Entropy production mapping on stretched DNA interacted with proteins.
This paper presents an entropy production mapping (EPM) method for detecting a higher-order structure change of a stretched and immobilized DNA molecule on a cover slip through measuring and mapping an increment of the orientational entropy (defined as "entropy production") of the Watson-Crick base pairs by the interaction of biological factors such as proteins; the stretched DNA molecule undergoes a higher-order structure change by the interaction, so that the orientational entropy at the interaction regions increases because the alignment of the base pairs is reduced at the regions. We demonstrated the utility of this "EPM method" by using a histone-lambda DNA system. It is revealed that the histone interaction region is clearly distinguished from no interaction regions on a stretched lambda DNA molecule immobilized on a cover slip.
Takeda
Yoshihiro
Y
East Tokyo Laboratory, Genesis Research Institute Inc., 717-86 Futamata, Ichikawa, Chiba 272-0001, Japan. takeda@clusterlab.jp
Mafuné
Fumitaka
F
Kondow
Tamotsu
T
D000465:Algorithms; D001665:Binding Sites; D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure*; D004548:Elasticity; D004735:Energy Transfer; D019277:Entropy; D006657:Histones / Q000737:chemistry* / Q000648:ultrastructure*; D007090:Image Interpretation, Computer-Assisted / Q000379:methods*; D046911:Macromolecular Substances / Q000737:chemistry; D008956:Models, Chemical; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D011487:Protein Conformation; D013314:Stress, Mechanical
D006657:Histones; D046911:Macromolecular Substances; D004247:DNA