Solid-Phase Synthesis of DNA Chemical Sensor

Abstract:

Oligonucleotides are essential components of many applications in molecular biology. The synthesis chemistry is robust and commercial oligonucleotide synthesizers have taken advantage of the chemistry to provide oligonucleotides of high quality and purity. This paper established nucleic acid synthesis platform to carry out the synthesis of the labeled nucleic acid probes based on the DNA synthesizer and solid-phase synthesis technology. We chose to study the automated synthesis starting from DMT protected FAM labeled amidite attached to controlled pore glass (CPG) support and the standard trityl-off oligonucleotide synthesis cycle was performed, yielding the solid-supported oligonucleotide. The reported automated solid-phase oligonucleotide synthesis procedure successfully employs the common iterative synthesis, deblocking, activation, coupling, capping, oxidation, and isolation steps in standard oligonucleotide synthesis. The automated synthetic approach can also be applied to oligonucleotides of different length, composition of nucleotide, demonstrating the universality of the method. Moreover, the synthesis involved the use of commercially available, safe, stable, and inexpensive reagents, particularly advantageous and attractive for their use in automated solid-phase synthesis. The synthesis allows custom tailoring of their structure to the requirements of biological assays within hours, as opposed to traditional approaches that require weeks or months of work in the laboratory. Therefore it will become much easier to investigate biological interactions and optimize for objectives such as the receptor mediated targeting of oligonucleotides.

• Periodical: Advanced Materials Research (Volume 815)
• Pages: 305-311
• DOI: https://doi.org/10.4028/www.scientific.net/AMR.815.305
• Online since: October 2013
• Authors: Hui Yong Zhang
• Keywords: DNA Synthesis, Label, Solid-Phase

References

[1] S. Zheng, J. H. Choi, S. M. Lee, K. S. Hwang, S. K. KimT. S. Kim, Analysis of DNA hybridization regarding the conformation of molecular layer with piezoelectric microcantilevers Lab on a Chip 11(2011) 63-69.

DOI: 10.1039/c0lc00122h

[2] S. T. Koev, W. E. BentleyR. Ghodssi, Interferometric readout of multiple cantilever sensors in liquid samples Sensor Actuat B-Chem 146(2010) 245-252.

DOI: 10.1016/j.snb.2010.02.038

[3] K. H. KangP. Shrotriya, Surface Stress Development Associated with Hybridization of Monomolecular DNA Film Imece 2009: Proceedings of the Asme International Mechanical Engineering Congress and Exposition, Vol 11 2010) 319-325.

[4] C. TuerkL. Gold, SYSTEMATIC EVOLUTION OF LIGANDS BY EXPONENTIAL ENRICHMENT - RNA LIGANDS TO BACTERIOPHAGE-T4 DNA-POLYMERASE Science 249(1990) 505-510.

DOI: 10.1126/science.2200121

[5] X. Zeng, X. Zhang, W. Yang, H. JiaY. Li, Fluorescence detection of adenosine triphosphate through an aptamer–molecular beacon multiple probe Analytical Biochemistry 424(2012) 8-11.

DOI: 10.1016/j.ab.2012.01.021

[6] H. Yang, J. Ji, Y. Liu, J. L. KongB. H. Liu, An aptamer-based biosensor for sensitive thrombin detection Electrochem. Commun. 11(2009) 38-40.

DOI: 10.1016/j.elecom.2008.10.024

[7] H. Cho, B. R. Baker, S. Wachsmann-Hogiu, C. V. Pagba, T. A. Laurence, S. M. Lane, L. P. LeeJ. B. H. Tok, Aptamer-Based SERRS Sensor for Thrombin Detection Nano Lett. 8(2008) 4386-4390.

DOI: 10.1021/nl802245w

[8] X. H. Cheng, T. Bing, X. J. LiuD. H. Shangguan, A label-free fluorescence sensor for probing the interaction of oligonucleotides with target molecules Anal. Chim. Acta 633(2009) 97-102.

DOI: 10.1016/j.aca.2008.11.031

[9] J. Chen, Z. Fang, J. LiuL. Zeng, A simple and rapid biosensor for ochratoxin A based on a structure-switching signaling aptamer Food Control 25(2012) 555-560.

DOI: 10.1016/j.foodcont.2011.11.039

[10] S. C. Stinson, DNA SYNTHESIZERS BASED ON 2-CHEMISTRIES Chemical & Engineering News 59(1981) 17-18.

[11] D. HarrisJ. E. Shively, CONSTRUCTION AND PERFORMANCE OF A SOLID-PHASE DNA SYNTHESIZER BASED ON THE PHOSPHOTRIESTER CHEMISTRY Federation Proceedings 42(1983) 1955-(1955).

[12] R. M. Cook, DNA SYNTHESIZERS PROVIDE CATALYST FOR GENETIC RESEARCH GAINS Research & Development 26(1984) 106-109.

[13] G. S. KubikM. A. Hollingsworth, Core lab modifications to a 96-well DNA synthesizer Molecular Biology of the Cell 11(2000) 131A-131A.

[14] S. Goforth, DNA synthesizers Scientist 16(2002) 44-44.

[15] I. Okamoto, K. SeioM. Sekine, Improved synthesis of oligonucleotides containing 2-thiouridine derivatives by use of diluted iodine solution Tetrahedron Letters 47(2006) 583-585.

DOI: 10.1016/j.tetlet.2005.11.044