Multiplexed DNA sequencing and diagnostics by hybridization with enriched stable isotope labels

Different strategies of covalent attachment of oligonucleotide probe onto glass beads and the hybridization properties

The glass bead is a new biochip support material for immobilization biomolecules, due to its independence and convenient rearrangement. In order to optimize the immobilization efficiency of oligonucleotides onto glass beads and obtain the highest hybridization efficiency, three commonly used coupling strategies have been studied for covalently attaching oligonucleotides onto large glass beads. Glass beads with 250 microm diameter were amino-silaned with 2% 3-aminopropyltrimethoxysilane (APTMS) and then reacted separately with glutaraldehyde, succinic anhydride and 1,4-phenylene diisothiocyanate (PDITC) to derive CHO beads, COOH beads and isothiocyanate-modified beads (NCS-Beads) accordingly. Afterwards, amino-terminal oligonucleotides were covalently attached onto the surface of beads achieved by three strategies mentioned above. The immobilization efficiency were studied to compare the three strategies, which turned out 2.55 x 10(13) probes/cm2 for CHO-Beads, 3.21 x 10(13) probes/cm2 for COOH beads and 6.68 x 10(13) probes/cm2 for NCS beads. It meant that the immobilization efficiency based on NCS beads was most acceptable. And the method, developed by attaching amino-terminal oligonucleotides onto these cyanate active beads, could be regarded as an efficient one for immobilizing oligonucleotides onto a solid surface. Moreover, in this paper, the hybridization properties of NCS bead-based oligonucleotides have been studied by employing Cy5-tagged complementary oligonucleotides. It was found that the high probe density NCS beads led to low hybridization efficiency possibly due to the existence of steric crowding. In addition, the equilibrium binding constant KA was determined by employing Langmuir isotherm model, which was 7.0 x 10(6) M(-1) for NCS beads with the density of 6.7 x 10(13) probes/cm2. Furthermore, it only took 60 min to reach hybridization equilibrium. These large microspheres (>100 microm) can be employed in the mesofluidic systems for automated heterogeneous assays.

Accurate mass measurement of DNA oligonucleotide ions using high-resolution time-of-flight mass spectrometry

Matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) time-of-flight mass spectrometry (TOFMS) play an essential role in the analysis of biological molecules, not only peptides and proteins, but also DNA and RNA. Tandem mass spectrometry used for sequence analysis has been a major focus of technological developments in mass spectrometry, but accurate mass measurements by high-resolution TOFMS are equally important. This paper describes the role that high mass measurement accuracy can play in DNA composition assignment and discusses the influence of several parameters on mass measurement accuracy in both MALDI and ESI mass spectra. Five oligonucleotides (5-13mers) were used to test the resolving power and mass measurement accuracy obtained with MALDI and ESI instruments with reflectron TOF mass analyzers. The results from the experimental studies and additional theoretical calculations provide a basis to predict the practical utility of high-resolution TOFMS for the analysis of larger oligonucleotides.

Analysing genetic information with DNA arrays

The large amount of DNA sequence information produced in recent years has created a need for high-throughput methods in biology and genetics. These include sequencing, comparing gene sequences and genotyping. DNA arrays promise a highly parallel means for analysis of DNA that is fast and cost-effective, and offers scope for application to complex systems and processes. Recent years have seen continued transfer of technology from the microelectronics industry. Rapid application of the technology to genotyping, antisense oligonucleotide selection and gene expression analysis has illustrated the general power of this approach.

Functional genomics in the post-genome era

As the biomedical research community enters the post-genome era, studying gene expression patterns and phenotypes in model organisms will be an important part of analyzing the role of genes in human health and disease. New technologies involving DNA chips will improve the ability to evaluate the differential expression of a large number of genes simultaneously. Also, new approaches for generating mutations in mice will significantly decrease the cost and increase the rate of generating mutant lines that model human disease.