Excerpt from: J. Am. Chem. Soc. 1996, 119:10989

(with permission from and Copyright by American Chemical Society, 1996.)

Molecular Dynamics Simulation of DNA Stretching is Consistent with the Tension Observed for Extension and Strand Separation and Predicts a Novel Ladder Structure

Michael W. Konrad and Joel I. Bolonick

Abstract: Molecular dynamics simulations were used to model the response of several double stranded dodecamers to gradually increasing tension applied to the opposing 3' ends of the two polynucleotide strands. At forces between 0.80 and 1.45 nN, depending on sequence, the strands separated completely. The separation force for one of the dodecamers studied has been measured and is close to that seen in the simulation. Before strand separation, at forces between 0.065 to 0.090 nN, again depending on sequence, there was an abrupt extension and transition to a novel ladder structure in which bases of one strand were stacked on those of the other strand. Sudden extensions have been observed in very long DNA molecules at forces similar to those seen in the simulations. After the abrupt extension but before strand separation the ladder structure became more regular and the phosphate backbones more linear. Throughout the entire molecular extension most hydrogen bonded base pairs remained intact.

This graph is a color version of the black and white Figure 1 in the article. Note the sudden extension (blue line) at a tension of about 0.08 nN, which is labeled "helix->ladder". The internal energy (red line) is generally increasing, since of course we are putting energy into the molecule as we pull it apart. The energy increases and then decreases as the transition to a new , more favorable structure is accomplished.

The change in molecular structure as the DNA is stretched is presented to the left. The mural of four stick models was selected from the start of the simulation, just before the transition at 0.077 nN, just after at 0.094 nM, and later at 0.22 nN. The mural is a color version of Figure 2 in the article (lucky for you it costs no extra to show color here on the Web, while in the Journal it cost us an arm and a leg to have even one color figure, which we saved for Figure 5).


The structure of the DNA helix when fully stretched (last of the structures in the previous mural), is a ladder with tilted base pairs. This may not been so obvious in the lower magnification but here (Figure 5 in the article) we see that the original intra-strand base stacking has changed to an inter-strand pattern in which bases on one strand are stacked on those of the other strand.


(Excerpted with permission from J. Am. Chem. Soc. 1996, 119:10989. Copyright 1996 American Chemical Society.)


The atomic coordinates of the relaxed and stretched DNA in PDB format are given in the following two files. If you want to use a PDB viewer you must download the files, save in text format, and then remove the two html commands at the beginning and end of the files (the lines with <...>).