1
|
Zhang Y, Ji Z, Wang X, Cao Y, Pan H. Single-Molecule Study of DNAzyme Reveals Its Intrinsic Conformational Dynamics. Int J Mol Sci 2023; 24:ijms24021212. [PMID: 36674728 PMCID: PMC9864658 DOI: 10.3390/ijms24021212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 01/11/2023] Open
Abstract
DNAzyme is a class of DNA molecules that can perform catalytic functions with high selectivity towards specific metal ions. Due to its potential applications for biosensors and medical therapeutics, DNAzyme has been extensively studied to characterize the relationships between its biochemical properties and functions. Similar to protein enzymes and ribozymes, DNAzymes have been found to undergo conformational changes in a metal-ion-dependent manner for catalysis. Despite the important role the conformation plays in the catalysis process, such structural and dynamic information might not be revealed by conventional approaches. Here, by using the single-molecule fluorescence resonance energy transfer (smFRET) technique, we were able to investigate the detailed conformational dynamics of a uranyl-specific DNAzyme 39E. We observed conformation switches of 39E to a folded state with the addition of Mg2+ and to an extended state with the addition of UO22+. Furthermore, 39E can switch to a more compact configuration with or without divalent metal ions. Our findings reveal that 39E can undergo conformational changes spontaneously between different configurations.
Collapse
Affiliation(s)
- Yiming Zhang
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, China
- Wenzhou–Kean University, Wenzhou 325060, China
| | - Zongzhou Ji
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, China
- Northeastern University, Shenyang 110819, China
| | - Xin Wang
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, China
| | - Yi Cao
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, China
- Jinan Microecological Biomedicine Shandong Laboratory, Shounuo City Light West Block, Qingdao Road 3716#, Huaiyin District, Jinan 250117, China
- National Laboratory of Solid–State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
| | - Hai Pan
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, China
- Correspondence:
| |
Collapse
|
2
|
Ultrasenstive SERS biosensor based on Zn 2+ from ZnO nanoparticle assisted DNA enzyme amplification for detection of miRNA. Anal Chim Acta 2022; 1228:340340. [PMID: 36127003 DOI: 10.1016/j.aca.2022.340340] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 08/13/2022] [Accepted: 08/31/2022] [Indexed: 11/23/2022]
Abstract
In this work, a simple and sensitive SERS biosensor was proposed for ultrasensitive detecting miRNA 122 based on ZnO nanoparticle amplification strategy and the full utilization of DNA chain. Firstly, ZnO@S1/S2 and CoFe2O4@S3 complexes can flock together with the assistance of target miRNA. Accompanied with the incremental amount of miRNA, the quantity of ZnO@S1/S2 would increase. Therefore, a significant amplification capability can be obtained by converting ZnO complexes into Zn2+ with the assistance of HCl. In this case, the DNA chain S2 can be obtained by the ZnO dissolving. In addition, through a clever design, the obtained Zn2+ can be further utilized to induce DNA enzyme cycle amplification to cleave S5 into DNA chain which was similar with DNA S2. This step greatly avoided the waste of DNA chains and improved the utilization efficiency of DNA chains. The S2 and abundant S2 analogues can complement with S4 on the Raman sensing interface to imbed lots of Raman probe DOX for obtaining strong Raman signal. By this way, with the increased number of miRNA, the S2 and abundant S2 analogues would increase, so the amount of DOX would increase to produce strong Raman signal to quantitatively detect target miRNA. As a result, this SERS biosensor based on Zn+ amplification and high utilization efficiency of DNA chain can obtain a low detection limit of 6.82 aM and wide linear range from 10 aM to 10 pM, which shown great potential in the clinical application and medical diagnosis.
Collapse
|
3
|
Abstract
This article provides a comprehensive review of biosensing with DNAzymes, providing an overview of different sensing applications while highlighting major progress and seminal contributions to the field of portable biosensor devices and point-of-care diagnostics. Specifically, the field of functional nucleic acids is introduced, with a specific focus on DNAzymes. The incorporation of DNAzymes into bioassays is then described, followed by a detailed overview of recent advances in the development of in vivo sensing platforms and portable sensors incorporating DNAzymes for molecular recognition. Finally, a critical perspective on the field, and a summary of where DNAzyme-based devices may make the biggest impact are provided.
Collapse
Affiliation(s)
- Erin M McConnell
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada.
| | | | | | | | | | | |
Collapse
|
4
|
Almarhoon Z, Al Rasheed HH, El-Faham A. Ultrasonically Assisted N-Cyanoacylation and Synthesis of Alkyl(4-(3-cyano-4,6-dimethyl-2-oxopyridin-1(2 H)-yl)benzoyl)amino Acid Ester Derivatives. ACS OMEGA 2020; 5:30671-30678. [PMID: 33283115 PMCID: PMC7711942 DOI: 10.1021/acsomega.0c04730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 11/04/2020] [Indexed: 06/12/2023]
Abstract
This work represents the use of N-3-(3,5-dimethyl-1H-pyrazol-1-yl)-3-oxopropanenitrile as a cyanoacetylating agent for the synthesis of cyanoacetamide benzoic acid and benzophenone derivatives by two different methods, namely, conventional heating and ultrasonication. The cyanoacetamide derivatives were subjected to cyclization to produce N-substituted 2-pyridone derivatives under conventional heating and by an ultrasonic method as well. The ultrasonic method afforded the products in less reaction time with high yields and purities compared to the conventional method, as observed from their spectral data. N-(4-Carboxy phenyl)-4,6-dimethyl-3-cyano-2-pyridone was coupled with different amino acid esters by the OxymaPure/DIC methodology under traditional and ultrasonic conditions. Again, ultrasonication assisted the coupling step and afforded the products with higher yields and purities compared to the traditional method. Fourier transform infrared spectroscopy, NMR (1H and 13C), elemental analysis, and LC-MS were used to determine the structures of all compounds. Finally, a feature of this protocol is exploring the utilization of ultrasonication as an eco-friendly alternative conventional heating method for N-cyanoacylation and synthesis of N-substituted pyridinone derivatives and as a coupling method for the formation of an amide bond, which might be of interest for many researchers.
Collapse
Affiliation(s)
- Zainab Almarhoon
- Department
of Chemistry, College of Science, King Saud
University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Hessa H. Al Rasheed
- Department
of Chemistry, College of Science, King Saud
University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Ayman El-Faham
- Department
of Chemistry, College of Science, King Saud
University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
- Chemistry
Department, Faculty of Science, Alexandria
University, P.O. Box 426, Ibrahimia 12321, Alexandria, Egypt
| |
Collapse
|
5
|
Feng XN, Cui YX, Zhang J, Tang AN, Mao HB, Kong DM. Chiral Interaction Is a Decisive Factor To Replace d-DNA with l-DNA Aptamers. Anal Chem 2020; 92:6470-6477. [PMID: 32249564 DOI: 10.1021/acs.analchem.9b05676] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Nucleic acid aptamers have been widely used in various fields such as biosensing, DNA chip, and medical diagnosis. However, the high susceptibility of nucleic acids to ubiquitous nucleases reduces the biostability of aptamers and limits their applications in biological contexts. Therefore, improving the biostability of aptamers becomes an urgent need. Herein, we present a simple strategy to resolve this problem by directly replacing the d-DNA-based aptamers with left-handed l-DNA. By testing several reported aptamers against respective targets, we found that our proposed strategy stood up well for nonchiral small molecule targets (e.g., Hemin and cationic porphyrin) and chiral targets whose interactions with aptamers are chirality-independent (e.g., ATP). We also found that the l-DNA aptamers were indeed endowed with greatly improved biostability due to the extraordinary resistance of l-DNA to nuclease digestion. With respect to other small-molecule targets whose interactions with aptamers are chirality-dependent (e.g., kanamycin) and biomacromolecules (e.g., tyrosine kinase-7), however, the proposed strategy was not entirely effective likely due to the participation of the DNA backbone chirality into the target recognition. In spite of this limitation, this strategy indeed paves an easy way to screen highly biostable aptamers important for the applications in many fields.
Collapse
Affiliation(s)
- Xue-Nan Feng
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Yun-Xi Cui
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Jing Zhang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - An-Na Tang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Han-Bin Mao
- Department of Chemistry & Biochemistry, Kent State University, Kent, Ohio 44242, United States
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| |
Collapse
|
6
|
Zou S, Lei Y, Ma W, Chen B, Cheng H, Jia R, Li Z, He X, Wang K. Extracellular pH-manipulated in situ reconfiguration of aptamer functionalized DNA monomer enables specifically improved affinity, detection and drug delivery. Analyst 2020; 145:2562-2569. [PMID: 32167102 DOI: 10.1039/d0an00101e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Aptamers are promising in cancer diagnosis and therapy, but their poor affinity under physiological conditions is a challenge. In view of the acidic microenvironment of solid tumors, we herein developed an extracellular pH-manipulated multivalent approach to exclusively improve the affinity to target cells at physiological temperature. Specifically, an aptamer based DNA monomer (AptDM) with split i-motif fragments overhanging was rationally designed, it possessed pH-responsiveness and doxorubicin loading capacity. At neutral pH, AptDMs existed as well dispersed small units, showing weakly undesired binding and internalization. In acidic extracellular conditions, AptDMs tended to crosslink of each other into multivalent DNA assemblies (MDAs) via formation of an intermolecular i-motif structure. Due to the multivalent effect, the resulting MDAs showed greatly enhanced affinity (Kd = 9.96 ± 1.06 nM) and stable binding ability at 37 °C, thus allowing highly sensitive diagnosis, efficient drug delivery, and improved inhibition to target tumor cells, but decreased cytotoxicity to nontarget cells. It is believed that this multivalent approach may boost the development of novel aptamer functionalized nanodevices for clinical validation.
Collapse
Affiliation(s)
- Shanzi Zou
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, China.
| | | | | | | | | | | | | | | | | |
Collapse
|
7
|
Pan J, Li Q, Zhou D, Chen J. Label-free and highly sensitive fluorescence detection of lead(ii) based on DNAzyme and exonuclease III-assisted cascade signal amplification. NEW J CHEM 2019. [DOI: 10.1039/c8nj06522e] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A Pb2+ biosensor has been constructed based on Exo III-assisted cascade signal amplification using 2-amino-5,6,7-trimethyl-1,8-naphthyridine as the signal indicator.
Collapse
Affiliation(s)
- Jiafeng Pan
- Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management
- Guangdong Institute of Eco-Environmental Science & Technology
- Guangzhou 510650
- China
| | - Qiong Li
- Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management
- Guangdong Institute of Eco-Environmental Science & Technology
- Guangzhou 510650
- China
- College of Bioscience and Biotechnology
| | - Danhua Zhou
- Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management
- Guangdong Institute of Eco-Environmental Science & Technology
- Guangzhou 510650
- China
- College of Natural Resources and Environment
| | - Junhua Chen
- Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management
- Guangdong Institute of Eco-Environmental Science & Technology
- Guangzhou 510650
- China
| |
Collapse
|
8
|
Mueh M, Maasch M, Knieb RA, Goringer HU, Damm C. Detection of African Trypanosomes Using Asymmetric Double-Split Ring Based THz Sensors. ACTA ACUST UNITED AC 2017. [DOI: 10.1109/jerm.2017.2771152] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
9
|
Saran R, Kleinke K, Zhou W, Yu T, Liu J. A Silver-Specific DNAzyme with a New Silver Aptamer and Salt-Promoted Activity. Biochemistry 2017; 56:1955-1962. [PMID: 28345892 DOI: 10.1021/acs.biochem.6b01131] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Most RNA-cleaving DNAzymes require a metal ion to interact with the scissile phosphate for activity. Therefore, few unmodified DNAzymes work with thiophilic metals because of their low affinity for phosphate. Recently, an Ag+-specific Ag10c DNAzyme was reported via in vitro selection. Herein, Ag10c is characterized to rationalize the role of the strongly thiophilic Ag+. Systematic mutation studies indicate that Ag10c is a highly conserved DNAzyme and its Ag+ binding is unrelated to C-Ag+-C interaction. Its activity is enhanced by increasing Na+ concentrations in buffer. At the same metal concentration, activity decreases in the following order: Li+ > Na+ > K+. Ag10c binds one Na+ ion and two Ag+ ions for catalysis. The pH-rate profile has a slope of ∼1, indicating a single deprotonation step. Phosphorothioate substitution at the scissile phosphate suggests that Na+ interacts with the pro-Rp oxygen of the phosphate, and dimethyl sulfate footprinting indicates that the DNAzyme loop is a silver aptamer binding two Ag+ ions. Therefore, Ag+ exerts its function allosterically, while the scissile phosphate interacts with Na+, Li+, Na+, or Mg2+. This work suggests the possibility of isolating thiophilic metal aptamers based on DNAzyme selection, and it also demonstrates a new Ag+ aptamer.
Collapse
Affiliation(s)
- Runjhun Saran
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
| | - Kimberly Kleinke
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
| | - Wenhu Zhou
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
| | - Tianmeng Yu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
| |
Collapse
|
10
|
Banerji B, Chandrasekhar K, Killi SK, Pramanik SK, Uttam P, Sen S, Maiti NC. Silver-catalysed azide-alkyne cycloaddition (AgAAC): assessing the mechanism by density functional theory calculations. ROYAL SOCIETY OPEN SCIENCE 2016; 3:160090. [PMID: 27703683 PMCID: PMC5043300 DOI: 10.1098/rsos.160090] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 07/18/2016] [Indexed: 05/04/2023]
Abstract
'Click reactions' are the copper catalysed dipolar cycloaddition reaction of azides and alkynes to incorporate nitrogens into a cyclic hydrocarbon scaffold forming a triazole ring. Owing to its efficiency and versatility, this reaction and the products, triazole-containing heterocycles, have immense importance in medicinal chemistry. Copper is the only known catalyst to carry out this reaction, the mechanism of which remains unclear. We report here that the 'click reactions' can also be catalysed by silver halides in non-aqueous medium. It constitutes an alternative to the well-known CuAAC click reaction. The yield of the reaction varies on the type of counter ion present in the silver salt. This reaction exhibits significant features, such as high regioselectivity, mild reaction conditions, easy availability of substrates and reasonably good yields. In this communication, the findings of a new catalyst along with the effect of solvent and counter ions will help to decipher the still obscure mechanism of this important reaction.
Collapse
Affiliation(s)
- Biswadip Banerji
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology; 4, Raja S.C. Mullick Road, Kolkata, India
- Academy of Scientific and Innovative Research, CSIR-Indian Institute of Chemical Biology; 4, Raja S.C. Mullick Road, Kolkata, India
- Author for correspondence: Biswadip Banerji e-mail:
| | - K. Chandrasekhar
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology; 4, Raja S.C. Mullick Road, Kolkata, India
| | - Sunil Kumar Killi
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology; 4, Raja S.C. Mullick Road, Kolkata, India
| | - Sumit Kumar Pramanik
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology; 4, Raja S.C. Mullick Road, Kolkata, India
| | - Pal Uttam
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology; 4, Raja S.C. Mullick Road, Kolkata, India
| | - Sudeshna Sen
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology; 4, Raja S.C. Mullick Road, Kolkata, India
| | - Nakul Chandra Maiti
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology; 4, Raja S.C. Mullick Road, Kolkata, India
| |
Collapse
|
11
|
Cui L, Peng R, Fu T, Zhang X, Wu C, Chen H, Liang H, Yang C, Tan W. Biostable L-DNAzyme for Sensing of Metal Ions in Biological Systems. Anal Chem 2016; 88:1850-5. [PMID: 26691677 PMCID: PMC4892185 DOI: 10.1021/acs.analchem.5b04170] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 12/22/2015] [Indexed: 12/13/2022]
Abstract
DNAzymes, an important type of metal ion-dependent functional nucleic acid, are widely applied in bioanalysis and biomedicine. However, the use of DNAzymes in practical applications has been impeded by the intrinsic drawbacks of natural nucleic acids, such as interferences from nuclease digestion and protein binding, as well as undesired intermolecular interactions with other nucleic acids. On the basis of reciprocal chiral substrate specificity, the enantiomer of D-DNAzyme, L-DNAzyme, could initiate catalytic cleavage activity with the same achiral metal ion as a cofactor. Meanwhile, by using the advantage of nonbiological L-DNAzyme, which is not subject to the interferences of biological matrixes, as recognition units, a facile and stable L-DNAzyme sensor was proposed for sensing metal ions in complex biological samples and live cells.
Collapse
Affiliation(s)
- Liang Cui
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio
Sensing and Chemometrics, College of Chemistry and Chemical Engineering,
College of Biology, and Collaborative Research Center of Molecular
Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Ruizi Peng
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio
Sensing and Chemometrics, College of Chemistry and Chemical Engineering,
College of Biology, and Collaborative Research Center of Molecular
Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Ting Fu
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio
Sensing and Chemometrics, College of Chemistry and Chemical Engineering,
College of Biology, and Collaborative Research Center of Molecular
Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Xiaobing Zhang
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio
Sensing and Chemometrics, College of Chemistry and Chemical Engineering,
College of Biology, and Collaborative Research Center of Molecular
Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Cuichen Wu
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio
Sensing and Chemometrics, College of Chemistry and Chemical Engineering,
College of Biology, and Collaborative Research Center of Molecular
Engineering for Theranostics, Hunan University, Changsha 410082, China
- Department
of Chemistry and Department of Physiology and Functional Genomics,
Center for Research at the Bio/Nano Interface, Health Cancer Center, University
of Florida, Gainesville, Florida 32611-7200, United States
| | - Huapei Chen
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio
Sensing and Chemometrics, College of Chemistry and Chemical Engineering,
College of Biology, and Collaborative Research Center of Molecular
Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Hao Liang
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio
Sensing and Chemometrics, College of Chemistry and Chemical Engineering,
College of Biology, and Collaborative Research Center of Molecular
Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Chaoyong
James Yang
- State
Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory
for Chemical Biology of Fujian Province, The MOE Key Laboratory of
Spectrochemical Analysis & Instrumentation, Department of Chemical
Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Weihong Tan
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio
Sensing and Chemometrics, College of Chemistry and Chemical Engineering,
College of Biology, and Collaborative Research Center of Molecular
Engineering for Theranostics, Hunan University, Changsha 410082, China
- Department
of Chemistry and Department of Physiology and Functional Genomics,
Center for Research at the Bio/Nano Interface, Health Cancer Center, University
of Florida, Gainesville, Florida 32611-7200, United States
| |
Collapse
|
12
|
Wu P, Yu Y, McGhee CE, Tan LH, Lu Y. Applications of synchrotron-based spectroscopic techniques in studying nucleic acids and nucleic acid-functionalized nanomaterials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2014; 26:7849-72. [PMID: 25205057 PMCID: PMC4275547 DOI: 10.1002/adma.201304891] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 06/02/2014] [Indexed: 05/22/2023]
Abstract
In this review, we summarize recent progress in the application of synchrotron-based spectroscopic techniques for nucleic acid research that takes advantage of high-flux and high-brilliance electromagnetic radiation from synchrotron sources. The first section of the review focuses on the characterization of the structure and folding processes of nucleic acids using different types of synchrotron-based spectroscopies, such as X-ray absorption spectroscopy, X-ray emission spectroscopy, X-ray photoelectron spectroscopy, synchrotron radiation circular dichroism, X-ray footprinting and small-angle X-ray scattering. In the second section, the characterization of nucleic acid-based nanostructures, nucleic acid-functionalized nanomaterials and nucleic acid-lipid interactions using these spectroscopic techniques is summarized. Insights gained from these studies are described and future directions of this field are also discussed.
Collapse
Affiliation(s)
- Peiwen Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yang Yu
- Center of Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Claire E. McGhee
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Li Huey Tan
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yi Lu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Center of Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| |
Collapse
|
13
|
James C, Rush AM, Insley T, Vuković L, Adamiak L, Král P, Gianneschi NC. Poly(oligonucleotide). J Am Chem Soc 2014; 136:11216-9. [PMID: 25077676 PMCID: PMC4140503 DOI: 10.1021/ja503142s] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Indexed: 01/01/2023]
Abstract
Here we report the preparation of poly(oligonucleotide) brush polymers and amphiphilic brush copolymers from nucleic acid monomers via graft-through polymerization. We describe the polymerization of PNA-norbornyl monomers to yield poly-PNA (poly(peptide nucleic acid)) via ring-opening metathesis polymerization (ROMP) with the initiator, (IMesH2)(C5H5N)2(Cl)2RuCHPh.1 In addition, we present the preparation of poly-PNA nanoparticles from amphiphilic block copolymers and describe their hybridization to a complementary single-stranded DNA (ssDNA) oligonucleotide.
Collapse
Affiliation(s)
- Carrie
R. James
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| | - Anthony M. Rush
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| | - Thomas Insley
- Department of Chemistry, Department of Physics University
of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Lela Vuković
- Department of Chemistry, Department of Physics University
of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Lisa Adamiak
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| | - Petr Král
- Department of Chemistry, Department of Physics University
of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Nathan C. Gianneschi
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| |
Collapse
|
14
|
Tang S, Lu W, Gu F, Tong P, Yan Z, Zhang L. A novel electrochemical sensor for lead ion based on cascade DNA and quantum dots amplification. Electrochim Acta 2014. [DOI: 10.1016/j.electacta.2014.04.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
|
15
|
Lee JW, Cho JH, Cho EJ. Aptamer-based optical switch for biosensors. ANALYTICAL SCIENCE AND TECHNOLOGY 2014. [DOI: 10.5806/ast.2014.27.3.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
16
|
Abstract
![]()
The successes of electronic digital logic have transformed every
aspect of human life over the last half-century. The word “computer”
now signifies a ubiquitous electronic device, rather than a human
occupation. Yet evidently humans, large assemblies of molecules, can
compute, and it has been a thrilling challenge to develop smaller,
simpler, synthetic assemblies of molecules that can do useful computation.
When we say that molecules compute, what we usually mean is that such
molecules respond to certain inputs, for example, the presence or
absence of other molecules, in a precisely defined but potentially
complex fashion. The simplest way for a chemist to think about computing
molecules is as sensors that can integrate the presence or absence
of multiple analytes into a change in a single reporting property.
Here we review several forms of molecular computing developed in our
laboratories. When we began our work, combinatorial approaches
to using DNA for
computing were used to search for solutions to constraint satisfaction
problems. We chose to work instead on logic circuits, building bottom-up
from units based on catalytic nucleic acids, focusing on DNA secondary
structures in the design of individual circuit elements, and reserving
the combinatorial opportunities of DNA for the representation of multiple
signals propagating in a large circuit. Such circuit design directly
corresponds to the intuition about sensors transforming the detection
of analytes into reporting properties. While this approach was unusual
at the time, it has been adopted since by other groups working on
biomolecular computing with different nucleic acid chemistries. We created logic gates by modularly combining deoxyribozymes (DNA-based
enzymes cleaving or combining other oligonucleotides), in the role
of reporting elements, with stem–loops as input detection elements.
For instance, a deoxyribozyme that normally exhibits an oligonucleotide
substrate recognition region is modified such that a stem–loop
closes onto the substrate recognition region, making it unavailable
for the substrate and thus rendering the deoxyribozyme inactive. But
a conformational change can then be induced by an input oligonucleotide,
complementary to the loop, to open the stem, allow the substrate to
bind, and allow its cleavage to proceed, which is eventually reported
via fluorescence. In this Account, several designs of this form are
reviewed, along with their application in the construction of large
circuits that exhibited complex logical and temporal relationships
between the inputs and the outputs. Intelligent (in the sense
of being capable of nontrivial information
processing) theranostic (therapy + diagnostic) applications have always
been the ultimate motivation for developing computing (i.e., decision-making)
circuits, and we review our experiments with logic-gate elements bound
to cell surfaces that evaluate the proximal presence of multiple markers
on lymphocytes.
Collapse
Affiliation(s)
- Milan N. Stojanovic
- Departments
of Medicine, Biomedical Engineering, and Systems Biology, Columbia University, New York, New York 10032, United States
| | - Darko Stefanovic
- Department
of Computer Science and Center for Biomedical Engineering, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Sergei Rudchenko
- Hospital for Special Surgery, New York, New York 10021, United States
| |
Collapse
|
17
|
Tan LH, Xing H, Lu Y. DNA as a powerful tool for morphology control, spatial positioning, and dynamic assembly of nanoparticles. Acc Chem Res 2014; 47:1881-90. [PMID: 24871359 PMCID: PMC4066914 DOI: 10.1021/ar500081k] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
Several properties of nanomaterials, such as
morphologies (e.g.,
shapes and surface structures) and distance dependent properties (e.g.,
plasmonic and quantum confinement effects), make nanomaterials uniquely
qualified as potential choices for future applications from catalysis
to biomedicine. To realize the full potential of these nanomaterials,
it is important to demonstrate fine control of the morphology of individual
nanoparticles, as well as precise spatial control of the position,
orientation, and distances between multiple nanoparticles. In addition,
dynamic control of nanomaterial assembly in response to multiple stimuli,
with minimal or no error, and the reversibility of the assemblies
are also required. In this Account, we summarize recent progress of
using DNA as a powerful programmable tool to realize the above goals.
First, inspired by the discovery of genetic codes in biology, we have
discovered DNA sequence combinations to control different morphologies
of nanoparticles during their growth process and have shown that these
effects are synergistic or competitive, depending on the sequence
combination. The DNA, which guides the growth of the nanomaterial,
is stable and retains its biorecognition ability. Second, by taking
advantage of different reactivities of phosphorothioate and phosphodiester
backbone, we have placed phosphorothioate at selective positions on
different DNA nanostructures including DNA tetrahedrons. Bifunctional
linkers have been used to conjugate phosphorothioate on one end and
bind nanoparticles or proteins on the other end. In doing so, precise
control of distances between two or more nanoparticles or proteins
with nanometer resolution can be achieved. Furthermore, by developing
facile methods to functionalize two hemispheres of Janus nanoparticles
with two different DNA sequences regioselectively, we have demonstrated
directional control of nanomaterial assembly, where DNA strands with
specific hybridization serve as orthogonal linkers. Third, by using
functional DNA that includes DNAzyme, aptamer, and aptazyme, dynamic
control of assemblies of gold nanoparticles, quantum dots, carbon
nanotubes, and iron oxide nanoparticles in response to one or more
stimuli cooperatively have been achieved, resulting in colorimetric,
fluorescent, electrochemical, and magnetic resonance signals for a
wide range of targets, such as metal ions, small molecules, proteins,
and intact cells. Fourth, by mimicking biology, we have employed DNAzymes
as proofreading units to remove errors in nanoparticle assembly and
further used DNAzyme cascade reactions to modify or repair DNA sequences
involved in the assembly. Finally, by taking advantage of different
affinities of biotin and desthiobiotin toward streptavidin, we have
demonstrated reversible assembly of proteins on DNA origami.
Collapse
Affiliation(s)
- Li Huey Tan
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Hang Xing
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| |
Collapse
|
18
|
Sett A, Das S, Bora U. Functional nucleic-acid-based sensors for environmental monitoring. Appl Biochem Biotechnol 2014; 174:1073-91. [PMID: 24903959 DOI: 10.1007/s12010-014-0990-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 05/19/2014] [Indexed: 01/16/2023]
Abstract
Efforts to replace conventional chromatographic methods for environmental monitoring with cheaper and easy to use biosensors for precise detection and estimation of hazardous environmental toxicants, water or air borne pathogens as well as various other chemicals and biologics are gaining momentum. Out of the various types of biosensors classified according to their bio-recognition principle, nucleic-acid-based sensors have shown high potential in terms of cost, sensitivity, and specificity. The discovery of catalytic activities of RNA (ribozymes) and DNA (DNAzymes) which could be triggered by divalent metallic ions paved the way for their extensive use in detection of heavy metal contaminants in environment. This was followed with the invention of small oligonucleotide sequences called aptamers which can fold into specific 3D conformation under suitable conditions after binding to target molecules. Due to their high affinity, specificity, reusability, stability, and non-immunogenicity to vast array of targets like small and macromolecules from organic, inorganic, and biological origin, they can often be exploited as sensors in industrial waste management, pollution control, and environmental toxicology. Further, rational combination of the catalytic activity of DNAzymes and RNAzymes along with the sequence-specific binding ability of aptamers have given rise to the most advanced form of functional nucleic-acid-based sensors called aptazymes. Functional nucleic-acid-based sensors (FNASs) can be conjugated with fluorescent molecules, metallic nanoparticles, or quantum dots to aid in rapid detection of a variety of target molecules by target-induced structure switch (TISS) mode. Although intensive research is being carried out for further improvements of FNAs as sensors, challenges remain in integrating such bio-recognition element with advanced transduction platform to enable its use as a networked analytical system for tailor made analysis of environmental monitoring.
Collapse
Affiliation(s)
- Arghya Sett
- Bioengineering Research Laboratory, Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | | | | |
Collapse
|
19
|
Romero-López C, Díaz-González R, Berzal-Herranz A. RNA Selection and EvolutionIn Vitro:Powerful Techniques for the Analysis and Identification of new Molecular Tools. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.1080/13102818.2007.10817461] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
|
20
|
Detection of lead(II) ions with a DNAzyme and isothermal strand displacement signal amplification. Biosens Bioelectron 2014; 53:245-9. [DOI: 10.1016/j.bios.2013.09.055] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Revised: 09/23/2013] [Accepted: 09/24/2013] [Indexed: 11/20/2022]
|
21
|
Comparison of nuclease activities of redox active and inactive binuclear mixed-polypyridyl complexes: zinc(II)/H2O2 and cadmium(II)/H2O2 systems display efficient nuclease activities. TRANSIT METAL CHEM 2014. [DOI: 10.1007/s11243-014-9803-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
22
|
Xu L, Yin H, Ma W, Wang L, Kuang H, Xu C. MRI Biosensor for Lead Detection Based on the DNAzyme-Induced Catalytic Reaction. J Phys Chem B 2013; 117:14367-71. [DOI: 10.1021/jp4087656] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Liguang Xu
- State Key Lab of Food Science and Technology,
School of Food Science and Technology, Jiangnan University, Wuxi, JiangSu 214122, People’s Republic of China
| | - Honghong Yin
- State Key Lab of Food Science and Technology,
School of Food Science and Technology, Jiangnan University, Wuxi, JiangSu 214122, People’s Republic of China
| | - Wei Ma
- State Key Lab of Food Science and Technology,
School of Food Science and Technology, Jiangnan University, Wuxi, JiangSu 214122, People’s Republic of China
| | - Libing Wang
- State Key Lab of Food Science and Technology,
School of Food Science and Technology, Jiangnan University, Wuxi, JiangSu 214122, People’s Republic of China
| | - Hua Kuang
- State Key Lab of Food Science and Technology,
School of Food Science and Technology, Jiangnan University, Wuxi, JiangSu 214122, People’s Republic of China
| | - Chuanlai Xu
- State Key Lab of Food Science and Technology,
School of Food Science and Technology, Jiangnan University, Wuxi, JiangSu 214122, People’s Republic of China
| |
Collapse
|
23
|
Huang Fu ZZ, Hao LJ, Wu YM, Qiao HY, Yi Z, Li XY, Chu X. Highly sensitive fluorescent immunoassay of human immunoglobulin G based on PbS nanoparticles and DNAzyme. ANAL SCI 2013; 29:499-504. [PMID: 23665621 DOI: 10.2116/analsci.29.499] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This paper reports a highly sensitive fluorescent immunoassay for the detection of human immunoglobulin G based on PbS nanoparticles and DNAzyme. A sandwich immunoassay format was performed on a microtiter plate. Goat anti-human IgG was coated onto the polystyrene microtiter plate. The human IgG analyte was first captured by the goat anti-human IgG, and then sandwiched by a goat anti-human IgG antibody labeled with PbS nanoparticles. After being dissolved with HNO3, the released Pb(2+) made the substrate chain of the DNAzyme labeled with the fluorophore dissociate from the enzyme strand of the DNAzyme labeled with the quencher, which resulted in fluorescence recovery. Then, the human IgG could be detected indirectly from the fluorescent signals. Under the optimized conditions, the linear range of the developed immunosensor was from 1 ng mL(-1) to 10 μg mL(-1) with a detection limit of 0.8 ng mL(-1). This immunosensor could be used to detect the amount of human IgG in human serum samples.
Collapse
Affiliation(s)
- Zhen-Zhen Huang Fu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P.R. China
| | | | | | | | | | | | | |
Collapse
|
24
|
Gu H, Furukawa K, Weinberg Z, Berenson DF, Breaker RR. Small, highly active DNAs that hydrolyze DNA. J Am Chem Soc 2013; 135:9121-9. [PMID: 23679108 PMCID: PMC3763483 DOI: 10.1021/ja403585e] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
DNA phosphoester bonds are exceedingly resistant to hydrolysis in the absence of chemical or enzymatic catalysts. This property is particularly important for organisms with large genomes, as resistance to hydrolytic degradation permits the long-term storage of genetic information. Here we report the creation and analysis of two classes of engineered deoxyribozymes that selectively and rapidly hydrolyze DNA. Members of class I deoxyribozymes carry a catalytic core composed of only 15 conserved nucleotides and attain an observed rate constant (k(obs)) of ~1 min(-1) when incubated near neutral pH in the presence of Zn(2+). Natural DNA sequences conforming to the class I consensus sequence and structure were found that undergo hydrolysis under selection conditions (2 mM Zn(2+), pH 7), which demonstrates that the inherent structure of certain DNA regions might promote catalytic reactions, leading to genomic instability.
Collapse
Affiliation(s)
- Hongzhou Gu
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, 06520 United States
- Howard Hughes Medical Institute, New Haven, Connecticut, 06520 United States
| | - Kazuhiro Furukawa
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, 06520 United States
| | - Zasha Weinberg
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, 06520 United States
- Howard Hughes Medical Institute, New Haven, Connecticut, 06520 United States
| | - Daniel F. Berenson
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, 06520 United States
| | - Ronald R. Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, 06520 United States
- Howard Hughes Medical Institute, New Haven, Connecticut, 06520 United States
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, 06520 United States
| |
Collapse
|
25
|
Yu HZ, Li Y, Ou LML. Reading disc-based bioassays with standard computer drives. Acc Chem Res 2013; 46:258-68. [PMID: 23025412 DOI: 10.1021/ar300104b] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Traditional methods of disease diagnosis are both time-consuming and labor-intensive, and many tests require expensive instrumentation and trained professionals, which restricts their use to biomedical laboratories. Because patients can wait several days (even weeks) for the results, the consequences of delayed treatment could be disastrous. Therefore, affordable and simple point-of-care (POC) biosensor devices could fill a diagnostic niche in the clinic or even at home, as personal glucose meters do for diabetics. These devices would allow patients to check their own health conditions and enable physicians to make prompt treatment decisions, which could improve the chances for rapid recovery and cure. Compact discs (CDs) provide inexpensive substrate materials for the preparation of microarray biochips, and conventional computer drives/disc players can be adapted as precise optical reading devices for signal processing. Researchers can employ the polycarbonate (PC) base of a CD as an alternative substrate to glass slides or silicon wafers for the preparation of microanalytical devices. Using the characteristic optical phenomena occurring on the metal layer of a CD, researchers can develop biosensors based on advanced spectroscopic readout (interferometry or surface plasmon resonance). If researchers integrate microfluidic functions with CD mechanics, they can control fluid transfer through the spinning motion of the disc, leading to "lab-on-a-CD" devices. Over the last decade, our laboratory has focused on the construction of POC biosensor devices from off-the-shelf CDs or DVDs and standard computer drives. Besides the initial studies of the suitability of CDs for surface and materials chemistry research (fabrication of self-assembled monolayers and oxide nanostructures), we have demonstrated that an ordinary optical drive, without modification of either the hardware or the software driver, can function as the signal transducing element for reading disc-based bioassays quantitatively. In this Account, we first provide a brief introduction to CD-related materials chemistry and microfluidics research. Then we describe the mild chemistry developed in our laboratory for the preparation of computer-readable biomolecular screening assays: photochemical activation of the polycarbonate (PC) disc surface and immobilization and delivery of probe and target biomolecules. We thoroughly discuss the analysis of the molecular recognition events: researchers can "read" these devices quantitatively with an unmodified optical drive of any personal computer. Finally, and critically, we illustrate our digitized molecular diagnosis approach with three trial systems: DNA hybridization, antibody-antigen binding, and ultrasensitive lead detection with a DNAzyme assay. These examples demonstrate the broad potential of this new analytical/diagnostic tool for medical screening, on-site food/water safety testing, and remote environmental monitoring.
Collapse
Affiliation(s)
- Hua-Zhong Yu
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Yunchao Li
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
- Department of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Lily M.-L. Ou
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| |
Collapse
|
26
|
Ameta S, Jäschke A. An RNA catalyst that reacts with a mechanistic inhibitor of serine proteases. Chem Sci 2013. [DOI: 10.1039/c2sc21588h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
27
|
Ma DL, Ma VPY, Chan DSH, Leung KH, He HZ, Leung CH. Recent advances in luminescent heavy metal complexes for sensing. Coord Chem Rev 2012. [DOI: 10.1016/j.ccr.2012.07.005] [Citation(s) in RCA: 241] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
28
|
|
29
|
Gu H, Furukawa K, Breaker RR. Engineered allosteric ribozymes that sense the bacterial second messenger cyclic diguanosyl 5'-monophosphate. Anal Chem 2012; 84:4935-41. [PMID: 22519888 DOI: 10.1021/ac300415k] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A series of allosteric ribozymes that respond to the bacterial second messenger cyclic diguanosyl-5'-monophosphate (c-di-GMP) have been created by using in vitro selection. An RNA library was generated by using random-sequence bridges to join a hammerhead self-cleaving ribozyme to an aptamer from a natural c-di-GMP riboswitch. Specific bridge sequences, called communication modules, emerged through two in vitro selection efforts that either activate or inhibit ribozyme self-cleavage upon ligand binding to the aptamer. Representative RNAs were found that exhibit EC(50) (half-maximal effective concentration) values for c-di-GMP as low as 90 nM and IC(50) (half-maximal inhibitory concentration) values as low as 180 nM. The allosteric RNAs display molecular recognition characteristics that mimic the high discriminatory ability of the natural aptamer. Some engineered RNAs operate with ribozyme rate constants approaching that of the parent hammerhead ribozyme. By use of these allosteric ribozymes, cytoplasmic concentrations of c-di-GMP in three mutant strains of Escherichia coli were quantitatively estimated from cell lysates. Our findings demonstrate that engineered c-di-GMP-sensing ribozymes can be used as convenient tools to monitor c-di-GMP levels from complex biological or chemical samples. Moreover, these ribozymes could be employed in high-throughput screens to identify compounds that trigger c-di-GMP riboswitch function.
Collapse
Affiliation(s)
- Hongzhou Gu
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, United States
| | | | | |
Collapse
|
30
|
Liao D, Jiao H, Wang B, Lin Q, Yu C. KF polymerase-based fluorescence aptasensor for the label-free adenosine detection. Analyst 2011; 137:978-82. [PMID: 22183639 DOI: 10.1039/c2an15809d] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We have developed a simple, inexpensive, and label-free method for the selective detection of adenosine. Klenow fragment polymerase (KF polymerase) is a commonly-used 5' to 3' DNA polymerase, it also has 3' to 5' exonuclease activity that can digest single-stranded DNA. An adenosine binding DNA aptamer was employed, the aptamer was split into two pieces of single-stranded DNA (aptamer-A1 + aptamer-A2). Without the addition of adenosine, aptamer-A1 and aptamer-A2 existed as single-stranded DNA which could be efficiently degraded by the exonuclease activity of KF polymerase. Much reduced background fluorescence was obtained when SYBR Green dye was added. However, in the presence of adenosine, aptamer-A1 and aptamer-A2 bound to adenosine, and hybridization of the complementary sequences resulted in the formation of a duplex DNA structure, which could initiate DNA polymerization. The addition of SYBR Green dye resulted in a very high fluorescence enhancement, which could be used for the quantification of adenosine.
Collapse
Affiliation(s)
- Dongli Liao
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, PR China
| | | | | | | | | |
Collapse
|
31
|
Lam CH, Hipolito CJ, Hollenstein M, Perrin DM. A divalent metal-dependent self-cleaving DNAzyme with a tyrosine side chain. Org Biomol Chem 2011; 9:6949-54. [PMID: 21670811 DOI: 10.1039/c1ob05359k] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The enzymatic incorporation of a phenol-modified 2'-deoxyuridine triphosphate gave rise to a modified DNA library that was subsequently used in an in vitro selection for ribophosphodiester-cleaving DNAzymes in the presence of divalent zinc and magnesium cations. After 11 rounds of selection, cloning and sequencing resulted in 14 distinct sequences, the most active of which was Dz11-17PheO. Dz11-17PheO self-cleaved an embedded ribocytidine with an observed rate constant of 0.20 ± 0.02 min(-1) in the presence of 10 mM Mg(2+) and 1 mM Zn(2+) at room temperature. The activity was inhibited at low concentrations of Hg(2+) cations and somewhat higher concentrations of Eu(3+) cations.
Collapse
Affiliation(s)
- Curtis H Lam
- Chemistry Department, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | | | | | | |
Collapse
|
32
|
Tjioe L, Meininger A, Joshi T, Spiccia L, Graham B. Efficient Plasmid DNA Cleavage by Copper(II) Complexes of 1,4,7-Triazacyclononane Ligands Featuring Xylyl-Linked Guanidinium Groups. Inorg Chem 2011; 50:4327-39. [DOI: 10.1021/ic102301n] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Linda Tjioe
- School of Chemistry, Monash University, Clayton, Victoria 3800, Australia
| | - Anja Meininger
- School of Chemistry, Monash University, Clayton, Victoria 3800, Australia
| | - Tanmaya Joshi
- School of Chemistry, Monash University, Clayton, Victoria 3800, Australia
| | - Leone Spiccia
- School of Chemistry, Monash University, Clayton, Victoria 3800, Australia
| | - Bim Graham
- Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| |
Collapse
|
33
|
Ma DL, Chan DSH, Man BYW, Leung CH. Oligonucleotide-based luminescent detection of metal ions. Chem Asian J 2011; 6:986-1003. [PMID: 21337527 DOI: 10.1002/asia.201000870] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Indexed: 01/20/2023]
Abstract
Metal ions are prevalent in biological systems and are critically involved in essential life processes. However, excess concentrations of metals can pose a serious danger to living organisms. Oligonucleotides represent a versatile sensing platform for the detection of various molecular entities including metal ions. This review summarizes the recent advances in the development of oligonucleotide-based luminescent detection methods for metal ions.
Collapse
Affiliation(s)
- Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, China.
| | | | | | | |
Collapse
|
34
|
Wang H, Ou LML, Suo Y, Yu HZ. Computer-Readable DNAzyme Assay on Disc for ppb-Level Lead Detection. Anal Chem 2011; 83:1557-63. [DOI: 10.1021/ac103177w] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Honglun Wang
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810001, P.R. China
| | - Lily M. L. Ou
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Yourui Suo
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810001, P.R. China
| | - Hua-Zhong Yu
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| |
Collapse
|
35
|
Kuwahara M, Sugimoto N. Molecular evolution of functional nucleic acids with chemical modifications. Molecules 2010; 15:5423-44. [PMID: 20714306 PMCID: PMC6257756 DOI: 10.3390/molecules15085423] [Citation(s) in RCA: 104] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Revised: 07/14/2010] [Accepted: 08/06/2010] [Indexed: 01/10/2023] Open
Abstract
Nucleic acids are attractive materials for creating functional molecules that have applications as catalysts, specific binders, and molecular switches. Nucleic acids having such functions can be obtained by random screening, typically using in vitro selection methods. These methods have helped explore the potential abilities of nucleic acids and steadily contributed to their evolution, i.e., creation of RNA/DNA enzymes, aptamers, and aptazymes. Chemical modification would be a key means to further increase their performance, e.g., expansion of function diversity, enhancement of activity, and improvement of biostability for biological use. Indeed, in the past two decades, random screening involving chemical modification, post-SELEX chemical modification, and rational design methods have been advanced, and combining and integrating these methods may produce a new class of functional nucleic acids. This review focuses on the effectiveness of chemical modifications on the evolution of nucleic acids as functional molecules and the outlook for related technologies.
Collapse
Affiliation(s)
- Masayasu Kuwahara
- Chemistry Laboratory of Artificial Biomolecules (CLAB), Graduate School of Engineering, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER) and Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-Ku, Kobe 650-0047, Japan; E-Mail: (N.S.)
| |
Collapse
|
36
|
Marton S, Reyes-Darias JA, Sánchez-Luque FJ, Romero-López C, Berzal-Herranz A. In vitro and ex vivo selection procedures for identifying potentially therapeutic DNA and RNA molecules. Molecules 2010; 15:4610-38. [PMID: 20657381 PMCID: PMC6257598 DOI: 10.3390/molecules15074610] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Revised: 06/17/2010] [Accepted: 06/24/2010] [Indexed: 02/05/2023] Open
Abstract
It was only relatively recently discovered that nucleic acids participate in a variety of biological functions, besides the storage and transmission of genetic information. Quite apart from the nucleotide sequence, it is now clear that the structure of a nucleic acid plays an essential role in its functionality, enabling catalysis and specific binding reactions. In vitro selection and evolution strategies have been extremely useful in the analysis of functional RNA and DNA molecules, helping to expand our knowledge of their functional repertoire and to identify and optimize DNA and RNA molecules with potential therapeutic and diagnostic applications. The great progress made in this field has prompted the development of ex vivo methods for selecting functional nucleic acids in the cellular environment. This review summarizes the most important and most recent applications of in vitro and ex vivo selection strategies aimed at exploring the therapeutic potential of nucleic acids.
Collapse
Affiliation(s)
- Soledad Marton
- Instituto de Parasitología y Biomedicina López-Neyra, CSIC, P.T. Ciencias de la Salud, Av. del Conocimiento s/n, Armilla, 18100 Granada, Spain.
| | | | | | | | | |
Collapse
|
37
|
A novel 1,2,4-triazole-based copper(II) complex: Synthesis, characterization, magnetic property and nuclease activity. J Inorg Biochem 2010; 104:171-9. [DOI: 10.1016/j.jinorgbio.2009.10.020] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2009] [Revised: 10/21/2009] [Accepted: 10/26/2009] [Indexed: 11/20/2022]
|
38
|
Hall B, Micheletti JM, Satya P, Ogle K, Pollard J, Ellington AD. Design, Synthesis, and Amplification of DNA Pools for In Vitro Selection. ACTA ACUST UNITED AC 2009; Chapter 9:Unit 9.2. [DOI: 10.1002/0471142700.nc0902s39] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Bradley Hall
- Department of Chemistry and Biochemistry, University of Texas Austin Texas
| | | | - Pooja Satya
- Freshman Research Initiative, University of Texas Austin Texas
| | - Krystal Ogle
- Freshman Research Initiative, University of Texas Austin Texas
| | - Jack Pollard
- 3rd Millennium Corporation Cambridge Massachusetts
| | | |
Collapse
|
39
|
Hall B, Micheletti JM, Satya P, Ogle K, Pollard J, Ellington AD. Design, synthesis, and amplification of DNA pools for in vitro selection. ACTA ACUST UNITED AC 2009; Chapter 24:Unit 24.2. [PMID: 19816932 DOI: 10.1002/0471142727.mb2402s88] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Preparation of a random-sequence DNA pool is presented. The degree of randomization and the length of the random sequence are discussed, as is synthesis of the pool using a DNA synthesizer or via commercial synthesis companies. Purification of a single-stranded pool and conversion to a double-stranded pool are presented as step-by-step protocols. Support protocols describe determination of the complexity and skewing of the pool, and optimization of amplification conditions.
Collapse
Affiliation(s)
- Bradley Hall
- Department of Chemistry and Biochemistry, University of Texas, Austin, Texas, USA
| | | | | | | | | | | |
Collapse
|
40
|
Sun J, Deng SY, Zhang L, He J, Jiang L, Mao ZW, Ji LN. DNA affinity and cleavage by naphthalene-based mononuclear and dinuclear copper(II) complexes. J COORD CHEM 2009. [DOI: 10.1080/00958970903055875] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Jing Sun
- a MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry and Chemical Engineering , Sun Yat-Sen University , Guangzhou 510275, China
- b School of Pharmaceutical Sciences , Guangdong Medical College , Dongguan 523808, China
| | - Shu-Yi Deng
- a MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry and Chemical Engineering , Sun Yat-Sen University , Guangzhou 510275, China
| | - Li Zhang
- a MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry and Chemical Engineering , Sun Yat-Sen University , Guangzhou 510275, China
| | - Juan He
- a MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry and Chemical Engineering , Sun Yat-Sen University , Guangzhou 510275, China
| | - Long Jiang
- a MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry and Chemical Engineering , Sun Yat-Sen University , Guangzhou 510275, China
| | - Zong-Wan Mao
- a MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry and Chemical Engineering , Sun Yat-Sen University , Guangzhou 510275, China
| | - Liang-Nian Ji
- a MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry and Chemical Engineering , Sun Yat-Sen University , Guangzhou 510275, China
| |
Collapse
|
41
|
Kuwahara M, Takeshima H, Nagashima JI, Minezaki S, Ozaki H, Sawai H. Transcription and reverse transcription of artificial nucleic acids involving backbone modification by template-directed DNA polymerase reactions. Bioorg Med Chem 2009; 17:3782-8. [PMID: 19427792 DOI: 10.1016/j.bmc.2009.04.045] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2009] [Revised: 04/21/2009] [Accepted: 04/22/2009] [Indexed: 12/22/2022]
Abstract
Oligodeoxyribonucleotides (ODN) where the phosphodiester linkage had been replaced with an amide-type linker [-CH(2)C=ONH-] or an amine-type linker [-CH(2)CH(2)NH-] were synthesized to investigate the effect of these backbone modifications on polymerase reactions. In addition, a triphosphate analogue of thymidine dinucleotide with the amide-type linker was synthesized and enzymatic insertion of the amide linkage into ODN was attempted using this analogue for the polymerase reaction. Primer extension reactions using three types of thermostable DNA polymerases, KOD(exo-), Vent(exo-) and Taq were performed for the assays. Analysis of these data indicate that (i) the polymerase reaction tends to be affected much more by insertion of the cationic flexible amine-type linker than by insertion of the neutral rigid amide-type linker; (ii) the backbone modification has a greater effect on the polymerase reaction when it is adjacent to the 3'-end of a primer as the elongation terminus than when it is on the template, as well as in base or sugar modification; (iii) although the modified linker in the modified DNA template is passed beyond by the polymerase, it still affects the extension reaction several bases downstream from its location; (iv) the modified linker in the template, in some cases, also affects the extension reaction upstream from its location; (v) further improvement of the chemical structure is required for dinucleotide-mimic incorporation.
Collapse
Affiliation(s)
- Masayasu Kuwahara
- Department of Chemistry and Chemical Biology, Graduate School of Engineering, Gunma University, Gunma 376-8515, Japan.
| | | | | | | | | | | |
Collapse
|
42
|
Chemiluminescence flow biosensor for hydrogen peroxide using DNAzyme immobilized on eggshell membrane as a thermally stable biocatalyst. Biosens Bioelectron 2009; 24:2534-40. [DOI: 10.1016/j.bios.2009.01.010] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2008] [Revised: 12/30/2008] [Accepted: 01/05/2009] [Indexed: 11/17/2022]
|
43
|
Abstract
Redox-active enzymes perform many key biological reactions. The electron transfer process is complex, not only because of its versatility, but also because of the intricate and delicate modulation exerted by the protein scaffold on the redox properties of the catalytic sites. Nowadays, there is a wealth of information available about the catalytic mechanisms of redox-active enzymes and the time is propitious for the development of projects based on the protein engineering of redox-active enzymes. In this review, we aim to provide an updated account of the available methods used for protein engineering, including both genetic and chemical tools, which are usually reviewed separately. Specific applications to redox-active enzymes are mentioned within each technology, with emphasis on those cases where the generation of novel functionality was pursued. Finally, we focus on two emerging fields in the protein engineering of redox-active enzymes: the construction of novel nucleic acid-based catalysts and the remodeling of intra-molecular electron transfer networks. We consider that the future development of these areas will represent fine examples of the concurrence of chemical and genetic tools.
Collapse
Affiliation(s)
- Gloria Saab-Rincón
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | | |
Collapse
|
44
|
|
45
|
Chaput JC, Woodbury NW, Stearns LA, Williams BAR. Creating protein biocatalysts as tools for future industrial applications. Expert Opin Biol Ther 2008; 8:1087-98. [PMID: 18613761 DOI: 10.1517/14712598.8.8.1087] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND Biocatalysts provide an economical and energy-efficient alternative to traditional chemical manufacturing processes. For processes where biocatalysts currently do not exist or existing protein catalysts function poorly, there is a tremendous need to discover new protein catalysts that function in industrial settings. The protein engineering community has traditionally relied on cell-based techniques in 96-well format to evolve new catalysts or improve existing enzymes. OBJECTIVE This review examines recent progress made in many display technologies, providing powerful alternatives for generating novel enzymes with altered specificity or altogether new types of function. METHODS Library creation methods and display technologies that are commonly used in conjunction with enzyme evolution are discussed. CONCLUSION We conclude with an expert opinion on future trans-disciplinary approaches that combine directed evolution with computational design as novel platforms for rapidly discovering new types of catalytic function.
Collapse
Affiliation(s)
- John C Chaput
- Center for BioOptical Nanotechnology, The Biodesign Institute, Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-5201, USA.
| | | | | | | |
Collapse
|
46
|
Hasegawa T, Hagihara M, Fukuda M, Nakano S, Fujieda N, Morii T. Context-dependent fluorescence detection of a phosphorylated tyrosine residue by a ribonucleopeptide. J Am Chem Soc 2008; 130:8804-12. [PMID: 18597435 DOI: 10.1021/ja801734f] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tools for selective recognition and sensing of specific phosphorylated tyrosine residues on the protein surface are essential for understanding signal transduction cascades in the cell. A stable complex of RNA and peptide, a ribonucleopeptide (RNP), provides effective approaches to tailor RNP receptors and fluorescent RNP sensors for small molecules. In vitro selection of an RNA-derived pool of RNP afforded RNP receptors specific for a phosphotyrosine residue within a defined amino-acid sequence Gly-Tyr-Ser-Arg. The RNP receptor for the specific phosphotyrosine residue was successfully converted to a fluorescent RNP sensor for sequence-specific recognition of a phosphorylated tyrosine by screening a pool of fluorescent phosphotyrosine-binding RNPs generated by a combination of the RNA subunits of phosphotyrosine-binding RNPs and various fluorophore-modified peptide subunits. The phosphotyrosine-binding RNP receptor and fluorescent RNP sensor constructed from the RNP receptor not only discriminated phosphotyrosine against tyrosine, phosphoserine, or phosphothreonine, but also showed specific recognition of amino acid residues surrounding the phosphotyrosine residue. A fluorescent RNP sensor for one of the tyrosine phosphorylation sites of p100 coactivator showed a binding affinity to the target site ~95-fold higher than the other tyrosine phosphorylation site. The fluorescent RNP sensor has an ability to function as a specific fluorescent sensor for the phosphorylated tyrosine residue within a defined amino-acid sequence in HeLa cell extracts.
Collapse
Affiliation(s)
- Tetsuya Hasegawa
- Institute of Advanced Energy, Institute of Sustainability Science, and Pioneering Research Unit for Next Generation, Kyoto University, Uji, Kyoto 611-0011, Japan
| | | | | | | | | | | |
Collapse
|
47
|
Kuwahara M, Obika S, Nagashima JI, Ohta Y, Suto Y, Ozaki H, Sawai H, Imanishi T. Systematic analysis of enzymatic DNA polymerization using oligo-DNA templates and triphosphate analogs involving 2',4'-bridged nucleosides. Nucleic Acids Res 2008; 36:4257-65. [PMID: 18583360 PMCID: PMC2490744 DOI: 10.1093/nar/gkn404] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2008] [Revised: 06/07/2008] [Accepted: 06/09/2008] [Indexed: 11/16/2022] Open
Abstract
In order to systematically analyze the effects of nucleoside modification of sugar moieties in DNA polymerase reactions, we synthesized 16 modified templates containing 2',4'-bridged nucleotides and three types of 2',4'-bridged nucleoside-5'-triphospates with different bridging structures. Among the five types of thermostable DNA polymerases used, Taq, Phusion HF, Vent(exo-), KOD Dash and KOD(exo-), the KOD Dash and KOD(exo-) DNA polymerases could smoothly read through the modified templates containing 2'-O,4'-C-methylene-linked nucleotides at intervals of a few nucleotides, even at standard enzyme concentrations for 5 min. Although the Vent(exo-) DNA polymerase also read through these modified templates, kinetic study indicates that the KOD(exo-) DNA polymerase was found to be far superior to the Vent(exo-) DNA polymerase in accurate incorporation of nucleotides. When either of the DNA polymerase was used, the presence of 2',4'-bridged nucleotides on a template strand substantially decreased the reaction rates of nucleotide incorporations. The modified templates containing sequences of seven successive 2',4'-bridged nucleotides could not be completely transcribed by any of the DNA polymerases used; yields of longer elongated products decreased in the order of steric bulkiness of the modified sugars. Successive incorporation of 2',4'-bridged nucleotides into extending strands using 2',4'-bridged nucleoside-5'-triphospates was much more difficult. These data indicate that the sugar modification would have a greater effect on the polymerase reaction when it is adjacent to the elongation terminus than when it is on the template as well, as in base modification.
Collapse
Affiliation(s)
- Masayasu Kuwahara
- Department of Chemistry and Chemical Biology, Graduate School of Engineering, Gunma University, Gunma 376-8515, Japan.
| | | | | | | | | | | | | | | |
Collapse
|
48
|
Pollard J, Bell SD, Ellington AD. Design, synthesis, and amplification of DNA pools for in vitro selection. ACTA ACUST UNITED AC 2008; Chapter 9:Unit 9.2. [PMID: 18428880 DOI: 10.1002/0471142700.nc0902s00] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Preparation of a random-sequence DNA pool is presented. The degree of randomization and the length of the random sequence are discussed, as is synthesis of the pool using a DNA synthesizer. Purification of a single-stranded pool and conversion to a double-stranded pool are presented as step-by-step protocols. Support protocols describe determination of the complexity and skewing of the pool, and optimization of amplification conditions.
Collapse
Affiliation(s)
- J Pollard
- Harvard University, Cambridge, Massachusetts, USA
| | | | | |
Collapse
|
49
|
Vant-Hull B, Gold L, Zichi DA. Theoretical principles of in vitro selection using combinatorial nucleic acid libraries. ACTA ACUST UNITED AC 2008; Chapter 9:Unit 9.1. [PMID: 18428805 DOI: 10.1002/0471142700.nc0901s00] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A new paradigm for drug discovery and biological research has developed from technologies that integrate combinatorial chemistry with rounds of selection and amplification, a technique called in vitro selection or systematic evolution of ligands by exponential enrichment (SELEX). This overview unit discusses nucleic acid libraries that can be used, affinity probability distributions, an equilibrium model for SELEX, and optimal conditions including concentrations and signal-to-noise ratios.
Collapse
Affiliation(s)
- B Vant-Hull
- NeXstar Pharmaceuticals, Boulder, Colorado, USA
| | | | | |
Collapse
|
50
|
Wanekaya AK, Chen W, Mulchandani A. Recent biosensing developments in environmental security. ACTA ACUST UNITED AC 2008; 10:703-12. [PMID: 18528536 DOI: 10.1039/b806830p] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Environmental security is one of the fundamental requirements of our well being. However, it still remains a major global challenge. Therefore, in addition to reducing and/or eliminating the amounts of toxic discharges into the environment, there is need to develop techniques that can detect and monitor these environmental pollutants in a sensitive and selective manner to enable effective remediation. Because of their integrated nature, biosensors are ideal for environmental monitoring and detection as they can be portable and provide selective and sensitive rapid responses in real time. In this review we discuss the main concepts behind the development of biosensors that have most relevant applications in the field of environmental monitoring and detection. We also review and document recent trends and challenges in biosensor research and development particularly in the detection of species of environmental significance such as organophosphate nerve agents, heavy metals, organic contaminants, pathogenic microorganisms and their toxins. Special focus will be given to the trends that have the most promising applications in environmental security. We conclude by highlighting the directions towards which future biosensors research in environmental security sector might proceed.
Collapse
Affiliation(s)
- Adam K Wanekaya
- Chemistry Department, Missouri State University, Springfield, MO 65897, USA.
| | | | | |
Collapse
|