DSSR-PyMOL cartoon-block schematics: PDB entry 2kh1

PDB-id

2kh1; SNAP-derived features in text and JSON formats

Class

DNA

Method

NMR

Summary

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

Reference

Dallmann A, Pfaffe M, Mahrwald R, Kovalenko SA, Ernsting NP (2009): "Local THz Time Domain Spectroscopy of Duplex DNA via Fluorescence of an Embedded Probe." J.Phys.Chem.B, 113, 15619-15628. doi: 10.1021/jp906037g.

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).