Diffusion-ordered nuclear magnetic resonance spectroscopy for analysis of DNA secondary structural elements.
Structure determination of secondary DNA structural elements, such as G-quadruplexes, gains an increasing importance as fundamental physiological roles are being associated with the formation of such structures in vivo. A truncated native DNA sequence generally requires further optimization to obtain a candidate with desired nuclear magnetic resonance (NMR) properties for structural analysis in solution. The optimum sequence is expected to form one dominant, stable molecular entity in solution with well-resolved NMR peaks. However, DNA sequences are prone to form structures composed of one, two, three, or four strands depending on sequence and solution conditions. The thorough characterization of the molecularity (stoichiometry and molecular weight) and appropriate solution conditions for sequences with different modifications traditionally applies analytical techniques that generally do not represent the solution conditions for NMR structure determination. Here we present the application of diffusion-ordered NMR spectroscopy as a useful analytical tool for the optimization and analysis of DNA secondary structural elements, specifically, the DNA G-quadruplex structures, including those formed in the human telomeric sequence and in the promoter regions of bcl-2 and c-myc genes.
Ambrus
Attila
A
Department of Pharmacology and Toxicology, University of Arizona, Tucson, AZ 85721, USA. ambrus@pharmacy.arizona.edu
Yang
Danzhou
D
D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D004058:Diffusion; D019254:Genes, bcl-2; D016259:Genes, myc; D006801:Humans; D046911:Macromolecular Substances / Q000737:chemistry; D009154:Mutation; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D009690:Nucleic Acid Conformation; D011401:Promoter Regions, Genetic; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D016615:Telomere / Q000737:chemistry / Q000235:genetics
D046911:Macromolecular Substances; D004247:DNA