2KH0

2-Hydroxy-7-nitrofluorene covalently linked into a 13mer DNA duplex - solution structure of the face-down orientation

2KH0 の概要

• エントリーDOI: 10.2210/pdb2kh0/pdb
• 関連するPDBエントリー: 2KGZ 2KH1
• 分子名称: 5'-D(*GP*CP*TP*GP*CP*AP*(3DR)P*AP*CP*GP*TP*CP*G)-3', 5'-D(*CP*GP*AP*CP*GP*TP*(3DR)P*TP*GP*CP*AP*GP*C)-3', 7-nitro-9H-fluoren-2-ol (3 entities in total)
• 機能のキーワード: dna, solution structure, base pair mimic, conformational flexibility
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 7914.19

構造登録者

Dallmann, A.,Pfaffe, M.,Muegge, C.,Mahrwald, R.,Kovalenko, S.A.,Ernsting, N.P. (登録日: 2009-03-23, 公開日: 2009-12-01, 最終更新日: 2024-05-22)

主引用文献

Dallmann, A.,Pfaffe, M.,Mahrwald, R.,Kovalenko, S.A.,Ernsting, N.P.
Local THz Time Domain Spectroscopy of Duplex DNA via Fluorescence of an Embedded Probe
J.Phys.Chem.B, 113:15619-15628, 2009

PubMed Abstract: We demonstrate that THz vibrational activity of a biopolymer can be measured locally, on the effective length scale for polar solvation, with an embedded molecular probe. For this purpose, the polarity probe 2-hydroxy-7-nitrofluorene was linked into a 13mer DNA duplex opposite an abasic site. The NMR solution structure shows that the fluorene moiety occupies a well-defined position in place of a base pair but can flip around the long axis on a millisecond time scale. Femtosecond optical pump-probe experiments are used to measure the time-resolved Stokes shift of emission from the probe. The dynamic shifts for solution in H(2)O and D(2)O are quantified. Their difference is much larger than that expected for free water, implying that only bound water is observed. A weak 26 cm(-1) spectral oscillation of the emission band is observed, which is not present when the probe is free in solution and is therefore caused by the supramolecular structure (DNA and hydration water).

PubMed: 19764701
DOI: 10.1021/jp906037g

実験手法

SOLUTION NMR