DNA Technology and Systems Biology

The detection of small amounts of DNA, the discovery of small changes in the structure of the DNA detected, and the sequencing of the DNA from individual patients, promises to revolutionize the diagnosis, management, and treatment of human disease. This will replace the "one size fits all" medicine that has patients being subjected to tests before a diagnosis is made, or suffering the side effects of medicines arising from their individuality.

Realizing the benefits of this revolution requires that the cost, speed, and sensitivity of DNA detection tools be enhanced, by orders of magnitude. In collaboration with its corporate collaborators, the FfAME is investigating and qualifying new technologies to meet the most demanding specifications for medicine of the future.

Expanding protein functionality through directed evolution

Directed evolution is a powerful technique for improving the activity, specificity and/or stability of proteins. We are developing a new method that integrates molecular phylogenetics to design DNA sequence libraries that will include the functional diversity of large, highly divergent protein families while still maintaining a high proportion of active variants (NIH).

Chemistry for massively parallel sequencing

One way to reduce the cost of personalized DNA sequencing is to sequence many genes at the same time. The Foundation is investigating a new way to do this through creative combinations of chemistry and enzymology (NIH).

Improved microarrays

FfAME scientists have invented chemistries that improve the selectivity and sensitivity of nucleic acid detection in singleplexed formats. These also improve the performance of multiplexed arrays. These chemistries are being implemented on the medium density arrays prepared using ink jet DNA array synthesizers.

Sequencing during synthesis

FfAME scientists have developed what is today the only practical reversible terminator-polymerase combination that can support highly parallel sequencing-during synthesis.

Light-activated fluorescent reporters

FfAME scientist are developing light activated fluorescent reporters that should permit detection of specific components of a transcriptome inside living cells.

Nucleic acid "parts kits"

FfAME scientists have invented chemical solutions to many specific problems in nucleic acid manipulation and analysis. These include: (a) 5'-protecting groups to replace dimethoxytrityl groups, removing a step per nucleotide in the chemical synthesis of DNA; (b) universal nucleobases that provide near perfect non-discrimination between purines and pyrimidines; (c) universal supports that permit the inclusion of non-standard nucleotides without the need for separate support synthesis; (d) new split-and-pool syntheses to allows random sequences to be sequenced non-destructively; (e) a new class of nucleic acid analog that binds with specificity to standard DNA, but not to itself; (f) new click chemistry that permits instant attachment of nucleic acids to other nucleic acid or to the solid support; (g) tags that do not cross react with adventitious nucleic acids in complex biological media; (h) nucleotide-polymerase combinations that support highly multiplexed PCR; (i) single molecule sequencing of RNA through degradation.

Polymerases

Many architectures for the detection and quantitation of nucleic acids rely on DNA polymerases and reverse transcriptases that incorporate nucleic acid analogs. To date, most systems biology laboratories rely on commercial polymerases. Unfortunately, natural polymerases do not necessarily meet the specifications required for systems biology. Through a combination of directed evolution and evolutionary guidance, FfAME scientists have developed polymerases that accept unnatural nucleic acids without these collateral disadvantages.

Template-directed primer assembly

FfAME scientists have developed a new tool that allows the template to generate the primers for detection and amplification. This generates probes with the specificities of 12-16mers, but the discriminating power of 4-8mers.