Show simple item record

dc.contributor.advisorKamal Youcef-Toumi.en_US
dc.contributor.authorBurns, Daniel Jamesen_US
dc.contributor.otherMassachusetts Institute of Technology. Dept. of Mechanical Engineering.en_US
dc.date.accessioned2006-03-29T18:52:05Z
dc.date.available2006-03-29T18:52:05Z
dc.date.copyright2004en_US
dc.date.issued2004en_US
dc.identifier.urihttp://hdl.handle.net/1721.1/32520
dc.descriptionThesis (S.M.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2004.en_US
dc.descriptionIncludes bibliographical references (p. 91-103).en_US
dc.description.abstractA novel DNA sequencing method is proposed based on the specific binding nature of nucleotides and measured by an atomic force microscope (AFM). A single molecule of DNA is denatured and immobilized on an atomically fiat surface, and a force probe functionalized with a nucleotide is scanned along the molecule to detect locations of the probe nucleotide's complement. To increase the spatial resolution of the atomic force microscope so that individual bases can be distinguished, a single-walled carbon nanotube is grown from the AFM probe and functionalized with a single nucleotide. The carbon nanotube diameter is of the order as the nucleotide base spacing--providing the necessary spatial resolution for single molecule sequencing. The absolute force detection limit of the microscope is thermal noise-limited and derived herein from the equipartition theorem. The calculated minimum detectable force is less than experimentally obtained nucleotide binding forces, indicating that the AFM is capable of directly measuring single nucleotide interactions. A model of the oscillating AFM probe dynamics is developed, allowing a methodical approach to determining attractive forces with a chemically-specific sensor. This attractive force detection is performed by measuring the phase lag of the oscillating probe near the sample surface as compared to the resonating probe in free air. As grown, the carbon nanotubes are too long to be used as reliable force probes, therefore a method for shortening carbon nanotubes is presented utilizing high voltages to remove material. Measuring the length of the nanotube is performed with a novel technique that exploits the nanotube's unique elastic buckling property.en_US
dc.description.abstract(cont.) This measurement technique characterizes the length of the nanotube while the probe is still mounted on the AFM and alleviates the need for a secondary microscope. The shortening procedure developed is performed in conjunction with the nucleotide functionalization, creating a precise and chemically-specific force probe. Experiments are performed on synthetic DNA of a known sequence to validate the proposed approach. A functionalized carbon nanotube force probe is scanned along single molecules of synthetic DNA to determine locations of target bases.en_US
dc.description.statementofresponsibilityby Daniel J. Burns.en_US
dc.format.extent103 p.en_US
dc.format.extent5602861 bytes
dc.format.extent5608539 bytes
dc.format.mimetypeapplication/pdf
dc.format.mimetypeapplication/pdf
dc.language.isoengen_US
dc.publisherMassachusetts Institute of Technologyen_US
dc.rightsM.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission.en_US
dc.rights.urihttp://dspace.mit.edu/handle/1721.1/7582
dc.subjectMechanical Engineering.en_US
dc.titleOn single-molecule DNA sequencing with atomic force microscopy using functionalized carbon nanotube probesen_US
dc.title.alternativeOn single-molecule deoxyribonucleic acid sequencing with AFM using functionalized carbon nanotube probesen_US
dc.typeThesisen_US
dc.description.degreeS.M.en_US
dc.contributor.departmentMassachusetts Institute of Technology. Department of Mechanical Engineering
dc.identifier.oclc62127350en_US


Files in this item

Thumbnail

This item appears in the following Collection(s)

Show simple item record