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Our genomics products and services include the use of custom synthesized microarrays based on the
µParaflo®
on-chip synthesis technology
which enables the total customization of content on each individual microarray to suit your needs. In addition, the flexibility of µParaflo®
enables the incorporation of modifications within the probes, which significantly
expands the range of applications for these microarrays. Listed below are applications of custom microarrays containing non-standard probes along with selected references.
| Microarray Type |
Application Examples |
Reference |
| DNA oligonucleotides |
|
1 |
| RNA oligonucleotides |
- Aptamer screening of high affinity binding sequences
- Antisense oligonucleotide binding arrays
- Protein/peptide-RNA binding assays
- Profiling of RNA-DNA and RNA-RNA interactions
|
2,3 |
| Phosphorothioate oligonucleotides |
- Antisense oligonucleotide screening
- Profiling binding with proteins
|
4 |
| Duplex DNA sequences |
- Probing DNA-protein interactions (transcription factor chips)
|
5 |
| Modified oligonucleotides |
- RNA modifications such as 2’-F and 2’-OMe oligos for novel aptamers and antisense sequences
- Methylation modification of nucleobases for probing interactions of these sequences with other biological molecules; effect of modification on the properties of the sequences as substrate of enzymatic reactions
- O- or N-methylation of nucleobases for investigation of base pair properties of mutagenic sequences
|
6 |
| 5’- or 3’-labeling |
- Fluoro-dye or biotin labeling at selected sites as signal references in quantitation by relative intensities of probes and targets
- Thiol, amino, and biotin labels for further modifications of the oligonucleotides on chip
- Phosphorylation enabling of ligation
|
7 |
| 5’ to 3’ reverse synthesis |
- Primer extension for SNP detection
- DNA Sequencing
- PCR genotyping
- Other Enzymatic assays
|
8 |
- Tian, J., Gong, H., Sheng, N., Zhou, X., Gulari, E., Gao, X., and Church, G. (2004) Accurate multiplex gene synthesis from programmable DNA chips.Nature 432, 1050-1054. [abstract]
- (a) Burgstaller, P., Jenne, A., and Blind, M. (2002) Aptamers and aptazymes: accelerating small molecule drug discovery. Curr. Opin. Drug Discov. Devel. 5, 690-700. (b) Murphy, MB., Fuller, S. T., Richardson, P. M., and
Doyle, S. A. (2003) An improved method for the in vitro evolution of aptamers and applications in protein detection and purification. Nucleic Acids Res. 31, e110.
- (a) Tolstrup, N., Nielsen, P. S., Kolberg, J. G., Frankel, A. M., Vissing, H., and Kauppinen, S. (2003) OligoDesign: Optimal design of LNA (locked nucleic acid) oligonucleotide capture probes for gene expression
profiling. Nucleic Acids Res. 31, 3758-3762. (b) Vester, B., and Wengel, J. (2004) LNA (locked nucleic acid): high-affinity targeting of complementary RNA and DNA. Biochemistry 43, 13233-13241.
- Bassett, S. E., Fennewald, S.M., King, D.J., Li, X., Herzog, N. K., Shope, R., Aronson, J. F., Luxon, B. A., and Gorenstein, D. G. (2004) Combinatorial selection and edited combinatorial selection of phosphorothioate
aptamers targeting human nuclear factor-kappaB RelA/p50 and RelA/RelA. Biochemistry 43, 9105-9015.
- (a) Bulyk, M. L., Huang, X., Choo, Y., and Church, G. M. (2001) Exploring the DNA-binding specificities of zinc fingers with DNA microarrays. Proc. Natl. Acad. Sci. USA 98, 7158-7163. (b) Mukherjee, S., Berger, M. F.,
Jona, G., Wang, X. S., Muzzey, D., Snyder, M., Young, R. A., and Bulyk, M. L. (2004) Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays. Nat. Genet. 36, 1331-1339.
- (a) Harborth, J., Elbashir, S. M., Vandenburgh, K., Manninga, H., Scaringe, S. A., Weber, K., and Tuschl, T. (2003) Sequence, chemical, and structural variation of small interfering RNAs and short hairpin RNAs and the
effect on mammalian gene silencing. Antisense Nucleic Acid Drug Dev. 13, 83-105. (b) Grunweller, A., Wyszko, E., Bieber, B., Jahnel, R., Erdmann, V.A., and Kurreck, J. (2003) Comparison of different antisense strategies in
mammalian cells using locked nucleic acids, 2'-O-methyl RNA, phosphorothioates and small interfering RNA. Nucleic Acids Res. 31, 3185-3193.
- Research at Atactic Technologies.
- Hirschhorn, J. N., Sklar, P., Lindblad-Toh, K., Lim, Y. M., Ruiz-Gutierrez, M., Bolk, S., Langhorst, B., Schaffner, S., Winchester, E., and Lander, E. S. (2000) SBE-TAGS: an array-based method for efficient single-nucleotide
polymorphism genotyping. Proc. Natl. Acad. Sci. USA 97, 12164-12169.
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