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DNA Topoisomerases02:02

DNA Topoisomerases

36.4K
Topoisomerases are enzymes that relax overwound DNA molecules during various cell processes, including DNA replication and transcription. These enzymes regulate positive and negative DNA supercoiling without changing the nucleotide sequence. DNA overwinding in a clockwise direction results in positively supercoiled DNA, whereas underwinding in a counterclockwise direction produces negatively supercoiled DNA.
Types and Mechanism of action
Topoisomerases are divided into two main types. ...
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The DNA Replication Fork01:02

The DNA Replication Fork

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An organism’s genome needs to be duplicated in an efficient and error-free manner for its growth and survival. The replication fork is a Y-shaped active region where two strands of DNA are separated and replicated continuously. The coupling of DNA unzipping and complementary strand synthesis is a characteristic feature of a replication fork.   Organisms with small circular DNA, such as E. coli, often have a single origin of replication; therefore, they have only two replication...
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The DNA Replication Fork01:02

The DNA Replication Fork

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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...
17.0K
Replication in Prokaryotes01:32

Replication in Prokaryotes

28.5K
DNA replication has three main steps: initiation, elongation, and termination. Replication in prokaryotes begins when initiator proteins bind to the single origin of replication (ori) on the cell's circular chromosome. Replication then proceeds around the entire circle of the chromosome in each direction from the two replication forks, resulting in two DNA molecules.
Many Proteins Work Together to Replicate the Chromosome
Replication is coordinated and carried out by a host of specialized...
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Replication in Prokaryotes02:35

Replication in Prokaryotes

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Single-Molecule Real-Time Visualization of DNA Unwinding by CMG Helicase
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自由端を持つDNAの超らせん化

Daniela Moretti1, Giada Forte2, Giuseppe Gonnella1

  • 1Dipartimento Interateneo di Fisica, Università degli Studi di Bari and INFN, Sezione di Bari, via Amendola 173, Bari, I-70126, Italy. daniela.moretti@uniba.it.

Soft matter
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まとめ
この要約は機械生成です。

開鎖DNAへのトルク印加は超らせん遷移を誘発する。DNAは膨潤相からプレクトネミック相へ移行し、非線形なツイストと局在化したライトダイナミクスを示し、実験的検証の可能性がある。

キーワード:
DNA超らせん化開鎖DNAトルク相転移プレクトネミック相ツイストライト

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Studying DNA Looping by Single-Molecule FRET
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Tools to Study the Role of Architectural Protein HMGB1 in the Processing of Helix Distorting, Site-specific DNA Interstrand Crosslinks
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科学分野:

  • 生物物理学
  • 高分子物理学
  • 計算生物学

背景:

  • DNAの超らせん化はゲノム機能に不可欠である。
  • トルク下でのDNA力学の理解は不可欠である。
  • 開鎖DNA末端のダイナミクスは特有の課題を提示する。

研究 の 目的:

  • 一定トルク下での開鎖DNAにおける超らせんダイナミクスを調査する。
  • 定常状態のツイストとライトプロファイルを解析する。
  • DNA相間の遷移を探索する。

主な方法:

  • 粗視化ブラウンダイナミクスシミュレーション。
  • 平均場理論解析。
  • 印加トルク下でのDNAポリマーのモデリング。

主要な成果:

  • 相転移（膨潤相からプレクトネミック相へ）の臨界トルク閾値を観測した。
  • プレクトネミック相における非線形かつ不均一なツイストプロファイルを特定した。
  • 拡散的なツイスト蓄積と無視できるライト拡散を示した。

結論:

  • DNAの超らせん化は、自由端があってもトルク依存性である。
  • プレクトネーム形成はトルク印加点付近に局在する。
  • 結果は、単一分子実験との比較のための枠組みを提供する。