1
|
Kim J, Ahn SY, Um SH. Bead-Immobilized Multimodal Molecular Beacon-Equipped DNA Machinery for Specific RNA Target Detection: A Prototypical Molecular Nanobiosensor. NANOMATERIALS 2021; 11:nano11061617. [PMID: 34203018 PMCID: PMC8235652 DOI: 10.3390/nano11061617] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/12/2021] [Accepted: 06/18/2021] [Indexed: 12/28/2022]
Abstract
A variety of nanostructured diagnostic tools have been developed for the precise detection of known genetic variants. Molecular beacon systems are very promising tools due to their specific selectivity coupled with relatively lower cost and time requirements than existing molecular detection tools such as next generation sequencing or real-time PCR (polymerase chain reaction). However, they are prone to errors induced by secondary structure responses to environmental fluctuations, such as temperature and pH. Herein, we report a temperature-insensitive, bead-immobilized, molecular beacon-equipped novel DNA nanostructure for detection of cancer miRNA variants with the consideration of thermodynamics. This system consists of three parts: a molecular beacon for cancer-specific RNA capture, a stem body as a core template, and a single bead for solid-support. This DNA system was selectively bound to nanosized beads using avidin-biotin chemistry. Synthetic DNA nanostructures, designed based on the principle of fluorescence-resonance enhanced transfer, were effectively applied for in vitro cancer-specific RNA detection. Several parameters were optimized for higher performance, with a focus on thermodynamic stability. Theoretical issues regarding the secondary structure of a single molecular beacon and its combinatory forms were also studied. This study provides design guidelines for new sensing systems of miRNA variation for next-generation biotechnological applications.
Collapse
Affiliation(s)
- Jeonghun Kim
- School of Chemical Engineering, Sungkyunkwan University, Suwon 16419, Gyeonggi-do, Korea; (J.K.); (S.Y.A.)
| | - So Yeon Ahn
- School of Chemical Engineering, Sungkyunkwan University, Suwon 16419, Gyeonggi-do, Korea; (J.K.); (S.Y.A.)
| | - Soong Ho Um
- School of Chemical Engineering, Sungkyunkwan University, Suwon 16419, Gyeonggi-do, Korea; (J.K.); (S.Y.A.)
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Gyeonggi-do, Korea
- Correspondence:
| |
Collapse
|
2
|
Zhou W, Feng M, Valadez A, Li X. One-Step Surface Modification to Graft DNA Codes on Paper: The Method, Mechanism, and Its Application. Anal Chem 2020; 92:7045-7053. [PMID: 32207965 DOI: 10.1021/acs.analchem.0c00317] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Glass slides have been widely used for DNA immobilization in DNA microarray and numerous bioassays for decades, whereas they are faced with limitations of low probe density, time-consuming modification steps, and expensive instruments. In this work, a simple one-step surface modification method using 3-aminopropyl trimethoxysilane (APTMS) has been developed and applied to graft DNA codes on paper. Higher DNA immobilization efficiency was obtained in comparison with that in a conventional method using glass slides. Fluorescence detection, X-ray photoelectron spectroscopy (XPS), infrared spectra (FT-IR), and pH influence studies were employed to characterize the surface modification and subsequent DNA immobilization, which further reveals a mechanism in which this method lies in ionic interactions between the positively charged APTMS-modified paper surface and negatively charged DNA probes. Furthermore, an APTMS-modified paper-based device has been developed to demonstrate application in low-cost detection of a foodborne pathogen, Giardia lamblia, with high sensitivity (the detection limit of 22 nM) and high specificity. Compared with conventional methods using redundant cross-linking reactions, our method is simpler, faster, versatile, and lower-cost, enabling broad applications of paper-based bioassays especially for point-of-care detection in resource-poor settings.
Collapse
Affiliation(s)
- Wan Zhou
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, 500 West University Avenue, El Paso, Texas 79968, United States
| | - Mengli Feng
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, 500 West University Avenue, El Paso, Texas 79968, United States
| | - Alejandra Valadez
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, 500 West University Avenue, El Paso, Texas 79968, United States
| | - XiuJun Li
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, 500 West University Avenue, El Paso, Texas 79968, United States.,Biomedical Engineering, The University of Texas at El Paso, 500 West University Avenue, El Paso, Texas 79968, United States.,Border Biomedical Research Center, The University of Texas at El Paso, 500 West University Avenue, El Paso, Texas 79968, United States.,Environmental Science and Engineering, The University of Texas at El Paso, 500 West University Avenue, El Paso, Texas 79968, United States
| |
Collapse
|
3
|
Runsewe D, Betancourt T, Irvin JA. Biomedical Application of Electroactive Polymers in Electrochemical Sensors: A Review. MATERIALS (BASEL, SWITZERLAND) 2019; 12:E2629. [PMID: 31426613 PMCID: PMC6720215 DOI: 10.3390/ma12162629] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/01/2019] [Accepted: 08/07/2019] [Indexed: 02/07/2023]
Abstract
Conducting polymers are of interest due to their unique behavior on exposure to electric fields, which has led to their use in flexible electronics, sensors, and biomaterials. The unique electroactive properties of conducting polymers allow them to be used to prepare biosensors that enable real time, point of care (POC) testing. Potential advantages of these devices include their low cost and low detection limit, ultimately resulting in increased access to treatment. This article presents a review of the characteristics of conducting polymer-based biosensors and the recent advances in their application in the recognition of disease biomarkers.
Collapse
Affiliation(s)
- Damilola Runsewe
- Materials Science, Engineering and Commercialization Program, Texas State University, San Marcos, TX 78666, USA
| | - Tania Betancourt
- Materials Science, Engineering and Commercialization Program, Texas State University, San Marcos, TX 78666, USA.
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA.
| | - Jennifer A Irvin
- Materials Science, Engineering and Commercialization Program, Texas State University, San Marcos, TX 78666, USA.
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA.
| |
Collapse
|
4
|
Caputo TM, Battista E, Netti PA, Causa F. Supramolecular Microgels with Molecular Beacons at the Interface for Ultrasensitive, Amplification-Free, and SNP-Selective miRNA Fluorescence Detection. ACS APPLIED MATERIALS & INTERFACES 2019; 11:17147-17156. [PMID: 31021070 DOI: 10.1021/acsami.8b22635] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In this study, a supramolecular structure with femtomolar biorecognition properties is proposed for use in analytical devices. It is obtained by an innovative interface between synthetic hydrogel polymers and molecular beacon (mb) probes. Supramolecularly structured microgels are synthetized with a core-shell architecture with specific dyes polymerized in a desired compartment. Mb probes are opportunely conjugated at the microgel interface so that their recognition mechanism is preserved and their spatial distribution is optimized to avoid crowding effects. The miR-21, a microRNA involved in various biological processes and usually used as a biomarker in early cancer diagnosis, has been selected as the target. The results demonstrate that by tuning the spatial distribution of molecular probes immobilized on the microgel and/or the amount of microgels, the assay shows scalable sensitivity reaching a limit of detection down to about 10 fM, without amplification steps and with detection time as short as 1 h. The assay results specific toward single mutated targets, and it is stable in the presence of high-interfering oligonucleotides concentrations. The miRNA target is also detected in human serum with performances similar to those observed in PBS buffer because of microgel antifouling properties without the need of any surface treatment. All tests were performed in a low sample volume (20 μL). As a result, mb-microgel represents an innovative biosensor to precisely quantify microRNAs in a direct (mix&read), scalable, and selective way. Such an approach paves the way for creating innovative biosensing interfaces with other probes, such as hairpins, aptamers, and PNA.
Collapse
Affiliation(s)
- Tania M Caputo
- Center for Advanced Biomaterials for Healthcare@CRIB , Istituto Italiano di Tecnologia (IIT) , Largo Barsanti e Matteucci 53 , 80125 Naples , Italy
| | - Edmondo Battista
- Center for Advanced Biomaterials for Healthcare@CRIB , Istituto Italiano di Tecnologia (IIT) , Largo Barsanti e Matteucci 53 , 80125 Naples , Italy
- InterdisciplinaryResearch Centre on Biomaterials (CRIB) , Università degli Studi di Napoli "Federico II" , Piazzale Tecchio 80 , 80125 Naples , Italy
| | - Paolo A Netti
- Center for Advanced Biomaterials for Healthcare@CRIB , Istituto Italiano di Tecnologia (IIT) , Largo Barsanti e Matteucci 53 , 80125 Naples , Italy
- InterdisciplinaryResearch Centre on Biomaterials (CRIB) , Università degli Studi di Napoli "Federico II" , Piazzale Tecchio 80 , 80125 Naples , Italy
- Dipartimento di Ingegneria Chimica del Materiali e della Produzione Industriale (DICMAPI) , University "Federico II" , Piazzale Tecchio 80 , 80125 Naples , Italy
| | - Filippo Causa
- Center for Advanced Biomaterials for Healthcare@CRIB , Istituto Italiano di Tecnologia (IIT) , Largo Barsanti e Matteucci 53 , 80125 Naples , Italy
- InterdisciplinaryResearch Centre on Biomaterials (CRIB) , Università degli Studi di Napoli "Federico II" , Piazzale Tecchio 80 , 80125 Naples , Italy
- Dipartimento di Ingegneria Chimica del Materiali e della Produzione Industriale (DICMAPI) , University "Federico II" , Piazzale Tecchio 80 , 80125 Naples , Italy
| |
Collapse
|
5
|
Zhang B, Wang Q, Wu J, Chen Y, Wang J. Detection of nucleic acids with a novel stem-loop primer rolling circle amplification technique. Biotechniques 2018; 64:69-80. [PMID: 29571284 DOI: 10.2144/btn-2017-0104] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 01/19/2018] [Indexed: 11/23/2022] Open
Abstract
This paper presents a new rolling circle amplification (RCA) technique using stem-loop primers (SLP). The technique enables detection of target DNA by either linear or exponential amplification (SLP-lRCA and SLP-eRCA) in both liquid and solid phases. For solid-phase detection, SLP-eRCA detects nucleic acids in four steps: (1) covalently immobilize an array of capture probes (CP) on a solid support; (2) hybridize the CP array with the DNA sample; (3) incubate the CP array with an RCA reaction containing two SLPs; (4) image the CP array. SLP-eRCA detects nucleic acids in liquid phase in one step: a real-time RCA reaction containing the DNA sample and two SLPs. Both liquid- and solid-phase detection methods employ a general rolling circle and an SLP. The other SLP is specific to the target. The technique was verified by detecting synthesized oligonucleotides and six different human papillomaviruses (HPVs), both in liquid phase and on a solid surface. The technique also detected two high-risk HPVs (HPV16 and HPV18) in cervical carcinoma cells (HeLa and SiHa) and clinical samples. This study provides proof-of-concept for the new RCA technique for nucleic acid detection, which overcomes major limitations of current RCA approaches.
Collapse
Affiliation(s)
- Beibei Zhang
- State Key Laboratory of Bioelectronics, Southeast University, 210096, Nanjing, China
| | - Qiao Wang
- State Key Laboratory of Bioelectronics, Southeast University, 210096, Nanjing, China
| | - Jian Wu
- State Key Laboratory of Bioelectronics, Southeast University, 210096, Nanjing, China
| | - Yin Chen
- School of Medical Technology, Xuzhou Medical University, 221004, Xuzhou, China
| | - Jinke Wang
- State Key Laboratory of Bioelectronics, Southeast University, 210096, Nanjing, China
| |
Collapse
|
6
|
Waidely E, Al-Youbi AO, Bashammakh AS, El-Shahawi MS, Leblanc RM. Alpha-l-Fucosidase Immunoassay for Early Detection of Hepatocellular Carcinoma. Anal Chem 2017; 89:9459-9466. [DOI: 10.1021/acs.analchem.7b02284] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Eric Waidely
- Department
of Chemistry, University of Miami, 1301 Memorial Drive, Cox Science
Center, Coral Gables, Florida 33146, United States
| | - Abdulrahman O. Al-Youbi
- Department
of Chemistry, King Abdulaziz University, P.O. Box 80200, Jeddah 21589, Kingdom of Saudi Arabia
| | - Abdulaziz S. Bashammakh
- Department
of Chemistry, King Abdulaziz University, P.O. Box 80200, Jeddah 21589, Kingdom of Saudi Arabia
| | - Mohammad S. El-Shahawi
- Department
of Chemistry, King Abdulaziz University, P.O. Box 80200, Jeddah 21589, Kingdom of Saudi Arabia
| | - Roger M. Leblanc
- Department
of Chemistry, University of Miami, 1301 Memorial Drive, Cox Science
Center, Coral Gables, Florida 33146, United States
| |
Collapse
|
7
|
Su Q, Nöll G. A sandwich-like strategy for the label-free detection of oligonucleotides by surface plasmon fluorescence spectroscopy (SPFS). Analyst 2016; 141:5784-5791. [PMID: 27484040 PMCID: PMC5166564 DOI: 10.1039/c6an01129b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cutting surface-bound optical molecular beacons results in a sandwich-like detection strategy with lower background fluorescence.
For the detection of oligonucleotides a sandwich-like detection strategy has been developed by which the background fluorescence is significantly lowered in comparison with surface-bound molecular beacons. Surface bound optical molecular beacons are DNA hairpin structures comprising a stem and a loop. The end of the stem is modified with a fluorophore and a thiol anchor for chemisorption on gold surfaces. In the closed state the fluorophore is in close proximity to the gold surface, and most of the fluorescence is quenched. After hybridization with a target the hairpin opens, the fluorophore and surface become separated, and the fluorescence drastically increases. Using this detection method the sensitivity is limited by the difference in the fluorescence intensity in the closed and open state. As the background fluorescence is mainly caused by non-quenched fluorophores, a strategy to reduce the background fluorescence is to cut the beacon in two halves. First a thiolated ssDNA capture probe strand (first half) is chemisorbed to a gold surface together with relatively short thiol spacers. Next the target is hybridized by one end to the surface-anchored capture probe and by the other to a fluorophore-labeled reporter probe DNA (second half). The signal readout is done by surface plasmon fluorescence spectroscopy (SPFS). Using this detection strategy the background fluorescence can be significantly lowered, and the detection limit is lowered by more than one order of magnitude. The detection of a target takes only a few minutes and the sensor chips can be used for multiple detection steps without a significant decrease in performance.
Collapse
Affiliation(s)
- Qiang Su
- Nöll Junior Research Group, Organic Chemistry, Chem. Biol. Dept., Faculty IV, Siegen University, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
| | | |
Collapse
|
8
|
Cao Q, Teng Y, Yang X, Wang J, Wang E. A label-free fluorescent molecular beacon based on DNA-Ag nanoclusters for the construction of versatile Biosensors. Biosens Bioelectron 2015; 74:318-21. [DOI: 10.1016/j.bios.2015.06.044] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 06/18/2015] [Accepted: 06/19/2015] [Indexed: 01/21/2023]
|
9
|
Glotov AS, Sinitsyna ES, Danilova MM, Vashukova ES, Walter JG, Stahl F, Baranov VS, Vlakh EG, Tennikova TB. Detection of human genome mutations associated with pregnancy complications using 3-D microarray based on macroporous polymer monoliths. Talanta 2015; 147:537-46. [PMID: 26592644 DOI: 10.1016/j.talanta.2015.09.066] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 09/21/2015] [Accepted: 09/27/2015] [Indexed: 01/13/2023]
Abstract
Analysis of variations in DNA structure using a low-density microarray technology for routine diagnostic in evidence-based medicine is still relevant. In this work the applicability of 3-D macroporous monolithic methacrylate-based platforms for detection of different pathogenic genomic substitutions was studied. The detection of nucleotide replacements in F5 (Leiden G/A, rs6025), MTHFR (C/T, rs1801133) and ITGB3 (T/C, rs5918), involved in coagulation, and COMT (C/G, rs4818), TPH2 (T/A, rs11178997), PON1 (T/A rs854560), AGTR2 (C/A, rs11091046) and SERPINE1 (5G/4G, rs1799889), associated with pregnancy complications, was performed. The effect of such parameters as amount and type of oligonucleotide probe, amount of PCR product on signal-to-noise ratio, as well as mismatch discrimination was analyzed. Sensitivity and specificity of mutation detections were coincided and equal to 98.6%. The analysis of SERPINE1 and MTHFR genotypes by both NGS and developed microarray was performed and compared.
Collapse
Affiliation(s)
- A S Glotov
- Faculty of Biology, Saint-Petersburg State University, St. Petersburg, Russia; D.O. Ott Research Institute of Obstetrics and Gynecology, Russian Academy of Medical Sciences, St. Petersburg, Russia
| | - E S Sinitsyna
- Institute of Chemistry, Saint-Petersburg State University, St. Petersburg, Russia; Institute of Macromolecular Compound, Russian Academy of Sciences, St. Petersburg, Russia
| | - M M Danilova
- D.O. Ott Research Institute of Obstetrics and Gynecology, Russian Academy of Medical Sciences, St. Petersburg, Russia
| | - E S Vashukova
- D.O. Ott Research Institute of Obstetrics and Gynecology, Russian Academy of Medical Sciences, St. Petersburg, Russia
| | - J G Walter
- Institute for Technical Chemistry, Leibniz University, Hannover, Germany
| | - F Stahl
- Institute for Technical Chemistry, Leibniz University, Hannover, Germany
| | - V S Baranov
- Faculty of Biology, Saint-Petersburg State University, St. Petersburg, Russia; D.O. Ott Research Institute of Obstetrics and Gynecology, Russian Academy of Medical Sciences, St. Petersburg, Russia
| | - E G Vlakh
- Institute of Chemistry, Saint-Petersburg State University, St. Petersburg, Russia; Institute of Macromolecular Compound, Russian Academy of Sciences, St. Petersburg, Russia
| | - T B Tennikova
- Institute of Chemistry, Saint-Petersburg State University, St. Petersburg, Russia; Institute of Macromolecular Compound, Russian Academy of Sciences, St. Petersburg, Russia.
| |
Collapse
|
10
|
Guo Q, Bai Z, Liu Y, Sun Q. A molecular beacon microarray based on a quantum dot label for detecting single nucleotide polymorphisms. Biosens Bioelectron 2015; 77:107-10. [PMID: 26397421 DOI: 10.1016/j.bios.2015.09.031] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Revised: 09/11/2015] [Accepted: 09/12/2015] [Indexed: 11/29/2022]
Abstract
In this work, we report the application of streptavidin-coated quantum dot (strAV-QD) in molecular beacon (MB) microarray assays by using the strAV-QD to label the immobilized MB, avoiding target labeling and meanwhile obviating the use of amplification. The MBs are stem-loop structured oligodeoxynucleotides, modified with a thiol and a biotin at two terminals of the stem. With the strAV-QD labeling an "opened" MB rather than a "closed" MB via streptavidin-biotin reaction, a sensitive and specific detection of label-free target DNA sequence is demonstrated by the MB microarray, with a signal-to-background ratio of 8. The immobilized MBs can be perfectly regenerated, allowing the reuse of the microarray. The MB microarray also is able to detect single nucleotide polymorphisms, exhibiting genotype-dependent fluorescence signals. It is demonstrated that the MB microarray can perform as a 4-to-2 encoder, compressing the genotype information into two outputs.
Collapse
Affiliation(s)
- Qingsheng Guo
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Zhixiong Bai
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Yuqian Liu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Qingjiang Sun
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China.
| |
Collapse
|
11
|
Wang L, Kong W, Yang M, Han J, Chen S. Safety issues and new rapid detection methods in traditional Chinese medicinal materials. Acta Pharm Sin B 2015; 5:38-46. [PMID: 26579423 PMCID: PMC4629208 DOI: 10.1016/j.apsb.2014.12.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 11/25/2014] [Accepted: 12/12/2014] [Indexed: 11/29/2022] Open
Abstract
The safety of traditional Chinese medicine (TCM) is a major strategic issue that involves human health. With the continuous improvement in disease prevention and treatment, the export of TCM and its related products has increased dramatically in China. However, the frequent safety issues of Chinese medicine have become the 'bottleneck' impeding the modernization of TCM. It was proved that mycotoxins seriously affect TCM safety; the pesticide residues of TCM are a key problem in TCM international trade; adulterants have also been detected, which is related to market circulation. These three factors have greatly affected TCM safety. In this study, fast, highly effective, economically-feasible and accurate detection methods concerning TCM safety issues were reviewed, especially on the authenticity, mycotoxins and pesticide residues of medicinal materials.
Collapse
Key Words
- 2D DNA barcodes
- AA, aristolochic acid, Afs, aflatoxins
- Authentication
- DON, deoxynivalenol, GICA, gold immunochromatographic assay
- LOD, limit of detection, OTA, ochratoxin A
- Mycotoxins
- PAs, pyrrolizidine alkaloids, SNP, single nucleotide polymorphism
- Pesticide residues
- Rapid detection
- SSCP, single-strand conformation polymorphism, ZEN, zearalenone
- Safety issue
- Traceability
- Traditional Chinese medicine
Collapse
Affiliation(s)
- Lili Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Weijun Kong
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Meihua Yang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Jianping Han
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Shilin Chen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| |
Collapse
|
12
|
|
13
|
Xing X, Zhou Y, Liu X, Pang D, Tang H. Graphene oxide and metal-mediated base pairs based "molecular beacon" integrating with exonuclease I for fluorescence turn-on detection of biothiols. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:3412-3420. [PMID: 24788855 DOI: 10.1002/smll.201302938] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 01/18/2014] [Indexed: 06/03/2023]
Abstract
A novel fluorescence turn-on strategy, based on the resistance of metal-mediated molecular-beacons (MBs) toward nuclease digestion and the remarkable difference in the affinity of graphene oxide (GO) with MBs and the mononucleotides, is designed for the biothiols assay. Specifically, the metal-mediated base pairs facilitate the dye labeled MBs to fold into a hairpin structure preventing the digestion by exonuclease I, and thus allow the fluorescence quenching. The competition binding by biothiols removes metal ions from the base pairs, causing the nuclease reaction, and less decrease in the fluorescence is obtained after incubating with GO due to the weak affinity of the product-mononucleotides to GO. Hg(2+)-mediated MBs were firstly designed for the biothiols detection, and glutathione (GSH) was applied as the model target. Under the optimal conditions, the approach exhibits high sensitivity to GSH with a detection limit of 1.53 nM. Ag(+)-mediated MBs based sensor was also constructed to demonstrate its versatility, and cysteine was studied as the model target. The satisfactory results in the determination of biothiols in serum demonstrate that the method possesses great potential for detecting thiols in biological fluids. This new approach is expected to promote the exploitation of metal-mediated base pairs-based biosensors in biochemical and biomedical studies.
Collapse
Affiliation(s)
- Xiaojing Xing
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan Institute of Biotechnology, and State, Key Laboratory of Virology, Wuhan University, Wuhan, 430072, P. R. China
| | | | | | | | | |
Collapse
|
14
|
Dual hairpin-like molecular beacon based on coralyne-adenosine interaction for sensing melamine in dairy products. Talanta 2014; 129:398-403. [PMID: 25127611 DOI: 10.1016/j.talanta.2014.05.046] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 05/18/2014] [Accepted: 05/21/2014] [Indexed: 11/20/2022]
Abstract
This study presents a novel dual hairpin-like molecular beacon (MB) for the selective and sensitive detection of melamine (MA) based on the conjugation of MA and thymine. In this protocol, the coordination between coralyne and adenosine (A) leaded a dual hairpin-like MB and the fluorophore-quencher pair is close proximity resulting in the fluorescence quenching. With the addition of MA, it conjugated with thymine in the loop part of dual hairpin-like MB by triple H-bonds, triggering the dissociation of the dual hairpin-like MB. The resulting spatial separation of the fluorophore from quencher induced the enhancement in fluorescence emission. Under the optimized conditions, the sensor exhibited a wide linear range of 8×10(-9)-1.6×10(-5) M (R(2)=0.9969) towards MA, with a low detection limit of 5 nM, approximately 4000 times lower than the Drug Administration and the US Food estimated MA safety limit. The real milk samples were also investigated with a satisfying result.
Collapse
|
15
|
Rao AN, Grainger DW. BIOPHYSICAL PROPERTIES OF NUCLEIC ACIDS AT SURFACES RELEVANT TO MICROARRAY PERFORMANCE. Biomater Sci 2014; 2:436-471. [PMID: 24765522 PMCID: PMC3992954 DOI: 10.1039/c3bm60181a] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Both clinical and analytical metrics produced by microarray-based assay technology have recognized problems in reproducibility, reliability and analytical sensitivity. These issues are often attributed to poor understanding and control of nucleic acid behaviors and properties at solid-liquid interfaces. Nucleic acid hybridization, central to DNA and RNA microarray formats, depends on the properties and behaviors of single strand (ss) nucleic acids (e.g., probe oligomeric DNA) bound to surfaces. ssDNA's persistence length, radius of gyration, electrostatics, conformations on different surfaces and under various assay conditions, its chain flexibility and curvature, charging effects in ionic solutions, and fluorescent labeling all influence its physical chemistry and hybridization under assay conditions. Nucleic acid (e.g., both RNA and DNA) target interactions with immobilized ssDNA strands are highly impacted by these biophysical states. Furthermore, the kinetics, thermodynamics, and enthalpic and entropic contributions to DNA hybridization reflect global probe/target structures and interaction dynamics. Here we review several biophysical issues relevant to oligomeric nucleic acid molecular behaviors at surfaces and their influences on duplex formation that influence microarray assay performance. Correlation of biophysical aspects of single and double-stranded nucleic acids with their complexes in bulk solution is common. Such analysis at surfaces is not commonly reported, despite its importance to microarray assays. We seek to provide further insight into nucleic acid-surface challenges facing microarray diagnostic formats that have hindered their clinical adoption and compromise their research quality and value as genomics tools.
Collapse
Affiliation(s)
- Archana N. Rao
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, UT 84112 USA
| | - David W. Grainger
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, UT 84112 USA
- Department of Bioengineering, University of Utah, Salt Lake City, UT 84112 USA
| |
Collapse
|
16
|
Dai X, Libera M. Dip-pen microarraying of molecular beacon probes on microgel thin-film substrates. Analyst 2014; 139:5568-75. [DOI: 10.1039/c4an01220h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Micron-sized spots of molecular beacon probes are patterned on PEG microgel thin films using dip-pen nanolithography.
Collapse
Affiliation(s)
- Xiaoguang Dai
- Department of Chemical Engineering and Materials Science
- Stevens Institute of Technology
- Hoboken, USA
| | - Matthew Libera
- Department of Chemical Engineering and Materials Science
- Stevens Institute of Technology
- Hoboken, USA
| |
Collapse
|
17
|
A quencher-free molecular beacon design based on pyrene excimer fluorescence using pyrene-labeled UNA (unlocked nucleic acid). Bioorg Med Chem 2013; 21:6186-90. [DOI: 10.1016/j.bmc.2013.04.062] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 04/08/2013] [Accepted: 04/16/2013] [Indexed: 11/18/2022]
|
18
|
Chen J, Huang Y, Shi M, Zhao S, Zhao Y. Highly sensitive multiplexed DNA detection using multi-walled carbon nanotube-based multicolor nanobeacon. Talanta 2013; 109:160-6. [PMID: 23618154 DOI: 10.1016/j.talanta.2013.02.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Revised: 01/26/2013] [Accepted: 02/01/2013] [Indexed: 01/06/2023]
Abstract
A highly sensitive and selective multi-walled carbon nanotube (MWCNT)-based multicolor fluorescent nanobeacon is developed for multiplexed analysis of DNA in homogeneous solution. In this work, three different dye-labeled DNA hairpins were adsorbed on MWCNTs surface via π-stacking, which brings the dyes and MWCNTs into close proximity and leads to the quenching of fluorescence of the dyes. When target DNAs were added to the solution, the target DNAs specifically hybridize with the probes to form stable DNA duplexes, which weakens the interactions between the probes and MWCNTs, and results in the fluorescence recovery of the dyes. By using three 15-mer DNA fragments as proof-of-principle analytes, the proposed method showed good analytical performance. The limits of detection obtained were in the range of 35-42 pM. Moreover, this method also exhibits an excellent ability to discriminate between single nucleotide polymorphisms.
Collapse
Affiliation(s)
- Jia Chen
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education), College of Chemistry and Chemical Engineering, Guangxi Normal University, Guilin 541004, China
| | | | | | | | | |
Collapse
|
19
|
Wang W, Yuan X, Zhang W, Gao Q, Qi H, Zhang C. Cascade signal amplification for ultra-sensitive impedimetric detection of DNA hybridization using a hairpin DNA as probe. Electrochim Acta 2012. [DOI: 10.1016/j.electacta.2012.06.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
|
20
|
Matharu Z, Bandodkar AJ, Gupta V, Malhotra BD. Fundamentals and application of ordered molecular assemblies to affinity biosensing. Chem Soc Rev 2012; 41:1363-402. [DOI: 10.1039/c1cs15145b] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
21
|
Duan D, Zheng KX, Shen Y, Cao R, Jiang L, Lu Z, Yan X, Li J. Label-free high-throughput microRNA expression profiling from total RNA. Nucleic Acids Res 2011; 39:e154. [PMID: 21976734 PMCID: PMC3239174 DOI: 10.1093/nar/gkr774] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
MicroRNAs (miRNAs) are key biological regulators and promising disease markers whose detection technologies hold great potentials in advancing fundamental research and medical diagnostics. Currently, miRNAs in biological samples have to be labeled before being applied to most high-throughput assays. Although effective, these labeling-based approaches are usually labor-intensive, time-consuming and liable to bias. Besides, the cross-hybridization of co-existing miRNA precursors (pre-miRNAs) is not adequately addressed in most assays that use total RNA as input. Here, we present a hybridization-triggered fluorescence strategy for label-free, microarray-based high-throughput miRNA expression profiling. The total RNA is directly applied to the microarray with a short fluorophore-linked oligonucleotide Universal Tag which can be selectively captured by the target-bound probes via base-stacking effects. This Stacking-Hybridized Universal Tag (SHUT) assay has been successfully used to analyze as little as 100 ng total RNA from human tissues, and found to be highly specific to homogenous miRNAs. Superb discrimination toward single-base mismatch at the 5′ or 3′ end has been demonstrated. Importantly, the pre-miRNAs generated negligible signals, validating the direct use of total RNA.
Collapse
Affiliation(s)
- Demin Duan
- Suzhou Institute of Nano-tech and Nano-bionics, Chinese Academy of Sciences, 398 Ruoshui Road, Suzhou, 215123, China
| | | | | | | | | | | | | | | |
Collapse
|
22
|
Sato Y, Nishizawa S, Teramae N. Label-Free Molecular Beacon System Based on DNAs Containing Abasic Sites and Fluorescent Ligands That Bind Abasic Sites. Chemistry 2011; 17:11650-6. [DOI: 10.1002/chem.201100384] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Revised: 05/31/2011] [Indexed: 01/13/2023]
|
23
|
Huang C, Stakenborg T, Cheng Y, Colle F, Steylaerts T, Jans K, Van Dorpe P, Lagae L. Label-free genosensor based on immobilized DNA hairpins on gold surface. Biosens Bioelectron 2010; 26:3121-6. [PMID: 21208795 DOI: 10.1016/j.bios.2010.12.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2010] [Revised: 11/18/2010] [Accepted: 12/03/2010] [Indexed: 10/18/2022]
Abstract
In this report, we demonstrate a label-free genosensor based on DNA hairpins coupled to gold coated sensor surfaces. The hairpin probes were labeled with a thiolated moiety for immobilization at the 5' end and with a fluorophore for signal transduction at the 3' end. In the absence of the complement, the fluorophore is quenched by energy transfer to the gold surface. Addition of the target sequence leads to the hairpin unfolding, and releases the fluorescent signal. This built-in property, using a gold film as both the immobilizing substrate and quenching agent, has the advantage of simplicity in design and ease of further integration. Our results showed that lengths of both the stem and the loop structures have significant effects on the sensor performance. Hybridization kinetics was investigated for various probe/target lengths and concentrations. An optimized hairpin probe gave a fluorescent signal increase of 39 folds after hybridization, which is much higher than the earlier reported results. A limit of detection (LOD) down to 0.3 nM for the complementary target DNA detection has been achieved. The developed sensor was further successfully applied for the detection of single-base mismatch targets, as well as for the direct detection of PCR products.
Collapse
|
24
|
Cederquist KB, Keating CD. Hybridization efficiency of molecular beacons bound to gold nanowires: effect of surface coverage and target length. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:18273-80. [PMID: 21038880 PMCID: PMC2994276 DOI: 10.1021/la1031703] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Revised: 10/13/2010] [Indexed: 05/22/2023]
Abstract
Surface-bound nucleic acid probes designed to adopt specific secondary structures are becoming increasingly important in a range of biosensing applications but remain less well characterized than traditional single-stranded probes, which are typically designed to avoid secondary structure. We report the hybridization efficiency for surface-immobilized hairpin DNA probes. Our probes are molecular beacons, carrying a 3' dye moiety and a 5' thiol for attachment to gold nanowires, which serve as both scaffolds for probe attachment and quenchers. Hybridization efficiency was dependent on probe surface coverage, reaching a maximum of ∼90% at intermediate coverages of (1-2) × 10(12) probes/cm(2) and dropping to ≤20% at higher or lower coverages. Fluorescence intensity did not track with the number of target molecules bound, and was highest for high probe coverage despite the lower bound targets per square centimeter. Backfilling with short thiolated oligoethylene glycol spacers increased hybridization efficiency at low hairpin probe coverages (∼(3-4) × 10(11) probes/cm(2)), but not at higher probe coverages (1 × 10(12)/cm(2)). We also evaluated the effect of target length by adding up to 50 nonhybridizing nucleotides to the 3' or 5' end of the complementary target sequence. Additional nucleotides on the 3' end of the complementary target sequence (i.e., the end near the nanowire surface) had a much greater impact on hybridization efficiency as compared to nucleotides added to the 5' end. This work provides guidance in designing sensors in which surface-bound probes designed to adopt secondary structures are used to detect target sequences from solution.
Collapse
Affiliation(s)
- Kristin B. Cederquist
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Christine D. Keating
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| |
Collapse
|
25
|
Li F, Huang Y, Yang Q, Zhong Z, Li D, Wang L, Song S, Fan C. A graphene-enhanced molecular beacon for homogeneous DNA detection. NANOSCALE 2010; 2:1021-6. [PMID: 20648302 DOI: 10.1039/b9nr00401g] [Citation(s) in RCA: 150] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
In this work, we report the design of a novel graphene-based molecular beacon (MB) that could sensitively and selectively detect specific DNA sequences. The ability of water-soluble graphene oxide (GO) to differentiated hairpin and dsDNA offered a new approach to detect DNA. We found that the background fluorescence of MB was significantly suppressed in the presence of GO, which increased the signal-to-background ratio, hence the sensitivity. Moreover, the single-mismatch differentiation ability of hairpin DNA was maintained, leading to high selectivity of this new method.
Collapse
Affiliation(s)
- Fan Li
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | | | | | | | | | | | | | | |
Collapse
|
26
|
Shi H, He X, Yang X, Wang K, Wang Q, Guo Q, Huo X. Protein analysis based on molecular beacon probes and biofunctionalized nanoparticles. Sci China Chem 2010; 53:704-719. [PMID: 32214997 PMCID: PMC7088759 DOI: 10.1007/s11426-010-0110-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2010] [Accepted: 02/07/2010] [Indexed: 01/10/2023]
Abstract
With the completion of the human genome-sequencing project, there has been a resulting change in the focus of studies from genomics to proteomics. By utilizing the inherent advantages of molecular beacon probes and biofunctionalized nanoparticles, a series of novel principles, methods and techniques have been exploited for bioanalytical and biomedical studies. This review mainly discusses the applications of molecular beacon probes and biofunctionalized nanoparticles-based technologies for real-time, in-situ, highly sensitive and highly selective protein analysis, including the nonspecific or specific protein detection and separation, protein/DNA interaction studies, cell surface protein recognition, and antigen-antibody binding process-based bacteria assays. The introduction of molecular beacon probes and biofunctionalized nanoparticles into the protein analysis area would necessarily advance the proteomics research.
Collapse
Affiliation(s)
- Hui Shi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082 China
- College of Chemistry and Chemical Engineering, Biomedical Engineering Center, Hunan University, Changsha, 410082 China
- Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Changsha, 410082 China
| | - XiaoXiao He
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082 China
- College of Chemistry and Chemical Engineering, Biomedical Engineering Center, Hunan University, Changsha, 410082 China
- Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Changsha, 410082 China
| | - XiaoHai Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082 China
- College of Chemistry and Chemical Engineering, Biomedical Engineering Center, Hunan University, Changsha, 410082 China
- Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Changsha, 410082 China
| | - KeMin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082 China
- College of Chemistry and Chemical Engineering, Biomedical Engineering Center, Hunan University, Changsha, 410082 China
- Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Changsha, 410082 China
| | - Qing Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082 China
- College of Chemistry and Chemical Engineering, Biomedical Engineering Center, Hunan University, Changsha, 410082 China
- Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Changsha, 410082 China
| | - QiuPing Guo
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082 China
- College of Chemistry and Chemical Engineering, Biomedical Engineering Center, Hunan University, Changsha, 410082 China
- Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Changsha, 410082 China
| | - XiQin Huo
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082 China
- College of Chemistry and Chemical Engineering, Biomedical Engineering Center, Hunan University, Changsha, 410082 China
- Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Changsha, 410082 China
| |
Collapse
|
27
|
Landré JBP, Blaess MF, Kohl M, Schlicksbier T, Ruryk A, Kinscherf R, Claus RA, Hermetter A, Keller M, Bauer M, Deigner HP. Addressable bipartite molecular hook (ABMH): immobilized hairpin probes with sensitivity below 50 fM. Anal Biochem 2010; 397:60-6. [PMID: 19825358 DOI: 10.1016/j.ab.2009.10.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Revised: 09/17/2009] [Accepted: 10/06/2009] [Indexed: 12/01/2022]
Abstract
Sensitivity and specificity of nucleic acid binding probes immobilized on solid supports are essential features of microarrays. Whereas conventional biochips apply nonquenched linear probes (cDNA, oligonucleotides), hairpin structures containing a fluorophore-quencher system comprise important prerequisites required for ideal transcriptional probes. We describe here the generation of addressable bipartite molecular hook (ABMH) probes and the characterization of their performance analyzing biological and clinical samples, also in comparison to linear oligonucleotide arrays. ABMH can be immobilized subsequent to reaction with the target sequence or the reaction carried out directly with the immobilized probe; target sequences are recognized with excellent sensitivity, specificity, and a detection limit below 50 fM. Due to excellent sensitivity and specificity, ABMH represent ideal candidates for the nonamplified microarray-based detection of low abundance nucleic acids, e.g., required in diagnostic assays.
Collapse
|
28
|
Gong H, Zhong T, Gao L, Li X, Bi L, Kraatz HB. Unlabeled hairpin DNA probe for electrochemical detection of single-nucleotide mismatches based on MutS-DNA interactions. Anal Chem 2010; 81:8639-43. [PMID: 19769379 DOI: 10.1021/ac901371n] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The paper described a label-free assay for the detection of single-nucleotide mismatches in which an unlabeled hairpin DNA probe and a MutS protein conjugate (His6-MutS-linker peptide-streptavidin binding peptide (HMLS)) are exploited for the detection of mismatches by electrochemical impedance spectroscopy (EIS). We demonstrate this method for eight single-nucleotide mismatches. Upon hybridization of the target strand with the hairpin DNA probe, the stem-loop structure is opened forming a duplex DNA. In duplexes containing a single nucleotide mismatch, the mismatch is present at the solvent exposed side, enabling more effective HMLS recognition and binding. The binding event is evaluated by EIS and analyzed with the help of Randles' equivalent circuits. The differences in the charge transfer resistance DeltaR(CT) before and after protein binding to the duplex DNA allows the unequivocal detection of all eight single-nucleotide mismatches. DeltaR(CT) allows the discrimination of a C-A mismatch with the concentration of the target strand as low as 100 pM.
Collapse
Affiliation(s)
- He Gong
- Department of Chemistry, Beijing Normal University, Beijing, China 100875
| | | | | | | | | | | |
Collapse
|
29
|
Ozkumur E, Ahn S, Yalçin A, Lopez CA, Cevik E, Irani RJ, DeLisi C, Chiari M, Unlü MS. Label-free microarray imaging for direct detection of DNA hybridization and single-nucleotide mismatches. Biosens Bioelectron 2010; 25:1789-95. [PMID: 20097056 DOI: 10.1016/j.bios.2009.12.032] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2009] [Revised: 12/09/2009] [Accepted: 12/23/2009] [Indexed: 10/20/2022]
Abstract
A novel method is proposed for direct detection of DNA hybridization on microarrays. Optical interferometry is used for label-free sensing of biomolecular accumulation on glass surfaces, enabling dynamic detection of interactions. Capabilities of the presented method are demonstrated by high-throughput sensing of solid-phase hybridization of oligonucleotides. Hybridization of surface immobilized probes with 20 base pair-long target oligonucleotides was detected by comparing the label-free microarray images taken before and after hybridization. Through dynamic data acquisition during denaturation by washing the sample with low ionic concentration buffer, melting of duplexes with a single-nucleotide mismatch was distinguished from perfectly matching duplexes with high confidence interval (>97%). The presented technique is simple, robust, and accurate, and eliminates the need of using labels or secondary reagents to monitor the oligonucleotide hybridization.
Collapse
Affiliation(s)
- Emre Ozkumur
- Department of Electrical & Computer Engineering, Boston University, Boston, MA 02215, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Zhu Z, Yang R, You M, Zhang X, Wu Y, Tan W. Single-walled carbon nanotube as an effective quencher. Anal Bioanal Chem 2009; 396:73-83. [DOI: 10.1007/s00216-009-3192-z] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2009] [Revised: 09/22/2009] [Accepted: 09/24/2009] [Indexed: 12/25/2022]
|
31
|
Utilizing RNA/DNA hybridization to directly quantify mRNA levels in microbial fermentation samples. J Microbiol Methods 2009; 79:205-10. [DOI: 10.1016/j.mimet.2009.09.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2009] [Revised: 09/01/2009] [Accepted: 09/02/2009] [Indexed: 11/22/2022]
|
32
|
Goulko AA, Li F, Chris Le X. Bioanalytical applications of aptamer and molecular-beacon probes in fluorescence-affinity assays. Trends Analyt Chem 2009. [DOI: 10.1016/j.trac.2009.03.014] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
33
|
Martinez K, Estevez MC, Wu Y, Phillips JA, Medley CD, Tan W. Locked nucleic acid based beacons for surface interaction studies and biosensor development. Anal Chem 2009; 81:3448-54. [PMID: 19351140 DOI: 10.1021/ac8027239] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA sensors and microarrays permit fast, simple, and real-time detection of nucleic acids through the design and use of increasingly sensitive, selective, and robust molecular probes. Specifically, molecular beacons (MBs) have been employed for this purpose; however, their potential in the development of solid-surface-based biosensors has not been fully realized. This is mainly a consequence of the beacon's poor stability because of the hairpin structure once immobilized onto a solid surface, commonly resulting in a low signal enhancement. Here, we report the design of a new MB that overcomes some of the limitations of MBs for surface immobilization. Essentially, this new design adds locked nucleic acid bases (LNAs) to the beacon structure, resulting in a LNA molecular beacon (LMB) with robust stability after surface immobilization. To test the efficacy of LMBs against that of regular molecular beacons (RMBs), the properties of selectivity, sensitivity, thermal stability, hybridization kinetics, and robustness for the detection of target sequences were compared and evaluated. A 25-fold enhancement was achieved for the LMB on surface with detection limits reaching the low nanomolar range. In addition, the LMB-based biosensor was shown to possess better stability, reproducibility, selectivity, and robustness when compared to the RMB. Therefore, as an alternative to conventional DNA and as a prospective tool for use in both DNA microarrays and biosensors, these results demonstrate the potential of the locked nucleic acid bases for nucleic acid design for surface immobilization.
Collapse
Affiliation(s)
- Karen Martinez
- Center for Research at the Bio/Nano Interface, Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA
| | | | | | | | | | | |
Collapse
|
34
|
Li K, Liu B. Conjugated Polyelectrolyte Amplified Thiazole Orange Emission for Label Free Sequence Specific DNA Detection with Single Nucleotide Polymorphism Selectivity. Anal Chem 2009; 81:4099-105. [DOI: 10.1021/ac9003985] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kai Li
- Department of Chemical and Biomolecular Engineering, 4 Engineering Drive 4, National University of Singapore, Singapore 117576, Singapore
| | - Bin Liu
- Department of Chemical and Biomolecular Engineering, 4 Engineering Drive 4, National University of Singapore, Singapore 117576, Singapore
| |
Collapse
|
35
|
Tang J, Xiao P. Polymerizing immobilization of acrylamide-modified nucleic acids and its application. Biosens Bioelectron 2009; 24:1817-24. [DOI: 10.1016/j.bios.2008.09.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2008] [Revised: 09/17/2008] [Accepted: 09/17/2008] [Indexed: 11/29/2022]
|
36
|
Wang HN, Dinh TV. Multiplex detection of breast cancer biomarkers using plasmonic molecular sentinel nanoprobes. NANOTECHNOLOGY 2009; 20:065101. [PMID: 19417369 PMCID: PMC4022306 DOI: 10.1088/0957-4484/20/6/065101] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We have demonstrated for the first time the feasibility of multiplex detection using the surface-enhanced Raman scattering-based molecular sentinel (MS) technology in a homogeneous solution. Two MS nanoprobes tagged with different Raman labels were used to detect the presence of the erbB-2 and ki-67 breast cancer biomarkers. The multiplexing capability of the MS technique was demonstrated by mixing the two MS nanoprobes and tested in the presence of single or multiple DNA targets.
Collapse
Affiliation(s)
- Hsin-Neng Wang
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
- Fitzpatrick Institute for Photonics, Duke University, Durham, NC 27708, USA
| | - Tuan Vo Dinh
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
- Fitzpatrick Institute for Photonics, Duke University, Durham, NC 27708, USA
- Departments of Chemistry, Duke University, Durham, NC 27708, USA
| |
Collapse
|
37
|
Wang K, Tang Z, Yang C, Kim Y, Fang X, Li W, Wu Y, Medley C, Cao Z, Li J, Colon P, Lin H, Tan W. Molekulartechnische DNA-Modifizierung: Molecular Beacons. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200800370] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
|
38
|
Abstract
Among the parameters which influence the success of a microarray experiment, the attachment of the nucleic acid captures to the support surface plays a decisive role.This article attempts to review the main concepts and ideas of the multiple variants which exist in terms of the immobilization chemistries used in nucleic acid microarray technology. Starting from the attachment of unmodified nucleic acids to modified glass slides by adsorption, further strategies for the coupling of nucleic acid capture molecules to a variety of support materials are surveyed with a focus on the reactive groups involved in the respective process.After a brief introduction, an overview is given about microarray substrates with special emphasis on the approaches used for the activation of these - usually chemically inert - materials. In the next sections strategies for the "undefined" and "defined" immobilization of captures on the substrates are described. While the latter approach tries to accomplish the coupling via a defined reactive moiety of the molecule to be immobilized, the former mentioned techniques involve multiply occurring reactive groups in the capture.The article finishes with an example for microarray manufacture, the production of aminopropyltriethoxysilane (APTES) functionalized glass substrates to which PDITC homobifunctional linker molecules are coupled; on their part providing reactive functional groups for the covalent immobilization of pre-synthesized, amino-modified oligonucleotides.This survey does not seek to be comprehensive rather it tries to present and provide key examples for the basic techniques, and to enable orientation if more detailed studies are needed. This review should not be considered as a guide to how to use the different chemistries described, but instead as a presentation of various principles and approaches applied in the still evolving field of nucleic acid microarray technology.
Collapse
Affiliation(s)
- Sascha Todt
- Center for Applied Genesensor-Technology, University of Bremen, , Bremen, Germany
| | | |
Collapse
|
39
|
Wang K, Tang Z, Yang CJ, Kim Y, Fang X, Li W, Wu Y, Medley CD, Cao Z, Li J, Colon P, Lin H, Tan W. Molecular engineering of DNA: molecular beacons. Angew Chem Int Ed Engl 2009; 48:856-70. [PMID: 19065690 PMCID: PMC2772660 DOI: 10.1002/anie.200800370] [Citation(s) in RCA: 492] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Molecular beacons (MBs) are specifically designed DNA hairpin structures that are widely used as fluorescent probes. Applications of MBs range from genetic screening, biosensor development, biochip construction, and the detection of single-nucleotide polymorphisms to mRNA monitoring in living cells. The inherent signal-transduction mechanism of MBs enables the analysis of target oligonucleotides without the separation of unbound probes. The MB stem-loop structure holds the fluorescence-donor and fluorescence-acceptor moieties in close proximity to one another, which results in resonant energy transfer. A spontaneous conformation change occurs upon hybridization to separate the two moieties and restore the fluorescence of the donor. Recent research has focused on the improvement of probe composition, intracellular gene quantitation, protein-DNA interaction studies, and protein recognition.
Collapse
Affiliation(s)
- Kemin Wang
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
- Biomedical Engineering Center, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 (P.R. China)
| | - Zhiwen Tang
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Chaoyong James Yang
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005 (P.R. China)
| | - Youngmi Kim
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Xiaohong Fang
- Institute of Chemistry, Chinese Academy of Sciences 2 Zhongguancun Beiyijie, Beijing 100190 (P.R. China)
| | - Wei Li
- Biomedical Engineering Center, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 (P.R. China)
| | - Yanrong Wu
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Colin D. Medley
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Zehui Cao
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Jun Li
- Biomedical Engineering Center, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 (P.R. China)
| | - Patrick Colon
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Hui Lin
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Weihong Tan
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
- Biomedical Engineering Center, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 (P.R. China)
| |
Collapse
|
40
|
Mahajan S, Richardson J, Brown T, Bartlett PN. SERS-Melting: A New Method for Discriminating Mutations in DNA Sequences. J Am Chem Soc 2008; 130:15589-601. [DOI: 10.1021/ja805517q] [Citation(s) in RCA: 150] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sumeet Mahajan
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - James Richardson
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Tom Brown
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Philip N. Bartlett
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| |
Collapse
|
41
|
Cederquist KB, Golightly RS, Keating CD. Molecular beacon-metal nanowire interface: effect of probe sequence and surface coverage on sensor performance. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:9162-71. [PMID: 18624416 PMCID: PMC2677025 DOI: 10.1021/la703854x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We report the effect of surface coverage and sequence on the performance of 5' thiolated, 3' fluorophore-labeled DNA hairpin probes bound to Au/Ag striped ("barcoded") metal nanowires. Coverage was controlled by varying probe concentration, buffer ionic strength, and by addition of short hydroxy-terminated alkanethiol diluent molecules during probe assembly onto the nanowire surface. Surface dilution of the surface-bound probes with a omega-hydroxyl alkanethiol, a commonly accepted practice in the surface-bound DNA literature, did not appreciably improve sensor performance as compared to similar probe coverages without hydroxyalkanethiol diluents; this finding underscores the differences between the molecular beacon probes used here and more traditional nonfluorescent, random coil probes. We found that intermediate probe coverage of approximately 10 (12) molecules/cm (2) gave the best discrimination between presence and absence of a target sequence. Because we are interested in multiplexed assays, we also compared several beacon probe sequences having different stabilities for secondary structure formation in solution; we found that both probe surface coverage and sensor performance varied for different probe sequences. When five different molecular beacon probes, each bound to barcoded nanowires, were used in a multiplexed, wash-free assay for target oligonucleotides corresponding to viral nucleic acid sequences, these differences in probe performance did not prevent accurate target identification. We anticipate that the findings described here will also be relevant to other applications involving molecular beacons or other structured nucleic acid probes immobilized on metal surfaces.
Collapse
Affiliation(s)
- Kristin B. Cederquist
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
| | | | - Christine D. Keating
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
| |
Collapse
|
42
|
Pan Z, Li Y, Shan Q, Hong X, Zhou D, Zhang M, Chen P, Xiao P, Lu Z. Fabrication of 3-D gel microarrays directly with raw polymerase chain reaction products by heat-directed polymerization. Electrophoresis 2008; 29:2424-36. [DOI: 10.1002/elps.200700570] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
43
|
Martinez K, Medley CD, Yang CJ, Tan W. Investigation of the hybrid molecular probe for intracellular studies. Anal Bioanal Chem 2008; 391:983-91. [PMID: 18421445 PMCID: PMC2748777 DOI: 10.1007/s00216-008-2067-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2007] [Revised: 03/04/2008] [Accepted: 03/10/2008] [Indexed: 10/22/2022]
Abstract
Monitoring gene expression in vivo is essential to the advancement of biological studies, medical diagnostics, and drug discovery. Adding to major efforts in developing molecular probes for mRNA monitoring, we have recently developed an alternative tool, the hybrid molecular probe (HMP). To optimize the probe, a series of experiments were performed to study the properties of HMP hybridization kinetics and stability. The results demonstrated the potential of the HMP as a prospective tool for use in both hybridization studies and in vitro and in vivo analyses. The HMP has shown no tendency to produce false positive signals, which is a major concern for living cell studies. Moreover, HMP has shown the ability to detect the mRNA expression of different genes inside single cells from both basal and stimulated genes. As an effective alternative to conventional molecular probes, the proven sensitivity, simplicity, and stability of HMPs show promise for their use in monitoring mRNA expression in living cells.
Collapse
Affiliation(s)
- Karen Martinez
- Center for Research at the Bio/Nano Interface, Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | | | | | | |
Collapse
|
44
|
Mao X, Jiang J, Xu X, Chu X, Luo Y, Shen G, Yu R. Enzymatic amplification detection of DNA based on “molecular beacon” biosensors. Biosens Bioelectron 2008; 23:1555-61. [DOI: 10.1016/j.bios.2008.01.019] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2007] [Revised: 12/13/2007] [Accepted: 01/14/2008] [Indexed: 11/29/2022]
|
45
|
Ricci F, Plaxco KW. E-DNA sensors for convenient, label-free electrochemical detection of hybridization. Mikrochim Acta 2008. [DOI: 10.1007/s00604-008-0015-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
46
|
Microarray-based label-free detection of RNA using bispyrene-modified 2'-O-methyl oligoribonucleotide as capture and detection probe. Bioorg Med Chem Lett 2008; 18:2590-3. [PMID: 18394885 DOI: 10.1016/j.bmcl.2008.03.040] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2007] [Revised: 02/19/2008] [Accepted: 03/14/2008] [Indexed: 11/22/2022]
Abstract
A novel oligonucleotide microarray that can detect RNAs without fluorescent labeling of sample RNAs was developed. As a capture and detection probe, bispyrene-modified 2'-O-methyl oligoribonucleotide (OMUpy2), whose fluorescence was dramatically increased when hybridized with its complementary RNA, was adopted. Fluorescence of the OMUpy2 tethered on the glass surface was enhanced as much as 22-fold by the addition of complementary oligoribonucleotide.
Collapse
|
47
|
Wang Y, Li C, Li X, Li Y, Kraatz HB. Unlabeled hairpin-DNA probe for the detection of single-nucleotide mismatches by electrochemical impedance spectroscopy. Anal Chem 2008; 80:2255-60. [PMID: 18290674 DOI: 10.1021/ac7024688] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An unlabeled hairpin-DNA probe was used for the detection of eight single-nucleotide mismatches by electrochemical impedance spectroscopy (EIS). Upon hybridization of the target strand with the hairpin DNA probe, the stem-loop structure is opened and forms a duplex DNA. Accordingly, the film thickness is increased, which causes differences in the electrical properties of the film before and after hybridization. Randles equivalent circuits were employed to evaluate the EIS result. The differences in the charge-transfer resistance DeltaR(CT) between hairpin DNA (before hybridization) and duplex DNA (after hybridization) shows the consequence of a large structural rearrangement from hairpin to duplex. If a single-nucleotide mismatch is present in the center of the duplex, the difference in charge-transfer resistance DeltaR(CT) between B-DNA in the absence and presence of Zn(2+) allows the unequivocal detection of all eight single-nucleotide mismatches. The detection limit was measured, and DeltaR(CT) allows the discrimination of a single-nucleotide mismatch with the concentration of the target strand as low as 10 pM.
Collapse
Affiliation(s)
- Ying Wang
- Department of Chemistry, Beijing Normal University, Beijing, China, 100875
| | | | | | | | | |
Collapse
|
48
|
Raab M, Hancock WO. Transport and detection of unlabeled nucleotide targets by microtubules functionalized with molecular beacons. Biotechnol Bioeng 2008; 99:764-73. [PMID: 17879297 DOI: 10.1002/bit.21645] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Shrinking biosensors down to microscale dimensions enables increases in sensitivity and the ability to analyze minute samples such as the contents of individual cells. The goal of the present study is to create mobile microscale biosensors by attaching molecular beacons to microtubules and using kinesin molecular motors to transport these functionalized microtubules across two-dimensional surfaces. Previous work has shown that microfluidic channels can be functionalized with kinesin motors such that microtubules can be transported and directed through these channels without the need for external power or pressure-driven pumping. In this work, we show that molecular beacons can be attached to microtubules such that both the fluorescence reporting capability of the beacon and the motility of the microtubules are retained. These molecular beacon-functionalized microtubules were able to bind ssDNA target sequences, transport them across surfaces, and report their presence by an increase in fluorescence that was detected by fluorescence microscopy. This work is an important step toward creating hybrid microdevices for sensitive virus detection or analyzing mRNA profiles of individual cells.
Collapse
Affiliation(s)
- Matthew Raab
- Department of Bioengineering, 229 Hallowell Building, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | | |
Collapse
|
49
|
Kim Y, Sohn D, Tan W. Molecular beacons in biomedical detection and clinical diagnosis. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2008; 1:105-116. [PMID: 18784800 PMCID: PMC2480550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 08/20/2007] [Accepted: 08/24/2007] [Indexed: 05/26/2023]
Abstract
Among the diverse nucleic acid probes, molecular beacons (MBs) have shown their excellent potential in a variety of basic researches and practical applications. Their excellent selectivity, sensitivity, and detection without separation have led them to be particularly useful in real-time intracellular monitoring of gene expression, development of biosensors, and clinical diagnostics. This paper will focus on the properties of various MBs and discuss their potential applications.
Collapse
Affiliation(s)
- Youngmi Kim
- Center for Research at the Bio/nano Interface, Department of Chemistry and UF Genetics Institute, Shands Cancer Center and McKnight Brain Institute, University of Florida Gainesville, FL, USA
| | | | | |
Collapse
|
50
|
Xiao P, Huang H, Zhou G, Lu Z. Gel immobilization of acrylamide-modified single-stranded DNA template for pyrosequencing. Electrophoresis 2007; 28:1903-12. [PMID: 17487922 DOI: 10.1002/elps.200600794] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A novel two-step process was developed to prepare ssDNA templates for pyrosequencing. First, PCR-amplified DNA templates modified with an acrylamide group and acrylamide monomers were copolymerized in 0.1 M NaOH solution to form polyacrylamide gel spots. Second, ssDNA templates for pyrosequencing were prepared by removing electrophoretically unbound complementary strands, unmodified PCR primers, inorganic pyrophosphate (PPi), and excess deoxyribonucleotides under alkali conditions. The results show that the 3-D polyacrylamide gel network has a high immobilization capacity and the modified PCR fragments are efficiently captured. After electrophoresis, gel spots copolymerized from 10 microL of the crude PCR products and the acrylamide monomers contain template molecules on the order of pmol, which generate enough light to be detected by a regular photomultiplier tube. The porous structure of gel spots facilitated the fast transportation of the enzyme, dNTPs and other reagents, and the solution-mimicking microenvironment guaranteed polymerase efficiency for pyrosequencing. Successful genotyping from the crude PCR products was demonstrated. This method can be applied in any laboratory; it is cheap, fast, simple, and has the potential to be incorporated into a DNA-chip format for high-throughput pyrosequencing analysis.
Collapse
Affiliation(s)
- Pengfeng Xiao
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, PR China.
| | | | | | | |
Collapse
|