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相关概念视频

RNA-seq03:21

RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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Ribosome Profiling02:24

Ribosome Profiling

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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
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RNA Structure01:19

RNA Structure

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The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...
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Nucleic Acid Structure01:25

Nucleic Acid Structure

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The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA...
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RNA Stability01:53

RNA Stability

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Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
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Types of RNA01:20

Types of RNA

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Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in regulating gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
RNA Performs Diverse...
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相关实验视频

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RNA Secondary Structure Prediction Using High-throughput SHAPE
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RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

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通过深度学习和溶液散射来预测RNA结构和动态.

Edan Patt1, Scott Classen2, Michal Hammel2

  • 1School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.

Biophysical journal
|December 26, 2024
PubMed
概括
此摘要是机器生成的。

由于灵活性和离子效应,预测溶液中的RNA结构具有挑战性. 一个新的工具SCOPER集成了深度学习和采样,以准确地建模RNA结构,并使用小角度X射线散射 (SAXS) 验证结构.

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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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科学领域:

  • 结构生物学是结构生物学.
  • 计算生物学是一种计算生物学.
  • 生物物理学的生物物理.

背景情况:

  • RNA分子表现出形状灵活性,使其难以预测在不同条件下溶液中的结构.
  • 微角X射线散射 (SAXS) 对于通过将实验数据与计算资料进行比较来验证预测的RNA结构至关重要.
  • 现有的方法难以准确地表示RNA可塑性,并且在结构模型中包含Mg2+等必不可少的离子.

研究的目的:

  • 开发一种先进的计算工具,SCOPER (RNA的溶液形状预测器),用于预测和验证溶液中的RNA结构.
  • 解决RNA形态可塑性和在结构建模中准确纳入离子的挑战.
  • 通过考虑溶液条件,提高SAXS对RNA结构的配置准确度.

主要方法:

  • 集成基于动力学的构造性采样与深度学习模型 (IonNet) 进行集成,用于预测Mg2+离子结合点.
  • 开发一个管道 (SCOPER) 来建模RNA溶液构造,包括离子相互作用和构造组合.
  • 将SCOPER与14个SAXS实验数据集进行比较,以评估其性能.

主要成果:

  • 通过结合Mg2+离子和采样RNA形态可塑性,SCOPER显著提高了SAXS配置匹配的质量.
  • 该研究表明,离子含量增加与RNA可塑性降低相关.
  • 精确调整可塑性和离子密度对于防止超匹配实验SAXS数据至关重要.

结论:

  • SCOPER提供了一种有效和准确的方法来验证RNA溶液结构,并生成纠正的原子模型,包括离子.
  • 当提供初始,足够准确的RNA结构时,该工具是有效的.
  • 了解离子度和RNA灵活性之间的相互作用是解决方案中准确的结构预测的关键.