Friday, March 22, 2013

Non-B DNA Structures Show Diverse Conformations and Complex Transition Kinetics Comparable to RNA or Proteins—A Perspective from Mechanical Unfolding and Refolding Experiments

Zhongbo Yu, Hanbin Mao

With the firm demonstration of the in vivo presence and biological functions of many non-B DNA structures, it is of great significance to understand their physiological roles from the perspective of structural conformation, stability, and transition kinetics. Although relatively simple in primary sequences compared to proteins, non-B DNA species show rather versatile conformations and dynamic transitions. As the most-studied non-B DNA species, the G-quadruplex displays a myriad of conformations that can interconvert between each other in different solutions. These features impose challenges for ensemble-average techniques, such as X-ray crystallography, NMR spectroscopy, and circular dichroism (CD), but leave room for single-molecular approaches to illustrate the structure, stability, and transition kinetics of individual non-B DNA species in a solution mixture. Deconvolution of the mixture can be further facilitated by statistical data treatment, such as iPoDNano (integrated population deconvolution with nanometer resolution), which resolves populations with subnanometer size differences. This Personal Account summarizes current mechanical unfolding and refolding methods to interrogate single non-B DNA species, with an emphasis on DNA G-quadruplexes and i-motifs. These single-molecule studies start to demonstrate that structures and transitions in non-B DNA species can approach the complexity of those in RNA or proteins, which provides solid justification for the biological functions carried out by non-B DNA species.

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