Molecular recognition using nanotube-adsorbed polymer complexes
Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, February 2013.
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| Format: | Thesis |
| Language: | eng |
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Massachusetts Institute of Technology
2013
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| Online Access: | http://hdl.handle.net/1721.1/79193 |
| _version_ | 1826193581408256000 |
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| author | Zhang, Jingqing, Ph. D. Massachusetts Institute of Technology |
| author2 | Michael S. Strano. |
| author_facet | Michael S. Strano. Zhang, Jingqing, Ph. D. Massachusetts Institute of Technology |
| author_sort | Zhang, Jingqing, Ph. D. Massachusetts Institute of Technology |
| collection | MIT |
| description | Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, February 2013. |
| first_indexed | 2024-09-23T09:41:22Z |
| format | Thesis |
| id | mit-1721.1/79193 |
| institution | Massachusetts Institute of Technology |
| language | eng |
| last_indexed | 2024-09-23T09:41:22Z |
| publishDate | 2013 |
| publisher | Massachusetts Institute of Technology |
| record_format | dspace |
| spelling | mit-1721.1/791932019-04-10T15:37:17Z Molecular recognition using nanotube-adsorbed polymer complexes Zhang, Jingqing, Ph. D. Massachusetts Institute of Technology Michael S. Strano. Massachusetts Institute of Technology. Department of Chemical Engineering. Massachusetts Institute of Technology. Department of Chemical Engineering. Chemical Engineering. Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, February 2013. Cataloged from PDF version of thesis. "December 2012." Includes bibliographical references (p. 234-249). We first reported the selective detection of single nitric oxide (NO) molecules using a specific DNA sequence of d(AT) 15 oligonucleotides, adsorbed to an array of near infrared fluorescent semiconducting single-walled carbon nanotubes (AT₁₅-SWCNT). While SWNT suspended with eight other variant DNA sequences show fluorescence quenching or enhancement from analytes such as dopamine, NADH, L-ascorbic acid, and riboflavin, d(AT)₁₅ imparts SWNT with a distinct selectivity toward NO. In contrast, the electrostatically neutral polyvinyl alcohol, enables no response to nitric oxide, but exhibits fluorescent enhancement to other molecules in the tested library. For AT₁₅ - SWCNT, a stepwise fluorescence decrease is observed when the nanotubes are exposed to NO, reporting the dynamics of single-molecule NO adsorption via SWCNT exciton quenching. We describe these quenching traces using a birth-and-death Markov model, and the maximum likelihood estimator of adsorption and desorption rates of NO is derived. Applying the method to simulated traces indicates that the resulting error in estimation is less than 5% under our experimental conditions, allowing for calibration using a series of NO concentrations. As expected, the adsorption rate is found to be linearly proportional to NO concentration, and the intrinsic single-SWCNT-site NO adsorption rate constant is 0.001 s-¹ [mu]M NO-¹. The ability to detect nitric oxide quantitatively at the single-molecule level may find applications in new cellular assays for the study of nitric oxide carcinogenesis and chemical signaling, as well as medical diagnostics for inflammation. Further, we also explored the concept of creating molecular recognition sites using polymer-SWCNT complexes. Molecular recognition is central to the design of therapeutics, chemical catalysis and sensor platforms, with the most common mechanisms involving biological structures such as antibodies[l] and aptamers[2, 3]. The key to this molecular recognition is a folded and constrained heteropolymer pinned, via intra-molecular forces, into a unique three-dimensional orientation that creates a binding pocket or interface to recognize a specific molecule. An alternate approach to constraining a polymer in three-dimensional space involves adsorbing it onto a cylindrical nanotube surface[4-7]. To date, however, the molecular recognition potential of these structured, nanotube-associated complexes has been unexplored. In this work, we demonstrate three distinct examples in which synthetic polymers create unique and highly selective molecular recognition sites once adsorbed onto a single-walled carbon nanotube (SWCNT) surface. The phenomenon is shown to be generic, with new recognition complexes demonstrated for riboflavin, L-thyroxine, and estradiol, predicted using a 2D thermodynamic model of surface interactions. The dissociation constants are continuously tunable by perturbing the chemical structure of the heteropolymer. The complexes can be used as new types of sensors based on modulation of SWCNT photoemission, as demonstrated using a complex for real time spatio-temporal detection of riboflavin in murine macrophages. Cardiac biomarkers troponin I and T are recognized as standard indicators for acute myocardial infarction (AMI, or heart attack), a condition that comprises 10% of U.S. emergency room visits [8]. There is significant interest in a rapid, point-of-cae (POC) device for troponin detection[9]. In this work we demonstrate a rapid, quantitative, and label-free assay specific for cardiac troponin T detection, using fluorescent single-walled carbon nanotubes (SWCNTs). Chitosan-wrapped carbon nanotubes are crosslinked to form a thin gel that is further functionalized with nitrilotriacetic acid (NTA) moieties. Upon chelation of Ni²+, the Ni²+ -NTA group binds to a hexa-histidine-modified troponin antibody, which specifically recognizes the target protein, troponin T. As the troponin T binds to the antibody, the local environment of the sensor changes, allowing for the detection through changes in SWCNT bandgap fluorescence intensity. In this work, we have developed the first near-infrared SWCNT sensor array for specific cTnT detection. Detection can be completed within 3 minutes, and the sensor responds linearly to the cTnT concentrations, with the experimental detection limit of 100 ng/ml (2.5 nM). This platform may provide a promising new tool for POC AMI detection in the future. Moreover, the work presented two useful methods of characterizing two commonly used functional groups, amines and carboxylic acids in soft gels, and this will be useful for other researchers studying hydrogel chemistry. In addition, we synthesized and characterized chitosan-gels both with and without NTA groups, and we compared fluorescence responses upon the addition of four different divalent cations, including Ni²+ , CO², Mg²+, and Mn²+. We proposed a model based Flory-Huggins theory, without any fitted parameters, that is able to describe the fluorescence increase as the Ni²+ concentration increases. The model suggests that the strong binding of Ni²+ onto NTA groups decreases the number of mobile ions in the gel, resulting in a reduction in the ionic chemical potential inside the gel. As a result, the gel de-swells, leading to a local SWCNT concentration increase and an increase in the SWCNT fluorescence signal. by Jingqing Zhang. Ph.D. 2013-06-17T19:46:29Z 2013-06-17T19:46:29Z 2012 2013 Thesis http://hdl.handle.net/1721.1/79193 844350009 eng M.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. http://dspace.mit.edu/handle/1721.1/7582 272 p. application/pdf Massachusetts Institute of Technology |
| spellingShingle | Chemical Engineering. Zhang, Jingqing, Ph. D. Massachusetts Institute of Technology Molecular recognition using nanotube-adsorbed polymer complexes |
| title | Molecular recognition using nanotube-adsorbed polymer complexes |
| title_full | Molecular recognition using nanotube-adsorbed polymer complexes |
| title_fullStr | Molecular recognition using nanotube-adsorbed polymer complexes |
| title_full_unstemmed | Molecular recognition using nanotube-adsorbed polymer complexes |
| title_short | Molecular recognition using nanotube-adsorbed polymer complexes |
| title_sort | molecular recognition using nanotube adsorbed polymer complexes |
| topic | Chemical Engineering. |
| url | http://hdl.handle.net/1721.1/79193 |
| work_keys_str_mv | AT zhangjingqingphdmassachusettsinstituteoftechnology molecularrecognitionusingnanotubeadsorbedpolymercomplexes |