Boston University scientists develop new application to characterize structure of DNA molecules

New technique provides insight into how DNA conforms to microarray surfaces

A team of researchers from Boston University has developed a new application to enable more precise measurement of the location of a fluorescent label in a DNA layer. According to their study, published in a recent issue of Proceedings of the National Academy of Sciences, the new technique provides insight into the shape of DNA molecules attached to a surface, such as microarrays used in genomics research. Determining specific information about how surface-bound DNA molecules conform may significantly improve the efficiency of DNA hybridization and microarray technology and thus impact emerging clinical and biotechnological fields.

The technique, called spectral self-interference fluorescence microscopy (SSFM), maps the interference spectrum from a fluorophore (fluorescent molecule) label located on a layered reflecting surface into a position with sub-nanometer accuracy. “Although a number of other methods have been used to determine the structure of the DNA layer, they are not very sensitive to variations in the shape of DNA molecules,” said Bennett Goldberg, professor of physics and study co-author. “Our group has developed SSFM to determine the precise measurement of the location of a fluorescent label relative to the microarray surface which provides us with specific information about the conformation of DNA molecules.”

Using SSFM, the team estimated the shape of coiled single-stranded DNA, the average tilt of double-stranded DNA of different lengths, and estimated the amount of hybridization. The data provide important new proof points for the capabilities of novel optical surface analysis methods of the behavior of DNA on microarray surfaces.

“Determining DNA conformation and hybridization behavior provide the information required to move DNA interfacial applications forward,” said M. Selim Unlu, electrical and computer engineering professor and study co-author. “Our research shows that locating a fluorescent label attached to a certain position within a DNA chain offers highly accurate information about the shape of DNA molecules bound to the surface of a microarray.”

Additional study investigators include Dr. Lev Moiseev, electrical and computer engineering research associate; Anna K. Swan, associate professor of electrical and computer engineering; and Charles R. Cantor, professor of biomedical engineering and co-director of the Center for Advanced Biotechnology at BU.