Topic of Contents

Some are based on the textbook and Wikipedia

  1. A nucleosome is the basic structural unit of DNA packaging in eukaryotes. The structure of a nucleosome consists of a segment of DNA wound around eight histone proteins and resembles thread wrapped around a spool. The nucleosome is the fundamental subunit of chromatin. Each nucleosome is composed of a little less than two turns of DNA wrapped around a set of eight proteins called histones, which are known as a histone octamer. Each histone octamer is composed of two copies each of the histone proteins H2A, H2B, H3, and H4.

    一个核小体是 DNA 在 真核生物 中包装的基本结构单元。核小体的结构由一段缠绕在八个组蛋白周围的 DNA 组成，类似于缠绕在卷轴上的线。核小体是 染色质 的基本亚单位。每个核小体由少于两圈缠绕在一组八个称为组蛋白的蛋白质周围的 DNA 组成，这组蛋白质被称为组蛋白八聚体。每个组蛋白八聚体由两份每种组蛋白 H2A、H2B、H3 和 H4 组成。

  2. DNA must be compacted into nucleosomes to fit within the cell nucleus. In addition to nucleosome wrapping, eukaryotic chromatin is further compacted by being folded into a series of more complex structures, eventually forming a chromosome. Each human cell contains about 30 million nucleosomes.

    DNA 必须被压缩成核小体以适应细胞核。除了核小体的包裹，真核 染色质 还通过折叠成一系列更复杂的结构来进一步压缩，最终形成染色体。每个人体细胞包含大约 3000 万个核小体。

  3. The nucleosome core particle consists of approximately 146 base pairs (bp) of DNA wrapped in 1.67 left-handed superhelical turns around a histone octamer, consisting of 2 copies each of the core histones H2A, H2B, H3, and H4. Core particles are connected by stretches of linker DNA, which can be up to about 80 bp long.

    核小体核心颗粒由大约 146 碱基对 (bp) 的 DNA 组成，绕着一个由 2 个拷贝核心组蛋白 H2A、H2B、H3 和 H4 组成的组蛋白八聚体以 1.67 个左手超螺旋包裹。核心颗粒通过长度可达约 80 bp 的 连接 DNA 连接在一起。

  4. The DNA of most organisms is usually negatively supercoiled. It becomes temporarily positively supercoiled when it is being replicated or transcribed.

Supercoiled DNA
Supercoiled DNA
Supercoiled DNA 
> 大多数生物的 DNA 通常是**负超螺旋**的。在复制或转录时，它会暂时变为正超螺旋。

  1. Supercoiled DNA forms two structures; a plectoneme or a toroid, or a combination of both. A negatively supercoiled DNA molecule will produce either a one-start left-handed helix, the toroid, or a two-start right-handed helix with terminal loops, the plectoneme. Plectonemes are typically more common in nature, and this is the shape most bacterial plasmids will take.

    超螺旋 DNA 形成两种结构；一个螺旋体或一个环形体，或者两者的结合。一个负超螺旋的 DNA 分子将产生一个单起始的左手螺旋，即环形体，或者一个双起始的右手螺旋，带有末端环的螺旋体。螺旋体在自然界中通常更为常见，这也是大多数细菌质粒将采取的形状。

  2. The DNA topoisomerases prevent and correct these types of topological problems. They do this by binding to DNA and cutting the sugar-phosphate backbone of either one (type I topoisomerases) or both (type II topoisomerases) of the DNA strands. This transient break allows the DNA to be untangled or unwound, and, at the end of these processes, the DNA backbone is resealed. Since the overall chemical composition and connectivity of the DNA do not change, the DNA substrate and product are chemical isomers, differing only in their topology.

    DNA 拓扑异构酶防止并纠正这些类型的拓扑问题。它们通过结合到 DNA 并切割糖-磷酸骨架，作用于其中一条（I 型拓扑异构酶）或两条（II 型拓扑异构酶）DNA 链来实现这一点。 这种暂时的断裂使得 DNA 能够解开或展开，在这些过程结束时，DNA 的主链重新封闭。由于 DNA 的整体化学成分和连接性没有改变，DNA 底物和产物是化学异构体，仅在其拓扑结构上有所不同。

  3. Topologically Domaincan also be called topologically associating domain (TAD), which is a self-interacting genomic region, meaning that DNA sequences within a TAD physically interact with each other more frequently than with sequences outside the TAD.

    拓扑结构域又可以被称为拓扑关联域(TAD)， 是一个自我交互的基因组区域，这意味着 DNA 序列 在 TAD 内的物理互动频率高于与 TAD 外序列的互动频率。

  4. The histone N-terminal tails stabilize DNA wrapping around the octamer → DNA is packaged into chromatin in a special way.

    组蛋白N端尾部稳定DNA绕绕八聚体的包裹 → DNA以一种特殊的方式包装成染色质。

  5. In the electron microscope, two states of chromatin are observed: fibers with a diameter of either 30 nm or 10 nm.

    The 30-nm fiber is a more compact version of chromatin that is frequently folded into large loops reaching out from a protein core or scaffold. In contrast, the 10-nm fiber is a less compact form of chromatin that resembles a regular series of “beads on a string.” These beads are nucleosomes, and these protein – DNA structures play a critical role in regulating the structure and function of chromosomes.

    在电子显微镜下，观察到染色质的两种状态：直径为 30 纳米或 10 纳米的纤维。

    30 纳米纤维是染色质的一种更紧凑的形式，经常折叠成从蛋白质核心或支架延伸出的大环。相比之下，10 纳米纤维是染色质的一种较不紧凑的形式，类似于一系列规则的“串珠”。这些珠子是核小体，这些蛋白质 - DNA 结构在调控染色体的结构和功能中起着关键作用。

  6. The supercoiling in nucleic acids is not spontaneously formed, as DNA is a semi-rigid elastic molecule that cannot change shape arbitrarily.

    核酸中的超螺旋并非自发形成，因为 DNA 是一种半刚性的弹性分子，不能任意改变形状。

  7. The formation of positive and negative supercoils is related to the interaction forces between various nucleic acid molecules inside DNA. If the force is repulsive, the helix is easily unwound, resulting in negative supercoiling; if the force is attractive, the helix is not easily unwound, resulting in positive supercoiling.

    形成正负超螺旋的因素与 DNA 内部各个核酸分子之间的相互作用力有关，若表现为斥力，则螺旋容易被解开，表现为负超螺旋；若表现为引力，则螺旋不易被解开，表现为正超螺旋。

  8. cccDNA (covalently closed circular DNA), a topological domain whose ends are impossible to rotate, is a special DNA structure that arises during the propagation of some viruses in the cell nucleus and may remain permanently there. It is a double-stranded DNA that originates in a linear form that is ligated by means of DNA ligase to a covalently closed ring. In most cases, transcription of viral DNA can occur from the circular form only. The cccDNA of viruses is also known as episomal DNA or occasionally as a minichromosome.

cccDNA
cccDNA
cccDNA 
<center><small>By Navneet Matharu, Nadav Ahituv - Matharu, Navneet (<span class="mw-formatted-date" title="2015-12-03">2015-12-03</span>). "<a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMCPMC4669122">Minor Loops in Major Folds: Enhancer–Promoter Looping, Chromatin Restructuring, and Their Association with Transcriptional Regulation and Disease</a>". PLOS Genetics 11 (12): e1005640. <span lang="en" dir="ltr"><a href="https://en.wikipedia.org/wiki/Digital_object_identifier" class="extiw" title="en:Digital object identifier">DOI</a></span>:<a rel="nofollow" class="external text" href="https://doi.org/10.1371/journal.pgen.1005640">10.1371/journal.pgen.1005640</a>. <span lang="en" dir="ltr"><a href="https://en.wikipedia.org/wiki/PubMed" class="extiw" title="en:PubMed"><span lang="en" dir="ltr">PMID</span></a></span> <a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pubmed/26632825">26632825</a>. <span lang="en" dir="ltr"><a href="https://en.wikipedia.org/wiki/PubMed_Central" class="extiw" title="en:PubMed Central"><span lang="en" dir="ltr">PMC</span></a></span>: <a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMCPMC4669122">PMC4669122</a>. <span lang="en" dir="ltr"><a href="https://en.wikipedia.org/wiki/ISSN" class="extiw" title="en:ISSN"><span lang="en" dir="ltr">ISSN</span></a></span> <a rel="nofollow" class="external text" href="https://www.worldcat.org/issn/1553-7404">1553-7404</a>., <a href="https://creativecommons.org/licenses/by-sa/4.0" title="Creative Commons Attribution-Share Alike 4.0">CC BY-SA 4.0</a>, <a href="https://commons.wikimedia.org/w/index.php?curid=59894646">Link</a></small></center>

> **cccDNA (共价闭合环状 DNA)** 是一种特殊的 DNA 结构，它是一种末端无法旋转的拓扑结构域，出现在某些病毒在细胞核中传播时，并可能永久保留在那里。它是一种双链DNA，起源于线性形式，通过 DNA 连接酶连接成一个 共价闭合的环。在大多数情况下，病毒 DNA 的 转录 只能从环状形式发生。病毒的 cccDNA 也被称为**外源性 DNA**，有时也称为**迷你染色体**。

  1. The superhelical density of DNA $\left( \sigma = \frac{\Delta Lk}{{Lk}^0}\right)$ is related to Linking Number ($Lk$). If the $Lk$ is changed, then the DNA becomes torsionally stressed. If $\Delta Lk \left(= Lk - {Lk}^0 \right) < 0$, the DNA is said to be “negatively supercoiled”. DNA in cells is usually negatively supercoiled by about 6%.

    DNA的超螺旋密度（$\sigma = \frac{\Delta Lk}{{Lk}^0}$）与连结数（$Lk$）有关。如果$Lk$发生变化，那么DNA就会产生扭转应力。如果$\Delta Lk \left(= Lk - {Lk}^0 \right) < 0$，则称DNA为“负超螺旋”。细胞中的 DNA 负超螺旋度约为 6%。

Volcabulary

All the words to be translated in Chapter 8 are listed in the summary of Week 02.

Thoughts

Partically based on online tools like Wikipedia and gpt-4o-latest.

Slide 01

Slide 01
Slide 01
Slide 01

This slide illustrates the migration of different forms of DNA during gel electrophoresis, highlighting how the conformation of DNA affects its movement through the gel matrix.

  1. Types of DNA Conformations:
    • Supercoiled DNA (represented in section A): This form is tightly coiled and compact, allowing it to migrate faster through the gel.
    • Relaxed Circular DNA (section B): This DNA is less compact than supercoiled DNA, resulting in slower migration.
    • Linear DNA (section C): This form has a distinct linear structure and migrates at a rate that is intermediate between supercoiled and relaxed circular DNA.
    • Open Circular DNA (section D): This form is similar to relaxed circular DNA but has some nicks or breaks, affecting its migration speed.
  2. Migration Behavior:
    • The slide notes that supercoiled DNA molecules are more compact than relaxed ones, which allows them to migrate more rapidly during gel electrophoresis. The more compact the DNA, the easier it moves through the gel’s pores.
  3. Gel Electrophoresis:
    • This technique separates DNA molecules based on size and conformation. Smaller and more compact DNA structures pass through the gel matrix more easily than larger or more relaxed structures.

这张幻灯片展示了在凝胶电泳过程中不同形式的 DNA 迁移情况，突出了 DNA 的构象如何影响其在凝胶基质中的迁移。

  1. DNA 构象类型：
    • 超螺旋 DNA（在 A 区域表示）：这种形式紧密缠绕、紧凑，使其能够更快地在凝胶中迁移。
    • 松弛环状 DNA（B 区域）：这种 DNA 比超螺旋 DNA 更松散，导致迁移速度较慢。
    • 线性 DNA（C 区域）：这种形式具有明显的线性结构，迁移速度介于超螺旋和松弛环状 DNA 之间。
    • 开放环状 DNA（D 区域）：这种形式类似于松弛环状 DNA，但有一些切口或断裂，影响其迁移速度。
  2. 迁移行为：
    • 幻灯片指出，超螺旋 DNA 分子比松弛的分子更紧凑，这使它们在凝胶电泳过程中迁移更快。DNA 越紧凑，就越容易穿过凝胶的孔隙。
  3. 凝胶电泳：
    • 这项技术根据大小和构象分离 DNA 分子。较小且更紧凑的 DNA 结构比较大或更松弛的结构更容易通过凝胶基质。

Slide 02

Slide 02
Slide 02
Slide 02

This slide focuses on the concept of topoisomers—different forms of DNA that have the same number of base pairs but differ in their linking number, which affects their degree of supercoiling. It illustrates how these variations can be observed through gel electrophoresis.

  1. Topoisomers:
    • Defined as DNA forms that differ in topology, specifically in linking number ($Lk$), while maintaining the same base pair count (bps).
    • They exhibit different degrees of supercoiling, which influences their physical properties.
  2. Gel Electrophoresis Results:
    • Lane 1: Contains highly supercoiled DNA. It migrates as a single band due to its compact structure, which allows it to move quickly through the gel.
    • Lane 2: Represents DNA that has undergone some relaxation but not as much as in lane 3. This DNA migrates to a different position compared to the highly supercoiled DNA.
    • Lane 3: Shows DNA that has been treated with a type I topoisomerase for a longer duration than the DNA in lane 2. This treatment reduces the supercoiling and results in a further change in migration pattern.
  3. Linking Number (Lk):
    • The linking number is a topological property that indicates how many times one strand of DNA winds around another.
    • The slide notes that the linking number changes by 1 from one band to the next in the gel, reflecting the gradual relaxation of the DNA as it is treated with topoisomerase.

这张幻灯片着重介绍了拓扑异构体的概念——这是指具有相同碱基对数目但连接数不同的 DNA 形式，连接数的不同会影响其超螺旋程度。

  1. 拓扑异构体：
    • 定义为在拓扑结构上不同的 DNA 形式，具体表现为连接数（$Lk$）不同，但碱基对数目相同。
    • 它们表现出不同程度的超螺旋，这影响了它们的物理特性。
  2. 凝胶电泳结果：
    • Lane 1：含有高度超螺旋的 DNA。由于其紧凑的结构，它以单一带状迁移，能够快速通过凝胶。
    • Lane 2：代表经历了一定程度松弛的 DNA，但不及 Lane 3。这种 DNA 与高度超螺旋的 DNA 相比迁移至不同位置。
    • Lane 3：展示了经过比 Lane 2 更长时间处理的 DNA，使用了 I 型拓扑异构酶。这种处理减少了超螺旋，并导致迁移模式的进一步改变。
  3. 连接数（Lk）：
    • 连接数是一个拓扑性质，指示一条 DNA 链绕另一条 DNA 链缠绕的次数。
    • 幻灯片指出，在凝胶中，从一个带到下一个带，连接数每次变化 1，反映了 DNA 在拓扑异构酶处理下逐渐松弛的过程。

Translation

All the summaries to be translated in Chapter 8 are listed in the summary of Week 02.