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The DNA Helix01:16

The DNA Helix

Overview
¹H NMR: Complex Splitting01:13

¹H NMR: Complex Splitting

A proton M that is coupled to a proton X results in doublet signals for M. However, NMR-active nuclei can be simultaneously coupled to more than one nonequivalent nucleus. When M is coupled to a second proton A, such as in styrene oxide, each peak in the doublet is split into another doublet.
Splitting diagrams or splitting tree diagrams are routinely used to depict such complex couplings. While drawing splitting diagrams, the splitting with the larger coupling constant is usually applied first.
¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between the...
The DNA Helix01:07

The DNA Helix

Deoxyribonucleic acid, or DNA, is the genetic material responsible for passing traits from generation to generation in all organisms and most viruses. DNA is composed of two strands of nucleotides that wind around each other to form a spring-like structure called a double helix. However, the double helix is not perfectly symmetrical. Instead, there are regularly occurring grooves in the structure. The major groove occurs where the sugar-phosphate backbones are relatively far apart. This space...
¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR01:15

¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR

The axial and equatorial protons in cyclohexane can be distinguished by performing a variable-temperature NMR experiment. In this process, except for one proton, the remaining eleven protons are replaced by deuterium. The deuterium substitution avoids the possible peak splitting caused by the spin-spin coupling between the adjacent protons. The remaining proton flips between the axial and equatorial positions.
Nucleic Acid Structure01:25

Nucleic Acid Structure

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
DNA has a double-helix structure. The...

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関連する実験動画

Updated: Jul 20, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

サイクルポリアミド-DNA複合体のNMR構造

Qing Zhang1, Tammy J Dwyer, Vickie Tsui

  • 1Department of Chemistry, University of California, Berkeley, California 94720-1460, USA.

Journal of the American Chemical Society
|June 24, 2004
PubMed
まとめ

この研究は,NMRと分子ダイナミクスを用いてDNAに結合したサイクルポリアミドの構造を明らかにしています. リガンドは緊密に結合し,構造的変化にもかかわらずDNAの柔軟性を示します.

科学分野:

  • 構造生物学 構造生物学とは
  • バイオケミストリー バイオケミストリー
  • 分子生物物理学 分子生物物理学

背景:

  • サイクルポリアミドは,DNA結合剤として研究されています.
  • リンガンド-DNAの相互作用を理解することは,薬剤設計において極めて重要です.

研究 の 目的:

  • 特定のDNAオリゴーマーと複合したサイクルポリアミドの溶液構造を決定する.
  • ポリアミド-DNA複合体の結合相互作用とダイナミクスを分析する.

主な方法:

  • 2D (1) H NMRデータを取得するために,核磁気共振 (NMR) スペクトロスコーピーを使用しました.
  • 距離制限は,MARDIGRASを使用してNOESYのクロスピーク強度から導かれました.
  • 構造を生成するために,溶剤モデルで抑制された分子ダイナミクス計算を行いました.

主要な成果:

  • DNA二重複に複合したサイクリックポリアミド (サイクロ-ガンマ-ImPyPy-ガンマ-PyPyPy-) の溶液構造が決定されました.
  • リガンドはDNA結合のためのナノモラー解離定数を示します.
  • 構造は,DNAの歪みを示し,サイクル化によりリガンドのリングの積み重ねが変化したが,無結合複合体と比較して同様のDNA相互作用を維持した.

さらに関連する動画

Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles
10:23

Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles

Published on: May 8, 2015

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
14:55

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

Published on: September 17, 2017

関連する実験動画

Last Updated: Jul 20, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles
10:23

Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles

Published on: May 8, 2015

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
14:55

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

Published on: September 17, 2017

  • 緩やかな結合解離とDNA開口の変動の減少が観察されました.

    • 結論:

    • サイクルポリアミドはDNAに安定的に結合し,軽微な構造変化を引き起こす.
    • サイクライゼーションはリガンド構成に影響しますが,全体的なDNA相互作用プロファイルには影響しません.
    • リガンド-DNA複合体は,リガンド結合とDNAの柔軟性とのダイナミックな相互作用を示しています.