[NMR paper] Probing the rate limiting step for intramolecular transfer of a transcription factor between specific sites on the same DNA molecule by 15Nz-exchange NMR spectroscopy.

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Probing the rate limiting step for intramolecular transfer of a transcription factor between specific sites on the same DNA molecule by 15Nz-exchange NMR spectroscopy.

Related Articles Probing the rate limiting step for intramolecular transfer of a transcription factor between specific sites on the same DNA molecule by 15Nz-exchange NMR spectroscopy.

J Am Chem Soc. 2014 Sep 25;

Authors: Ryu KS, Tugarinov V, Clore GM

Abstract
The kinetics of translocation of the homeodomain transcription factor HoxD9 between specific sites of the same or opposite polarities on the same DNA molecule have been studied by 15Nz-exchange NMR spectroscopy. We show that exchange occurs by two facilitated diffusion mech-anisms: a second-order intermolecular exchange reaction between specific sites located on different DNA molecules without the protein dissociating into free solution that pre-dominates at high concentrations of free DNA, and a first-order intramolecular process involving direct transfer be-tween specific sites located on the same DNA molecule. Control experiments using a mixture of two DNA molecules, each possessing only a single specific site, indicate that trans-fer between specific sites by full dissociation of HoxD9 into solution followed by reassociation is too slow to measure by z-exchange spectroscopy. Intramolecular transfer with com-parable rate constants occurs between sites of the same and opposing polarity indicating that both rotation-coupled slid-ing and hopping/flipping (analogous to geminate recombi-nation) occur. The half-life for intramolecular transfer (0.5 -1 s) is many orders of magnitude larger than the calculated transfer time (1-100 ?s) by sliding, leading us to conclude that the intramolecular transfer rates measured by z-exchange spectroscopy represent the rate-limiting step for a one base pair shift from the specific site to the immediately adjacent non-specific site. At zero concentration of added salt, the intramolecular transfer rate constants between sites of opposing polarity are smaller than those between sites of the same polarity, suggesting that hopping/flipping may be-come rate limiting at very low salt concentrations.


PMID: 25253516 [PubMed - as supplied by publisher]



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