Manipulation of Deoxyribonucleic Acid

Enormous progress has been made in developing the tools for DNA manipulation and characterization such as cloning, synthesis, and sequencing. Many of these processes are now fully automated, permitting exploration into the genetic analysis of complex cellular systems and organisms. Structural characterization and analytical techniques for separation, purification, cloning, etc. are now widespread and often commercially available.

DNA sequencing has made enormous progress in terms of efficiency and speed, thus enabling full characterization of the human genome and of other organisms. Automated chemical synthesis of artificial nucleic acid oligos is now commercially available and can be done with high accuracy for short pieces. Chemical modifications of the backbone or bases with a variety of functional groups can also be incorporated, which allow oligos to be linked to other molecules in inorganic systems such as bulk macroscopic surfaces and also nanoparticles. This has greatly furthered research and the development of pharmaceutical applications and permitted exploration of interdisciplinary studies with biology.

In addition to these analytical and synthetic techniques, there has been recent interest in manipulating and utilizing DNA as an information medium or a machine. DNA is an attractive system for this purpose as it has exquisite recognition properties in base pairing. In addition, DNA is involved in many information transfer processes in a cell such as self-replication. All the processes necessary for life are contained in DNA, as this is what is passed on from parent to offspring.

Engineered into the DNA are complex information components such as promoter and repressor elements that can turn on or off expression of a particular gene, allowing the cell or organism to react to DNA environment. As a result, controlling its hybridization is one simple way to access the machinery of biology. In addition, with the sequencing of the human genome, the formidable task of gene profiling has generated interest in developing rapid, inexpensive, and high-throughput characterization and manipulation tools. Described below are just a few examples of the tools developed for studying and manipulating DNA.

Microarray Chips. Recently, there has been tremendous interest in using gene chips to study genes for analysis of behavior of an organism. In order to study the presence of genes, multiple probe strands complementary to a given target strand are chemically tethered to a substrate. The slide is incubated with the set of target DNA strands, which hybridize to the corresponding probe strands. A reporter strand complementary to the overhang of the target strand is added. The reporter strand has fluorophore chemically attached to it, so when the target is present fluorescence increases. Because of the multitude of groups and companies using this technology, the generation of DNA microarrays by automated spotters and their analysis of large numbers of them has been standardized. As a result, thousands of genes can be probed simultaneously, enabling high-throughput analysis of an entire genome on a single chip.

Some groups have taken this further by developing methods for spatially controlling hybridization on an array by using an electric field. A DNA probe is chemically tethered to a site above an electrode on a surface. A voltage applied to the electrode attracts negatively charged DNA complement, thereby directing where the DNA is hybridized with single nucleotide resolution. Electric field interfacing to DNA on a surface has the advantages of multiplex control of hybridization events. Other electronic interfaces to DNA molecules for the purposes of control include orientation of DNA helices on metal surfaces by an applied electric field.