendency was lower (>∆G) in the cry11Ba and Bb genes. Proteins that are phylogenetically closer to Cry11Ba and Cry11Bb, such as Cry2Aa and Cry18Aa, maintained the same thermodynamic pattern. More distant proteins, such as Cry1Aa, Cry1Ab, Cry30Aa and Cry30Ca, featured different thermodynamic patterns in their DNA. Conclusion These results suggest the presence of thermodynamic variations associated to the formation of secondary structures and an evolutionary relationship with regions that encode highly conserved domains in Cry proteins. The findings of this study may have a role in the in silico design of cry gene assembly by DNA shuffling techniques.
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Ni Y, Cao B, Ma T, Niu G, Huo Y, Huang J, Chen D, Liu Y, Yu B, Zhang MQ, Niu H. Super-resolution imaging of a 2.5 kb non-repetitive DNA in situ in the nuclear genome using molecular beacon probes. eLife 2017; 6. [PMID: 28485713 PMCID: PMC5433842 DOI: 10.7554/elife.21660] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 04/24/2017] [Indexed: 12/17/2022] Open
Abstract
High-resolution visualization of short non-repetitive DNA in situ in the nuclear genome is essential for studying looping interactions and chromatin organization in single cells. Recent advances in fluorescence in situ hybridization (FISH) using Oligopaint probes have enabled super-resolution imaging of genomic domains with a resolution limit of 4.9 kb. To target shorter elements, we developed a simple FISH method that uses molecular beacon (MB) probes to facilitate the probe-target binding, while minimizing non-specific fluorescence. We used three-dimensional stochastic optical reconstruction microscopy (3D-STORM) with optimized imaging conditions to efficiently distinguish sparsely distributed Alexa-647 from background cellular autofluorescence. Utilizing 3D-STORM and only 29–34 individual MB probes, we observed 3D fine-scale nanostructures of 2.5 kb integrated or endogenous unique DNA in situ in human or mouse genome, respectively. We demonstrated our MB-based FISH method was capable of visualizing the so far shortest non-repetitive genomic sequence in 3D at super-resolution. DOI:http://dx.doi.org/10.7554/eLife.21660.001
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Affiliation(s)
- Yanxiang Ni
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China.,MOE Key laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic and Systems Biology, TNLIST; School of Medicine, Tsinghua University, Beijing, China.,School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Bo Cao
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Tszshan Ma
- MOE Key laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic and Systems Biology, TNLIST; School of Medicine, Tsinghua University, Beijing, China
| | - Gang Niu
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China.,LemonData Biotech, Shenzhen, China.,Phil Rivers Technology, Beijing, China
| | - Yingdong Huo
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Jiandong Huang
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Danni Chen
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Yi Liu
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Bin Yu
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Michael Q Zhang
- MOE Key laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic and Systems Biology, TNLIST; School of Medicine, Tsinghua University, Beijing, China.,Department of Biological Sciences, Center for Systems Biology, The University of Texas at Dallas, Dallas, United States
| | - Hanben Niu
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
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Parvin N, Jin Q, Wei Y, Yu R, Zheng B, Huang L, Zhang Y, Wang L, Zhang H, Gao M, Zhao H, Hu W, Li Y, Wang D. Few-Layer Graphdiyne Nanosheets Applied for Multiplexed Real-Time DNA Detection. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2017; 29:1606755. [PMID: 28295711 DOI: 10.1002/adma.201606755] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 01/13/2017] [Indexed: 06/06/2023]
Abstract
Despite recent progress in 2D nanomaterials-based biosensing, it remains challenging to achieve sensitive and high selective detection. This study develops few-layer graphdiyne (GD) nanosheets (NSs) that are used as novel sensing platforms for a variety of fluorophores real-time detection of DNA with low background and high signal-to-noise ratio, which show a distinguished fluorescence quenching ability and different affinities toward single-stranded DNA and double-stranded DNA. Importantly, for the first time, a few-layer GD NSs-based multiplexed DNA sensor is developed.
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Affiliation(s)
- Nargish Parvin
- State Key Laboratory of Biochemical Engineering, CAS Center for Excellence in Nanoscience, Institute of Process Engineering, Chinese Academy of Sciences, No. 1 Beiertiao, Zhongguancun, Beijing, 100190, P. R. China
| | - Quan Jin
- State Key Laboratory of Biochemical Engineering, CAS Center for Excellence in Nanoscience, Institute of Process Engineering, Chinese Academy of Sciences, No. 1 Beiertiao, Zhongguancun, Beijing, 100190, P. R. China
| | - Yanze Wei
- Department of Physical Chemistry, School of Metallurgical and Ecological Engineering, University of Science and Technology Beijing, No. 30, Xueyuan Road, Haidian District, Beijing, 100083, P. R. China
| | - Ranbo Yu
- Department of Physical Chemistry, School of Metallurgical and Ecological Engineering, University of Science and Technology Beijing, No. 30, Xueyuan Road, Haidian District, Beijing, 100083, P. R. China
| | - Bing Zheng
- Institute of Advanced Materials, Nanjing Tech University, Chemical Engineering Block, 5 Xinmofan Road, Nanjing, 210009, China
| | - Ling Huang
- Institute of Advanced Materials, Nanjing Tech University, Chemical Engineering Block, 5 Xinmofan Road, Nanjing, 210009, China
| | - Ying Zhang
- School of Materials Science and Engineering, Nanjing University of Posts and Telecommunications, No. 9 Wenyuan Road, Nanjing, 210046, P. R. China
| | - Lianhui Wang
- School of Materials Science and Engineering, Nanjing University of Posts and Telecommunications, No. 9 Wenyuan Road, Nanjing, 210046, P. R. China
| | - Hua Zhang
- Center for Programmable Materials, School of Materials Science and Engineering, Nanyang Technological University, No. 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Mingyuan Gao
- Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun North First Street 2, 100190, Beijing, P. R. China
| | - Huijun Zhao
- Centre for Clean Environment and Energy, Gold Coast Campus, Griffith University, Queensland, 4222, Australia
| | - Wenping Hu
- Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Department of Chemistry, School of Science and Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, 92 Weijin Road, Nankai District, Tianjin, 300072, China
| | - Yuliang Li
- Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun North First Street 2, 100190, Beijing, P. R. China
| | - Dan Wang
- State Key Laboratory of Biochemical Engineering, CAS Center for Excellence in Nanoscience, Institute of Process Engineering, Chinese Academy of Sciences, No. 1 Beiertiao, Zhongguancun, Beijing, 100190, P. R. China
- Centre for Clean Environment and Energy, Gold Coast Campus, Griffith University, Queensland, 4222, Australia
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Canalis E, Sanjay A, Yu J, Zanotti S. An Antibody to Notch2 Reverses the Osteopenic Phenotype of Hajdu-Cheney Mutant Male Mice. Endocrinology 2017; 158:730-742. [PMID: 28323963 PMCID: PMC5460801 DOI: 10.1210/en.2016-1787] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 01/20/2017] [Indexed: 11/19/2022]
Abstract
Notch receptors play a central role in skeletal development and bone remodeling. Hajdu-Cheney syndrome (HCS), a disease characterized by osteoporosis and fractures, is associated with gain-of-NOTCH2 function mutations. To study HCS, we created a mouse model harboring a point 6955C>T mutation in the Notch2 locus upstream of the proline, glutamic acid, serine, and threonine domain, leading to a Q2319X change at the amino acid level. Notch2Q2319X heterozygous mutants exhibited cancellous and cortical bone osteopenia. Microcomputed tomography demonstrated that the cancellous and cortical osteopenic phenotype was reversed by the administration of antibodies generated against the negative regulatory region (NRR) of Notch2, previously shown to neutralize Notch2 activity. Bone histomorphometry revealed that anti-Notch2 NRR antibodies decreased the osteoclast number and eroded surface in cancellous bone of Notch2Q2319X mice. An increase in osteoclasts on the endocortical surface of Notch2Q2319X mice was not observed in the presence of anti-Notch2 NRR antibodies. The anti-Notch2 NRR antibody decreased the induction of Notch target genes and Tnfsf11 messenger RNA levels in bone extracts and osteoblasts from Notch2Q2319X mice. In vitro experiments demonstrated increased osteoclastogenesis in Notch2Q2319X mutants in response to macrophage colony-stimulating factor and receptor activator of nuclear factor-κB ligand, and these effects were suppressed by the anti-Notch2 NRR. In conclusion, Notch2Q2319X mice exhibit cancellous and cortical bone osteopenia that can be corrected by the administration of anti-Notch2 NRR antibodies.
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Affiliation(s)
- Ernesto Canalis
- Departments of Orthopaedic Surgery and
- Medicine and
- the UConn Musculoskeletal Institute, UConn Health, Farmington, Connecticut 06030
| | - Archana Sanjay
- Departments of Orthopaedic Surgery and
- the UConn Musculoskeletal Institute, UConn Health, Farmington, Connecticut 06030
| | - Jungeun Yu
- Departments of Orthopaedic Surgery and
- the UConn Musculoskeletal Institute, UConn Health, Farmington, Connecticut 06030
| | - Stefano Zanotti
- Departments of Orthopaedic Surgery and
- Medicine and
- the UConn Musculoskeletal Institute, UConn Health, Farmington, Connecticut 06030
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69
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Canalis E, Zanotti S. Hairy and Enhancer of Split-Related With YRPW Motif-Like (HeyL) Is Dispensable for Bone Remodeling in Mice. J Cell Biochem 2017; 118:1819-1826. [PMID: 28019674 DOI: 10.1002/jcb.25859] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 12/22/2016] [Indexed: 12/14/2022]
Abstract
Notch induces Hairy Enhancer of Split (Hes)1 and Hes-related with YRPW motif (Hey) Hey1, Hey2 and Hey-like (HeyL) expression in osteoblasts, but it is not known whether any of these target genes mediates the effect of Notch in the skeleton. We demonstrated that Notch1 activation in osteoblasts/osteocytes induces Hes1, Hey1, Hey2, and HeyL, but HeyL was induced to a greater extent than other target genes. To characterize HeyL null mice for their skeletal phenotype, microcomputed tomography (µCT) and histomorphometric analysis of HeyL null and sex-matched littermate controls was performed. µCT demonstrated modest cancellous bone osteopenia in 1 month old male mice and normal microarchitecture in 3 month old male HeyL null mice. Female HeyL null mice were not different from controls at either 1 or 3 months of age. Bone histomorphometry did not demonstrate differences between HeyL null mice of either sex and littermate controls. In conclusion, HeyL null mice do not exhibit an obvious skeletal phenotype demonstrating that HeyL is dispensable for skeletal homeostasis. J. Cell. Biochem. 118: 1819-1826, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Ernesto Canalis
- Departments of Orthopaedic Surgery and Medicine, and the UConn Musculoskeletal Institute, UConn Health, Farmington, Connecticut, 06030-5456
| | - Stefano Zanotti
- Departments of Orthopaedic Surgery and Medicine, and the UConn Musculoskeletal Institute, UConn Health, Farmington, Connecticut, 06030-5456
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Mathur D, Medintz IL. Analyzing DNA Nanotechnology: A Call to Arms For The Analytical Chemistry Community. Anal Chem 2017; 89:2646-2663. [DOI: 10.1021/acs.analchem.6b04033] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Divita Mathur
- College of Science, George Mason University, Fairfax, Virginia 22030, United States
- Center
for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Code 6900, Washington, D.C. 20375, United States
| | - Igor L. Medintz
- Center
for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Code 6900, Washington, D.C. 20375, United States
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Ali A, Kamra M, Roy S, Muniyappa K, Bhattacharya S. Enhanced G-Quadruplex DNA Stabilization and Telomerase Inhibition by Novel Fluorescein Derived Salen and Salphen Based Ni(II) and Pd(II) Complexes. Bioconjug Chem 2017; 28:341-352. [PMID: 28165710 DOI: 10.1021/acs.bioconjchem.6b00433] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Metal based salen complexes have been considered as an important scaffold toward targeting of DNA structures. In the present work, we have synthesized nickel(II) and palladium(II) salen and salphen complexes by using readily available fluorescein as the backbone to provide an extended aromatic surface. The metal complexes exhibit affinity toward the human telomeric G-quadruplex DNA with promising inhibition of telomerase activity. This has been ascertained by their efficiency in the long term cell proliferation assay which showed significant cancer cell toxicity in the presence of the metal complexes. Confocal microscopy showed cellular internalization followed by localization in the nucleus and mitochondria. Considerable population at the sub-G1 phase of the cell cycle showed cell death via apoptotic pathway.
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Affiliation(s)
| | | | | | | | - Santanu Bhattacharya
- Director's Research Unit, Indian Association for the Cultivation of Science , Kolkata 700 032, India
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72
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Wang J, Dong P, Wu W, Pan X, Liang X. High-throughput thermal stability assessment of DNA hairpins based on high resolution melting. J Biomol Struct Dyn 2016; 36:1-13. [PMID: 28024437 DOI: 10.1080/07391102.2016.1266967] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
On the basis of high-resolution melting, a high-throughput approach to measure melting temperatures (Tms) of short DNA hairpins was developed. With this method, Tms of thousands of triloop, tetraloop, and pentaloop hairpins involving various loop sequences and various closing base pairs (cbp) were obtained in hours. The stability of triloop hairpins decreased with the change of cbp (5'-3') in the order of c-g > g-c > t-a ≥ a-t, showing that the cbp of 5'-Pyr-Pur-3' (Pyr = pyrimidine, Pur = purine) contributed more stability than 5'-Pur-Pyr-3'. For tetraloop hairpins, GNNA, GNAB, and CNNG (N = A, G, C, or T; B = G, C, or T) were found to be highly stable irrespective of the cbp type. TNNA was also stable in both g-c and a-t families, while CGNA only in the c-g family. Pentaloop hairpins of cTGNAGg, cGNYNAg (Y = T or C) and cCGNNAg were exceptionally stable motifs. In most cases, pyrimidine-rich loops were more favorable to stabilize the whole structure than purine-rich ones. The present approach showed a good performance in assessing the thermal stability of large amounts of DNA hairpins comprehensively. These data are useful to understand the sequence dependence of the stability of DNA secondary structures and promising to improve the structure simulation by consummating basic databases.
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Affiliation(s)
- Jing Wang
- a College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
| | - Ping Dong
- a College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
| | - Wei Wu
- a College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
| | - Xiaoming Pan
- a College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
| | - Xingguo Liang
- a College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
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73
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Pyrrolidinyl peptide nucleic acid terminally labeled with fluorophore and end-stacking quencher as a probe for highly specific DNA sequence discrimination. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.10.040] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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74
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Stancescu M, Fedotova TA, Hooyberghs J, Balaeff A, Kolpashchikov DM. Nonequilibrium Hybridization Enables Discrimination of a Point Mutation within 5-40 °C. J Am Chem Soc 2016; 138:13465-13468. [PMID: 27681667 DOI: 10.1021/jacs.6b05628] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Detection of point mutations and single nucleotide polymorphisms in DNA and RNA has a growing importance in biology, biotechnology, and medicine. For the application at hand, hybridization assays are often used. Traditionally, they differentiate point mutations only at elevated temperatures (>40 °C) and in narrow intervals (ΔT = 1-10 °C). The current study demonstrates that a specially designed multistranded DNA probe can differentiate point mutations in the range of 5-40 °C. This unprecedentedly broad ambient-temperature range is enabled by a controlled combination of (i) nonequilibrium hybridization conditions and (ii) a mismatch-induced increase of equilibration time in respect to that of a fully matched complex, which we dub "kinetic inversion".
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Affiliation(s)
- Maria Stancescu
- Chemistry Department, University of Central Florida , Orlando, Florida 32816, United States
| | - Tatiana A Fedotova
- Chemistry Department, University of Central Florida , Orlando, Florida 32816, United States
| | - Jef Hooyberghs
- Flemish Institute for Technological Research, VITO , Boeretang 200, Mol B-2400, Belgium.,Theoretical Physics, Hasselt University, Campus Diepenbeek , Agoralaan - Building D, Diepenbeek B-3590, Belgium
| | - Alexander Balaeff
- NanoScience Technology Center , 12424 Research Parkway, Suite 400, Orlando, Florida 32826, United States
| | - Dmitry M Kolpashchikov
- Chemistry Department, University of Central Florida , Orlando, Florida 32816, United States.,National Center for Forensic Science and Burnett School of Biomedical Sciences, University of Central Florida , Orlando, Florida 32816, United States
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75
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Zhou W, Ding J, Liu J. 2-Aminopurine-modified DNA homopolymers for robust and sensitive detection of mercury and silver. Biosens Bioelectron 2016; 87:171-177. [PMID: 27551997 DOI: 10.1016/j.bios.2016.08.033] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 08/09/2016] [Accepted: 08/11/2016] [Indexed: 01/11/2023]
Abstract
Heavy metal detection is a key topic in analytical chemistry. DNA-based metal recognition has advanced significantly producing many specific metal ligands, such as thymine for Hg2+ and cytosine for Ag+. For practical applications, however, robust sensors that can work in a diverse range of salt concentrations need to be developed, while most current sensing strategies cannot meet this requirement. In this work, 2-aminopurine (2AP) is used as a fluorescence label embedded in the middle of four 10-mer DNA homopolymers. 2AP can be quenched up to 98% in these DNA without an external quencher. The interaction between 2AP and all common metal ions is studied systematically for both free 2AP base and 2AP embedded DNA homopolymers. With such low background, Hg2+ induces up to 14-fold signal enhancement for the poly-T DNA, and Ag+ enhances up to 10-fold for the poly-C DNA. A detection limit of 3nM is achieved for both metals. With these four probes, silver and mercury can be readily discriminated from the rest. A comparison with other signaling methods was made using fluorescence resonance energy transfer, graphene oxide, and SYBR Green I staining, respectively, confirming the robustness of the 2AP label. Detection of Hg2+ in Lake Huron water was also achieved with a similar sensitivity. This work has provided a comprehensive fundamental understanding of using 2AP as a label for metal detection, and has achieved the highest fluorescence enhancement for non-protein targets.
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Affiliation(s)
- Wenhu Zhou
- School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, 410013 China; Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L3G1 Canada
| | - Jinsong Ding
- School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, 410013 China
| | - Juewen Liu
- School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, 410013 China; Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L3G1 Canada.
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Lin YJ, Wu YC, Mani V, Huang ST, Huang CH, Hu YC, Peter Shan HC. Designing anthraquinone–pyrrole redox intercalating probes for electrochemical gene detection. Biosens Bioelectron 2016; 79:294-9. [DOI: 10.1016/j.bios.2015.12.042] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/30/2015] [Accepted: 12/15/2015] [Indexed: 10/22/2022]
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77
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Durand G, Dausse E, Goux E, Fiore E, Peyrin E, Ravelet C, Toulmé JJ. A combinatorial approach to the repertoire of RNA kissing motifs; towards multiplex detection by switching hairpin aptamers. Nucleic Acids Res 2016; 44:4450-9. [PMID: 27067541 PMCID: PMC4872101 DOI: 10.1093/nar/gkw206] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/15/2016] [Indexed: 01/22/2023] Open
Abstract
Loop–loop (also known as kissing) interactions between RNA hairpins are involved in several mechanisms in both prokaryotes and eukaryotes such as the regulation of the plasmid copy number or the dimerization of retroviral genomes. The stability of kissing complexes relies on loop parameters (base composition, sequence and size) and base combination at the loop–loop helix - stem junctions. In order to identify kissing partners that could be used as regulatory elements or building blocks of RNA scaffolds, we analysed a pool of 5.2 × 106 RNA hairpins with randomized loops. We identified more than 50 pairs of kissing RNA hairpins. Two kissing motifs, 5′CCNY and 5′RYRY, generate highly stable complexes with KDs in the low nanomolar range. Such motifs were introduced in the apical loop of hairpin aptamers that switch between unfolded and folded state upon binding to their cognate target molecule, hence their name aptaswitch. The aptaswitch–ligand complex is specifically recognized by a second RNA hairpin named aptakiss through loop–loop interaction. Taking advantage of our kissing motif repertoire we engineered aptaswitch–aptakiss modules for purine derivatives, namely adenosine, GTP and theophylline and demonstrated that these molecules can be specifically and simultaneously detected by surface plasmon resonance or by fluorescence anisotropy.
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Affiliation(s)
- Guillaume Durand
- University of Bordeaux, ARNA Laboratory, 146 rue Léo Saignat, 33076 Bordeaux, France Inserm U1212, 146 rue Léo Saignat, 33076 Bordeaux, France CNRS UMR5320, 146 rue Léo Saignat, 33076 Bordeaux, France
| | - Eric Dausse
- University of Bordeaux, ARNA Laboratory, 146 rue Léo Saignat, 33076 Bordeaux, France Inserm U1212, 146 rue Léo Saignat, 33076 Bordeaux, France CNRS UMR5320, 146 rue Léo Saignat, 33076 Bordeaux, France
| | - Emma Goux
- University Grenoble Alpes, Département de Pharmacochimie Moléculaire, CNRS UMR5063, 38400 St Martin d'Hères, France
| | - Emmanuelle Fiore
- University Grenoble Alpes, Département de Pharmacochimie Moléculaire, CNRS UMR5063, 38400 St Martin d'Hères, France
| | - Eric Peyrin
- University Grenoble Alpes, Département de Pharmacochimie Moléculaire, CNRS UMR5063, 38400 St Martin d'Hères, France
| | - Corinne Ravelet
- University Grenoble Alpes, Département de Pharmacochimie Moléculaire, CNRS UMR5063, 38400 St Martin d'Hères, France
| | - Jean-Jacques Toulmé
- University of Bordeaux, ARNA Laboratory, 146 rue Léo Saignat, 33076 Bordeaux, France Inserm U1212, 146 rue Léo Saignat, 33076 Bordeaux, France CNRS UMR5320, 146 rue Léo Saignat, 33076 Bordeaux, France
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78
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A Biofunctional Molecular Beacon for Detecting Single Base Mutations in Cancer Cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2016; 5:e302. [PMID: 27045206 PMCID: PMC5014519 DOI: 10.1038/mtna.2016.18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 02/09/2016] [Indexed: 12/22/2022]
Abstract
The development of a convenient and sensitive biosensing system to detect
specific DNA sequences is an important issue in the field of genetic disease
therapy. As a classic DNA detection technique, molecular beacon (MB) is often
used in the biosensing system. However, it has intrinsic drawbacks, including
high assay cost, complicated chemical modification, and operational complexity.
In this study, we developed a simple and cost-effective label-free
multifunctional MB (LMMB) by integrating elements of polymerization primer,
template, target recognition, and G-quadruplex into one entity to detect target
DNA. The core technique was accomplished by introducing a G-hairpin that
features fragments of both G-quadruplex and target DNA recognition in the
G-hairpin stem. Hybridization between LMMB and target DNA triggered
conformational change between the G-hairpin and the common C-hairpin, resulting
in significant SYBR-green signal amplification. The hybridization continues to
the isothermal circular strand-displacement polymerization and accumulation of
the double-stranded fragments, causing the uninterrupted extension of the LMMB
without a need of chemical modification and other assistant DNA sequences. The
novel and programmable LMMB could detect target DNA with sensitivity at 250
pmol/l with a linear range from 2 to 100 nmol/l and the relative standard
deviation of 7.98%. The LMMB could sense a single base mutation from the normal
DNA, and polymerase chain reaction (PCR) amplicons of the mutant-type cell line
from the wild-type one. The total time required for preparation and assaying was
only 25 minutes. Apparently, the LMMB shows great potential for detecting DNA
and its mutations in biosamples, and therefore it opens up a new prospect for
genetic disease therapy.
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79
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Prakash V, Saha S, Chakraborty K, Krishnan Y. Rational design of a quantitative, pH-insensitive, nucleic acid based fluorescent chloride reporter. Chem Sci 2016; 7:1946-1953. [PMID: 30050672 PMCID: PMC6042475 DOI: 10.1039/c5sc04002g] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 12/01/2015] [Indexed: 12/29/2022] Open
Abstract
Chloride plays a major role in cellular homeostasis by regulating the lumenal pH of intracellular organelles. We have described a pH-independent, fluorescent chloride reporter called Clensor that has successfully measured resting chloride in organelles of living cells. Here, we describe the rational design of Clensor. Clensor integrates a chloride sensitive fluorophore called 10,10'-bis[3-carboxypropyl]-9,9'-biacridinium dinitrate (BAC) with the programmability, modularity and targetability available to nucleic acid scaffolds. We show that simple conjugation of BAC to a DNA backbone fails to yield a viable chloride-sensitive reporter. Fluorescence intensity and lifetime investigations on a series of BAC-functionalized structural variants yielded molecular insights that guided the rational design and successful realization of the chloride sensitive fluorescent reporter, Clensor. This study provides some general design principles that would aid the realization of diverse ion-sensitive nucleic acid reporters based on the sensing strategy of Clensor.
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Affiliation(s)
- Ved Prakash
- Department of Chemistry and the Grossman Institute , University of Chicago , 929E, 57th Street, E305A, GCIS , Chicago , Illinois 60637 , USA .
| | - Sonali Saha
- National Centre for Biological Sciences , TIFR, GKVK, Bellary Road , Bangalore 560065 , India
| | - Kasturi Chakraborty
- Department of Chemistry and the Grossman Institute , University of Chicago , 929E, 57th Street, E305A, GCIS , Chicago , Illinois 60637 , USA .
| | - Yamuna Krishnan
- Department of Chemistry and the Grossman Institute , University of Chicago , 929E, 57th Street, E305A, GCIS , Chicago , Illinois 60637 , USA .
- National Centre for Biological Sciences , TIFR, GKVK, Bellary Road , Bangalore 560065 , India
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80
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Huang L, Aryal GH, Tam-Chang SW, Publicover NG, Hunter KW. Self-assembled biosensor with universal reporter and dual-quenchers for detection of unlabelled nucleic acids. Analyst 2016; 141:1376-82. [PMID: 26757447 DOI: 10.1039/c5an02094h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A novel biosensor with universal reporter and dual quenchers was developed for rapid, sensitive, selective, and inexpensive detection of unlabelled nucleic acids. The biosensor is based on a single-strand DNA stem-loop motif with an extended universal reporter-binding region, a G-base rich stem region, and a universal address-binding region. The self-assembly of these stem-loop probes with fluorescence labeled universal reporter and a universal address region conjugated to gold nanoparticles forms the basis of a biosensor for DNA or microRNA targets in solution. The introduction of dual quenchers (G-base quenching and gold surface plasmon resonance-induced quenching) significantly reduces the fluorescence background to as low as 12% of its original fluorescence intensity and hence enhances the detection limit to 0.01 picomoles without signal ampilication.
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Affiliation(s)
- Liming Huang
- Department of Microbiology and Immunology, School of Medicine, University of Nevada, Reno, NV 89557, USA.
| | - Gyan H Aryal
- Department of Microbiology and Immunology, School of Medicine, University of Nevada, Reno, NV 89557, USA.
| | - Suk-Wah Tam-Chang
- Department of Microbiology and Immunology, School of Medicine, University of Nevada, Reno, NV 89557, USA.
| | - Nelson G Publicover
- Department of Microbiology and Immunology, School of Medicine, University of Nevada, Reno, NV 89557, USA.
| | - Kenneth W Hunter
- Department of Microbiology and Immunology, School of Medicine, University of Nevada, Reno, NV 89557, USA.
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81
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Pavan Kumar Y, Saha P, Saha D, Bessi I, Schwalbe H, Chowdhury S, Dash J. Fluorescent Dansyl-Guanosine Conjugates that Bindc-MYCPromoter G-Quadruplex and Downregulatec-MYCExpression. Chembiochem 2016; 17:388-93. [DOI: 10.1002/cbic.201500631] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Indexed: 01/15/2023]
Affiliation(s)
- Y. Pavan Kumar
- Department of Organic Chemistry; Indian Association for the Cultivation of Science; Jadavpur University; 2A ∞ B Raja S. C. Mullick Road Jadavpur Kolkata 700032 India
| | - Puja Saha
- Department of Organic Chemistry; Indian Association for the Cultivation of Science; Jadavpur University; 2A ∞ B Raja S. C. Mullick Road Jadavpur Kolkata 700032 India
| | - Dhurjhoti Saha
- CSIR-Institute of Genomics and Integrative Biology; Mathura Road Delhi 110 025 India
| | - Irene Bessi
- Institute of Organic Chemistry and Chemical Biology; Goethe University Frankfurt; and Center for Biomolecular Magnetic Resonance; Max-von-Laue Strasse 7 60438 Frankfurt am Main Germany
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical Biology; Goethe University Frankfurt; and Center for Biomolecular Magnetic Resonance; Max-von-Laue Strasse 7 60438 Frankfurt am Main Germany
| | - Shantanu Chowdhury
- CSIR-Institute of Genomics and Integrative Biology; Mathura Road Delhi 110 025 India
| | - Jyotirmayee Dash
- Department of Organic Chemistry; Indian Association for the Cultivation of Science; Jadavpur University; 2A ∞ B Raja S. C. Mullick Road Jadavpur Kolkata 700032 India
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82
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Canalis E, Bridgewater D, Schilling L, Zanotti S. Canonical Notch activation in osteocytes causes osteopetrosis. Am J Physiol Endocrinol Metab 2016; 310:E171-82. [PMID: 26578715 PMCID: PMC4719030 DOI: 10.1152/ajpendo.00395.2015] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 11/12/2015] [Indexed: 01/01/2023]
Abstract
Activation of Notch1 in cells of the osteoblastic lineage inhibits osteoblast differentiation/function and causes osteopenia, whereas its activation in osteocytes causes a distinct osteopetrotic phenotype. To explore mechanisms responsible, we established the contributions of canonical Notch signaling (Rbpjκ dependent) to osteocyte function. Transgenics expressing Cre recombinase under the control of the dentin matrix protein-1 (Dmp1) promoter were crossed with Rbpjκ conditional mice to generate Dmp1-Cre(+/-);Rbpjκ(Δ/Δ) mice. These mice did not have a skeletal phenotype, indicating that Rbpjκ is dispensable for osteocyte function. To study the Rbpjκ contribution to Notch activation, Rosa(Notch) mice, where a loxP-flanked STOP cassette is placed between the Rosa26 promoter and the NICD coding sequence, were crossed with Dmp1-Cre transgenic mice and studied in the context (Dmp1-Cre(+/-);Rosa(Notch);Rbpjκ(Δ/Δ)) or not (Dmp1-Cre(+/-);Rosa(Notch)) of Rbpjκ inactivation. Dmp1-Cre(+/-);Rosa(Notch) mice exhibited increased femoral trabecular bone volume and decreased osteoclasts and bone resorption. The phenotype was reversed in the context of the Rbpjκ inactivation, demonstrating that Notch canonical signaling was accountable for the phenotype. Notch activation downregulated Sost and Dkk1 and upregulated Axin2, Tnfrsf11b, and Tnfsf11 mRNA expression, and these effects were not observed in the context of the Rbpjκ inactivation. In conclusion, Notch activation in osteocytes suppresses bone resorption and increases bone volume by utilization of canonical signals that also result in the inhibition of Sost and Dkk1 and upregulation of Wnt signaling.
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Affiliation(s)
- Ernesto Canalis
- Department of Orthopedic Surgery and the University of Connecticut Musculoskeletal Institute, Farmington, Connecticut; and Department of Medicine, University of Connecticut Health, Farmington, Connecticut
| | - David Bridgewater
- Department of Orthopedic Surgery and the University of Connecticut Musculoskeletal Institute, Farmington, Connecticut; and
| | - Lauren Schilling
- Department of Orthopedic Surgery and the University of Connecticut Musculoskeletal Institute, Farmington, Connecticut; and
| | - Stefano Zanotti
- Department of Orthopedic Surgery and the University of Connecticut Musculoskeletal Institute, Farmington, Connecticut; and Department of Medicine, University of Connecticut Health, Farmington, Connecticut
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83
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Xu J, Carrocci TJ, Hoskins AA. Evolution and characterization of a benzylguanine-binding RNA aptamer. Chem Commun (Camb) 2016; 52:549-52. [PMID: 26538152 PMCID: PMC5020705 DOI: 10.1039/c5cc07605f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Repurposing the "protein-labeling toolkit" for RNA research could be a pragmatic approach for developing new RNA-labeling methods. We have evolved an RNA aptamer that tightly binds benzylguanine (bG), the key ligand for the protein SNAP-tag. The aptamer tightly binds bG fluorophores and can be purified from cellular RNA with bG agarose under native conditions.
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Affiliation(s)
- J Xu
- Department of Biochemistry, U. Wisconsin-Madison, 433 Babcock Dr., Madison, WI 53706, USA.
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84
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Canalis E, Schilling L, Yee SP, Lee SK, Zanotti S. Hajdu Cheney Mouse Mutants Exhibit Osteopenia, Increased Osteoclastogenesis, and Bone Resorption. J Biol Chem 2015; 291:1538-1551. [PMID: 26627824 DOI: 10.1074/jbc.m115.685453] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Indexed: 11/06/2022] Open
Abstract
Notch receptors are determinants of cell fate and function and play a central role in skeletal development and bone remodeling. Hajdu Cheney syndrome, a disease characterized by osteoporosis and fractures, is associated with NOTCH2 mutations resulting in a truncated stable protein and gain-of-function. We created a mouse model reproducing the Hajdu Cheney syndrome by introducing a 6955C→T mutation in the Notch2 locus leading to a Q2319X change at the amino acid level. Notch2(Q2319X) heterozygous mutants were smaller and had shorter femurs than controls; and at 1 month of age they exhibited cancellous and cortical bone osteopenia. As the mice matured, cancellous bone volume was restored partially in male but not female mice, whereas cortical osteopenia persisted in both sexes. Cancellous bone histomorphometry revealed an increased number of osteoclasts and bone resorption, without a decrease in osteoblast number or bone formation. Osteoblast differentiation and function were not affected in Notch2(Q2319X) cells. The pre-osteoclast cell pool, osteoclast differentiation, and bone resorption in response to receptor activator of nuclear factor κB ligand in vitro were increased in Notch2(Q2319X) mutants. These effects were suppressed by the γ-secretase inhibitor LY450139. In conclusion, Notch2(Q2319X) mice exhibit cancellous and cortical bone osteopenia, enhanced osteoclastogenesis, and increased bone resorption.
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Affiliation(s)
| | | | - Siu-Pok Yee
- Cell Biology, Genetics, and; Genome Sciences Biology
| | - Sun-Kyeong Lee
- Medicine,; Center on Aging, University of Connecticut Health Center, Farmington, Connecticut 06030
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85
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Zanotti S, Canalis E. The Dmp1-SOST Transgene Interacts With and Downregulates the Dmp1-Cre Transgene and the Rosa(Notch) Allele. J Cell Biochem 2015; 117:1222-32. [PMID: 26456319 DOI: 10.1002/jcb.25405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 10/08/2015] [Indexed: 11/10/2022]
Abstract
Activation of Notch1 in osteocytes of Rosa(Notch) mice, where a loxP-flanked STOP cassette and the Nicd coding sequence were targeted to the reverse orientation splice acceptor (Rosa)26 locus, causes osteopetrosis associated with suppressed Sost expression and enhanced Wnt signaling. To determine whether Sost downregulation mediates the effects of Notch activation in osteocytes, Rosa(Notch) mice were crossed with transgenics expressing Cre recombinase or SOST under the control of the dentin matrix protein (Dmp)1 promoter. Dmp1-SOST transgenics displayed vertebral osteopenia and a modest femoral cancellous and cortical bone phenotype, whereas hemizygous Dmp1-Cre transgenics heterozygous for the Rosa(Notch) allele (Dmp1-Cre;Rosa(Notch)) exhibited osteopetrosis. The phenotype of Notch activation in osteocytes was prevented in Dmp1-Cre;Rosa(Notch) mice hemizygous for the Dmp1-SOST transgene. The effect was associated with downregulated Notch signaling and suppressed Dmp1 and Rosa26 expression. To test whether SOST regulates Notch expression in osteocytes, cortical bone cultures from Dmp1-Cre;Rosa(Notch) mice or from Rosa(Notch) control littermates were exposed to recombinant human SOST. The addition of SOST had only modest effects on Notch target gene mRNA levels and suppressed Dmp1, but not Cre or Rosa26, expression. These findings suggest that prevention of the Dmp1-Cre;Rosa(Notch) skeletal phenotype by Dmp1-SOST is not secondary to SOST expression but to interactions among the Dmp1-SOST and Dmp1-Cre transgenes and the Rosa26 locus. In conclusion, the Dmp1-SOST transgene suppresses the expression of the Dmp1-Cre transgene and of Rosa26.
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Affiliation(s)
- Stefano Zanotti
- Departments of Orthopaedic Surgery and Medicine, and The UConn Musculoskeletal Institute, UConn Health, Farmington, 06030, Connecticut
| | - Ernesto Canalis
- Departments of Orthopaedic Surgery and Medicine, and The UConn Musculoskeletal Institute, UConn Health, Farmington, 06030, Connecticut
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86
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Schelvis JPM, Zhu X, Gindt YM. Enzyme-Substrate Binding Kinetics Indicate That Photolyase Recognizes an Extrahelical Cyclobutane Thymidine Dimer. Biochemistry 2015; 54:6176-85. [PMID: 26393415 DOI: 10.1021/acs.biochem.5b00927] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Escherichia coli DNA photolyase is a DNA-repair enzyme that repairs cyclobutane pyrimidine dimers (CPDs) that are formed on DNA upon exposure of cells to ultraviolet light. The light-driven electron-transfer mechanism by which photolyase catalyzes the CPD monomerization after the enzyme-substrate complex has formed has been studied extensively. However, much less is understood about how photolyase recognizes CPDs on DNA. It has been clearly established that photolyase, like many other DNA-repair proteins, requires flipping of the CPD site into an extrahelical position. Photolyase is unique in that it requires the two dimerized pyrimidine bases to flip rather than just a single damaged base. In this paper, we perform direct measurements of photolyase binding to CPD-containing undecamer DNA that has been labeled with a fluorophore. We find that the association constant of ∼2 × 10(6) M(-1) is independent of the location of the CPD on the undecamer DNA. The binding kinetics of photolyase are best described by two rate constants. The slower rate constant is ∼10(4) M(-1) s(-1) and is most likely due to steric interference of the fluorophore during the binding process. The faster rate constant is on the order of 2.5 × 10(5) M(-1) s(-1) and reflects the binding of photolyase to the CPD on the DNA. This result indicates that photolyase finds and binds to a CPD lesion 100-4000 times slower than other DNA-repair proteins. In light of the existing literature, we propose a mechanism in which photolyase recognizes a CPD that is flipped into an extrahelical position via a three-dimensional search.
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Affiliation(s)
- Johannes P M Schelvis
- Department of Chemistry and Biochemistry, Montclair State University , 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Xuling Zhu
- Department of Chemistry, New York University , 100 Washington Square East, New York, New York 10003, United States
| | - Yvonne M Gindt
- Department of Chemistry and Biochemistry, Montclair State University , 1 Normal Avenue, Montclair, New Jersey 07043, United States
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87
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Gracie K, Smith WE, Yip P, Sutter JU, Birch DJS, Graham D, Faulds K. Interaction of fluorescent dyes with DNA and spermine using fluorescence spectroscopy. Analyst 2015; 139:3735-43. [PMID: 24915043 DOI: 10.1039/c4an00680a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Oligonucleotides labelled with fluorescent dyes are widely used as probes for the identification of DNA sequences in detection methods using optical spectroscopies such as fluorescence and surface enhanced Raman scattering (SERS). Spermine is widely used in surface enhanced based assays as a charge reduction and aggregating agent as it interacts strongly with the phosphate backbone and has shown to enhance the signal of a labelled oligonucleotide. The fluorescence intensity of two commonly used labels, FAM and TAMRA, were compared when spermine was added under different experimental conditions. There was a marked difference upon conjugating the free dye to an oligonucleotide, when FAM was conjugated to an oligonucleotide there was around a six fold decrease in emission, compared to a six fold increase when TAMRA was conjugated to an oligonucleotide. Dye labelled single and double stranded DNA also behaved differently with double stranded DNA labelled with FAM being a much more efficient emitter in the mid pH range, however TAMRA becomes increasingly less efficient as the pH rises. Upon addition of the base spermine, signal enhancement from the FAM labelled oligonucleotide is observed. Increasing probe concentrations of TAMRA oligonucleotide above 0.5 μM led to signal reduction most likely through quenching, either by an interaction with guanine, or through self-quenching. By using different bases for comparison, spermine and triethylamine (TEA), different affects were observed in the measured fluorescence signals. When TEA was added to FAM, a reduction in the pH dependence of fluorescence was observed, which may be useful for mid pH range assays. With the drive to increase information content and decrease time and complexity of DNA assays it is likely that more assays will be carried out in complex media such as extracted DNA fragments and PCR product. This model study indicates that dye DNA and dye spermine interactions are dye specific and that extreme care with conditions is necessary particularly if it is intended to determine the concentrations of multiple analytes using probes labelled with different dyes.
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Affiliation(s)
- K Gracie
- Centre of Molecular Nanometrology, WestChem, Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, UK.
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88
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Tan C, Yu P, Hu Y, Chen J, Huang Y, Cai Y, Luo Z, Li B, Lu Q, Wang L, Liu Z, Zhang H. High-Yield Exfoliation of Ultrathin Two-Dimensional Ternary Chalcogenide Nanosheets for Highly Sensitive and Selective Fluorescence DNA Sensors. J Am Chem Soc 2015; 137:10430-6. [DOI: 10.1021/jacs.5b06982] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Chaoliang Tan
- School
of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Peng Yu
- School
of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Yanling Hu
- School
of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
- Key
Laboratory for Organic Electronics and Information Display (KLOEID)
and Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM) Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210046, China
| | - Junze Chen
- School
of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Ying Huang
- School
of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Yongqing Cai
- Institute
of High Performance Computing, A*STAR (Agency for Science, Technology and Research) 1 Fusionopolis Way, Singapore 138632, Singapore
| | - Zhimin Luo
- School
of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Bing Li
- Institute
of Materials Research and Engineering, A*STAR (Agency for Science, Technology and Research), 3 Research Link, Singapore 117602, Singapore
| | - Qipeng Lu
- School
of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Lianhui Wang
- Key
Laboratory for Organic Electronics and Information Display (KLOEID)
and Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM) Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210046, China
| | - Zheng Liu
- School
of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Hua Zhang
- School
of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
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89
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Wang H, Song S, Hao J, Song A. Hydrogels Triggered by Metal Ions as Precursors of Network CuS for DNA Detection. Chemistry 2015; 21:12194-201. [PMID: 26179250 DOI: 10.1002/chem.201500919] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Indexed: 11/09/2022]
Abstract
The gelation behavior of lithocholate (LC(-) ) with different metal ions in water was investigated. The microstructures of hydrogels were determined to be three-dimensional (3D) networks of fibrous aggregates. The formation of fibrils was speculated to be mainly driven by the coordination between carboxylate of LC(-) and metal ions, accompanied by the assistance of noncovalent interactions such as electrostatic and hydrophobic interactions. The hydrogels, which can maintain the mechanical strength at higher temperature, exhibit thermal stability. Their gelation capability was enhanced with the increase in acidity. The hydrogels of LC(-) and Cu(2+) mixtures served as the precursors for producing network nanostructures of CuS nanoparticles. These new CuS networks exhibit high fluorescence quenching ability and can act as an effective fluorescent sensing platform for ssDNA detection.
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Affiliation(s)
- Haiqiao Wang
- Key Laboratory of Colloid and Interface Chemistry and Key Laboratory of Special Aggregated Materials, Shandong University, Ministry of Education, Jinan 250100 (P.R. China)
| | - Shasha Song
- Key Laboratory of Colloid and Interface Chemistry and Key Laboratory of Special Aggregated Materials, Shandong University, Ministry of Education, Jinan 250100 (P.R. China)
| | - Jingcheng Hao
- Key Laboratory of Colloid and Interface Chemistry and Key Laboratory of Special Aggregated Materials, Shandong University, Ministry of Education, Jinan 250100 (P.R. China)
| | - Aixin Song
- Key Laboratory of Colloid and Interface Chemistry and Key Laboratory of Special Aggregated Materials, Shandong University, Ministry of Education, Jinan 250100 (P.R. China).
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90
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Mekler V, Severinov K. RNA polymerase molecular beacon as tool for studies of RNA polymerase-promoter interactions. Methods 2015; 86:19-26. [PMID: 25956222 DOI: 10.1016/j.ymeth.2015.04.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 04/27/2015] [Accepted: 04/28/2015] [Indexed: 10/23/2022] Open
Abstract
The molecular details of formation of transcription initiation complex upon the interaction of bacterial RNA polymerase (RNAP) with promoters are not completely understood. One way to address this problem is to understand how RNAP interacts with different parts of promoter DNA. A recently developed fluorometric RNAP molecular beacon assay allows one to monitor the RNAP interactions with various unlabeled DNA probes and quantitatively characterize partial RNAP-promoter interactions. This paper focuses on methodological aspects of application of this powerful assay to study the mechanism of transcription initiation complex formation by Escherichia coli RNA polymerase σ(70) holoenzyme and its regulation by bacterial and phage encoded factors.
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Affiliation(s)
- Vladimir Mekler
- Waksman Institute of Microbiology, Rutgers, State University of New Jersey, Piscataway, NJ 08854, USA.
| | - Konstantin Severinov
- Waksman Institute of Microbiology, Rutgers, State University of New Jersey, Piscataway, NJ 08854, USA; Skolkovo Institute of Science and Technology, 143025 Skolkovo, Russia; Institutes of Gene Biology and Molecular Genetics, Russian Academy of Sciences, 119334 Moscow, Russia.
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91
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Wang C, Zhai W, Wang Y, Yu P, Mao L. MnO2 nanosheets based fluorescent sensing platform with organic dyes as a probe with excellent analytical properties. Analyst 2015; 140:4021-9. [PMID: 25919222 DOI: 10.1039/c5an00581g] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Manganese dioxide (MnO2) nanosheets have recently been demonstrated to be particularly attractive for fluorescent sensing and imaging; however, almost all MnO2 nanosheets-based fluorescent assays have been developed with emissive nanoparticles as the probes. In this study, we developed a novel strategy to use organic dyes, instead of emissive nanoparticles, as the probe to construct a platform for biosensing with excellent analytical properties. With 5-carboxyfluorescein (FAM) as a model organic dye, we firstly investigate the effect of MnO2 nanosheets on the fluorescence of FAM and find that the fluorescence intensity of FAM is considerably suppressed by MnO2 nanosheets based on the inner filter effect (IFE). To demonstrate that the MnO2 nanosheets-based fluorescence sensing platform can easily achieve a high selectivity with organic dyes as the probe, we use single-stranded DNA (ssDNA) oligonucleotide as a typical biorecognition unit, which is labeled with the FAM probe to form FAM-ssDNA. The fluorescent intensity of FAM-ssDNA is first suppressed by MnO2 nanosheets through the combination of IFE and Förster resonant energy transfer (FRET), and then recovered with subsequent hybridization with the complementary DNA oligonucleotide. To demonstrate the potential applications of the MnO2 nanosheets-based fluorescence sensing platform with organic dyes as the probes, we developed methods for simple but effective microRNA and thrombin assays. With the platform demonstrated here, the limits of detection for miR124a and thrombin are 0.8 nM and 11 nM, respectively. Moreover, the fluorescent sensing assay for thrombin exhibits high selectivity. This study essentially demonstrates a new 2D nanostructure-based fluorescent sensing platform that is robust, technically simple, and easily manipulated to achieve high selectivity and sensitivity for practical applications.
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Affiliation(s)
- Chunxia Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, the Chinese Academy of Sciences, Beijing 100190, China.
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92
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Yang C, Spinelli N, Perrier S, Defrancq E, Peyrin E. Macrocyclic host-dye reporter for sensitive sandwich-type fluorescent aptamer sensor. Anal Chem 2015; 87:3139-43. [PMID: 25738735 DOI: 10.1021/acs.analchem.5b00341] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We describe herein a novel approach for the fluorescent detection of small molecules using a sandwich-type aptamer strategy based on a signaling macrocyclic host-dye system. One split adenosine aptamer fragment was 5'-conjugated to a β-cylodextrin (CD) molecule while the other nucleic acid fragment was labeled at the 3'-end by a dansyl molecule prone to be included into the macrocycle. The presence of the small target analyte governed the assembly of the two fragments, bringing the dye molecule and its specific receptor in close proximity and promoting the inclusion interaction. Upon the inclusion complex formation, the microenvironment of dansyl was modified in such a way that the fluorescent intensity increased. Concomitantly, this supplementary interaction at the aptamer extremities induced stabilizing effects on the ternary complex. We next proposed a bivalent signaling design where the two extremities of one split aptamer fragment were conjugated to the β-CD molecule while those of the other fragment were tagged by the dansyl dye. The dual reporting dye inclusion promoted an improvement of both the signal-to-background change and the assay sensitivity. Owing to the vast diversity of responsive host-macrocycle systems available, this aptasensor strategy has potential to be extended to the multiplexed analysis and to other kinds of transducers (such as electrochemical).
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Affiliation(s)
- Cheng Yang
- †Université Grenoble Alpes, CNRS, DPM UMR 5063, F-38041 Grenoble, France.,‡Université Grenoble Alpes, CNRS, DCM UMR 5250, F-38041 Grenoble, France
| | - Nicolas Spinelli
- ‡Université Grenoble Alpes, CNRS, DCM UMR 5250, F-38041 Grenoble, France
| | - Sandrine Perrier
- †Université Grenoble Alpes, CNRS, DPM UMR 5063, F-38041 Grenoble, France
| | - Eric Defrancq
- ‡Université Grenoble Alpes, CNRS, DCM UMR 5250, F-38041 Grenoble, France
| | - Eric Peyrin
- †Université Grenoble Alpes, CNRS, DPM UMR 5063, F-38041 Grenoble, France
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93
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Fluorogenic DNA ligase and base excision repair enzyme assays using substrates labeled with single fluorophores. Anal Biochem 2015; 477:69-77. [PMID: 25728944 DOI: 10.1016/j.ab.2015.02.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 02/19/2015] [Indexed: 01/27/2023]
Abstract
Continuing our work on fluorogenic substrates labeled with single fluorophores for nucleic acid modifying enzymes, here we describe the development of such substrates for DNA ligases and some base excision repair enzymes. These substrates are hairpin-type synthetic DNA molecules with a single fluorophore located on a base close to the 3' ends, an arrangement that results in strong fluorescence quenching. When such substrates are subjected to an enzymatic reaction, the position of the dyes relative to that end of the molecules is altered, resulting in significant fluorescence intensity changes. The ligase substrates described here were 5' phosphorylated and either blunt-ended or carrying short, self-complementary single-stranded 5' extensions. The ligation reactions resulted in the covalent joining of the ends of the molecules, decreasing the quenching effect of the terminal bases on the dyes. To generate fluorogenic substrates for the base excision repair enzymes formamido-pyrimidine-DNA glycosylase (FPG), human 8-oxo-G DNA glycosylase/AP lyase (hOGG1), endonuclease IV (EndoIV), and apurinic/apyrimidinic endonuclease (APE1), we introduced abasic sites or a modified nucleotide, 8-oxo-dG, at such positions that their enzymatic excision would result in the release of a short fluorescent fragment. This was also accompanied by strong fluorescence increases. Overall fluorescence changes ranged from approximately 4-fold (ligase reactions) to more than 20-fold (base excision repair reactions).
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94
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Zhang Y, Zheng B, Zhu C, Zhang X, Tan C, Li H, Chen B, Yang J, Chen J, Huang Y, Wang L, Zhang H. Single-layer transition metal dichalcogenide nanosheet-based nanosensors for rapid, sensitive, and multiplexed detection of DNA. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2015; 27:935-9. [PMID: 25504749 DOI: 10.1002/adma.201404568] [Citation(s) in RCA: 214] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 11/06/2014] [Indexed: 05/21/2023]
Abstract
Single-layer transition metal dichalcogenide nanosheets, including MoS2, TiS2, and TaS2, are used as novel sensing platforms for sensitive and selective detection of DNA, based on their high fluorescence-quenching ability and different affinities toward single-stranded DNA and double-stranded DNA. Importantly, for the first time, a single-layer TaS2 nanosheet-based multiplexed DNA sensor is also developed.
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Affiliation(s)
- Ying Zhang
- Key Laboratory for Organic Electronics and Information Displays and Institute of Advanced Materials, National Jiangsu Synergistic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China; School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
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95
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Assembling programmable FRET-based photonic networks using designer DNA scaffolds. Nat Commun 2014; 5:5615. [PMID: 25504073 PMCID: PMC4275599 DOI: 10.1038/ncomms6615] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 10/20/2014] [Indexed: 12/23/2022] Open
Abstract
DNA demonstrates a remarkable capacity for creating designer nanostructures and devices. A growing number of these structures utilize Förster resonance energy transfer (FRET) as part of the device's functionality, readout or characterization, and, as device sophistication increases so do the concomitant FRET requirements. Here we create multi-dye FRET cascades and assess how well DNA can marshal organic dyes into nanoantennae that focus excitonic energy. We evaluate 36 increasingly complex designs including linear, bifurcated, Holliday junction, 8-arm star and dendrimers involving up to five different dyes engaging in four-consecutive FRET steps, while systematically varying fluorophore spacing by Förster distance (R0). Decreasing R0 while augmenting cross-sectional collection area with multiple donors significantly increases terminal exciton delivery efficiency within dendrimers compared with the first linear constructs. Förster modelling confirms that best results are obtained when there are multiple interacting FRET pathways rather than independent channels by which excitons travel from initial donor(s) to final acceptor.
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96
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Turriani E, Höbartner C, Jovin TM. Mg2+-dependent conformational changes and product release during DNA-catalyzed RNA ligation monitored by Bimane fluorescence. Nucleic Acids Res 2014; 43:40-50. [PMID: 25505142 PMCID: PMC4288166 DOI: 10.1093/nar/gku1268] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Among the deoxyribozymes catalyzing the ligation of two RNA substrates, 7S11 generates a branched RNA containing a 2',5'-linkage. We have attached the small fluorogenic probe Bimane to the triphosphate terminated RNA substrate and utilized emission intensity and anisotropy to follow structural rearrangements leading to a catalytically active complex upon addition of Mg(2+). Bimane coupled to synthetic oligonucleotides is quenched by nearby guanines via photoinduced electron transfer. The degree of quenching is sensitive to changes in the base pairing of the residues involved and in their distances to the probe. These phenomena permit the characterization of various sequential processes in the assembly and function of 7S11: binding of Mg(2+) to the triphosphate moiety, release of quenching of the probe by the 5'-terminal G residues of R-RNA as they engage in secondary base-pair interactions, local rearrangement into a distinct active conformation, and continuous release of the Bimane-labeled pyrophosphate during the course of reaction at 37°C. It was possible to assign equilibrium and rate constants and structural interpretations to the sequence of conformational transitions and catalysis, information useful for optimizing the design of next generation deoxyribozymes. The fluorescent signatures, thermodynamic equilibria and catalytic function of numerous mutated (base/substituted) molecules were examined.
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Affiliation(s)
- Elisa Turriani
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, I-56126 Pisa, Italy Laboratory for Cellular Dynamics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Claudia Höbartner
- Max Planck Research Group Nucleic Acid Chemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany and Institute for Organic and Biomolecular Chemistry, Georg August University Göttingen, Tammannstrasse 2, 37077 Göttingen, Germany
| | - Thomas M Jovin
- Laboratory for Cellular Dynamics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
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97
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Ang YS, Yung LYL. Toehold-mediated internal control to probe the near-field interaction between the metallic nanoparticle and the fluorophore. NANOSCALE 2014; 6:12515-12523. [PMID: 25238596 DOI: 10.1039/c4nr03643c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Metallic nanoparticles (MNPs) are known to alter the emission of vicinal fluorophores through the near-field interaction, leading to either fluorescence quenching or enhancement. Much ambiguity remains in the experimental outcome of such a near-field interaction, particularly for bulk colloidal solution. It is hypothesized that the strong far-field interference from the inner filter effect of the MNPs could mask the true near-field MNP-fluorophore interaction significantly. Thus, in this work, a reliable internal control capable of decoupling the near-field interaction from far-field interference is established by the use of the DNA toehold concept to mediate the in situ assembly and disassembly of the MNP-fluorophore conjugate. A model gold nanoparticle (AuNP)-Cy3 system is used to investigate our proposed toehold-mediated internal control system. The maximum fluorescence enhancement is obtained for large-sized AuNP (58 nm) separated from Cy3 at an intermediate distance of 6.8 nm, while fluorescence quenching is observed for smaller-sized AuNP (11 nm and 23 nm), which is in agreement with the theoretical values reported in the literature. This work shows that the toehold-mediated internal control design can serve as a central system for evaluating the near-field interaction of other MNP-fluorophore combinations and facilitate the rational design of specific MNP-fluorophore systems for various applications.
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Affiliation(s)
- Y S Ang
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 10 Kent Ridge Crescent, Singapore 11920, Singapore.
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98
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Canalis E, Kranz L, Zanotti S. Nemo-like kinase regulates postnatal skeletal homeostasis. J Cell Physiol 2014; 229:1736-43. [PMID: 24664870 DOI: 10.1002/jcp.24625] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 03/20/2014] [Indexed: 01/04/2023]
Abstract
Nemo-like kinase (Nlk) is related to the mitogen-activated protein (MAP) kinases and known to regulate signaling pathways involved in osteoblastogenesis. In vitro Nlk suppresses osteoblastogenesis, but the consequences of the Nlk inactivation in the skeleton in vivo are unknown. To study the function of Nlk, Nlk(loxP/loxP) mice, where the Nlk exon2 is flanked by lox(P) sequences, were mated with mice expressing the Cre recombinase under the control of the paired-related homeobox gene 1 (Prx1) enhancer (Prx1-Cre), the Osterix (Osx-Cre) or the osteocalcin/bone gamma carboxyglutamate protein (Bglap-Cre) promoter. Prx1-Cre;Nlk(Δ/Δ) mice did not exhibit a skeletal phenotype except for a modest increase in trabecular number and connectivity observed only in 3-month-old male mice. Osx-Cre;Nlk(Δ/Δ) male and female mice exhibited an increase in trabecular bone volume secondary to an increased trabecular number at 3 months of age. Bone histomorphometry revealed a decrease in osteoclast number and eroded surface in male mice, and decreased osteoblast number and function in female mice. Expression of osteoprotegerin mRNA was increased in calvarial extracts, explaining the decreased osteoclast and osteoblast number. The conditional deletion of Nlk in mature osteoblasts (Bglap-Cre;Nlk(Δ/Δ) ) resulted in no skeletal phenotype in 1- to 6-month-old male or female mice. In conclusion, when expressed in undifferentiated osteoblasts, Nlk is a negative regulator of skeletal homeostasis possibly by targeting signals that regulate osteoclastogenesis and bone resorption.
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Affiliation(s)
- Ernesto Canalis
- Department of Research, Saint Francis Hospital and Medical Center, Hartford, Connecticut; The University of Connecticut School of Medicine, Farmington, Connecticut
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99
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He D, He X, Wang K, Yang X, Yang X, Li X, Zou Z. Nanometer-sized manganese oxide-quenched fluorescent oligonucleotides: an effective sensing platform for probing biomolecular interactions. Chem Commun (Camb) 2014; 50:11049-52. [PMID: 25098407 DOI: 10.1039/c4cc04573d] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We propose a novel template-assisted strategy to prepare nanometer-sized manganese oxide (nano-MnO2) by self-assembly of some MnO2 platelets and demonstrate its application as a new class of biosensing platform for probing DNA hybridization and aptamer-target interaction in a homogeneous solution.
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Affiliation(s)
- Dinggeng He
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Institute of Biology, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082, China.
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100
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Canalis E, Zanotti S, Smerdel-Ramoya A. Connective tissue growth factor is a target of notch signaling in cells of the osteoblastic lineage. Bone 2014; 64:273-80. [PMID: 24792956 PMCID: PMC4069863 DOI: 10.1016/j.bone.2014.04.028] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Revised: 04/03/2014] [Accepted: 04/23/2014] [Indexed: 12/15/2022]
Abstract
Connective tissue growth factor (Ctgf) or CCN2 is a protein synthesized by osteoblasts necessary for skeletal homeostasis, although its overexpression inhibits osteogenic signals and bone formation. Ctgf is induced by bone morphogenetic proteins, transforming growth factor β and Wnt; and in the present studies, we explored whether Notch regulated Ctgf expression in osteoblasts. We employed Rosa(Notch) mice, where the Notch intracellular domain (NICD) is expressed following the excision of a STOP cassette, placed between the Rosa26 promoter and NICD. Notch was activated by transduction of adenoviral vectors expressing Cre recombinase (Ad-CMV-Cre). Notch induced Ctgf mRNA levels in a time dependent manner and increased Ctgf heterogeneous nuclear RNA. Notch also destabilized Ctgf mRNA shortening its half-life from 13h to 3h. The effect of Notch on Ctgf expression was lost following Rbpjκ downregulation, demonstrating that it was mediated by Notch canonical signaling. However, downregulation of the classic Notch target genes Hes1, Hey1 and Hey2 did not modify the effect of Notch on Ctgf expression. Wild type osteoblasts exposed to immobilized Delta-like 1 displayed enhanced Notch signaling and increased Ctgf expression. In addition to the effects of Notch in vitro, Notch induced Ctgf in vivo, and calvariae and femurs from Rosa(Notch) mice mated with transgenics expressing the Cre recombinase in cells of the osteoblastic lineage exhibited increased expression of Ctgf. In conclusion, Ctgf is a target of Notch canonical signaling in osteoblasts, and may act in concert with Notch to regulate skeletal homeostasis.
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Affiliation(s)
- Ernesto Canalis
- Department of Research, Saint Francis Hospital and Medical Center, Hartford, CT, 06105; The University of Connecticut School of Medicine, Farmington, CT, 06030.
| | - Stefano Zanotti
- Department of Research, Saint Francis Hospital and Medical Center, Hartford, CT, 06105; The University of Connecticut School of Medicine, Farmington, CT, 06030.
| | - Anna Smerdel-Ramoya
- Department of Research, Saint Francis Hospital and Medical Center, Hartford, CT, 06105.
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