Force induced unzipping in biopolymers

Till recently, information about the inter- and intra- molecular forces involved in the stability of double stranded DNA (dsDNA) were obtained in vitro through the indirect physical and thermodynamic measurements like nuclear magnetic resonance spectroscopy, light scattering, crystallography, differential scanning calorimetry etc. These information are needed to understand two key biological processes i.e. replication and transcription, where a dsDNA is required to separate (fully or partially) into two single stranded DNA (ssDNA). It is believed that the stability of dsDNA is the result of hydrogen bonding between bases, backbone conformational constraints, electrostatic interactions and the coordination of water molecules. In recent years, single molecule force spectroscopy  (SMFS) experiments e.g. optical tweezers, atomic force microscope etc. have directly measured these forces and provided unprecedented insight about the mechanism involved in the process of DNA separation and its stability. Simple models e.g Poland Scheraga (PS) model or Peyrard-Bishop-Dauxious (PBD) model have described some of the essential macroscopic features of the meting profile of dsDNA quite effectively  and predicted that the force-induced melting transition is a first order transition. However, semi-microscopic information about the opening e.g. whether a dsDNA opens from the end or interior of the chain, distribution of partially opened region in the form of bubbles in the chain are  some of the intriguing issues in these studies. At present,  we are investigating the effects of these constrains on the melting profile of hetro-sequence of finite length single molecule experiments and provide the semi microscopic information about the formation of bubbles in the form of partially opened regions during the opening of a dsDNA