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New Findings from Stanford University in the Area of DNA Research Reported

May 30, 2014

By a News Reporter-Staff News Editor at Science Letter -- New research on DNA Research is the subject of a report. According to news originating from Stanford, California, by NewsRx correspondents, research stated, "Direct experimental measurements of conformational ensembles are critical for understanding macromolecular function, but traditional biophysical methods do not directly report the solution ensemble of a macromolecule. Small-angle X-ray scattering interferometry has the potential to overcome this limitation by providing the instantaneous distance distribution between pairs of gold-nanocrystal probes conjugated to a macromolecule in solution."

Our news journalists obtained a quote from the research from Stanford University, "Our X-ray interferometry experiments reveal an increasing bend angle of DNA duplexes with bulges of one, three, and five adenosine residues, consistent with previous FRET measurements, and further reveal an increasingly broad conformational ensemble with increasing bulge length. The distance distributions for the AAA bulge duplex (3A-DNA) with six different Au-Au pairs provide strong evidence against a simple elastic model in which fluctuations occur about a single conformational state. Instead, the measured distance distributions suggest a 3A-DNA ensemble with multiple conformational states predominantly across a region of conformational space with bend angles between 24 and 85 degrees and characteristic bend directions and helical twists and displacements. Additional X-ray interferometry experiments revealed perturbations to the ensemble from changes in ionic conditions and the bulge sequence, effects that can be understood in terms of electrostatic and stacking contributions to the ensemble and that demonstrate the sensitivity of X-ray interferometry. Combining X-ray interferometry ensemble data with molecular dynamics simulations gave atomic-level models of representative conformational states and of the molecular interactions that may shape the ensemble, and fluorescence measurements with 2-aminopurine-substituted 3A-DNA provided initial tests of these atomistic models."

According to the news editors, the research concluded: "More generally, X-ray interferometry will provide powerful benchmarks for testing and developing computational methods."

For more information on this research see: From a structural average to the conformational ensemble of a DNA bulge. Proceedings of the National Academy of Sciences of the United States of America, 2014;111(15):E1473-E1480. Proceedings of the National Academy of Sciences of the United States of America can be contacted at: Natl Acad Sciences, 2101 Constitution Ave NW, Washington, DC 20418, USA. (National Academy of Sciences -; Proceedings of the National Academy of Sciences of the United States of America -

The news correspondents report that additional information may be obtained from X.S. Shi, Stanford University, Biophys Program, Stanford, CA 94305, United States. Additional authors for this research include K.A. Beauchamp, P.B. Harbury and D. Herschlag (see also DNA Research).

Keywords for this news article include: Stanford, California, DNA Research, United States, North and Central America

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Source: Science Letter

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