Sequence-dependent DNA dynamics by scanning force microscopy time-resolved imaging.
Scanning force microscopy was used to study in fluid the conformational fluctuations of two double-stranded DNA molecules resulting from differently cut pBR322 circular DNAs. A new approach was conceived to monitor the thermodynamic equilibrium of the chain dynamics on different scale lengths. This method made it possible to demonstrate that both the observed DNA molecules were allowed to equilibrate only on their local small-scale dynamics during the time of the experiment. This capability of monitoring the length scale and the time scale of the equilibration processes in the dynamics of a DNA chain is relevant to give an insight in the thermodynamics of the DNA binding with proteins and synthetic ligands. It was also shown that the small-scale equilibration of the DNA chain during surface-restricted dynamics is enough to allow a valid measurement of the local sequence-dependent curvature.
Scipioni
Anita
A
Dipartimento di Chimica, Università "La Sapienza", Roma, Italy.
Zuccheri
Giampaolo
G
Anselmi
Claudio
C
Bergia
Anna
A
Samorì
Bruno
B
De Santis
Pasquale
P
D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D004270:DNA, Circular; D007091:Image Processing, Computer-Assisted; D018625:Microscopy, Atomic Force; D009038:Motion; D009690:Nucleic Acid Conformation; D013816:Thermodynamics; D013997:Time Factors
D004270:DNA, Circular; D004247:DNA