1
|
Xue C, Huang H, Wang L, Liao W, Jiang H, Wu ZS. Swelling of Serum-Stable DNA Nanoparticles upon Target-Induced Conformational Rearrangement of Sensing Probes for the Signal-On Detection of Cancer-Related Genes. Anal Chem 2022; 94:2749-2756. [PMID: 35099191 DOI: 10.1021/acs.analchem.1c03598] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Nuclease-resistant assay probes are of significant importance for biochemical analysis and disease diagnosis. In this contribution, a reconfigurable lipidic moiety-attached DNA nanoparticle (LDN) is constructed from a cholesterol-conjugated multifunctional hairpin-type DNA probe (Chol-DP) by hydrophobicity-mediated self-assembly. The LDN holds high serum stability and displays a low false-positive signal even in a complex biological milieu. The hydrophobic cholesterol moiety enables the hydrophobicity-mediated assembly, while hydrophilic DNA sequence serves as a recognition element and a polymerization template. The initiator-activated strand displacement amplification (SDA) reaction can convert the hairpin-shaped probe into rigid double-stranded DNA (dsDNA), causing the conformational rearrangement-based LDN swelling that can be used to reliably and fluorescently signal the cancer-related p53 gene. The size increase and structural reconfiguration are confirmed by dynamic light scattering (DLS) analysis and confocal microscopy imaging, respectively. Target p53 is specifically detected down to 10 pM. The whole assay process involved only several simple mixing steps. Recovery test and blind test further confirm the feasibility of the use of the LDN for the detection of target DNA in a complex biological milieu, indicating a promising nanotool for biomedical applications.
Collapse
Affiliation(s)
- Chang Xue
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Hong Huang
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Lei Wang
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China.,Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Wenqiang Liao
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Hao Jiang
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Zai-Sheng Wu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| |
Collapse
|
2
|
Wang HB, Bai HY, Dong GL, Liu YM. DNA-templated Au nanoclusters coupled with proximity-dependent hybridization and guanine-rich DNA induced quenching: a sensitive fluorescent biosensing platform for DNA detection. NANOSCALE ADVANCES 2019; 1:1482-1488. [PMID: 36132614 PMCID: PMC9419426 DOI: 10.1039/c8na00278a] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 01/28/2019] [Indexed: 06/09/2023]
Abstract
In this paper, the fluorescence signal of poly(A) DNA-templated Au nanoclusters (AuNCs) is found to be greatly quenched by photoinduced electron transfer (PET) when they are close to guanine (G)-rich DNA. Based on the findings, we have designed a low-cost fluorescence biosensing strategy for the sensitive detection of DNA. Highly luminescent and photo-stable poly(A) DNA-AuNCs were utilized as the fluorescent indicator and G-rich DNA was utilized as the fluorescent quencher. In the absence of target DNA, DNA-AuNCs failed to hybridize with the G-rich DNA and did not form the duplex DNA structure. Strong fluorescence intensity at 475 nm was observed due to the DNA-AuNCs being far away from the G-rich DNA. However, in the presence of target DNA, the DNA-AuNCs together with G-rich DNA could hybridize with the target DNA, leading to the 5' terminus of the DNA-AuNCs and the 3' terminus of G-rich DNA being in close proximity and promoting the cooperative hybridization. Therefore, a "Y" junction structure was formed and the G-rich sequences were brought close to the AuNCs. Therefore, the fluorescence intensity of the sensing system decreased significantly. Taking advantage of the poly(A) DNA-templated Au nanoclusters and G-rich DNA proximity-induced quenching, the strategy could be extended to determine other biomolecules by designing appropriate sequences of DNA probes.
Collapse
Affiliation(s)
- Hai-Bo Wang
- College of Chemistry and Chemical Engineering, Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal University Xinyang 464000 PR China +86 376 6391172 +86 376 6391172
| | - Hong-Yu Bai
- College of Chemistry and Chemical Engineering, Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal University Xinyang 464000 PR China +86 376 6391172 +86 376 6391172
| | - Gao-Li Dong
- College of Chemistry and Chemical Engineering, Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal University Xinyang 464000 PR China +86 376 6391172 +86 376 6391172
| | - Yan-Ming Liu
- College of Chemistry and Chemical Engineering, Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal University Xinyang 464000 PR China +86 376 6391172 +86 376 6391172
| |
Collapse
|
3
|
Shi Z, Zhang X, Cheng R, Zhang Q, Jin Y. High-throughout identification of telomere-binding ligands based on photo-induced electron transfer. RSC Adv 2016. [DOI: 10.1039/c5ra25612g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
A fast and cost-effective method is developed for high-throughout screening G-quadruplex-binding ligands based on the photo-induced electron transfer.
Collapse
Affiliation(s)
- Zhilu Shi
- Key Laboratory of Applied Surface and Colloid Chemistry
- Ministry of Education
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
| | - Xiafei Zhang
- Key Laboratory of Applied Surface and Colloid Chemistry
- Ministry of Education
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
| | - Rui Cheng
- Key Laboratory of Applied Surface and Colloid Chemistry
- Ministry of Education
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
| | - Qi Zhang
- Key Laboratory of Applied Surface and Colloid Chemistry
- Ministry of Education
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
| | - Yan Jin
- Key Laboratory of Applied Surface and Colloid Chemistry
- Ministry of Education
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
| |
Collapse
|
4
|
Zheng J, Yang R, Shi M, Wu C, Fang X, Li Y, Li J, Tan W. Rationally designed molecular beacons for bioanalytical and biomedical applications. Chem Soc Rev 2015; 44:3036-55. [PMID: 25777303 PMCID: PMC4431697 DOI: 10.1039/c5cs00020c] [Citation(s) in RCA: 248] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Nucleic acids hold promise as biomolecules for future applications in biomedicine and biotechnology. Their well-defined structures and compositions afford unique chemical properties and biological functions. Moreover, the specificity of hydrogen-bonded Watson-Crick interactions allows the construction of nucleic acid sequences with multiple functions. In particular, the development of nucleic acid probes as essential molecular engineering tools will make a significant contribution to advancements in biosensing, bioimaging and therapy. The molecular beacon (MB), first conceptualized by Tyagi and Kramer in 1996, is an excellent example of a double-stranded nucleic acid (dsDNA) probe. Although inactive in the absence of a target, dsDNA probes can report the presence of a specific target through hybridization or a specific recognition-triggered change in conformation. MB probes are typically fluorescently labeled oligonucleotides that range from 25 to 35 nucleotides (nt) in length, and their structure can be divided into three components: stem, loop and reporter. The intrinsic merit of MBs depends on predictable design, reproducibility of synthesis, simplicity of modification, and built-in signal transduction. Using resonance energy transfer (RET) for signal transduction, MBs are further endowed with increased sensitivity, rapid response and universality, making them ideal for chemical sensing, environmental monitoring and biological imaging, in contrast to other nucleic acid probes. Furthermore, integrating MBs with targeting ligands or molecular drugs can substantially support their in vivo applications in theranositics. In this review, we survey advances in bioanalytical and biomedical applications of rationally designed MBs, as they have evolved through the collaborative efforts of many researchers. We first discuss improvements to the three components of MBs: stem, loop and reporter. The current applications of MBs in biosensing, bioimaging and therapy will then be described. In particular, we emphasize recent progress in constructing MB-based biosensors in homogeneous solution or on solid surfaces. We expect that such rationally designed and functionalized MBs will open up new and exciting avenues for biological and medical research and applications.
Collapse
Affiliation(s)
- Jing Zheng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha 410082, China
| | | | | | | | | | | | | | | |
Collapse
|
5
|
Suzuki A, Saito M, Katoh R, Saito Y. Synthesis of 8-aza-3,7-dideaza-2′-deoxyadenosines possessing a new adenosine skeleton as an environmentally sensitive fluorescent nucleoside for monitoring the DNA minor groove. Org Biomol Chem 2015; 13:7459-68. [DOI: 10.1039/c5ob00862j] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Fluorescent ODN probes containing3n7zA(2) acted as effective reporter probes for homogeneous single nucleotide polymorphism (SNP) typing.
Collapse
Affiliation(s)
- Azusa Suzuki
- Department of Chemical Biology and Applied Chemistry
- College of Engineering
- Nihon University
- Koriyama
- Japan
| | - Mio Saito
- Department of Chemical Biology and Applied Chemistry
- College of Engineering
- Nihon University
- Koriyama
- Japan
| | - Ryuzi Katoh
- Department of Chemical Biology and Applied Chemistry
- College of Engineering
- Nihon University
- Koriyama
- Japan
| | - Yoshio Saito
- Department of Chemical Biology and Applied Chemistry
- College of Engineering
- Nihon University
- Koriyama
- Japan
| |
Collapse
|
6
|
Synthesis and characterization of a fluorescent adenosine derivative for detection of intermolecular RNA G-quadruplexes. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.01.048] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
7
|
Ozaki H, Hagiwara Y, Kuwahara M. Specific Amino Acid Sensing Using a Single Acridone-labeled DNA Aptamer. CHEM LETT 2012. [DOI: 10.1246/cl.2012.917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Hiroaki Ozaki
- Department of Chemistry and Chemical Biology, Graduate School of Engineering, Gunma University
| | - Yasuhisa Hagiwara
- Department of Chemistry and Chemical Biology, Graduate School of Engineering, Gunma University
| | - Masayasu Kuwahara
- Department of Chemistry and Chemical Biology, Graduate School of Engineering, Gunma University
| |
Collapse
|
8
|
Wang D, Tang W, Wu X, Wang X, Chen G, Chen Q, Li N, Liu F. Highly selective detection of single-nucleotide polymorphisms using a quartz crystal microbalance biosensor based on the toehold-mediated strand displacement reaction. Anal Chem 2012; 84:7008-14. [PMID: 22830619 DOI: 10.1021/ac301064g] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Toehold-mediated strand displacement reaction (SDR) is first introduced to develop a simple quartz crystal microbalance (QCM) biosensor without an enzyme or label at normal temperature for highly selective and sensitive detection of single-nucleotide polymorphism (SNP) in the p53 tumor suppressor gene. A hairpin capture probe with an external toehold is designed and immobilized on the gold electrode surface of QCM. A successive SDR is initiated by the target sequence hybridization with the toehold domain and ends with the unfolding of the capture probe. Finally, the open-loop capture probe hybridizes with the streptavidin-coupled reporter probe as an efficient mass amplifier to enhance the QCM signal. The proposed biosensor displays remarkable specificity to target the p53 gene fragment against single-base mutant sequences (e.g., the largest discrimination factor is 63 to C-C mismatch) and high sensitivity with the detection limit of 0.3 nM at 20 °C. As the crucial component of the fabricated biosensor for providing the high discrimination capability, the design rationale of the capture probe is further verified by fluorescence sensing and atomic force microscopy imaging. Additionally, a recovery of 84.1% is obtained when detecting the target sequence in spiked HeLa cells lysate, demonstrating the feasibility of employing this biosensor in detecting SNPs in biological samples.
Collapse
Affiliation(s)
- Dingzhong Wang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | | | | | | | | | | | | | | |
Collapse
|
9
|
Quencher-free molecular beacon tethering 7-hydroxycoumarin detects targets through protonation/deprotonation. Bioorg Med Chem 2012; 20:4310-5. [DOI: 10.1016/j.bmc.2012.05.052] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 05/23/2012] [Accepted: 05/23/2012] [Indexed: 12/11/2022]
|
10
|
Fan X, Lin F, Zhang Y, Zhao J, Li H, Yao S. A simple adenosine fluorescent aptasensor based on the quenching ability of guanine. NEW J CHEM 2012. [DOI: 10.1039/c2nj40501f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
11
|
Xiang D, Zhang C, Chen L, Ji X, He Z. Tricolour fluorescence detection of sequence-specific DNA with a new molecular beacon and a nucleic acid dye TOTO-3. Analyst 2012; 137:5898-905. [DOI: 10.1039/c2an35910c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
12
|
Østergaard ME, Hrdlicka PJ. Pyrene-functionalized oligonucleotides and locked nucleic acids (LNAs): tools for fundamental research, diagnostics, and nanotechnology. Chem Soc Rev 2011; 40:5771-88. [PMID: 21487621 PMCID: PMC3644995 DOI: 10.1039/c1cs15014f] [Citation(s) in RCA: 202] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Pyrene-functionalized oligonucleotides (PFOs) are increasingly explored as tools in fundamental research, diagnostics and nanotechnology. Their popularity is linked to the ability of pyrenes to function as polarity-sensitive and quenchable fluorophores, excimer-generating units, aromatic stacking moieties and nucleic acid duplex intercalators. These characteristics have enabled development of PFOs for detection of complementary DNA/RNA targets, discrimination of single nucleotide polymorphisms (SNPs), and generation of π-arrays on nucleic acid scaffolds. This critical review will highlight the physical properties and applications of PFOs that are likely to provide high degree of positional control of the chromophore in nucleic acid complexes. Particular emphasis will be placed on pyrene-functionalized Locked Nucleic Acids (LNAs) since these materials display interesting properties such as fluorescence quantum yields approaching unity and recognition of mixed-sequence double stranded DNA (144 references).
Collapse
|
13
|
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]
|
14
|
A simple and sensitive fluorescent sensing platform for Hg²+ ions assay based on G-quenching. Talanta 2011; 85:713-7. [PMID: 21645763 DOI: 10.1016/j.talanta.2011.04.063] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2011] [Revised: 04/19/2011] [Accepted: 04/21/2011] [Indexed: 11/22/2022]
Abstract
In this work, a novel fluorescence biosensor was demonstrated for detection of Hg(2+) ions with relatively high selectivity and sensitivity. The sensing scheme was based on G-quenching induced by Hg(2+) ions. In the presence of Hg(2+) ions, the single-stranded signal probe which has carboxylfluorescein (FAM) and guanine segment at its 5' and 3' ends, respectively, folded into duplex-like structure via the Hg(2+)-mediated coordination of T-Hg(2+)-T base pairs. It brought guannine segment close to the dye and caused a remarkable decrease of fluorescence signal. The sensor showed a sensitive response to Hg(2+) ions in a concentration range from 0.5 to 10 μM, and a detection limit of 0.5 nM was given. This homogeneous system required only a single-labeled oligonucleotide, operated by concise procedures, and possessed comparable sensitivity as previous approaches. Furthermore, the sensor exhibits a great perspective for future practical applications.
Collapse
|
15
|
Xie Y, Maxson T, Tor Y. Fluorescent nucleoside analogue displays enhanced emission upon pairing with guanine. Org Biomol Chem 2010; 8:5053-5. [PMID: 20862439 PMCID: PMC3032630 DOI: 10.1039/c0ob00413h] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A fluorescent nucleobase analogue, 7-aminoquinazoline-2,4-(1H,3H)-dione, is incorporated into a DNA oligonucleotide and senses mismatched pairing by displaying G-specific fluorescence enhancement.
Collapse
Affiliation(s)
- Yun Xie
- Department of Chemistry and Biochemistry, University of California, San
Diego, La Jolla, CA, 92093-0358, USA. ; Fax:
+1 858 534 0202; Tel: +1 858 534 6401
| | - Tucker Maxson
- Department of Chemistry and Biochemistry, University of California, San
Diego, La Jolla, CA, 92093-0358, USA. ; Fax:
+1 858 534 0202; Tel: +1 858 534 6401
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San
Diego, La Jolla, CA, 92093-0358, USA. ; Fax:
+1 858 534 0202; Tel: +1 858 534 6401
| |
Collapse
|
16
|
Singly and doubly labeled base-discriminating fluorescent oligonucleotide probes containing oxo-pyrene chromophore. Bioorg Med Chem Lett 2010; 20:3227-30. [DOI: 10.1016/j.bmcl.2010.04.063] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2010] [Revised: 04/13/2010] [Accepted: 04/16/2010] [Indexed: 12/13/2022]
|
17
|
Matsumoto K, Shinohara Y, Bag SS, Takeuchi Y, Morii T, Saito Y, Saito I. Pyrene-labeled deoxyguanosine as a fluorescence sensor to discriminate single and double stranded DNA structures: Design of ends free molecular beacons. Bioorg Med Chem Lett 2009; 19:6392-5. [DOI: 10.1016/j.bmcl.2009.09.060] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2009] [Revised: 09/11/2009] [Accepted: 09/16/2009] [Indexed: 01/04/2023]
|
18
|
Choi MS, Yoon M, Baeg JO, Kim J. Label-free dual assay of DNA sequences and potassium ions using an aptamer probe and a molecular light switch complex. Chem Commun (Camb) 2009:7419-21. [PMID: 20024248 DOI: 10.1039/b915994k] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A homogeneous assay is reported using Ru(phen)(2)(dppz)(2+) and a K(+)-binding aptamer for the selective and sensitive detection of a target oligonucleotide and potassium ions, based on reduction in fluorescence emission according to the formation of the G-quadruplex structure from the aptamer in the presence of K(+).
Collapse
Affiliation(s)
- Min Sun Choi
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 120-750, Korea
| | | | | | | |
Collapse
|
19
|
Lee IJ, Yi JW, Kim BH. Probe for i-motif structure and G-rich strands using end-stacking ability. Chem Commun (Camb) 2009:5383-5. [PMID: 19724792 DOI: 10.1039/b908624b] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We suggest a novel method for probing human i-motif structure based on a pi-stacking interaction between a base pair of two cytosines and a non-polar aromatic fluorophore, PyA, at the end position.
Collapse
Affiliation(s)
- Il Joon Lee
- Department of Chemistry, BK School of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, South Korea
| | | | | |
Collapse
|
20
|
|
21
|
Ends free and self-quenched molecular beacon with pyrene labeled pyrrolocytidine in the middle of the stem. Tetrahedron 2009. [DOI: 10.1016/j.tet.2008.10.093] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
22
|
Seo YJ, Lee IJ, Kim BH. Detection of structure-switching in G-quadruplexes using end-stacking ability. Bioorg Med Chem Lett 2008; 18:3910-3. [PMID: 18585032 DOI: 10.1016/j.bmcl.2008.06.033] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2008] [Revised: 06/04/2008] [Accepted: 06/11/2008] [Indexed: 10/21/2022]
Abstract
G-quadruplex-forming ODNs containing nonpolar aromatic fluorophore moiety, A(PY) at the dangling ends undergo pi-stacking on surface of G-quadruplex, and the fluorescence change can be used to distinguish the structure-switching between the mixed parallel/antiparallel structure and antiparallel structure.
Collapse
Affiliation(s)
- Young Jun Seo
- Department of Chemistry, BK School of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea
| | | | | |
Collapse
|
23
|
Srivatsan SG, Weizman H, Tor Y. A highly fluorescent nucleoside analog based on thieno[3,4-d]pyrimidine senses mismatched pairing. Org Biomol Chem 2008; 6:1334-8. [PMID: 18385838 PMCID: PMC5263222 DOI: 10.1039/b801054d] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A highly emissive nucleobase analog, based on a thieno[3,4-d]pyrimidine core, is enzymatically incorporated into RNA oilgonucleotides that function as base discriminating fluorescent probes.
Collapse
Affiliation(s)
- Seergazhi G Srivatsan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0358, USA
| | | | | |
Collapse
|