New Technique for Mapping DNA Molecules

  As a result of research conducted in Life Sciences Division's Chemical and Biological Physics Section, DNA molecules can now be mapped directly to high precision by a new technique using atomic force microscopy (AFM). Mapping is a process of finding the locations of specific sequences of chemical bases in a long strand of DNA, the genetic molecule that determines physical makeup.

  Conventional methods digest the DNA using an endonuclease protein, which cuts at a particular sequence, followed by sizing the fragments with electrophoresis. Finally, the order of the fragments in the original molecule must be determined. The method is limited both in precision and maximum allowed length of the DNA fragment. The new method reacts the DNA with a modified endonuclease that binds at the proper positions but does not cut. The molecules, which are then spread onto a flat surface, appear as strings with knots at the binding sites when they are imaged with AFM. The order of the fragments can therefore be read directly and their size determined to an accuracy of better than 1%.

  The new method can not only supply improved data and reduce bottlenecks for the Human Genome Program, but will be extended to longer DNAs, such as bacterial artificial chromosomes (BACs), and will also be used in examining DNA interactions with proteins (e.g., transcription factors) that control gene expression.

Contact: Dave Allison
Telephone: 423-574-6199
E-mail: x3a@ornl.gov