Molecular engineering approaches for DNA sequencing and analysis

Termination of DNA synthesis by N6-alkylated, not 3'-O-alkylated, photocleavable 2'-deoxyadenosine triphosphates

The Human Genome Project has facilitated the sequencing of many species, yet the current Sanger method is too expensive, labor intensive and time consuming to accomplish medical resequencing of human genomes en masse. Of the ‘next-generation’ technologies, cyclic reversible termination (CRT) is a promising method with the goal of producing accurate sequence information at a fraction of the cost and effort. The foundation of this approach is the reversible terminator (RT), its chemical and biological properties of which directly impact the performance of the sequencing technology. Here, we have discovered a novel paradigm in RT chemistry, the attachment of a photocleavable, 2-nitrobenzyl group to the N⁶-position of 2′-deoxyadenosine triphosphate (dATP), which, upon incorporation, terminates DNA synthesis. The 3′-OH group of the N⁶-(2-nitrobenzyl)-dATP remains unblocked, providing favorable incorporation and termination properties for several commercially available DNA polymerases while maintaining good discrimination against mismatch incorporations. Upon removal of the 2-nitrobenzyl group with UV light, the natural nucleotide is restored without molecular scarring. A five-base experiment, illustrating the exquisite, stepwise addition through a homopolymer repeat, demonstrates the applicability of the N⁶-(2-nitrobenzyl)-dATP as an ideal RT for CRT sequencing.

Single molecule transcription profiling with AFM

Established techniques for global gene expression profiling, such as microarrays, face fundamental sensitivity constraints. Due to greatly increasing interest in examining minute samples from micro-dissected tissues, including single cells, unorthodox approaches, including molecular nanotechnologies, are being explored in this application. Here, we examine the use of single molecule, ordered restriction mapping, combined with AFM, to measure gene transcription levels from very low abundance samples. We frame the problem mathematically, using coding theory, and present an analysis of the critical error sources that may serve as a guide to designing future studies. We follow with experiments detailing the construction of high density, single molecule, ordered restriction maps from plasmids and from cDNA molecules, using two different enzymes, a result not previously reported. We discuss these results in the context of our calculations.

Pharmacogenetics and pharmacogenomics: origin, status, and the hope for personalized medicine

Pharmacogenetics arose with studies of single genes, which had major effects on the action of particular drugs. It turned into pharmacogenomics through realization that the controls of most drug responses are multifactorial. Then, variable gene expression posed new problems, for example what do drugs do to genes, or how useful is any genetic pretesting of a person? A common disease may be caused by different groups of genes in different people, who therefore require different drugs for treatment. Personalized medicine is currently represented by a physician's attention to a patients age, sex, or ethnic background, that is groups showing smaller genetic variation than is typical for general humanity. Occasionally, there is also the use of single-gene pretesting of a patient before drug administration. Over time, improvements in multigenic testing promise to increase the role of personalized medicine. However, the many pharmacogenomic complexities, and particularly time-dependent changes of gene expression, will never allow personalized medicine to become an error-free entity.