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检索条件"主题词=RNA secondary structure prediction"

共 132 条记录，以下是111-120 订阅

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Rapid Generation of mirna Inhibitor Leads by Bioinformatics and Efficient High-Throughput Screening Methods

Rapid Generation of miRNA Inhibitor Leads by Bioinformatics ...

引用

作者： Christopher L. Haga Sai Pradeep Velagapudi Jessica L. Childs-Disney Jacqueline Strivelli Matthew D. Disney Donald G. Phinney

The discovery of micrornas (mirnas) has opened an entire new avenue for drug development. These short (15–22 nucleotides) noncoding rnas, which function in rna silencing and posttranscriptional regulation of gene expression, have been shown to critically affect numerous pathways in both development and disease progression. Current mirna drug development focuses on either reintroducing the mirna into cells through the use of a mirna mimic or inhibiting its function via use of a synthetic antagomir. Although these methods have shown some success as therapeutics, they face challenges particularly with regard to cellular uptake and for use as systemic reagents. We recently presented a novel mechanism of inhibiting miR-544 by directed inhibition of mirna biogenesis. We found that inhibition of DICER processing of miR-544 through the use of a small molecule abolished miR-544 function in regulating adaptation of breast cancer cells to hypoxic stress. Herein, we describe a protocol that utilizes bioinformatics to first identify lead small molecules that bind to DICER cleavage sites in pre-mirnas and then employ an efficient, high-throughput fluorescent-based screening system to determine the inhibitory potential of the lead compounds and their derivatives. less

关键词： High-throughput Screening Binding Assay Apoptosis Assay Statistical Calculation rna secondary structure prediction In Vitro Transcription Competition Dialysis EMSA Fluorescence Microscopy Luciferase Reporter Assay Real-time PCR Quantitative Reverse Transcription PCR Cell And Tissue Culture Reverse Transcription PCR Flow Cytometry Transfection FACS Nuclease Protection Assay PCR Data analysis Homo sapiens Bos taurus HEK Therapeutics mirna Microrna Small molecule DICER

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Invader Assay for rna Quantitation

Invader Assay for RNA Quantitation

引用

作者： Marilyn C. Olson Tsetska Takova LuAnne Chehak Michelle L. Curtis Sarah M. Olson Robert W. Kwiatkowski

The Invader® assay is a homogeneous, isothermal, signal amplification system for the quantitative detection of nucleic acids. The assay can directly detect either DNA or rna without target amplification or reverse transcription. It is based on the ability of Cleavase® enzymes to recognize as a substrate and cleave a specific nucleic acid structure generated through the hybridization of two oligonucleotides to the target sequence. The combination of sequence-specific oligo-nucleotide hybridization and structure-specific enzymatic cleavage results in a highly specific assay well suited for discriminating closely related gene sequences. This includes detection of single nucleotide polymorphisms directly from genomic DNA as well as highly homologous mrnas in closely related gene families. Because Cleavase® substrate recognition is structure, and not sequence dependent, cleavage and detection can be applied to virtually any DNA or rna sequence. less

关键词： Nucleic Acid structure Analysis Enzymatic Cleavage NCBI BLAST Sequence Analysis rna secondary structure prediction FRET HPLC Cell And Tissue Culture Cell Lysis rna Extraction Statistical Calculation Data analysis GenBank mrna Cleavase hybridizationcDNA Invader

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The Genetic Data Environment

The Genetic Data Environment

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作者： Jonathan A. Eisen

The Genetic Data Environment (GDE) is a software package designed for molecular sequence alignment and analysis (1). Four features make GDE stand out relative to other similar programs:*** is free. *** has a user-friendly and visually powerful multiple sequence alignment editor. *** can readily be performed on any sequence(s) or region(s) of sequences simply by selecting the sequence(s) or region(s) of interest and choosing the desired function from the pop-up menus. *** it comes with a variety of powerful sequence analysis tools, any additional programs of the user’s interest or updates for programs in use can be incorporated quickly and easily into the menu system (

关键词： Sequence Analysis Multiple Sequence Alignment Sequence Editing rna secondary structure prediction Database Comparison Sequence Analysis Tools Felis catus

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Free Energy Minimization to Predict rna secondary structures and Computational rna Design

Free Energy Minimization to Predict RNA Secondary Structures...

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作者： Alexander Churkin Lina Weinbrand Danny Barash

Determining the rna secondary structure from sequence data by computational predictions is a long-standing problem. Its solution has been approached in two distinctive ways. If a multiple sequence alignment of a collection of homologous sequences is available, the comparative method uses phylogeny to determine conserved base pairs that are more likely to form as a result of billions of years of evolution than by chance. In the case of single sequences, recursive algorithms that compute free energy structures by using empirically derived energy parameters have been developed. This latter approach of rna folding prediction by energy minimization is widely used to predict rna secondary structure from sequence. For a significant number of rna molecules, the secondary structure of the rna molecule is indicative of its function and its computational prediction by minimizing its free energy is important for its functional analysis. A general method for free energy minimization to predict rna secondary structures is dynamic programming, although other optimization methods have been developed as well along with empirically derived energy parameters. In this chapter, we introduce and illustrate by examples the approach of free energy minimization to predict rna secondary structures. less

关键词： rna secondary structure prediction Multiple Sequence Alignment rna structure prediction Mutagenesis Hepatitis C virus rna folding prediction Free energy minimization methods rna free energy parameters rna bioinformatics

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structure Analysis of Microrna Precursors

Structure Analysis of MicroRNA Precursors

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作者： Jacek Krol Wlodzimierz J. Krzyzosiak

Microrna biogenesis occurs in several steps from their precursors having irregular hairpin structures. The highly variable architecture of these stem-and-loop structures, which have terminal loops of various sizes and diverse structure destabilizing motifs present in their stem sections, may strongly influence the process of microrna liberation. In order to better understand this process, more details regarding its structural basis are required A substantial part of this information may be derived from the structure analysis of microrna precursor using biochemical methods. Here we show how the analysis with the use of various nucleases and metal ions is performed. The presented protocols include the design of DNA template-phage promoter fusions to generate natural precursor ends, and the tests performed to check the sequence and structure homogeneity of the in vitro transcripts prior to probing their structures. less

关键词： structure Analysis rna structure prediction In Vitro Transcription Gel Electrophoresis Autoradiography Phosphorimaging rna secondary structure prediction PCR mirna mirna precursor

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Utilization of SSCprofiler to Predict a New mirna Gene

Utilization of SSCprofiler to Predict a New miRNA Gene

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作者： Anastasis Oulas Panayiota Poirazi

Experimental identification provides a valuable yet slow and expensive method for predicting novel mirna genes. With the advent of computational procedures, it is now possible to capture characteristic features of mirna biogenesis in an in silico model, resulting thereafter in the fast and inexpensive prediction of multiple novel mirna gene candidates. These computational tools provide valuable clues to experimentalists, allowing them to narrow down their search space, making experimental verification less time consuming and less costly. Furthermore, the computational model itself can provide biological information as to which are the dominant features that characterize these regulatory units. Moreover, large-scale, high-throughput techniques, such as deep sequencing and tiling arrays, require computational methods to analyze this vast amount of data. Computational mirna gene prediction tools are often used in synergy with high-throughput methods, aiding in the discovery of putative mirna genes. This chapter focuses on a recently developed computational tool (SSCprofiler) for identifying mirna genes and provides an overview of the methodology undertaken by this tool, and defines a stepwise guideline on how to utilize SSCprofiler to predict novel mirnas in the human genome. less

关键词： Deep Sequencing Gene prediction structure prediction Genome Alignment Cell And Tissue Culture rna secondary structure prediction Genome Assembly Programming Language Homo sapiens Mus musculus Canis lupus familiaris Gallus gallus Takifugu Danio rerio Rattus norvegicus Pan troglodytes Hidden Markov model Web tool Expression data

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rna structure prediction, Analysis, and Design: An Introduction to Web-Based Tools

RNA Structure Prediction, Analysis, and Design: An Introduct...

引用

作者： Raphael Angelo Zambrano Carmen Hernandez-Perez Melissa K. Takahashi

Understanding rna structure has become critical in the study of rna in their roles as mediators of biological processes. To aid in these studies, computational algorithms that utilize thermodynamics have been developed to predict rna secondary structure. Due to the importance of intermolecular interactions, the algorithms have been expanded to determine and predict rna-rna hybridization. This chapter discusses popular webservers with the tools for rna secondary structure prediction, rna-rna hybridization, and design. We address key features that distinguish common-functioning programs and their purposes for the interests of the user. Ultimately, we hope this review elucidates web-based tools researchers may take advantage of in their investigations of rna structure and function. less

关键词： rna secondary structure prediction rna structure prediction Noncoding rna rna design tools

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Fast prediction of rna–rna Interaction Using Heuristic Algorithm

Fast Prediction of RNA–RNA Interaction Using Heuristic Algo...

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作者： Soheila Montaseri

Interaction between two rna molecules plays a crucial role in many medical and biological processes such as gene expression regulation. In this process, an rna molecule prohibits the translation of another rna molecule by establishing stable interactions with it. Some algorithms have been formed to predict the structure of the rna–rna interaction. High computational time is a common challenge in most of the presented algorithms. In this context, a heuristic method is introduced to accurately predict the interaction between two rnas based on minimum free energy (MFE). This algorithm uses a few dot matrices for finding the secondary structure of each rna and binding sites between two rnas. Furthermore, a parallel version of this method is presented. We describe the algorithm’s concurrency and parallelism for a multicore chip. The proposed algorithm has been performed on some datasets including CopA-CopT, R1inv-R2inv, Tar-Tar*, DIS-DIS, and Incrna54-RepZ in Escherichia coli bacteria. The method has high validity and efficiency, and it is run in low computational time in comparison to other approaches. less

关键词： rna secondary structure prediction Intarna Escherichia coli rna secondary structure rna–rna interaction Heuristic Parallel Minimum free energy

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Development of rna G-quadruplex (rG4)-targeting

Development of RNA G-quadruplex (rG4)-targeting

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作者： Mubarak I. Umar Chun-Yin Chan Chun Kit Kwok

rna G-quadruplex (rG4)-SELEX is a method that generates l-rna aptamers to target an rG4 structure of interest, which can be applied to inhibit G-quadruplex-mediated interactions that have important roles in gene regulation and function. Here we present a Protocol Extension substantially modifying an existing SELEX protocol to describe in detail the procedures involved in performing rG4-SELEX to identify rG4-specific binders that can effectively suppress rG4–peptide and rG4–protein associations. This Protocol Extension improves the speed of aptamer discovery and identification, offering a suite of techniques to characterize the aptamer secondary structure and monitor binding affinity and specificity, and demonstrating the utility of the l-rna aptamer. The previous protocol mainly describes the identification of rna aptamers against proteins of interest, whereas in this Protocol Extension we present the development of an unnatural rna aptamer against an rna structure of interest, with the potential to be applicable to other nucleic acid motifs or biomolecules. rG4-SELEX starts with a random d-rna library incubated with the l-rG4 target of interest, followed by binding, washing and elution of the library. Enriched d-aptamer candidates are sequenced and structurally characterized. Then, the l-aptamer is synthesized and used for different applications. rG4-SELEX can be carried out by an experienced molecular biologist with a basic understanding of nucleic acids. The development of rG4-targeting l-rna aptamers expands the current rG4 toolkit to explore innovative rG4-related applications, and opens new doors to discovering novel rG4 biology in the near future. The duration of each selection cycle as outlined in the protocol is ~2 d. less

关键词： In Vitro Transcription PCR TA cloning Data analysis Native PAGE SELEX Thin-layer Chromatography Shadowing (Histology) rna Extraction Agarose Gel Electrophoresis DNA Ligation Transfection TOPO Cloning Colony PCR Snapgene Sanger Sequencing ClustalO rna secondary structure prediction EMSA ImageJ GraphPad Prism Electrophoresis Sequence Analysis Tools Saccharomyces cerevisiae Sequencing rna Nucleic acids

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Identification of mirnas Bound to an rna of Interest by Microrna Capture Affinity Technology (miR-CATCH)

Identification of miRNAs Bound to an RNA of Interest by Micr...

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作者： Andrea Zeni Margherita Grasso Michela A. Denti

microrna capture affinity technology (miR-CATCH) uses affinity capture biotinylated antisense oligonucleotides to co-purify a target transcript together with all its endogenously bound mirnas. The miR-CATCH assay is performed to investigate mirnas bound to a specific mrna. This method allows to have a total vision of mirnas bound not only to the 3′UTR but also to the 5′UTR and Coding Region of target messenger rnas (mrnas). less

关键词： Cell Lysis Affinity Purification Cross-linking rna secondary structure prediction Real-time PCR Quantitative Reverse Transcription PCR Reverse Transcription PCR Cell And Tissue Culture Pull-down Assay Homo sapiens mirnas Post-transcriptional regulation miR-CATCH mirna target analysis

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