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Digital Electrical DNA Sensing
KTH, School of Electrical Engineering and Computer Science (EECS), Micro and Nanosystems.ORCID iD: 0000-0003-4364-794X
2019 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Molecule detection is a workhorse in life sciences and medicine, for example in cancer diagnosis and virus and bacterial detection. DNA analysis can provide vital information about the state of a host organism and its medical and health condition. A central challenge in DNA sensing lays in obtaining the following key detection characteristics in a single device: low limit of detection, small sample volume, high specificity, quantification, rapid time-to-result at a low cost.

Here we investigate whether direct electrical DNA sensing in a miniaturized detector can enable such performance. The detector consists of a gold-coated thin porous membrane, functionalized with oligonucleotides receptors, that is sandwiched between two off-stoichiometric thiol-ene-epoxy layers. The device works as follows. First, target DNA in the sample is specifically recognized by padlock probe hybridization and ligation. Second, the target-receptor circular molecules are amplified by rolling circle amplification (RCA), generating long ssDNA concatemers (RCP). Third, the RCPs are stretched through the membrane pores. Fourth, DNA metallization was used to form the gold nanowires bridging both sides of membrane pores after gold enhancement, which results in a conductive path that is measured with a simple resistance measurement. The thesis describes the engineering technology that enables low LoD detection of ssDNA using a digital measurement and details the development and optimization of the detector fabrication and operation, including structural design, materials, and microfluidic operation. We demonstrated a detector with sub-aM LoD, high specificity and simple operation in a miniaturized and uncomplicated format.

 Furthermore, the thesis studies the long-term liquid storage in nL scale well arrays fabricated in off-stoichiometric thiol-ene (OSTE). We demonstrated liquid storage with < 10 % loss of stored PBS buffer for 33 days and the on-demand electrically controlled liquid release.

The thesis presents the potential of a combination DNA detector with the method of liquid storage. Combining the on-chip liquid storage and DNA detection methods could provide a powerful alternative to conventional bio-detectors used in molecular diagnostics, and improved performance in multiplexed point-of-care sensing of (ultra-low abundant) biomolecules.

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2019. , p. 81
Series
TRITA-EECS-AVL ; 2019:38
Keywords [en]
DNA detection, thiol-ene-epoxy, rolling circle amplification, digital measurement, DNA stretching, microwell-array, gold nanowires, electrical measurement, specificity, limit of detection, liquid storage, disease diagnosis, lab-on-a-chip, point-of-care.
National Category
Engineering and Technology Medical and Health Sciences
Identifiers
URN: urn:nbn:se:kth:diva-250783ISBN: 978-91-7873-162-6 (print)OAI: oai:DiVA.org:kth-250783DiVA, id: diva2:1313776
Public defence
2019-06-11, Q2, Malvinas väg 10, Stockholm, 10:00 (English)
Opponent
Supervisors
Note

QC 20190508

Available from: 2019-05-08 Created: 2019-05-06 Last updated: 2019-05-14Bibliographically approved
List of papers
1. Efficient DNA-assisted synthesis of trans-membrane gold nanowires
Open this publication in new window or tab >>Efficient DNA-assisted synthesis of trans-membrane gold nanowires
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2018 (English)In: Microsystems & Nanoengineering, ISSN 2055-7434, Vol. 4, p. 1-8, article id UNSP 17084Article in journal (Refereed) Published
Abstract [en]

Whereas electric circuits and surface-based (bio)chemical sensors are mostly constructed in-plane due to ease of manufacturing, 3D microscale and nanoscale structures allow denser integration of electronic components and improved mass transport of the analyte to (bio)chemical sensor surfaces. This work reports the first out-of-plane metallic nanowire formation based on stretching of DNA through a porous membrane. We use rolling circle amplification (RCA) to generate long single-stranded DNA concatemers with one end anchored to the surface. The DNA strands are stretched through the pores in the membrane during liquid removal by forced convection. Because the liquid–air interface movement across the membrane occurs in every pore, DNA stretching across the membrane is highly efficient. The stretched DNA molecules are transformed into trans-membrane gold nanowires through gold nanoparticle hybridization and gold enhancement chemistry. A 50 fM oligonucleotide concentration, a value two orders of magnitude lower than previously reported for flat surface-based nanowire formation, was sufficient for nanowire formation. We observed nanowires in up to 2.7% of the membrane pores, leading to an across-membrane electrical conductivity reduction from open circuit to o20 Ω. The simple electrical read-out offers a high signal-to-noise ratio and can also be extended for use as a biosensor due to the high specificity and scope for multiplexing offered by RCA.

National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Identifiers
urn:nbn:se:kth:diva-227196 (URN)10.1038/micronano.2017.84 (DOI)000425451300001 ()
Funder
Swedish Research Council, SBE13-0125Swedish Foundation for Strategic Research , SBE13-0125EU, Horizon 2020, 675412
Note

Correction in: Microsystems & Nanoengineering (2018) 4:9 DOI: 10.1038/s41378-018-0012-7, WOS: 000434457800001

QC 20180601

Available from: 2018-05-04 Created: 2018-05-04 Last updated: 2019-05-08Bibliographically approved
2. Polymer Nanoliter Well Arrays for Liquid Storage and Rapid On-demand Electrochemical Release
Open this publication in new window or tab >>Polymer Nanoliter Well Arrays for Liquid Storage and Rapid On-demand Electrochemical Release
2018 (English)In: Sensors and actuators. B, Chemical, ISSN 0925-4005, E-ISSN 1873-3077, Vol. 267, p. 111-118Article in journal (Refereed) Published
Abstract [en]

Polymer microfluidic systems are of increasing importance in several applications in biomedicine and biosensing. The integrated encapsulation, storage, and controlled release of small amounts of liquid in such systems remains an unresolved technical challenge. Here, we report two methods for the room-temperature and adhesive-free sealing of 1–330 nanoliter volumes of liquid in off-stoichiometry thiol-ene polymer well arrays by spontaneous bonding to 200 nm thin gold films. Sealed well arrays were stored for more than one month in a liquid environment with <10% liquid loss, and for more than one week in air with minimal loss. We demonstrated that controlling the electrical potential and polarity over encapsulated wells allowed for selecting one of two well opening mechanisms: slow anodic electrochemical etching, or rapid electrolytic gas pressure-induced bursting of the gold film. The results may find potential applications in diagnostic testing, in vivo drug delivery, or in spatio-temporal release of chemical compounds in biological assays.

Place, publisher, year, edition, pages
Elsevier, 2018
Keywords
nanoliter liquid encapsulation, nanoliter liquid storage, electrochemical liquid release, off-stoichiometry thiol-ene (OSTE) polymer, nanoliter well arrays
National Category
Polymer Technologies Medical Biotechnology Biomedical Laboratory Science/Technology Electrical Engineering, Electronic Engineering, Information Engineering
Research subject
Electrical Engineering
Identifiers
urn:nbn:se:kth:diva-215017 (URN)10.1016/j.snb.2018.04.013 (DOI)000432775600014 ()2-s2.0-85045401734 (Scopus ID)
Note

QC 20180515

Available from: 2017-09-29 Created: 2017-09-29 Last updated: 2019-05-08Bibliographically approved
3. Direct Electrical Detection of sub-aM DNA concentrations
Open this publication in new window or tab >>Direct Electrical Detection of sub-aM DNA concentrations
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2019 (English)Article in journal (Other academic) Submitted
National Category
Electrical Engineering, Electronic Engineering, Information Engineering Medical and Health Sciences Nano Technology
Identifiers
urn:nbn:se:kth:diva-250773 (URN)
Note

QC 20190506

Available from: 2019-05-06 Created: 2019-05-06 Last updated: 2019-05-14Bibliographically approved

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Guo, Maoxiang

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