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相关概念视频

The DNA Helix01:16

The DNA Helix

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Overview
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DNA as a Genetic Template02:05

DNA as a Genetic Template

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Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...
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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
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Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

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For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...
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Molecular Shapes01:18

Molecular Shapes

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Molecules have characteristic shapes that are crucial for their function. The arrangement of various electron groups around the central atom dictates their molecular geometry. Electron pairs in the valence shell of a central atom will adopt an arrangement that minimizes repulsions between the electron pairs by maximizing the distance between them. The valence electrons form either bonding pairs, located primarily between bonded atoms, or lone pairs.
Two regions of electron density in a diatomic...
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Labeling DNA Probes03:31

Labeling DNA Probes

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DNA probes are fragments of DNA labeled with a reporter tag to enable their detection or purification. The resulting labeled DNA probes can then hybridize to target nucleic acid sequences through complementary base-pairing, and may be used to recover or identify these regions.
Radioisotopes, fluorophores, or small molecule binding partners like biotin or digoxigenin, are the most widely used reporter tags for labeling DNA probes. These labels can be attached to the probe DNA molecule via...
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发现具有多个DNA形状特征的DNA形状图案:概括,方法和验证.

Nanjun Chen1, Jixiang Yu1, Zhe Liu1

  • 1Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR.

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我们开发了新的计算工具来发现DNA形状动机,揭示了对基因调节和DNA-蛋白相互作用的见解. 这些方法提高了对DNA拓学的理解.

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科学领域:

  • 基因组学就是基因组学.
  • 生物信息学是一种生物信息学.
  • 计算生物学 计算生物学

背景情况:

  • 基因调控中,DNA动图至关重要,DNA结合蛋白 (DBPs) 与特定序列相互作用.
  • 反映内在DNA拓学的DNA形状特征,越来越多地被认为是它们在DNA-DBP相互作用中的作用.
  • 现有的高通量工具用于发现DNA形状图案,特别是那些整合多个特征的工具,是有限的.

研究的目的:

  • 开发和验证用于发现非冗余DNA形状图案的先进计算方法.
  • 将DNA形状动图的发现概括为同时容纳多个动图和多个形状特征.
  • 在基因调节的背景下,为分析DNA拓提供可访问的工具.

主要方法:

  • 现有的吉布斯采样方法的概括,用于多动机和多特征DNA形状的发现.
  • 开发一种新的预期最大化 (EM) 算法,用于DNA形状图案识别.
  • 实施混合EM-Gibbs采样方法,结合两种方法的优势.
  • 创建一个R包,以开放可访问性和实际应用开发的工具.

主要成果:

  • 提出的方法在DNA形状模式发现方面显示出有前途的性能,融合和效率.
  • 发现的DNA形状图案为低信号的ChIP-seq峰峰峰提供了新的见解,补充了基于序列的图案分析.
  • 该建模成功地捕捉了多个DNA形状特征之间的潜在相互作用.
  • 开发的R包为研究DNA-DBP相互作用的研究人员提供了一个有价值的平台.

结论:

  • 新的计算工具已成功开发用于发现DNA形状图案,解决现有方法的局限性.
  • 这些工具通过整合序列和形状信息来增强对DNA-DBP结合的理解.
  • 这些发现为基因调节提供了新的视角,突出了DNA拓学的作用.
  • 提供了一个可访问的R包,以促进进一步的实地研究和应用.