1
|
Wang Z, Cui R, Liu L, Li L, Li Z, Liu X, Guo Y. Nanopore-Based Single-Molecule Investigation of Cation Effect on the i-Motif Structure. J Phys Chem B 2024; 128:6830-6837. [PMID: 38959208 DOI: 10.1021/acs.jpcb.4c02021] [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: 07/05/2024]
Abstract
The i-motif, a secondary structure of a four-helix formed by cytosine-rich DNA (i-DNA) through C-C+ base pairing, is prevalent in human telomeres and promoters. This structure creates steric hindrance, thereby inhibiting both gene expression and protein coding. The conformation of i-DNA is intricately linked to the intracellular ionic environment. Hence, investigating its conformation under various ion conditions holds significant importance. In this study, we explored the impact of cations on the i-motif structure at the single-molecule level using the α-hemolysin (α-HL) nanochannel. Our findings reveal that the ability of i-DNA to fold into the i-motif structure follows the order Cs+ > Na+ > K+ > Li+ for monovalent cations. Furthermore, we observed the interconversion of single-stranded DNA (ss-DNA) and the i-motif structure at high and low concentrations of Mg2+ and Ba2+ electrolyte solutions. This study not only has the potential to extend the application of i-motif-based sensors in complex solution environments but also provides a new idea for the detection of metal ions.
Collapse
Affiliation(s)
- Zhenzhao Wang
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710127, P. R. China
| | - Rikun Cui
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710127, P. R. China
| | - Lili Liu
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710127, P. R. China
| | - Linna Li
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710127, P. R. China
| | - Zhen Li
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710127, P. R. China
| | - Xingtong Liu
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710127, P. R. China
| | - Yanli Guo
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710127, P. R. China
| |
Collapse
|
2
|
Li F, Luo Y, Xi G, Fu J, Tu J. Single-Molecule Analysis of DNA structures using nanopore sensors. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2022. [DOI: 10.1016/j.cjac.2022.100089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
3
|
Comparison of Duplex and Quadruplex Folding Structure Adenosine Aptamers for Carbon Nanotube Field Effect Transistor Aptasensors. NANOMATERIALS 2021; 11:nano11092280. [PMID: 34578596 PMCID: PMC8468449 DOI: 10.3390/nano11092280] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/25/2021] [Accepted: 08/30/2021] [Indexed: 12/24/2022]
Abstract
Carbon nanotube field effect transistor (CNT FET) aptasensors have been investigated for the detection of adenosine using two different aptamer sequences, a 35-mer and a 27-mer. We found limits of detection for adenosine of 100 pM and 320 nM for the 35-mer and 27-mer aptamers, with dissociation constants of 1.2 nM and 160 nM, respectively. Upon analyte recognition the 35-mer adenosine aptamer adopts a compact G-quadruplex structure while the 27-mer adenosine aptamer changes to a folded duplex. Using the CNT FET aptasensor platform adenosine could be detected with high sensitivity over the range of 100 pM to 10 µM, highlighting the suitability of the CNT FET aptasensor platform for high performance adenosine detection. The aptamer restructuring format is critical for high sensitivity with the G-quadraplex aptasensor having a 130-fold smaller dissociation constant than the duplex forming aptasensor.
Collapse
|
4
|
Tang J, Wu J, Zhu R, Wang Z, Zhao C, Tang P, Xie W, Wang D, Liang L. Reversible photo-regulation on the folding/unfolding of telomere G-quadruplexes with solid-state nanopores. Analyst 2021; 146:655-663. [PMID: 33206065 DOI: 10.1039/d0an01930e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The formation of G-quadruplexes (G4) in human telomere and other important biological regions inhibits the replication and transcription of DNA, thereby influencing further cell proliferation. The investigation of G4 formation and unfolding is vital for understanding their modulation in biological processes and life science. Photo regulation is a facile and sensitive approach for monitoring the structures of biomacromolecules and material surface properties. The nanopore-based technique is also prevalent for label-free single-molecule characterization with high accuracy. This study provides a combination of solid-state nanopore technology with light-switch as a platform for the modulation of human telomere G4 formation and splitting under switchable light exposure. The introduction of molecular switch, namely azobenzene moiety at different positions of the DNA sequence influences the formation and stability of G4. Three azobenzenes immobilized on each of the G-quartet plane (hTelo-3azo-p) or four azobenzenes on the same plane (hTelo-4azo-4p) of the human telomere G4 sequence realized the reversible control of G4 folding/unfolding at the temporal scale upon photo regulation, and the formation and splitting of G4 with hTelo-4azo-4p is slower and not thorough compared to that with hTelo-3azo-p due to the coplanar steric hindrance. Moreover, the G4 formation recorded with the combined nanopore and photo-responsive approach was also characterized with fluorescence, and the variation in the fluorescence intensity of the NMM and G4 complex exhibited a different tendency under reverse light irradiation due to the distinct interactions of NMM with the azobenzene-modified G4. Our study demonstrated a controllable and sensitive way for the manipulation of G4 structures, which will be inspiring for the intervention of G4-related cell senescence, cancer diagnosis and drug exploration.
Collapse
Affiliation(s)
- Jing Tang
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, P. R. China.
| | | | | | | | | | | | | | | | | |
Collapse
|
5
|
Reynaud L, Bouchet-Spinelli A, Raillon C, Buhot A. Sensing with Nanopores and Aptamers: A Way Forward. SENSORS 2020; 20:s20164495. [PMID: 32796729 PMCID: PMC7472324 DOI: 10.3390/s20164495] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/31/2020] [Accepted: 08/03/2020] [Indexed: 12/13/2022]
Abstract
In the 90s, the development of a novel single molecule technique based on nanopore sensing emerged. Preliminary improvements were based on the molecular or biological engineering of protein nanopores along with the use of nanotechnologies developed in the context of microelectronics. Since the last decade, the convergence between those two worlds has allowed for biomimetic approaches. In this respect, the combination of nanopores with aptamers, single-stranded oligonucleotides specifically selected towards molecular or cellular targets from an in vitro method, gained a lot of interest with potential applications for the single molecule detection and recognition in various domains like health, environment or security. The recent developments performed by combining nanopores and aptamers are highlighted in this review and some perspectives are drawn.
Collapse
|
6
|
Ji N, Shi HQ, Fang XY, Wu ZY. Exploring the interaction of G-quadruplex and porphyrin derivative by single protein nanopore sensing interface. Anal Chim Acta 2020; 1106:126-132. [DOI: 10.1016/j.aca.2020.01.053] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/18/2020] [Accepted: 01/23/2020] [Indexed: 11/26/2022]
|
7
|
Wang S, Liang L, Tang J, Cai Y, Zhao C, Fang S, Wang H, Weng T, Wang L, Wang D. Label-free single-molecule identification of telomere G-quadruplexes with a solid-state nanopore sensor. RSC Adv 2020; 10:27215-27224. [PMID: 35515777 PMCID: PMC9055465 DOI: 10.1039/d0ra05083k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 07/06/2020] [Indexed: 12/14/2022] Open
Abstract
Telomere sequences can spontaneously form G-quadruplexes (G4) in the presence of some cations. In view of their relevance to genetic processes and potential as therapeutic-targets, hitherto, a wealth of conventional techniques have been reported for interrogation of G4 conformation diversity and corresponding folding kinetics, most of which are limited in precision and sensitivity. This work introduces a label-free solid-state nanopore (SSN) approach for the determination of inter-, intra- and tandem molecular G4 with distinct base permutation in various cation buffers with a tailored aperture and meanwhile captures the single-molecule G4 folding process. SSN translocation properties elucidated that both inter- and intramolecular G4 generated higher current blockage with longer duration than flexible homopolymer nucleotide, and intramolecular G4 are structurally more stable with higher event frequency and longer blockage time than intermolecular ones; base arrangement played weak role in translocation behaviors; the same sequences with one, two and three G4 skeletons displayed an increase in current blockage and a gradual extension in dwell time with the increase of molecule size recorded in the same nanopore. We observed the conformation change of single-molecule G4 which indicated the existence of folding/unfolding equilibration in nanopore, and real-time test suggested a gradual formation of G4 with time. Our results could provide a continued and improved understanding of the underlying relevance of structural stability and G4 folding process by utilizing SSN platform which exhibits strategic potential advances over the other methods with high spatial and temporal resolution. Nanopore detection of single-molecule G-quadruplexes.![]()
Collapse
|
8
|
Bošković F, Zhu J, Chen K, Keyser UF. Monitoring G-Quadruplex Formation with DNA Carriers and Solid-State Nanopores. NANO LETTERS 2019; 19:7996-8001. [PMID: 31577148 DOI: 10.1021/acs.nanolett.9b03184] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
G-quadruplexes (Gqs) are guanine-rich DNA structures formed by single-stranded DNA. They are of paramount significance to gene expression regulation, but also drug targets for cancer and human viruses. Current ensemble and single-molecule methods require fluorescent labels, which can affect Gq folding kinetics. Here we introduce, a single-molecule Gq nanopore assay (smGNA) to detect Gqs and kinetics of Gq formation. We use ∼5 nm solid-state nanopores to detect various Gq structural variants attached to designed DNA carriers. Gqs can be identified by localizing their positions along designed DNA carriers, establishing smGNA as a tool for Gq mapping. In addition, smGNA allows for discrimination of (un)folded Gq structures, provides insights into single-molecule kinetics of Gq folding, and probes quadruplex-to-duplex structural transitions. smGNA can elucidate the formation of Gqs at the single-molecule level without labeling and has potential implications on the study of these structures both in single-stranded DNA and in genomic samples.
Collapse
Affiliation(s)
- Filip Bošković
- Cavendish Laboratory , University of Cambridge , JJ Thompson Avenue , Cambridge CB3 0HE , United Kingdom
| | - Jinbo Zhu
- Cavendish Laboratory , University of Cambridge , JJ Thompson Avenue , Cambridge CB3 0HE , United Kingdom
| | - Kaikai Chen
- Cavendish Laboratory , University of Cambridge , JJ Thompson Avenue , Cambridge CB3 0HE , United Kingdom
| | - Ulrich F Keyser
- Cavendish Laboratory , University of Cambridge , JJ Thompson Avenue , Cambridge CB3 0HE , United Kingdom
| |
Collapse
|
9
|
Abstract
Circular dichroism and stopped-flow UV spectroscopies were used to investigate the thermodynamic stability and the folding pathway of d[TGAG3TG3TAG3TG3TA2] at 25 °C in solutions containing 25 mM KCl. Under these conditions the oligonucleotide adopts a thermally stable, all-parallel G-quadruplex topography containing three stacked quartets. K+-induced folding shows three resolved relaxation times, each with distinctive spectral changes. Folding is complete within 200 s. These data indicate a folding pathway that involves at least two populated intermediates, one of which seems to be an antiparallel structure that rearranges to the final all-parallel conformation. Molecular dynamics reveals a stereochemically plausible folding pathway that does not involve complete unfolding of the intermediate. The rate of unfolding was determined using complementary DNA to trap transiently unfolded states to form a stable duplex. As assessed by 1D-1H NMR and fluorescence spectroscopy, unfolding is extremely slow with only one observable rate-limiting relaxation time.
Collapse
|
10
|
Si W, Yang H, Sha J, Zhang Y, Chen Y. Discrimination of single-stranded DNA homopolymers by sieving out G-quadruplex using tiny solid-state nanopores. Electrophoresis 2019; 40:2117-2124. [PMID: 30779188 DOI: 10.1002/elps.201800537] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 01/28/2019] [Accepted: 02/13/2019] [Indexed: 12/19/2022]
Abstract
Nanopore sensor has been developed as a promising technology for DNA sequencing at the single-base resolution. However, the discrimination of homopolymers composed of guanines from other nucleotides has not been clearly revealed due to the easily formed G-quadruplex in aqueous buffers. In this work, we report that a tiny silicon nitride nanopore was used to sieve out G tetramers to make sure only homopolymers composed of guanines could translocate through the nanopore, then the 20-nucleotide long ssDNA homopolymers could be identified and differentiated. It is found that the size of the nucleotide plays a major role in affecting the current blockade as well as the dwell time while DNA is translocating through the nanopore. By the comparison of translocation behavior of ssDNA homopolymers composed of nucleotides with different volumes, it is found that smaller nucleotides can lead to higher translocation speed and lower current blockage, which is also found and validated for the 105-nucleotide long homopolymers. The studies performed in this work will improve our understanding of nanopore-based DNA sequencing at single-base level.
Collapse
Affiliation(s)
- Wei Si
- School of Mechanical Engineering, Southeast University, Nanjing, P. R. China.,Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, P. R. China
| | - Haojie Yang
- School of Mechanical Engineering, Southeast University, Nanjing, P. R. China.,Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, P. R. China
| | - Jingjie Sha
- School of Mechanical Engineering, Southeast University, Nanjing, P. R. China.,Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, P. R. China
| | - Yin Zhang
- School of Mechanical Engineering, Southeast University, Nanjing, P. R. China.,Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, P. R. China
| | - Yunfei Chen
- School of Mechanical Engineering, Southeast University, Nanjing, P. R. China.,Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, P. R. China
| |
Collapse
|
11
|
Vu T, Davidson SL, Shim J. Investigation of compacted DNA structures induced by Na + and K + monovalent cations using biological nanopores. Analyst 2019; 143:906-913. [PMID: 29362734 DOI: 10.1039/c7an01857f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In aqueous solutions, an elongated, negatively charged DNA chain can quickly change its conformation into a compacted globule in the presence of positively charged molecules, or cations. This well-known process, called DNA compaction, is a method with great potential for gene therapy and delivery. Experimental conditions to induce these compacted DNA structures are often limited to the use of common compacting agents, such as cationic surfactants, polymers, and multivalent cations. In this study, we show that in highly concentrated buffers of 1 M monovalent cation solutions at pH 7.2 and 10, biological nanopores allow real-time sensing of individual compacted structures induced by K+ and Na+, the most abundant monovalent cations in human bodies. Herein, we studied the ratio between compacted and linear structures for 15-mer single-stranded DNA molecules containing only cytosine nucleotides, optimizing the probability of linear DNA chains being compacted. Since the binding affinity of each nucleotide to cation is different, the ability of the DNA strand to fold into a compacted structure greatly depends on the type of cations and nucleotides present. Our experimental results compare favorably with findings from previous molecular dynamics simulations for the DNA compacting potential of K+ and Na+ monovalent cations. We estimate that the majority of single-stranded DNA molecules in our experiment are compacted. From the current traces of nanopores, the ratio of compacted DNA to linear DNA molecules is approximately 30 : 1 and 15 : 1, at a pH of 7.2 and 10, respectively. Our comparative studies reveal that Na+ monovalent cations have a greater potential of compacting the 15C-ssDNA than K+ cations.
Collapse
Affiliation(s)
- Trang Vu
- Department of Biomedical Engineering, Rowan University, Glassboro, New Jersey 08028, USA.
| | | | | |
Collapse
|
12
|
Lipid bilayer membrane technologies: A review on single-molecule studies of DNA sequencing by using membrane nanopores. Mikrochim Acta 2017. [DOI: 10.1007/s00604-017-2321-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
13
|
Vu T, Davidson SL, Borgesi J, Maksudul M, Jeon TJ, Shim J. Piecing together the puzzle: nanopore technology in detection and quantification of cancer biomarkers. RSC Adv 2017. [DOI: 10.1039/c7ra08063h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
This mini-review paper is a comprehensive outline of nanopore technology applications in the detection and study of various cancer causal factors.
Collapse
Affiliation(s)
- Trang Vu
- Department of Biomedical Engineering
- Henry M. Rowan College of Engineering
- Rowan University
- Glassboro
- USA
| | - Shanna-Leigh Davidson
- Department of Biomedical Engineering
- Henry M. Rowan College of Engineering
- Rowan University
- Glassboro
- USA
| | - Julia Borgesi
- Department of Biomedical Engineering
- Henry M. Rowan College of Engineering
- Rowan University
- Glassboro
- USA
| | - Mowla Maksudul
- Department of Biomedical Engineering
- Henry M. Rowan College of Engineering
- Rowan University
- Glassboro
- USA
| | - Tae-Joon Jeon
- Department of Biological Engineering
- Inha University
- Incheon 22212
- Republic of Korea
| | - Jiwook Shim
- Department of Biomedical Engineering
- Henry M. Rowan College of Engineering
- Rowan University
- Glassboro
- USA
| |
Collapse
|
14
|
Šponer J, Bussi G, Stadlbauer P, Kührová P, Banáš P, Islam B, Haider S, Neidle S, Otyepka M. Folding of guanine quadruplex molecules-funnel-like mechanism or kinetic partitioning? An overview from MD simulation studies. Biochim Biophys Acta Gen Subj 2016; 1861:1246-1263. [PMID: 27979677 DOI: 10.1016/j.bbagen.2016.12.008] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 12/04/2016] [Accepted: 12/11/2016] [Indexed: 01/18/2023]
Abstract
BACKGROUND Guanine quadruplexes (GQs) play vital roles in many cellular processes and are of much interest as drug targets. In contrast to the availability of many structural studies, there is still limited knowledge on GQ folding. SCOPE OF REVIEW We review recent molecular dynamics (MD) simulation studies of the folding of GQs, with an emphasis paid to the human telomeric DNA GQ. We explain the basic principles and limitations of all types of MD methods used to study unfolding and folding in a way accessible to non-specialists. We discuss the potential role of G-hairpin, G-triplex and alternative GQ intermediates in the folding process. We argue that, in general, folding of GQs is fundamentally different from funneled folding of small fast-folding proteins, and can be best described by a kinetic partitioning (KP) mechanism. KP is a competition between at least two (but often many) well-separated and structurally different conformational ensembles. MAJOR CONCLUSIONS The KP mechanism is the only plausible way to explain experiments reporting long time-scales of GQ folding and the existence of long-lived sub-states. A significant part of the natural partitioning of the free energy landscape of GQs comes from the ability of the GQ-forming sequences to populate a large number of syn-anti patterns in their G-tracts. The extreme complexity of the KP of GQs typically prevents an appropriate description of the folding landscape using just a few order parameters or collective variables. GENERAL SIGNIFICANCE We reconcile available computational and experimental studies of GQ folding and formulate basic principles characterizing GQ folding landscapes. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.
Collapse
Affiliation(s)
- Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic; Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic.
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea 265, 34136 Trieste, Italy
| | - Petr Stadlbauer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic; Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Petra Kührová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Barira Islam
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Shozeb Haider
- UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Stephen Neidle
- UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic
| |
Collapse
|
15
|
Zhang X, Xu X, Yang Z, Burcke AJ, Gates KS, Chen SJ, Gu LQ. Mimicking Ribosomal Unfolding of RNA Pseudoknot in a Protein Channel. J Am Chem Soc 2015; 137:15742-52. [PMID: 26595106 PMCID: PMC4886178 DOI: 10.1021/jacs.5b07910] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Pseudoknots are a fundamental RNA tertiary structure with important roles in regulation of mRNA translation. Molecular force spectroscopic approaches such as optical tweezers can track the pseudoknot's unfolding intermediate states by pulling the RNA chain from both ends, but the kinetic unfolding pathway induced by this method may be different from that in vivo, which occurs during translation and proceeds from the 5' to 3' end. Here we developed a ribosome-mimicking, nanopore pulling assay for dissecting the vectorial unfolding mechanism of pseudoknots. The pseudoknot unfolding pathway in the nanopore, either from the 5' to 3' end or in the reverse direction, can be controlled by a DNA leader that is attached to the pseudoknot at the 5' or 3' ends. The different nanopore conductance between DNA and RNA translocation serves as a marker for the position and structure of the unfolding RNA in the pore. With this design, we provided evidence that the pseudoknot unfolding is a two-step, multistate, metal ion-regulated process depending on the pulling direction. Most notably, unfolding in both directions is rate-limited by the unzipping of the first helix domain (first step), which is Helix-1 in the 5' → 3' direction and Helix-2 in the 3' → 5' direction, suggesting that the initial unfolding step in either pulling direction needs to overcome an energy barrier contributed by the noncanonical triplex base-pairs and coaxial stacking interactions for the tertiary structure stabilization. These findings provide new insights into RNA vectorial unfolding mechanisms, which play an important role in biological functions including frameshifting.
Collapse
Affiliation(s)
- Xinyue Zhang
- Department of Bioengineering and Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri 65211, United States
| | - Xiaojun Xu
- Department of Physics, Department of Biochemistry, and Informatics Institute, University of Missouri, Columbia, Missouri 65211, United States
| | - Zhiyu Yang
- Department of Chemistry and Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Andrew J. Burcke
- Department of Bioengineering and Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri 65211, United States
| | - Kent S. Gates
- Department of Chemistry and Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Shi-Jie Chen
- Department of Physics, Department of Biochemistry, and Informatics Institute, University of Missouri, Columbia, Missouri 65211, United States
| | - Li-Qun Gu
- Department of Bioengineering and Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri 65211, United States
| |
Collapse
|
16
|
Wang Y, Gu LQ. Biomedical diagnosis perspective of epigenetic detections using alpha-hemolysin nanopore. AIMS MATERIALS SCIENCE 2015; 2:448-472. [PMID: 30931380 PMCID: PMC6436813 DOI: 10.3934/matersci.2015.4.448] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The α-hemolysin nanopore has been studied for applications in DNA sequencing, various single-molecule detections, biomolecular interactions, and biochips. The detection of single molecules in a clinical setting could dramatically improve cancer detection and diagnosis as well as develop personalized medicine practices for patients. This brief review shortly presents the current solid state and protein nanopore platforms and their applications like biosensing and sequencing. We then elaborate on various epigenetic detections (like microRNA, G-quadruplex, DNA damages, DNA modifications) with the most widely used alpha-hemolysin pore from a biomedical diagnosis perspective. In these detections, a nanopore electrical current signature was generated by the interaction of a target with the pore. The signature often was evidenced by the difference in the event duration, current level, or both of them. An ideal signature would provide obvious differences in the nanopore signals between the target and the background molecules. The development of cancer biomarker detection techniques and nanopore devices have the potential to advance clinical research and resolve health problems. However, several challenges arise in applying nanopore devices to clinical studies, including super low physiological concentrations of biomarkers resulting in low sensitivity, complex biological sample contents resulting in false signals, and fast translocating speed through the pore resulting in poor detections. These issues and possible solutions are discussed.
Collapse
Affiliation(s)
- Yong Wang
- Department of Biological Engineering, Dalton Cardiovascular Research Center, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Li-qun Gu
- Department of Biological Engineering, Dalton Cardiovascular Research Center, University of Missouri-Columbia, Columbia, MO 65211, USA
| |
Collapse
|
17
|
Pederson ED, Barbalas J, Drown BS, Culbertson MJ, Keranen Burden LM, Kasianowicz JJ, Burden DL. Proximal Capture Dynamics for a Single Biological Nanopore Sensor. J Phys Chem B 2015. [DOI: 10.1021/acs.jpcb.5b04955] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
| | - Jonathan Barbalas
- Chemistry
Department, Wheaton College, Wheaton, Illinois 60187, United States
| | - Bryon S. Drown
- Chemistry
Department, Wheaton College, Wheaton, Illinois 60187, United States
| | | | | | - John J. Kasianowicz
- Semiconductor
Electronics Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8120, United States
| | - Daniel L. Burden
- Chemistry
Department, Wheaton College, Wheaton, Illinois 60187, United States
| |
Collapse
|
18
|
Ma J, Qiu Y, Yuan Z, Zhang Y, Sha J, Liu L, Sun L, Ni Z, Yi H, Li D, Chen Y. Detection of short single-strand DNA homopolymers with ultrathin Si3N4 nanopores. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:022719. [PMID: 26382444 DOI: 10.1103/physreve.92.022719] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Indexed: 06/05/2023]
Abstract
A series of nanopores with diameters ranging from 2.5 to 63 nm are fabricated on a reduced Si3N4 membrane by focused ion beam and high energy electron beam. Through measuring the blocked ionic currents for DNA strands threading linearly through those solid-state nanopores, it is found that the blockade ionic current is proportional to the square of the hydrodynamic diameter of the DNA strand. With the nanopore diameter reduced to be comparable with that of DNA strands, the hydrodynamic diameter of the DNA becomes smaller, which is attributed to the size confinement effects. The duration time for the linear DNA translocation events increases monotonically with the nanopore length. By comparing the spatial configurations of DNA strands through nanopores with different diameters, it is found that the nanopore with large diameter has enough space to allow the DNA strand to translocate through with complex conformation. With the decrease of the nanopore diameter, the folded part of the DNA is prone to be straightened by the nanopore, which leads to the increase in the occurrence frequency of the linear DNA translocation events. Reducing the diameter of the nanopore to 2.5 nm allows the detection and discrimination of three nucleotide "G" and three nucleotide "T" homopolymer DNA strands based on differences in their physical dimensions.
Collapse
Affiliation(s)
- Jian Ma
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| | - Yinghua Qiu
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| | - Zhishan Yuan
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| | - Yin Zhang
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| | - Jingjie Sha
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| | - Lei Liu
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| | - Litao Sun
- China Education Council Key Laboratory of MEMS, Southeast University, Nanjing 210096, China
| | - Zhonghua Ni
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| | - Hong Yi
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| | - Deyu Li
- Department of Mechanical Engineering, Vanderbilt University, Nashville, Tennessee 37235-1592, USA
| | - Yunfei Chen
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| |
Collapse
|
19
|
Ding Y, Fleming AM, Burrows CJ. α-Hemolysin nanopore studies reveal strong interactions between biogenic polyamines and DNA hairpins. Mikrochim Acta 2015; 183:973-979. [PMID: 27217593 DOI: 10.1007/s00604-015-1516-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The α-hemolysin (α-HL) nanopore analyzes DNA as it is electrophoretically driven through the pore. The respective current vs. time (i-t) traces depends on the DNA sequence, its secondary structures, or on the physical conditions of the analysis. The current study describes analysis of a DNA hairpin with a 5'-extension with the α-HL nanopore in the presence of the polyamines spermine (Spm), spermidine (Spd), and putrescine (Put). These studies identified a new i-t trace characteristic of the DNA-polyamine complex. Voltage-dependent studies determined that the hairpin-Spm complex formed with excess Spm was not unzipped and translocated through the pore even when the voltage was increased to 180 mV. The DNA hairpin sample was titrated with Spm, Spd, or Put that showed a dose-dependent response in the characteristic event patterns for hairpins bound to Spm or Spd, but not for Put. Plots of the event types vs. count were used to calculate binding constants for the Spm or Spd hairpin interactions under these conditions. The titration also demonstrated that the event rate decreased ~10-fold when the Spm or Spd concentration was increased from 0 to 4 mM. These observations impose practical limitations on the ability to use Spm or Spd for DNA studies with the α-HL nanopore.
Collapse
Affiliation(s)
- Yun Ding
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850, USA
| | - Aaron M Fleming
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850, USA
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850, USA
| |
Collapse
|
20
|
Sawaya S, Boocock J, Black MA, Gemmell NJ. Exploring possible DNA structures in real-time polymerase kinetics using Pacific Biosciences sequencer data. BMC Bioinformatics 2015; 16:21. [PMID: 25626999 PMCID: PMC4384361 DOI: 10.1186/s12859-014-0449-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 12/30/2014] [Indexed: 12/01/2022] Open
Abstract
Background Pausing of DNA polymerase can indicate the presence of a DNA structure that differs from the canonical double-helix. Here we detail a method to investigate how polymerase pausing in the Pacific Biosciences sequencer reads can be related to DNA sequences. The Pacific Biosciences sequencer uses optics to view a polymerase and its interaction with a single DNA molecule in real-time, offering a unique way to detect potential alternative DNA structures. Results We have developed a new way to examine polymerase kinetics data and relate it to the DNA sequence by using a wavelet transform of read information from the sequencer. We use this method to examine how polymerase kinetics are related to nucleotide base composition. We then examine tandem repeat sequences known for their ability to form different DNA structures: (CGG)n and (CG)n repeats which can, respectively, form G-quadruplex DNA and Z-DNA. We find pausing around the (CGG)n repeat that may indicate the presence of G-quadruplexes in some of the sequencer reads. The (CG)n repeat does not appear to cause polymerase pausing, but its kinetics signature nevertheless suggests the possibility that alternative nucleotide conformations may sometimes be present. Conclusion We discuss the implications of using our method to discover DNA sequences capable of forming alternative structures. The analyses presented here can be reproduced on any Pacific Biosciences kinetics data for any DNA pattern of interest using an R package that we have made publicly available.
Collapse
Affiliation(s)
- Sterling Sawaya
- Institute for Behavioral Genetics, University of Colorado, Boulder, USA. .,Department of Anatomy, and Allan Wilson Centre for Molecular Ecology and Evolution, University of Otago, Dunedin, New Zealand.
| | - James Boocock
- Department of Biochemistry, University of Otago, Dunedin, New Zealand.
| | - Michael A Black
- Department of Biochemistry, University of Otago, Dunedin, New Zealand.
| | - Neil J Gemmell
- Department of Anatomy, and Allan Wilson Centre for Molecular Ecology and Evolution, University of Otago, Dunedin, New Zealand.
| |
Collapse
|
21
|
Shim J, Kim Y, Humphreys GI, Nardulli AM, Kosari F, Vasmatzis G, Taylor WR, Ahlquist DA, Myong S, Bashir R. Nanopore-based assay for detection of methylation in double-stranded DNA fragments. ACS NANO 2015; 9:290-300. [PMID: 25569824 DOI: 10.1021/nn5045596] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
DNA methylation is an epigenetic modification of DNA in which methyl groups are added at the 5-carbon position of cytosine. Aberrant DNA methylation, which has been associated with carcinogenesis, can be assessed in various biological fluids and potentially can be used as markers for detection of cancer. Analytically sensitive and specific assays for methylation targeting low-abundance and fragmented DNA are needed for optimal clinical diagnosis and prognosis. We present a nanopore-based direct methylation detection assay that circumvents bisulfite conversion and polymerase chain reaction amplification. Building on our prior work, we used methyl-binding proteins (MBPs), which selectively label the methylated DNA. The nanopore-based assay selectively detects methylated DNA/MBP complexes through a 19 nm nanopore with significantly deeper and prolonged nanopore ionic current blocking, while unmethylated DNA molecules were not detectable due to their smaller diameter. Discrimination of hypermethylated and unmethylated DNA on 90, 60, and 30 bp DNA fragments was demonstrated using sub-10 nm nanopores. Hypermethylated DNA fragments fully bound with MBPs are differentiated from unmethylated DNA at 2.1- to 6.5-fold current blockades and 4.5- to 23.3-fold transport durations. Furthermore, these nanopore assays can detect the CpG dyad in DNA fragments and could someday profile the position of methylated CpG sites on DNA fragments.
Collapse
Affiliation(s)
- Jiwook Shim
- Department of Bioengineering, ‡Micro and Nanotechnology Laboratory, and §Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign Urbana, Illinois 61801, United States
| | | | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Wolna AH, Fleming AM, Burrows CJ. Single-molecule analysis of thymine dimer-containing G-quadruplexes formed from the human telomere sequence. Biochemistry 2014; 53:7484-93. [PMID: 25407781 PMCID: PMC4263424 DOI: 10.1021/bi501072m] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 11/14/2014] [Indexed: 02/06/2023]
Abstract
The human telomere plays crucial roles in maintaining genome stability. In the presence of suitable cations, the repetitive 5'-TTAGGG-3' human telomere sequence can fold into G-quadruplexes that adopt the hybrid, basket, or propeller fold. The telomere sequence is hypersensitive to UV-induced thymine dimer (T=T) formation, yet it does not cause telomere shortening. In this work, the potential structural disruption and thermodynamic stability of the T=T-containing natural telomere sequences were studied to understand why this damage is tolerated in telomeres. First, established methods, such as thermal melting measurements, electrophoretic mobility shift assays, and circular dichroism spectroscopy, were utilized to determine the effects of the damage on these structures. Second, a single-molecule ion channel recording technique using α-hemolysin (α-HL) was employed to examine further the structural differences between the damaged sequences. It was observed that the damage caused slightly lower thermal stabilities and subtle changes in the circular dichroism spectra for hybrid and basket folds. The α-HL experiments determined that T=Ts disrupt double-chain reversal loop formation but are tolerated in edgewise and diagonal loops. The largest change was observed for the T=T-containing natural telomere sequence when the propeller fold (all double-chain reversal loops) was studied. On the basis of the α-HL experiments, it was determined that a triplexlike structure exists under conditions that favor a propeller structure. The biological significance of these observations is discussed.
Collapse
Affiliation(s)
- Anna H. Wolna
- Department of Chemistry, University of
Utah, 315 South 1400
East, Salt Lake City, Utah 84112-0850, United States
| | - Aaron M. Fleming
- Department of Chemistry, University of
Utah, 315 South 1400
East, Salt Lake City, Utah 84112-0850, United States
| | - Cynthia J. Burrows
- Department of Chemistry, University of
Utah, 315 South 1400
East, Salt Lake City, Utah 84112-0850, United States
| |
Collapse
|
23
|
Shasha C, Henley RY, Stoloff DH, Rynearson KD, Hermann T, Wanunu M. Nanopore-based conformational analysis of a viral RNA drug target. ACS NANO 2014; 8:6425-6430. [PMID: 24861167 PMCID: PMC4729693 DOI: 10.1021/nn501969r] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Nanopores are single-molecule sensors that show exceptional promise as a biomolecular analysis tool by enabling label-free detection of small amounts of sample. In this paper, we demonstrate that nanopores are capable of detecting the conformation of an antiviral RNA drug target. The hepatitis C virus uses an internal ribosome entry site (IRES) motif in order to initiate translation by docking to ribosomes in its host cell. The IRES is therefore a viable and important drug target. Drug-induced changes to the conformation of the HCV IRES motif, from a bent to a straight conformation, have been shown to inhibit HCV replication. However, there is presently no straightforward method to analyze the effect of candidate small-molecule drugs on the RNA conformation. In this paper, we show that RNA translocation dynamics through a 3 nm diameter nanopore is conformation-sensitive by demonstrating a difference in transport times between bent and straight conformations of a short viral RNA motif. Detection is possible because bent RNA is stalled in the 3 nm pore, resulting in longer molecular dwell times than straight RNA. Control experiments show that binding of a weaker drug does not produce a conformational change, as consistent with independent fluorescence measurements. Nanopore measurements of RNA conformation can thus be useful for probing the structure of various RNA motifs, as well as structural changes to the RNA upon small-molecule binding.
Collapse
Affiliation(s)
- Carolyn Shasha
- Departments of Physics and Chemistry/Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Robert Y. Henley
- Departments of Physics and Chemistry/Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Daniel H. Stoloff
- Departments of Physics and Chemistry/Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Kevin D. Rynearson
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Thomas Hermann
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Meni Wanunu
- Departments of Physics and Chemistry/Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| |
Collapse
|
24
|
Larkin J, Carson S, Stoloff DH, Wanunu M. Nanopore-Based Analysis of Chemically Modified DNA and Nucleic Acid Drug Targets. Isr J Chem 2013. [DOI: 10.1002/ijch.201300006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
25
|
Stoloff DH, Wanunu M. Recent trends in nanopores for biotechnology. Curr Opin Biotechnol 2012; 24:699-704. [PMID: 23266100 DOI: 10.1016/j.copbio.2012.11.008] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 11/20/2012] [Indexed: 10/27/2022]
Abstract
Nanopore technology employs a nanoscale hole in an insulating membrane to stochastically sense with high throughput individual biomolecules in solution. The generality of the nanopore detection principle and the ease of single-molecule detection suggest many potential applications of nanopores in biotechnology. Recent progress has been made with nanopore fabrication and sophistication, as well as with applications in DNA/protein mapping, biomolecular structure analysis, protein detection, and DNA sequencing. In addition, concepts for DNA sequencing devices have been suggested, and computational efforts have been made. The state of the nanopore field is maturing and given the right type of nanopore and operating conditions, nearly every application could revolutionize medicine in terms of speed, cost, and quality. In this review, we summarize progress in nanopores for biotechnological applications over the past 2-3 years.
Collapse
Affiliation(s)
- Daniel H Stoloff
- Department of Physics, Northeastern University, Boston, MA, United States
| | | |
Collapse
|