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B-DNA Helix Stability in a Solvent-Free Environment

  • Erin Shammel Baker
  • Michael T. Bowers
Focus: From Mobilities To Proteomes

Abstract

B-DNA is the most common DNA helix conformation under physiological conditions. However, when the amount of water in a DNA solution is decreased, B-to-A helix transitions have been observed. To understand what type of helix conformations exist in a solvent-free environment, a series of poly d(CG) n and mixed sequence DNA duplexes from 18 to 30 bp were examined with circular dichroism (CD), ESI-MS, ion mobility, and molecular dynamics. From the CD spectra, it was observed that all sequences had B-form helices in solution. However, the solvent-free results were more complex. For the poly d(CG) n series, the 18 bp duplex had an A-form helix conformation, both A- and B-helices were present for the 22 bp duplex, and only B-helices were observed for the 26 and 30 bp duplexes. Since these sequences were all present as B-DNA in solution, the observed solvent-free structures illustrate that smaller helices with fewer base pairs convert to A-DNA more easily than larger helices in the absence of solvent. A similar trend was observed for the mixed sequence duplexes where both an A- and B-helix were present for the 18 bp duplex, while only B-helices occur for the larger 22, 26, and 30 bp duplexes. Since the solvent-free B-helices appear at smaller sizes for the mixed sequences than for the pure d(CG) n duplexes, the pure d(CG) n duplexes have a greater A-philicity.

Keywords

Circular Dichroism Experimental Cross Section Mixed Sequence Drift Cell Collisional Cross Section 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© American Society for Mass Spectrometry 2007

Authors and Affiliations

  1. 1.Department of Chemistry and BiochemistryUniversity of CaliforniaSanta BarbaraUSA

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