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https://www.readbyqxmd.com/read/28431642/pcr-based-detection-methods-for-single-nucleotide-polymorphism-or-mutation-real-time-pcr-and-its-substantial-contribution-toward-technological-refinement
#1
Kazuyuki Matsuda
Single-nucleotide polymorphisms (SNPs) and single-nucleotide mutations result from the substitution of only a single base. The SNP or mutation can be relevant to disease susceptibility, pathogenesis of disease, and efficacy of specific drugs. It is important to detect SNPs or mutations clinically. Methods to distinguish/detect SNPs or mutations should be highly specific and sensitive. In this regard, polymerase chain reaction (PCR) has provided the necessary analytical performance for many molecular analyses...
2017: Advances in Clinical Chemistry
https://www.readbyqxmd.com/read/28431179/mirna-regulation-in-gliomas-usual-suspects-in-glial-tumorigenesis-and-evolving-clinical-applications
#2
Heather Ames, Marc K Halushka, Fausto J Rodriguez
In recent years, an increasing role for noncoding small RNAs (miRNA) has been uncovered in carcinogenesis. These oligonucleotides can promote degradation and/or inhibit translation of key mRNAs. Recent studies have also highlighted a possible role for miRNAs in adult and pediatric brain tumors, including high- and low-grade gliomas, medulloblastoma, ependymoma, and neoplasms associated with neurofibromatosis type 1. Gliomas represent the most common category of primary intraparenchymal brain tumors, and, for example, manipulation of signaling pathways, through inhibition of PTEN transcription appears to be an important function of miRNA dysregulation through miR-21, miR-106b, and miR-26a...
April 1, 2017: Journal of Neuropathology and Experimental Neurology
https://www.readbyqxmd.com/read/28429017/oligonucleotide-promoted-peptide-bond-formation-using-a-trna-mimicking-approach
#3
H-P Mattelaer, C-A Mattelaer, N Papastavrou, W Dehaen, P Herdewijn
TransferRNA's role in protein translation is the prime example of an Informational Leaving Group (ILG). A simplified model produced oligophenylalanine with a modified uracil as an ILG in the presence of specific oligonucleotides. Our preliminary studies contribute to the importance of hybrid species in bridging the gap between peptides and nucleic acids.
April 21, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28428333/the-microrna-199a-214-cluster-targets-e-cadherin-and-claudin-2-and-promotes-high-glucose-induced-peritoneal-fibrosis
#4
Mingwen Che, Tiantian Shi, Shidong Feng, Huan Li, Xiaomin Zhang, Ning Feng, Weijuan Lou, Jianhua Dou, Guangbo Tang, Chen Huang, Guoshuang Xu, Qi Qian, Shiren Sun, Lijie He, Hanmin Wang
Serum response factor (SRF) was found to be involved in the phenotypic transition and fibrosis of the peritoneal membrane during treatment with peritoneal dialysis (PD), but the exact mechanism remains unclear. SRF regulates microRNAs (miRNAs) that contain the SRF-binding consensus (CArG) element in the promoter region. Therefore, we investigated whether the miR-199a/214 gene cluster, which contains a CArG element in its promoter, is directly regulated by SRF. High-glucose (HG) treatment significantly unregulated the expression of the miR-199a-5p/214-3p gene cluster in human peritoneal mesothelial cells (HPMCs)...
April 20, 2017: Journal of the American Society of Nephrology: JASN
https://www.readbyqxmd.com/read/28427878/localized-degradation-of-foreign-dna-strands-in-cells-only-excising-the-first-nucleotide-of-5-region
#5
Hui Li, Wei Shen, Michael Hon-Wah Lam, Haojun Liang
Intracellular delivery of foreign DNA probes sharply increases the efficiency of various biodetection protocols. Spherical nucleic acid (SNA) conjugate is a new type of probe that consists of a dense oligonucleotide shell attached typically to a gold nanoparticle core. They are widely used as novel labels for in vitro biodetection and intracellular assay. However, the degradation of foreign DNA still remains a challenge that can cause significant signal leakage (false positive signal). Hence, the site and behavior of intracellular degradation need to be investigated...
April 17, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/28426096/managing-the-sequence-specificity-of-antisense-oligonucleotides-in-drug-discovery
#6
Peter H Hagedorn, Bo R Hansen, Troels Koch, Morten Lindow
All drugs perturb the expression of many genes in the cells that are exposed to them. These gene expression changes can be divided into effects resulting from engaging the intended target and effects resulting from engaging unintended targets. For antisense oligonucleotides, developments in bioinformatics algorithms, and the quality of sequence databases, allow oligonucleotide sequences to be analyzed computationally, in terms of the predictability of their interactions with intended and unintended RNA targets...
March 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28426093/biophysical-properties-thermal-stability-and-functional-impact-of-8-oxo-7-8-dihydroguanine-on-oligonucleotides-of-rna-a-study-of-duplex-hairpins-and-the-aptamer-for-preq1-as-models
#7
Yu J Choi, Krzysztof S Gibala, Tewoderos Ayele, Katherine V Deventer, Marino J E Resendiz
A better understanding of the effects that oxidative lesions have on RNA is of importance to understand their role in the development/progression of disease. 8-oxo-7,8-dihydroguanine was incorporated into RNA to understand its structural and functional impact on RNA:RNA and RNA:DNA duplexes, hairpins and pseudoknots. One to three modifications were incorporated into dodecamers of RNA [AAGA GGG AUGAC] resulting in thermal destabilization (Δ T m - 10°C per lesion). Hairpins with tetraloops c-UUCG*-g* ( ), a-ACCG-g* ( ), c-UUG*G*-g* ( ) and c-ACG*G*-g* ( ) were modified and used to determine thermal stabilities, concluding that: (i) modifying the stem leads to destabilization unless adenosine is the opposing basepair of 8-oxoGua; (ii) modification at the loop is position- and sequence-dependent and varies from slight stabilization to large destabilization, in some cases leading to formation of other secondary structures (hairpin→duplex)...
February 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28425985/the-cellular-senescence-of-leukemia-initiating-cells-from-acute-lymphoblastic-leukemia-is-postponed-by-%C3%AE-arrestin1-binding-with-p300-sp1-to-regulate-htert-transcription
#8
Shan Liu, Haiyan Liu, Ru Qin, Yi Shu, Zhidai Liu, Penghui Zhang, Caiwen Duan, Dengli Hong, Jie Yu, Lin Zou
Although we previously reported that the self-renewal of leukemia-initiating cells of B-lineage acute lymphoblastic leukemia (B-ALL LICs) was regulated by β-Arrestin1, a multiple-function protein, the cellular senescence is critical for LICs fate and leukemia progress, and worthy for further investigation. Here we found that depletion of β-Arrestin1 extended the population doubling time and the percentage of senile cells, the signatures of cellular senescence, of B-ALL LICs. Moreover, lack of β-Arrestin1 enhanced the expression of proteins (CBX, HIRA) and genes (P53, P16) related to senescence in leukemic Reh cells and B-ALL-LICs-derived leukemic mice...
April 20, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28425453/aptamer-mediated-impairment-of-egfr-integrin-%C3%AE-v%C3%AE-3-complex-inhibits-vasculogenic-mimicry-and-growth-of-triple-negative-breast-cancers
#9
Simona Camorani, Elvira Crescenzi, Matteo Gramanzini, Monica Fedele, Antonella Zannetti, Laura Cerchia
Current treatment options for triple-negative breast cancers (TNBCs) is limited by the absence of well-defined biomarkers, excluding a targeted therapy. Notably, epidermal growth factor receptor (EGFR) is overexpressed in a great proportion of TNBCs and is a negative prognostic factor. In clinical trials, however, existing EGFR inhibitors showed disappointing outcome. Oligonucleotide aptamers are a valid alternative to antibodies for diagnostic and therapeutic uses. Here, we prove that, when applied to aggressive TNBC cell lines with unique stem-like plasticity, the anti-EGFR CL4 aptamer, but not erlotinib or cetuximab, prevents the vasculogenic mimicry (VM) capability of the cells and destroys previously formed channels in three-dimensional culture...
April 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28418770/gene-silencing-activity-and-hepatic-accumulation-of-antisense-oligonucleotides-bearing-cholesterol-conjugated-thiono-triester-at-the-gap-region
#10
Mado Nakajima, Takeshi Kasuya, Shinnichi Yokota, Reina Onishi, Tatsuya Ikehara, Akira Kugimiya, Ayahisa Watanabe
Cholesterol (Chol) conjugation to the 5' or 3' end of antisense oligonucleotide (ASO) enables delivery to the liver, and Chol conjugation at the gap region can also be expected to improve delivery to the liver. In this study, we synthesized ASOs bearing the Chol-conjugated thiono triester and evaluated their activity and hepatic accumulation. We found that Chol conjugations at the gap region improved in vitro activity and hepatic accumulation when compared to unconjugated ASOs. However, Chol conjugation with phosphorothioate linkage did not improve in vivo activity in the liver, suggesting the importance of cleaving the phosphodiester between ASO and Chol...
April 18, 2017: Nucleic Acid Therapeutics
https://www.readbyqxmd.com/read/28418733/feasibility-of-spect-ct-imaging-to-study-the-pharmacokinetics-of-antisense-oligonucleotides-in-a-mouse-model-of-duchenne-muscular-dystrophy
#11
Evita van de Steeg, Tilman Läppchen, Begoña Aguilera, Harm T Jansen, Daan Muilwijk, Rick Vermue, José W van der Hoorn, Katia Donato, Raffaella Rossin, Peter C de Visser, Maria L H Vlaming
Antisense oligonucleotides (AONs) are promising candidates for treatment of Duchenne muscular dystrophy (DMD), a severe and progressive disease resulting in premature death. However, more knowledge on the pharmacokinetics of new AON drug candidates is desired for effective application in the clinic. We assessed the feasibility of using noninvasive single-photon emission computed tomography-computed tomography (SPECT-CT) imaging to determine AON pharmacokinetics in vivo. To this end, a 2'-O-methyl phosphorothioate AON was radiolabeled with (123)I or (111)In, and administered to mdx mice, a rodent model of DMD...
April 18, 2017: Nucleic Acid Therapeutics
https://www.readbyqxmd.com/read/28418099/influence-of-divalent-counterions-on-the-dynamics-in-dna-probed-by-a-minor-groove-binder
#12
Sneha Paul, Tasnim Ahmed, Anunay Samanta
Dynamics in DNA to which water, counterions and DNA motions contribute is a topic of considerable interest as it is closely related to the efficiency of biological functions performed by it. Simulation studies and experiments suggest that counterion dynamics in DNA probed by a minor groove binder is similar for various monovalent counterions. As the influence of higher valent counterions, which are also present around DNA and known to bind more strongly to it compared to the monovalent ions, on the dynamics in DNA has not been studied so far, we investigate in this work the dynamics in presence of Mg2+ and Ca2+, chosen for their relative abundance in the cell, using 4', 6-diamidino-2-phenylindole (DAPI), a minor groove-binder, as fluorescence probe...
April 18, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
https://www.readbyqxmd.com/read/28417633/ph-responsive-graphene-oxide-dna-nano-system-for-living-cell-imaging-and-detection
#13
Chen Shao, Jia Liang, Sihui He, Tianqi Luan, Jiantao Yu, Haoran Zhao, Jingyuan Xu, Leilei Tian
The interaction between GO and DNA is very sensitive to the environment. For example, under the acidic condition, the affinity from GO to DNA will be enhanced, weakening the capability of GO on distinguishing DNAs with different confor-mations. Such effect impedes the development of sensitive pH biosensors based on GO-DNA nano-systems. In this work, we systematically studied the affinity between GO and i-motif forming oligonucleotides (IFOs) under different pH values and developed a herring sperm DNA (HSD) treatment method...
April 18, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28412171/gender-specific-amelioration-of-sma-phenotype-upon-disruption-of-a-deep-intronic-structure-by-an-oligonucleotide
#14
Matthew D Howell, Eric W Ottesen, Natalia N Singh, Rachel L Anderson, Ravindra N Singh
Spinal muscular atrophy (SMA), the leading genetic disease of children, is caused by low levels of survival motor neuron (SMN) protein. Here, we employ A15/283, an antisense oligonucleotide targeting a deep intronic sequence/structure, to examine the impact of restoration of SMN in a mild SMA mouse model. We show gender-specific amelioration of tail necrosis upon subcutaneous administrations of A15/283 into SMA mice at postnatal days 1 and 3. We also demonstrate that a modest increase in SMN due to early administrations of A15/283 dramatically improves testicular development and spermatogenesis...
April 13, 2017: Molecular Therapy: the Journal of the American Society of Gene Therapy
https://www.readbyqxmd.com/read/28411847/the-molecular-revolution-in-cutaneous-biology-era%C3%A2-of-cytogenetics-and-copy-number%C3%A2-analysis
#15
REVIEW
Jürgen Bauer
Development of karyotyping techniques in the 1950s sparked groundbreaking reports of chromosomal aberrations in cancer, such as the Philadelphia chromosome in chronic myelogenous leukemia in 1960, followed by a number of others. Spatial resolution of karyotyping is limited and vital tumor cells are required for metaphase preparation. To overcome these limitations, DNA hybridization techniques were developed. In situ hybridization of radioactively or fluorescence labeled RNA probes onto tumor samples allowed the identification of specific genomic regions, translocations and copy number alterations...
May 2017: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/28411643/transgultaminase-mediated-nanoarmoring-of-enzymes-by-pegylation
#16
Antonella Grigoletto, Anna Mero, Katia Maso, Gianfranco Pasut
PEGylation, the covalent attachment of polyethylene glycol to bioactive molecules, is one of the leading approaches used to prolong pharmacokinetics, to improve the stability, and to reduce the immunogenicity of therapeutic proteins. PEG-conjugated products are associated with better therapy outcomes and improved patient compliance. Widely applied in clinical practice, the technology is mainly used to modify proteins, peptides, and oligonucleotides but also other drug delivery systems such as the liposomal one...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28410209/mir-106b-inhibitors-sensitize-trail-induced-apoptosis-in-hepatocellular-carcinoma-through-increase-of-death-receptor-4
#17
Changlong Xu, Liang Shi, Weilai Chen, Peipei Fang, Jie Li, Lingxiang Jin, Zhenzhen Pan, Chenwei Pan
TNF-related apoptosis-inducing ligand (TRAIL), which is a member of the TNF superfamily, can induce tumor cell apoptosis. However, multiple types of tumor, including hepatocellular carcinoma, show tolerance to TRAIL. Previous studies have demonstrated that tumor cells usually change their expression profile of microRNA (miRNA) to obtain the ability of tolerance to drugs. However, whether such change of miRNA on TRAIL sensitivity is seen in hepatocellular carcinoma still needs to be explored. In this study, we observed overexpression of miR-106b in both HCC patients' tumor tissues and cell lines...
March 30, 2017: Oncotarget
https://www.readbyqxmd.com/read/28409554/lncrna-ccat1-upregulates-proliferation-and-invasion-in-melanoma-cells-via-suppressing-mir-33a
#18
Li Lv, Jian-Qin Jia, Jin Chen
It is increasingly evident that various long non-coding RNAs (lncRNAs) participate in the tumorigenesis of multiple tumors, including melanoma. LncRNA has been validated as oncogenic factor in multifarious tumor, however, the potential regulatory mechanism of CCAT1 in melanoma is still unclear. The purpose of this study is to investigate the regulation of CCAT1 on melanoma genesis. The expression of CCAT1 in melanoma tissue and cell lines was measured using qRT-PCR. Interference oligonucleotide or mimics sequences were applied to up- or down-regulate RNA expression...
April 12, 2017: Oncology Research
https://www.readbyqxmd.com/read/28409453/sirna-mediated-silencing-of-peroxisomal-genes-in-mammalian-cells
#19
Tina A Schrader, Michael Schrader
RNAi technologies are a valuable tool in the identification and investigation of proteins that are involved in peroxisome biogenesis and function. Small interfering RNA (siRNA) has developed into the most commonly used RNAi tool for the induction of transient, short-term silencing of protein coding genes. Although siRNA can induce gene knockdown in a variety of mammalian cell lines, their utility is limited by efficient uptake of synthetic oligonucleotides into the cells. Here, we describe different transfection methods that have been successfully used by us to silence peroxisomal genes in a variety of cell lines, including primary human skin fibroblasts, which are usually difficult to transfect...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28409342/zebrafish-as-a-model-of-kidney-disease
#20
Elvin E Morales, Rebecca A Wingert
Animal models have been an invaluable means to advance biomedical research as they provide experimental avenues for cellular and molecular investigations of disease pathology. The zebrafish (Danio rerio) is a good alternative to mammalian models that can be used to apply powerful genetic experimental methods normally used in invertebrates to answer questions about vertebrate development and disease. In the case of the kidney, the zebrafish has proven itself to be an applicable and versatile experimental system, mainly due to the simplicity of its pronephros, which contains two nephrons that possess conserved structural and physiological aspects with mammalian nephrons...
2017: Results and Problems in Cell Differentiation
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