DNA-based nanomechanical devices and DNA enzymatic detection of oligonucleotides

Ye Tian, Purdue University

Abstract

DNA has been extensively explored in the past decades not only for its genetic properties but also for its superb physical/chemical properties. A variety of discoveries in DNA chemistry have made it possible to use DNA in more practical applications, such as nanofabrication, nanomechanical devices, bioanalysis, etc. In this research, three aspects of DNA technology were studied: DNA nanomechanical device, DNA-based detection method development and DNA nanostructure fabrication. The concept of DNA molecular gears was first brought out in this work. Two gears with diameter of 6.7 nm were entirely composed of DNA strands; and could roll against each other, if fueled by other DNA strands. Another DNA nanodevice was also implemented, in which a DNA enzyme (DNAzyme) could autonomously and continuously move along a DNA track. The DNAzyme extracted chemical energy from its track and used this energy to fuel the motion. The concept of DNAzyme was also used in DNA-based detection of DNA oligonucleotides. A DNAzyme that can cleave a RNA substrate was coupled with a catalytic molecular beacon (MB) reporter. An analyte DNA could activate one DNAzyme, and then activate multiple copies of MB and give rise to a strong fluorescence signal. A detection limit of 10 pM DNA was achieved. A following work using two steps of signal amplification improved the detection limit to 1 pM. An analyte DNA first activated the reaction to generate multiple copies of DNAzyme, and the DNAzymes worked simultaneously to further amplify a colorimetric signal. Finally, branched structures with long DNA duplex arms have been constructed through biotin-streptavidin binding and characterized by gel electrophoresis and atomic force microscopy imaging. A novel synthetic method for tandem repetitive DNA duplex without template was also introduced, in which a combination of a DNA ligase and a restriction endonuclease were used to provide DNA polymerase activity.

Degree

Ph.D.

Advisors

Mao, Purdue University.

Subject Area

Analytical chemistry

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