DNA Hybridization on Surfaces

DNA microarrays were designed to work off the process of hybridization. Every sequence of DNA has a complimentary sequence that will bind to it in the Watson-Crick configuration to form a double helix. The process of two strands of DNA binding in the Watson-Crick conformation to form a double helix is called hybridization.

A DNA microarray consists of thousands of strands of DNA attached to a glass plate. Each strand has a specific sequence and location on the chip. In a microarray experiment, an unknown sample of DNA is given a fluorescent tag and allowed to hybridize with the DNA attached to the microarray surface. Due to the precise nature of Watson-Crick binding, the tagged DNA should only hybridize with its complimentary sequences. Scientists can then determine what sequences are in the DNA by where spots are glowing on the microarray. In theory, this system should be robust with consistent results, practice has shown, however, that microarray results are not as reproducible as expected.

The mechanism of hybridization in the bulk differs from that of a microarray surface.

 

Based on the current understanding of bulk hybridization, microarray results should be consistent since they work on the principle of hybridization. The hybridization environment that exists on a microarray surface, however, is very different from the environment in which bulk hybridization occurs. Microarray hybridization involves a surface, competing probes, competing targets with similar sequences, and strands of varying lengths. The aim of this study is to use computer simulations to characterize hybridization in the bulk and then to add the complexities of a microarray system to these simulations to see what affects these complexities have.

This study took a single DNA duplex and calculated the reversible work required to for the duplex to hybridize. The system was then altered by switching one base to create a mismatch in the duplex; the reversible work of hybridization was calculated for the new system and compared against the results for the perfect duplex. Artificial tensions were then added to stretch and compress the duplex. These simulations were then performed in the presence of a surface with one strand tethered to the surface. After calculating the effects of a surface, the system was changed to calculate the effects of uneven strand length and multiple targets and probes.

DNA samples hybridize on a local level, introducing hybridization competition and strand shifting.