J Phys Chem B vol. 113, Issues 8 and 9

31P NMR Investigation of Backbone Dynamics in DNA Binding Sites†

Ye Tian‡, Michael Kayatta§, Katharine Shultis, Alejandro Gonzalez§, Leonard J. Mueller‡ and Mary E. Hatcher*

J. Phys. Chem. B, 2009, 113 (9), pp 2596–2603
DOI: 10.1021/jp711203m
Abstract: The backbone conformation of DNA plays an important role in the indirect readout mechanisms for protein−DNA recognition events. Thus, investigating the backbone dynamics of each step in DNA binding sequences provides useful information necessary for the characterization of these interactions. Here, we use 31P dynamic NMR to characterize the backbone conformation and dynamics in the Dickerson dodecamer, a sequence containing the EcoRI binding site, and confirm solid-state 2H NMR results showing that the C3pG4 and C9pG10 steps experience unique dynamics and that these dynamics are quenched upon cytosine methylation. In addition, we show that cytosine methylation affects the conformation and dynamics of neighboring nucleotide steps, but this effect is localized to only near neighbors and base-pairing partners. Last, we have been able to characterize the percent BII in each backbone step and illustrate that the C3pG4 and C9pG10 favor the noncanonical BII conformation, even at low temperatures. Our results demonstrate that 31P dynamic NMR provides a robust and efficient method for characterizing the backbone dynamics in DNA. This allows simple, rapid determination of sequence-dependent dynamical information, providing a useful method for studying trends in protein−DNA recognition events.




Molecular Mechanism for Formation of Polyaniline Lamella from a Lyotropic Liquid Crystal: An NMR Study

Li Shi, Xiaodong Wu*, Lude Lu, Xujie Yang and Xin Wang*
J. Phys. Chem. B, 2009, 113 (9), pp 2725–2733
DOI: 10.1021/jp9002824

Abstract: Polyaniline (PANI) microlamellas with an average interlamellar distance of 2.6 nm were prepared from a nematic lyotropic liquid crystal system composed by sodium dodecyl sulfate (SDS) aqueous solution. To reveal the formation mechanism of these lamellas, a series of NMR studies have been performed. At first, variable-temperature (VT) 13C NMR experiments have suggested that, prior to polymerization, anilines are predominantly located in the vicinity of the SDS polar head region with a limited mobility at low temperature, whereas they become more mobile and penetrate into the SDS hydrophobic domain at elevated temperature. Subsequent in situ 13C NMR measurements at 310 K have indicated that the overall polymerization can be taken place in two stages. In the beginning, the reaction sites are within the SDS micelles, resulting in the formation of oligomeric PANI species with benzenoid and quinoid structures. Interestingly, these oligomeric species fall off from the micellar hydrophobic domains and reorganize into layered structures with the support of SDS. In the second stage, further polymerization can be continued within the interlayers. This paper provides a good example in studying the roles of surfactants at the nucleation stage qualitatively during the synthesis of morphology-specific polymers with the application of NMR techniques, a period difficult to be examined by other approaches currently.