Software Application: 2D Single Molecules

2D Single Molecules is a software (freeware) we have developed for the processing data of AFM single molecule experiments (or any other technique allowing the visualization of single molecules, e.g. fluorescence microscopy or scanning electron microscopy (SEM) for giant DNA or other biomolecules: *.jpg, *.bmp files may be processed). Images of molecules may be zoomed and the molecule contour can be easily drawn by dragging a mouse cursor. The drawn contour curves are subdivided into equal vectors of a changeable length.

Figure 1. 2D Single Molecules Software screenshot.

Single Molecule data:

    • Center of Mass Position;
    • Radius of Gyration (<s2>1/2);
    • End-to-End Distance (<r2>1/2);
    • Contour Length (L);
    • Degree of Polymerization (N);
    • Molecular Weight (MM).

All these characteristics can be calculated for the selected molecule and for any number of selected molecules.


Statistical Analysis

Statistical Analysis of molecular dimensions can be performed by processing two or more molecules in the same image. The molecules may be gathered together from several different images for simultaneous processing. Radius of Gyration and End-to-End Distance are calculated as root mean square values. Contour Length and Molecular Weight values are number- (Ln>, Mn) and weight-averaged (Lw, Mw) values.


Persistence Length and Ideal End-to-End distance

There is an option for the use of the model of ideal worm-like coil to compare experimental results with the molecular dimensions predicted by the model. We consider two cases: (1) 2D-equilibrated molecule, and (2) 3D->2D projected (trapped) conformation. The freeware calculates the persistence length of the chains Lp using the drawn contour of the chains. In the next step the Lp and Ln experimental values are used to estimate rms End-to-End Distance for the case (1) and for the case (2). Then the values, experimental and estimated from the model, are compared by the freeware.

The freeware has an option to save the drawn contours of single molecules with a link to its original image. Processed molecules can be collected from different data files and combined in the same file to perform the statistical analysis.

The freeware is temporarily not available for download directly from this site because of the policy of our provider. If you wish to receive the freeware, please, contact Sergiy Minko or Yuri Roiter.

Authors acknowledge the support from the North Atlantic Treaty Organization under NSF Grant DGE-0411649 awarded in 2004.

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