1
|
Adil O, Eddington SB, Gagnon KT, Shamsi MH. Microprobes for Label-Free Detection of Short Tandem Repeats: An Insight into Alleviating Secondary Structure Effects. Anal Chem 2023; 95:13528-13536. [PMID: 37651633 DOI: 10.1021/acs.analchem.3c01886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Overgrowth of short tandem repeat sequences in our genes can cause various neurodegenerative disorders. Such repeat sequences are ideal targets for the label-free electrochemical detection of such potential expansions. However, their length- and sequence-dependent secondary structures may interfere with the interfacial charge transfer of a detection platform, making them complex targets. In addition, the gene contains sporadic repeats that may result in false-positive signals. Therefore, it is necessary to design a platform capable of mitigating these effects and ultimately enhancing the specificity of tandem repeats. Here, we analyzed three different backbones of nucleic acid microprobes [DNA, peptide nucleic acid, and lock-nucleic acid (LNA)] to detect in vitro transcribed RNA carrying CAG repeats, which are associated with Huntington's disease, based on the charge-transfer resistance of the interface. We found that the LNA microprobe can distinguish lengths down to the attomolar concentration level and alleviate the effect of secondary structures and sporadic repeats in the sequence, thus distinguishing the "tandem repeats" specifically. Additionally, the control experiments conducted with and without Mg2+ demonstrated the LNA microprobe to perform better in the presence of the divalent cation. The results suggest that the LNA-based platform may eventually lead to the development of a reliable and straightforward biosensor for genetic neurodegenerative disorders.
Collapse
Affiliation(s)
- Omair Adil
- School of Chemical and Biomolecular Sciences, 1245 Lincoln Dr, Southern Illinois University at Carbondale, Carbondale, Illinois 62901, United States
| | - Seth B Eddington
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27101, United States
| | - Keith T Gagnon
- School of Chemical and Biomolecular Sciences, 1245 Lincoln Dr, Southern Illinois University at Carbondale, Carbondale, Illinois 62901, United States
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27101, United States
| | - Mohtashim H Shamsi
- School of Chemical and Biomolecular Sciences, 1245 Lincoln Dr, Southern Illinois University at Carbondale, Carbondale, Illinois 62901, United States
| |
Collapse
|
2
|
Walden K, Martin ME, LaBee L, Provorse Long M. Hydration and Charge-Transfer Effects of Alkaline Earth Metal Ions Binding to a Carboxylate Anion, Phosphate Anion, and Guanine Nucleobase. J Phys Chem B 2021; 125:12135-12146. [PMID: 34706195 DOI: 10.1021/acs.jpcb.1c05757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To investigate the ability of alkaline earth metal ions to tune ion-mediated DNA adsorption, hydrated Mg2+, Ca2+, Sr2+, and Ba2+ ions bound to a carboxylate anion, phosphate anion, and guanine nucleobase were modeled using density functional theory (DFT) and a combined explicit and continuum solvent model. The large first solvation shell of Ba2+ requires a larger solute cavity defined by a solvent-accessible surface, which is used to model all hydrated ions. Alkaline earth metal ions bind indirectly or directly to each binding site. DFT binding energies decrease with increasing ion size, which is likely due to ion size and hydration structure, rather than quantum effects such as charge transfer. However, charge transfer explains weaker ion binding to guanine compared to phosphate or carboxylate. Overall, carboxylate and phosphate anions are expected to compete equally for hydrated Mg2+, Ca2+, Sr2+, and Ba2+ ions and larger alkaline earth metal ions may induce weaker ion-mediated adsorption. The ion size and hydration structure of alkaline earth metal ions may effectively tune ion-mediated adsorption processes, such as DNA adsorption to functionalized surfaces.
Collapse
Affiliation(s)
- Kathryn Walden
- Department of Chemistry, University of Central Arkansas, Conway, Arkansas 72035, United States
| | - Madison E Martin
- Department of Chemistry, University of Central Arkansas, Conway, Arkansas 72035, United States
| | - Lacey LaBee
- Department of Chemistry, University of Central Arkansas, Conway, Arkansas 72035, United States
| | - Makenzie Provorse Long
- Department of Chemistry, University of Central Arkansas, Conway, Arkansas 72035, United States
| |
Collapse
|
3
|
Banasiak A, Colleran J. Determination of Integrity, Stability and Density of the DNA Layers Immobilised at Glassy Carbon and Gold Electrodes Using Ferrocyanide. ELECTROANAL 2020. [DOI: 10.1002/elan.202060077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Anna Banasiak
- Applied Electrochemistry Group Technological University Dublin, FOCAS Institute Camden Row Dublin 8 D08 CKP1 Ireland
| | - John Colleran
- Applied Electrochemistry Group Technological University Dublin, FOCAS Institute Camden Row Dublin 8 D08 CKP1 Ireland
- School of Chemical and Pharmaceutical Sciences Technological University Dublin, City Campus – Kevin Street Dublin 8 D08 NF82 Ireland
| |
Collapse
|
4
|
A novel colorimetric aptasensor for detection of chloramphenicol based on lanthanum ion-assisted gold nanoparticle aggregation and smartphone imaging. Anal Bioanal Chem 2019; 411:7511-7518. [PMID: 31641824 DOI: 10.1007/s00216-019-02149-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 08/14/2019] [Accepted: 09/10/2019] [Indexed: 12/29/2022]
Abstract
A label-free, rapid response colorimetric aptasensor for sensitive detection of chloramphenicol (CAP) was proposed, which was based on the strategy of ssDNA-modified gold nanoparticle (AuNP) aggregation assisted by lanthanum (La3+) ions. The AuNPs generated a color change that could be monitored in the red, green, and blue and analyzed by the smartphone imaging app. La3+, as a trigger agent, strongly combined with the phosphate groups of the surface of ssDNA-AuNPs probe, which helps create AuNP aggregation and the color change of AuNPs from red to blue. On the contrary, when mixing with CAP, the aptamer (Apt) bound to CAP to form a rigid structure of the Apt-CAP complex, and La3+ attached to the phosphate groups of the complex, which prevented the aptamer from binding to the surface of the AuNPs. As a result, the color of the AuNPs changed to violet-red. Finally, UV-vis absorption spectroscopy and the smartphone imaging app were employed to determine CAP with a lower detection limit of 7.65 nM and 5.88 nM, respectively. The proposed strategy featuring high selectivity and strong anti-interference ability for detection of CAP in practical samples was achieved. It is worth mentioning that the simple and portable colorimetric aptasensor will be used for facilitating on-site detection of food samples.
Collapse
|
5
|
Bhai S, Ganguly B. Role of backbones on the interaction of metal ions with deoxyribonucleic acid and peptide nucleic acid: A DFT study. J Mol Graph Model 2019; 93:107445. [PMID: 31494536 DOI: 10.1016/j.jmgm.2019.107445] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 08/28/2019] [Accepted: 08/28/2019] [Indexed: 11/30/2022]
Abstract
Metal ion interaction with deoxyribonucleic acid and peptide nucleic acid were studied using B3LYP-D3/6-311++g(d,p)//B3LYP/6-31 + G(d) level of theory in aqueous phase employing polarized continuum (PCM) model. This study reports the role of backbones on deoxyribonucleic acid and peptide nucleic acid for complexation with different metal ions. The systematic study performed with DFT calculations reveals that central binding (Type-4) shows the strongest binding compared to the other binding modes because of the involvement of the backbone as well as the nitrogenous bases. The charged backbone of DNA nucleotides contributes significantly towards binding with the metal ions. The deoxyguanosine monophosphate (dGMP) clearly indicates the strongest binding upon complexation with Mg2+ (-49.6 kcal/mol), Zn2+ (-45.3 kcal/mol) and Cu2+ (-148.4 kcal/mol), respectively. The neutral backbone of PNA also assists to complex the metal ions with PNA nucleotides. The Mg2+ and Cu2+ prefer to bind with the PNA-Cytosine (-32.9 kcal/mol & -132.9 kcal/mol) in central binding mode (type-4). PNA-Adenine-Zn2+ (-29.1 kcal/mol) is the preferred binding mode (type-4) compared to other modes of interaction for this metal ion with PNA-Adenine nucleotide. The Cu2+ ion showed the superior complexation ability with deoxyribonucleic acid and peptide nucleic acid compared to Mg2+ and Zn2+ ions. The cation-π complexation with the bases of nucleotides was also obtained with Cu2+ ion. The AIM (atoms in molecule) theory has been applied to examine the nature of the interaction of Mg2+, Zn2+, and Cu2+ ion to the deoxyribonucleic acid and peptide nucleic acid. The alkaline earth metal, Mg2+ ion shows electrostatic nature while interaction with deoxyribonucleic acid and peptide nucleic acid, however, the transition metal ions (Zn2+, Cu2+) showed partly covalent nature as well with deoxyribonucleic acid and peptide nucleic acid. The optical properties calculated for the binding of metal ions with deoxyribonucleic acid and peptide nucleic acid showed a diagnostic signature to ascertain the interaction of metal ions with such nucleotides. Cu2+ ion showed larger red shifts in the absorption spectrum values upon complexation with the DNAs and PNAs. The calculated results suggest that such metal ions would prefer to bind with the DNA compared to PNA in DNA-PNA duplexes. The preference for the binding of metal ions with DNA nucleotides is largely attributed to the contribution of charged backbones compared to the neutral PNA backbones.
Collapse
Affiliation(s)
- Surjit Bhai
- Computation and Simulation Unit (Analytical and Environmental Science Division and Centralized Instrument Facility), CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, 364 002, India
| | - Bishwajit Ganguly
- Computation and Simulation Unit (Analytical and Environmental Science Division and Centralized Instrument Facility), CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, 364 002, India.
| |
Collapse
|
6
|
Alshanski I, Blaszkiewicz J, Mervinetsky E, Rademann J, Yitzchaik S, Hurevich M. Sulfation Patterns of Saccharides and Heavy Metal Ion Binding. Chemistry 2019; 25:12083-12090. [DOI: 10.1002/chem.201901538] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 05/30/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Israel Alshanski
- Institute of Chemistry and Center for Nanoscience and NanotechnologyThe Hebrew University of Jerusalem, Safra Campus Givat Ram, Jerusalem 91904 Israel
| | - Joanna Blaszkiewicz
- Medicinal ChemistryFreie Universität Berlin Königin-Luise-Strasse 2+4 Berlin 14195 Germany
| | - Evgeniy Mervinetsky
- Institute of Chemistry and Center for Nanoscience and NanotechnologyThe Hebrew University of Jerusalem, Safra Campus Givat Ram, Jerusalem 91904 Israel
| | - Jörg Rademann
- Medicinal ChemistryFreie Universität Berlin Königin-Luise-Strasse 2+4 Berlin 14195 Germany
| | - Shlomo Yitzchaik
- Institute of Chemistry and Center for Nanoscience and NanotechnologyThe Hebrew University of Jerusalem, Safra Campus Givat Ram, Jerusalem 91904 Israel
| | - Mattan Hurevich
- Institute of Chemistry and Center for Nanoscience and NanotechnologyThe Hebrew University of Jerusalem, Safra Campus Givat Ram, Jerusalem 91904 Israel
| |
Collapse
|
7
|
Zhao L, Yin S, Ma Z. Ca 2+-Triggered pH-Response Sodium Alginate Hydrogel Precipitation for Amplified Sandwich-Type Impedimetric Immunosensor of Tumor Marker. ACS Sens 2019; 4:450-455. [PMID: 30638376 DOI: 10.1021/acssensors.8b01465] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Signal amplification is of great significance in the ultrasensitive electrochemical impedimetric immunoassays for tumor marker detection. A cascaded signal amplification approach was designed using gold nanoparticle-CaCO3 microspheres (AuNP-CaCO3) to trigger pH-responsive alginate hydrogel precipitation for sandwich-type impedimetric immunosensor. AuNP-CaCO3 exerts a large hindrance effect and can release Ca2+ ions under weak acidic conditions, and thus can serve as a multifunctional label. The hindrance effect of AuNP-CaCO3 can significantly enhance the impedance response as the initial signal amplification. Then, part of CaCO3 dissolves under weak acid conditions and releases Ca2+, which can cross-link with alginate to generate an insoluble alginate hydrogel precipitate on the sensing interface, significantly increasing the impedance signal. The impedance signal can be further amplified by making the hydrogel negatively charged based on the pH-responsive surface charge properties of the alginate hydrogel. Benefiting from the cascaded signal amplification, this impedimetric immunosensor exhibits a linear range from 1.0 fg mL-1 to 100 ng mL-1, an detection limit of 0.09 fg mL-1, and ultrahigh sensitivity of 973.01 Ω (lg(ng mL-1))-1 toward the assay of prostate specific antigen (PSA).
Collapse
Affiliation(s)
- Lihua Zhao
- Department of Chemistry, Capital Normal University, Beijing 100048, China
| | - Shuang Yin
- Department of Chemistry, Capital Normal University, Beijing 100048, China
| | - Zhanfang Ma
- Department of Chemistry, Capital Normal University, Beijing 100048, China
| |
Collapse
|
8
|
Hao Y, Zhou B, Tang Y, Yang P. Dual-functional aluminum(III)-based electrochemiluminescent detection of gene mutation. Mikrochim Acta 2017. [DOI: 10.1007/s00604-017-2507-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
9
|
Kamal A, She Z, Sharma R, Kraatz HB. A study of the interactions of Hg(II) with T-T mispair containing hairpin loops. Electrochim Acta 2017. [DOI: 10.1016/j.electacta.2017.05.058] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
10
|
Kamal A, She Z, Sharma R, Kraatz HB. Interactions of Hg(ii) with oligonucleotides having thymine-thymine mispairs. Optimization of an impedimetric Hg(ii) sensor. Analyst 2017; 142:1827-1834. [PMID: 28474033 DOI: 10.1039/c7an00238f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The present work describes the effect of the number of thymine-thymine mispairs in single strand DNA probes on Hg(ii) interactions and further to develop a highly sensitive DNA based impedimetric sensor for Hg(ii) detection. To achieve this goal, the influence of the number of T-T mispairs on the signal response prompted by DNA-Hg(ii) binding interactions was examined on three designed DNA probes: 5'-OH-(CH2)6-S-S-(CH2)6-AGTCCACACGTTCCTTACGC-3', 5'-OH-(CH2)6-S-S-(CH2)6-AGTCCACATTTTCCTTTTGC-3', 5'-OH-(CH2)6-S-S-(CH2)6-AGTCCATTTTTTCCTTTTTT-3' having 2T-T, 4T-T and 6T-T mispairs with identical length, respectively. This study revealed that the number of T-T mispairs plays a critical role in maximizing the signal intensity of DNA-Hg(ii) binding interactions. Based on these results, DNA comprising maximum number of T-T mispairs was further utilized for construction of the Hg(ii) sensor, which exhibited a linear correlation between the change in charge transfer resistance (ΔRCT) and the concentration of Hg(ii) over the range of 1.0 × 10-5 M to 1.0 × 10-10 M with a lower detection limit of 3.2 × 10-11 M. The selectivity was tested against 12 different metal ions including Hg(ii). The ΔRCT response from Hg(ii) is 3 times higher than the nearest competitor Pb(ii) and approximately 10 times than other ions. The potential application of such a robust and label-free DNA sensor was demonstrated by analyzing environmental samples collected from Lake Ontario.
Collapse
Affiliation(s)
- Ajar Kamal
- Department of Physical and Environmental Sciences, University of Toronto, Scarborough, Toronto M1C 1A4, Canada.
| | - Zhe She
- Department of Physical and Environmental Sciences, University of Toronto, Scarborough, Toronto M1C 1A4, Canada.
| | - Renu Sharma
- Department of Physical and Environmental Sciences, University of Toronto, Scarborough, Toronto M1C 1A4, Canada.
| | - Heinz-Bernhard Kraatz
- Department of Physical and Environmental Sciences, University of Toronto, Scarborough, Toronto M1C 1A4, Canada.
| |
Collapse
|
11
|
Léon JC, She Z, Kamal A, Shamsi MH, Müller J, Kraatz HB. DNA Films Containing the Artificial Nucleobase Imidazole Mediate Charge Transfer in a Silver(I)-Responsive Way. Angew Chem Int Ed Engl 2017; 56:6098-6102. [DOI: 10.1002/anie.201700248] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 03/03/2017] [Indexed: 12/22/2022]
Affiliation(s)
- J. Christian Léon
- Institut für Anorganische und Analytische Chemie; Westfälische Wilhelms-Universität Münster; Corrensstrasse 28/30 48149 Münster Germany
| | - Zhe She
- Department of Physical and Environmental Sciences; University of Toronto; Scarborough 1265 Military Trail Toronto Ontario M1C 1A4 Canada
| | - Ajar Kamal
- Department of Physical and Environmental Sciences; University of Toronto; Scarborough 1265 Military Trail Toronto Ontario M1C 1A4 Canada
| | - Mohtashim Hassan Shamsi
- Department of Physical and Environmental Sciences; University of Toronto; Scarborough 1265 Military Trail Toronto Ontario M1C 1A4 Canada
- Current address: Department of Chemistry and Biochemistry; Southern Illinois University Carbondale; Carbondale USA
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie; Westfälische Wilhelms-Universität Münster; Corrensstrasse 28/30 48149 Münster Germany
| | - Heinz-Bernhard Kraatz
- Department of Physical and Environmental Sciences; University of Toronto; Scarborough 1265 Military Trail Toronto Ontario M1C 1A4 Canada
| |
Collapse
|
12
|
Léon JC, She Z, Kamal A, Shamsi MH, Müller J, Kraatz HB. DNA-Filme mit der künstlichen Nucleobase Imidazol vermitteln Ladungstransfer in einer Silber(I)-abhängigen Weise. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201700248] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- J. Christian Léon
- Institut für Anorganische und Analytische Chemie; Westfälische Wilhelms-Universität Münster; Corrensstraße 28/30 48149 Münster Deutschland
| | - Zhe She
- Department of Physical and Environmental Sciences; University of Toronto; Scarborough 1265 Military Trail Toronto Ontario M1C 1A4 Kanada
| | - Ajar Kamal
- Department of Physical and Environmental Sciences; University of Toronto; Scarborough 1265 Military Trail Toronto Ontario M1C 1A4 Kanada
| | - Mohtashim Hassan Shamsi
- Department of Physical and Environmental Sciences; University of Toronto; Scarborough 1265 Military Trail Toronto Ontario M1C 1A4 Kanada
- Department of Chemistry and Biochemistry; Southern Illinois University Carbondale; Carbondale USA
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie; Westfälische Wilhelms-Universität Münster; Corrensstraße 28/30 48149 Münster Deutschland
| | - Heinz-Bernhard Kraatz
- Department of Physical and Environmental Sciences; University of Toronto; Scarborough 1265 Military Trail Toronto Ontario M1C 1A4 Kanada
| |
Collapse
|
13
|
Jain P, Chakma B, Singh N, Patra S, Goswami P. Metal-DNA Interactions Improve signal in High-Resolution Melting of DNA for Species Differentiation of Plasmodium Parasite. Mol Biotechnol 2017; 59:179-191. [PMID: 28421327 DOI: 10.1007/s12033-017-0004-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The success of high-resolution melting (HRM) analysis for distinguishing similar DNAs with minor base mismatch differences is limited. Here, metal-mediated structural change in DNA has been exploited to amplify HRM signals leading to differentiation of target DNAs in an orthologous gene corresponding to four Plasmodium species. Conserved 26-mer ssDNAs from ldh gene of the four Plasmodium species were employed as targets. A capture probe (CP) that is fully complementary to the Plasmodium falciparum target (FT) and has two base mismatches each, with the targets of Plasmodium vivax (VT), Plasmodium malariae, (MT), and Plasmodium ovale (OT), was considered. The DNA duplexes were treated with metal ions for structural perturbation and analyzed by HRM. Distinct resolution of melting fluorescence signal in otherwise identical HRM profiles for each of the DNA duplexes was achieved by using Ca+2 or Mg+2 ions, where, Ca+2 conferred higher resolution. The increase in resolution for CP-FT versus CP-OT, CP-FT versus CP-VT, CP-FT versus CP-MT, CP-VT versus CP-OT, and CP-MT versus CP-OT with Ca-DNA as compared to control was 67.3-, 20.4-, 22.0-, 10.9-, and 8.3-fold, respectively. The signal resolution was the highest at pH 8. The method could detect 0.25 pmol/µl of the target DNA. Structural analysis showed that Ca+2 and Mg+2 ions perturbed the structure of DNA. This perturbation helped to improve HRM signal resolution among DNA targets corresponding to the orthologous gene of four Plasmodium species. This novel approach has potential application not only for Plasmodium species-specific diagnosis but also for differentiation of DNAs with minor sequence variation.
Collapse
Affiliation(s)
- Priyamvada Jain
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, India
| | - Babina Chakma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, India
| | - Naveen Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, India
| | - Sanjukta Patra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, India
| | - Pranab Goswami
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, India.
| |
Collapse
|
14
|
Guo Z, Wei Y, Yang R, Liu JH, Huang XJ. Hydroxylation/carbonylation carbonaceous microspheres: A route without the need for an external functionalization to a “hunter” of lead(II) for electrochemical detection. Electrochim Acta 2013. [DOI: 10.1016/j.electacta.2012.08.106] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
15
|
Hu Y, Yang T, Li Q, Guan Q, Jiao K. Conjugated self-doped polyaniline–DNA hybrid as trigger for highly sensitive reagentless and electrochemical self-signal amplifying DNA hybridization sensing. Analyst 2013; 138:1067-74. [DOI: 10.1039/c2an36620g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
16
|
Shamsi MH, Kraatz HB. Interactions of Metal Ions with DNA and Some Applications. J Inorg Organomet Polym Mater 2012. [DOI: 10.1007/s10904-012-9694-8] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
|
17
|
Alam MN, Shamsi MH, Kraatz HB. Scanning positional variations in single-nucleotide polymorphism of DNA: an electrochemical study. Analyst 2012; 137:4220-5. [DOI: 10.1039/c2an35420a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
18
|
Li Z, Niu T, Zhang Z, Feng G, Bi S. Effect of monovalent cations (Li+, Na+, K+, Cs+) on self-assembly of thiol-modified double-stranded and single-stranded DNA on gold electrode. Analyst 2012; 137:1680-91. [DOI: 10.1039/c2an15716k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
19
|
Zhao ZQ, Chen X, Yang Q, Liu JH, Huang XJ. Selective adsorption toward toxic metal ions results in selective response: electrochemical studies on a polypyrrole/reduced graphene oxide nanocomposite. Chem Commun (Camb) 2012; 48:2180-2. [DOI: 10.1039/c1cc16735a] [Citation(s) in RCA: 181] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
|
20
|
Gebala M, Schuhmann W. Understanding properties of electrified interfaces as a prerequisite for label-free DNA hybridization detection. Phys Chem Chem Phys 2012; 14:14933-42. [DOI: 10.1039/c2cp42382k] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
21
|
Shervedani RK, Pourbeyram S, Sabzyan H. Electrochemical probe of natural DNA attached onto the gold–thiol SAMs via Zr(IV) ion glue. J Electroanal Chem (Lausanne) 2011. [DOI: 10.1016/j.jelechem.2011.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
22
|
Shamsi MH, Kraatz HB. Electrochemical identification of artificial oligonucleotides related to bovine species. Potential for identification of species based on mismatches in the mitochondrial cytochrome C1 oxidase gene. Analyst 2011; 136:4724-31. [PMID: 21847503 DOI: 10.1039/c1an15414a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Our studies show that electrochemical impedance spectroscopy (EIS) and scanning electrochemical microscopy (SECM) of films of ds-DNA on gold allow us to distinguish between mitochondrial DNA fragments of the cytochrome c(1) oxidase (mt-Cox1) of three related species of the subfamily 'Bovinae' (Bos taurus, Bison bison, and Bison bonasus). In EIS, a perfectly matched DNA gives rise to a considerably larger charge transfer resistance R(ct) compared to mismatched pairings. Differences in charge transfer resistance, ΔR(ct), before and after the addition of Zn(2+) ions provide an additional tool for identification. In addition, all ds-DNA films were studied by SECM and their kinetic parameters were determined. Perfectly matched ds-DNAs are readily distinguished from mismatched duplexes by their lower rate constants. Our system can be used multiple times by dehybridization and rehybridization of capture strands up to the 250 pmole level.
Collapse
|
23
|
Shamsi MH, Kraatz HB. The effects of oligonucleotide overhangs on the surface hybridization in DNA films: an impedance study. Analyst 2011; 136:3107-12. [PMID: 21701715 DOI: 10.1039/c1an15253j] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
While oligonucleotide hybridization and effects of nucleobase mismatches have been the intense focus of a number of electrochemical studies, the effects of the target strand length on the electrochemical response of oligonucleotide films have not been addressed yet. In this report, we have studied the electrochemical impedance of the oligonucleotide films having overhangs on either the target or the surface bound capture strand. Each system gives different impedance responses, which were interpreted with the help of modified Randles' equivalent. Results indicate that comparable sizes of target and capture strands ensure the higher hybridization efficiency and film order. The presence of nucleobase overhangs at the bottom of the film causes lower changes in charge transfer resistance (ΔR(CT)) after hybridization due to lower hybridization efficiency and presumably non-uniformity in the film. Nucleobase overhangs at the top of the film result in higher ΔR(CT) due to higher film order and accumulation of negative charges but appear not to cause any steric congestion.
Collapse
Affiliation(s)
- Mohtashim Hassan Shamsi
- Department of Chemistry, University of Western Ontario, 1151 Richmond, Street, London, Ontario, Canada N6A 5B7
| | | |
Collapse
|
24
|
Gebala M, Schuhmann W. Controlled orientation of DNA in a binary SAM as a key for the successful determination of DNA hybridization by means of electrochemical impedance spectroscopy. Chemphyschem 2010; 11:2887-95. [PMID: 20677315 DOI: 10.1002/cphc.201000210] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Determination of DNA hybridization at electrode surfaces modified with thiol-tethered single-stranded DNA (ssDNA) capture probes and co-assembled with short-chain thiol derivatives using electrochemical impedance spectroscopy requires a careful design of the electrode/electrolyte interface as well as an in-depth understanding of the processes at the interface during DNA hybridization. The influence of the electrode potential, the ssDNA coverage, the ionic strength, the nature of the thiol derivative and especially the Debye length are shown to have a significant impact on the impedance spectra. A mixed monolayer comprising--in addition to the ssDNA capture probe--both mercaptohexanol (MCH) and mercaptopropionic acid (MPA) is suggested as an interface design which allows a high efficiency of the DNA hybridization concomitantly with a reliable modulation of the charge-transfer resistance of the electrode upon hybridization.
Collapse
Affiliation(s)
- Magdalena Gebala
- Analytische Chemie-Elektroanalytik & Sensorik, Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum, Germany
| | | |
Collapse
|
25
|
Gao L, Li C, Li X, Kraatz HB. Electrochemical impedance study of the interaction of metal ions with unlabeled PNA. Chem Commun (Camb) 2010; 46:6344-6. [PMID: 20680217 DOI: 10.1039/c0cc00986e] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The interactions of the metal ions Mg(2+), Zn(2+), Ni(2+), and Co(2+) with thin films of peptide nucleic acids (PNAs) were studied by electrochemical impedance spectroscopy (EIS), and the results show that Zn(2+), Ni(2+) and Co(2+) interacted favorably with the PNA film involving the backbone and the nucleobases with the exception of Mg(2+) for which the interaction with the backbone appears to be dominant.
Collapse
Affiliation(s)
- Lan Gao
- Department of Chemistry, Beijing Normal University, Beijing, 100875, China
| | | | | | | |
Collapse
|
26
|
Shamsi MH, Kraatz HB. Probing nucleobase mismatch variations by electrochemical techniques: exploring the effects of position and nature of the single-nucleotide mismatch. Analyst 2010; 135:2280-5. [PMID: 20672148 DOI: 10.1039/c0an00184h] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electrochemical impedance spectroscopy (EIS) has been used as an ultrasensitive tool for label-free detection of single-nucleotide mismatches in double-stranded DNA (ds-DNA) films. In this study, we have explored the effects of the position and of the type of single-nucleotide mismatch in ds-DNA on gold surfaces and were able to distinguish mismatch positions and mismatch pairs. The single-nucleotide mismatches A-C, A-A and A-G were introduced at three positions within the sequence in bottom, middle and top positions of ds-DNA, the films were studied by EIS, and the impedance results were interpreted with the help of equivalent circuits. The DeltaR(ct), the difference in charge transfer resistance before and after the addition of Zn(2+), was used to distinguish single-nucleotide mismatch within the DNA sequences. Importantly, the mismatch pair is easily distinguishable at the middle position. A purine-pyrimidine mismatch can be distinguished from purine-purine mismatch by its lower DeltaR(ct) value. In addition, all ds-DNA films were studied by scanning electrochemical microscopy in the absence and presence of Zn(2+), allowing us to distinguish a range of mismatched films from matched ds-DNA film.
Collapse
Affiliation(s)
- Mohtashim H Shamsi
- Department of Chemistry, University of Western Ontario, 1151 Richmond Street, London, Ontario, Canada N6A 5B7
| | | |
Collapse
|
27
|
Li C, Li X, Liu X, Kraatz HB. Exploiting the interaction of metal ions and peptide nucleic acids-DNA duplexes for the detection of a single nucleotide mismatch by electrochemical impedance spectroscopy. Anal Chem 2010; 82:1166-9. [PMID: 20055458 DOI: 10.1021/ac902813y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The interaction of the metal ions Mg(2+), Zn(2+), Ni(2+), and Co(2+) with DNA-peptide nucleic acid (PNA) films on a gold surface is studied by electrochemical impedance spectroscopy in the presence of [Fe(CN)(6)](3-/4-) as the redox probe. Impedance data were analyzed with the help of a modified Randles' equivalent circuit. Changes in the charge-transfer resistance, R(CT), decreases in the order of Ni(2+) > Co(2+) > Zn(2+) > Mg(2+). We interpret these results in terms of stronger interactions for Ni(2+) with the DNA-PNA film compared to the other metal ions, potentially involving interactions with the nucleobases, presumably with the N7 of purines or the N3 of pyrimidines. On the basis of these observations, Ni(2+) was chosen to probe the detection of a C-T mismatch in 15-mer PNA-DNA films. Using Ni(2+), it is possible to detect a single C-T mismatch. The resulting DeltaR(CT) is larger for the PNA-DNA hybrid compared to that for the identical 15-mer DNA-DNA hybrid.
Collapse
Affiliation(s)
- Congjuan Li
- Department of Chemistry, School of Environment, Beijing Normal University, Beijing, 100875, China
| | | | | | | |
Collapse
|
28
|
Nguyen TH, Chen KL, Elimelech M. Adsorption Kinetics and Reversibility of Linear Plasmid DNA on Silica Surfaces: Influence of Alkaline Earth and Transition Metal Ions. Biomacromolecules 2010; 11:1225-30. [DOI: 10.1021/bm901427n] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Thanh H. Nguyen
- Department of Civil and Environmental Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, Department of Geography and Environmental Engineering, Johns Hopkins University, Baltimore, Maryland 21218, and Department of Chemical Engineering, Environmental Engineering Program, Yale University, New Haven, Connecticut 06520
| | - Kai Loon Chen
- Department of Civil and Environmental Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, Department of Geography and Environmental Engineering, Johns Hopkins University, Baltimore, Maryland 21218, and Department of Chemical Engineering, Environmental Engineering Program, Yale University, New Haven, Connecticut 06520
| | - Menachem Elimelech
- Department of Civil and Environmental Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, Department of Geography and Environmental Engineering, Johns Hopkins University, Baltimore, Maryland 21218, and Department of Chemical Engineering, Environmental Engineering Program, Yale University, New Haven, Connecticut 06520
| |
Collapse
|
29
|
Bonanni A, Pumera M, Miyahara Y. Rapid, Sensitive, and Label-Free Impedimetric Detection of a Single-Nucleotide Polymorphism Correlated to Kidney Disease. Anal Chem 2010; 82:3772-9. [DOI: 10.1021/ac100165q] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Alessandra Bonanni
- International Center for Materials Nanoarchitectonics (MANA)/Biomaterials Center, National Institute for Material Science (NIMS), Ibaraki, Japan
| | - Martin Pumera
- International Center for Materials Nanoarchitectonics (MANA)/Biomaterials Center, National Institute for Material Science (NIMS), Ibaraki, Japan
| | - Yuji Miyahara
- International Center for Materials Nanoarchitectonics (MANA)/Biomaterials Center, National Institute for Material Science (NIMS), Ibaraki, Japan
| |
Collapse
|
30
|
Park JY, Park SM. DNA hybridization sensors based on electrochemical impedance spectroscopy as a detection tool. SENSORS (BASEL, SWITZERLAND) 2009; 9:9513-32. [PMID: 22303136 PMCID: PMC3267184 DOI: 10.3390/s91209513] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Revised: 10/28/2009] [Accepted: 11/11/2009] [Indexed: 12/18/2022]
Abstract
Recent advances in label free DNA hybridization sensors employing electrochemical impedance spectroscopy (EIS) as a detection tool are reviewed. These sensors are based on the modulation of the blocking ability of an electrode modified with a probe DNA by an analyte, i.e., target DNA. The probe DNA is immobilized on a self-assembled monolayer, a conducting polymer film, or a layer of nanostructures on the electrode such that desired probe DNA would selectively hybridize with target DNA. The rate of charge transfer from the electrode thus modified to a redox indicator, e.g., [Fe(CN)(6)](3-/4-), which is measured by EIS in the form of charge transfer resistance (R(ct)), is modulated by whether or not, as well as how much, the intended target DNA is selectively hybridized. Efforts made to enhance the selectivity as well as the sensitivity of DNA sensors and to reduce the EIS measurement time are briefly described along with brief future perspectives in developing DNA sensors.
Collapse
Affiliation(s)
- Jin-Young Park
- Department of Chemistry, Pohang University of Science & Technology, Pohang 790-784, Korea; E-Mail:
| | - Su-Moon Park
- Interdisciplinary School of Green Energy Engineering, Ulsan National Institute of Science & Technology, Ulsan 689-805, Korea
| |
Collapse
|