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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 Structure01:23

RNA Structure

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Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. 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): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
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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.
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RNA Stability01:53

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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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相关实验视频

Updated: Jun 3, 2025

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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通过深度学习和解决方案分散来预测RNA结构和动力学.

Edan Patt1, Scott Classen2, Michal Hammel2

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

bioRxiv : the preprint server for biology
|January 7, 2025
PubMed
概括
此摘要是机器生成的。

SCOPER通过整合构型采样和离子结合预测来预测溶液中的RNA结构. 这种方法使用小角度X射线散射 (SAXS) 数据准确验证RNA结构.

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科学领域:

  • 计算生物学 计算生物学
  • 结构生物学 结构生物学
  • 生物物理学的生物物理.

背景情况:

  • RNA分子表现出灵活性,使得在不同的条件下对它们的溶液构造进行建模具有挑战性.
  • 预测精确的RNA结构需要考虑离子和形状可塑性,这些常常在当前模型中缺失.
  • 小角度X射线散射 (SAXS) 是验证溶液中预测的RNA结构的关键实验技术.

研究的目的:

  • 开发一个计算管道,SCOPER,用于预测和验证溶液中的RNA结构.
  • 在RNA结构预测中解决缺少离子和形态可塑性的挑战.
  • 为了提高SAXS对RNA结构的配置匹配的准确性.

主要方法:

  • 集成基于动力学的构造采样与深度学习模型IonNet,用于预测Mg2+离子结合点.
  • 与14个实验SAXS数据集对比SCOPER的基准测试.
  • 分析离子含量对RNA可塑性的影响.

主要成果:

  • SCOPER通过结合Mg2+离子和 conformational采样,显著提高了SAXS配置匹配的质量.
  • 增加的离子含量被观察到降低RNA可塑性.
  • 该研究强调了调整可塑性和离子密度的重要性,以防止超匹配实验SAXS数据.

结论:

  • SCOPER提供了一种有效的工具,用于验证RNA结构的溶液状态.
  • 管道生成了RNA的纠正原子模型,包括必需的离子.
  • 对RNA结构的准确验证需要考虑离子相互作用和构造动力学.