Zhang's technological vision would enable scientists to sequence billions of base pairs of DNA in a single day. This is the size of an average mammalian genome and is approximately 10,000 times more bases per day than can be sequenced using current technologies. By increasing the speed of sequencing and reducing its cost, genetic research may develop a more significant role in everyday medical practice.
In Zhang's sequencing project, billions of base pairs of genomic DNA could be sequenced on a single, cookie crumb-sized one centimeter by one centimeter chip. The technique uses hybridization, a process of joining two complementary strands of DNA, to sequence DNA by applying a sample to single stranded DNA probes attached to a chip.
An atomic force microscope (AFM), like a caffeinated speed reader, can then rapidly scan the surface of the chip to see where DNA from the sample has hybridized to the probes. Wherever sample DNA binds to the probes, the sequence is registered.
"Traditional approaches to sequencing by hybridization are limited by the number of probes that can be placed on a chip," said Jian Gu, a research staff member in the Center for Applied NanoBioscience at the Biodesign Institute and co-leader of the project.
By using nanoprinting techniques developed by Gu, the researchers hope to increase the number probes they can fit on a chip. "Right now, we have a mechanical printing technology that could put down billions of probes on a chip surface at very low cost," said Gu.
It is estimated that a single base pair can be sequenced for every DNA probe, which means that optimizing the nanoprinting process is critical to the goal of a $1,000 genome, according to Zhang.
The researchers' first goal is a proof of principal for their approach. They plan to synthesize a universal DNA nanoarray on a 100 micrometer by 100 micrometer chip, about the si
Source:Arizona State University