2KH0

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

Summary for 2KH0

• Entry DOI: 10.2210/pdb2kh0/pdb
• Related: 2KGZ 2KH1
• Descriptor: 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)
• Functional Keywords: dna, solution structure, base pair mimic, conformational flexibility
• Total number of polymer chains: 2
• Total formula weight: 7914.19

Authors

Dallmann, A.,Pfaffe, M.,Muegge, C.,Mahrwald, R.,Kovalenko, S.A.,Ernsting, N.P. (deposition date: 2009-03-23, release date: 2009-12-01, Last modification date: 2024-05-22)

Primary citation

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

Experimental method

SOLUTION NMR