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相关概念视频

RNA Structure01:19

RNA Structure

4.8K
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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Bacterial RNA Polymerase00:43

Bacterial RNA Polymerase

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Unlike eukaryotes, bacteria use a single RNA Polymerase (RNAP) to transcribe all genes. The different subunits of bacterial RNAPhave distinct functions. The multisubunit structure of the bacterial RNAP helps the enzyme to maintain catalytic function, facilitate assembly, interact with DNA and RNA, and self-regulate its activity.
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...
29.4K
Bacterial Transcription01:53

Bacterial Transcription

28.1K
RNA polymerase (RNAP) carries out DNA-dependent RNA synthesis in both bacteria and eukaryotes. Bacteria do not have a membrane-bound nucleus. So, transcription and translation occur simultaneously, on the same DNA template.
Transcription can be divided into three main stages, each involving distinct DNA sequences to guide the polymerase. These are:
28.1K
Protein Folding01:25

Protein Folding

7.9K
Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
7.9K
Ribosomal RNA Synthesis02:53

Ribosomal RNA Synthesis

13.2K
Ribosome synthesis is a highly complex and coordinated process involving more than 200 assembly factors. The synthesis and processing of ribosomal components occurs not only in the nucleolus but also in the nucleoplasm and the cytoplasm of eukaryotic cells.
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...
13.2K
Leaky Scanning02:28

Leaky Scanning

5.1K
During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R...
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相关实验视频

Updated: Jun 22, 2025

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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RiboDiffusion:基于三级结构的RNA反折叠与产生性扩散模型.

Han Huang1,2, Ziqian Lin1,3, Dongchen He1

  • 1Department of Computer Science and Engineering, CUHK, Hong Kong SAR, 999077, China.

Bioinformatics (Oxford, England)
|June 28, 2024
PubMed
概括

RiboDiffusion是一种新的生成模型,从3D结构设计RNA序列,改善合成生物学和治疗学的RNA反折叠. 它在序列恢复和多样性之间提供了平衡,优于现有的方法.

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Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation
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Analyzing and Building Nucleic Acid Structures with 3DNA
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Analyzing and Building Nucleic Acid Structures with 3DNA

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科学领域:

  • 计算生物学 计算生物学
  • 合成生物学 合成生物学
  • 生物技术是生物技术.

背景情况:

  • RNA在生物学中的关键作用推动了合成生物学和治疗学的应用.
  • 反向RNA折叠问题,即为特定结构设计功能序列,仍然是一个挑战,特别是在3D构造中.
  • 现有的计算方法主要集中在二次结构上,直接基于3D结构的设计面临数据稀缺性和结构灵活性问题.

研究的目的:

  • 开发一种新的生成模型,RiboDiffusion,用于使用3D结构信息进行RNA逆折叠.
  • 为了使RNA序列的设计符合指定的3D骨干结构.
  • 探索序列恢复和RNA设计中的多样性之间的权衡.

主要方法:

  • RiboDiffusion采用一种生成扩散模型,集成图形神经网络用于结构和变压器用于序列.
  • 该模型反复地将随机序列改进为受3DRNA骨干结构条件的目标序列.
  • 测试组通过RNA聚类 (序列/结构相似性) 来分层,以评估模型性能.

主要成果:

  • 在序列恢复方面,RiboDiffusion显著优于基线方法,在基于相似性的分割上显示了11-16%的相对改善.
  • 该模型在各种RNA长度和类型中展示了一致的性能.
  • 在形折叠验证证实,生成的序列可以采用目标3DRNA骨干.

结论:

  • RiboDiffusion为3D结构的RNA逆折叠提供了一种强大的新方法.
  • 该方法有效地导航序列空间,以找到满足结构约束的新型RNA候选者.
  • 这种工具在合成生物学和治疗开发中推进RNA设计方面具有重大潜力.