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Marpaung DSS, Sinaga AOY, Damayanti D, Taharuddin T. Bridging biological samples to functional nucleic acid biosensor applications: current enzymatic-based strategies for single-stranded DNA generation. ANAL SCI 2024; 40:1225-1237. [PMID: 38607600 DOI: 10.1007/s44211-024-00566-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/13/2024] [Indexed: 04/13/2024]
Abstract
The escalating threat of emerging diseases, often stemming from contaminants and lethal pathogens, has precipitated a heightened demand for sophisticated diagnostic tools. Within this landscape, the functional nucleic acid (FNA) biosensor, harnessing the power of single-stranded DNA (ssDNA), has emerged as a preeminent choice for target analyte detection. However, the dependence on ssDNA has raised difficulties in realizing it in biological samples. Therefore, the production of high-quality ssDNA from biological samples is critical. This review aims to discuss strategies for generating ssDNA from biological samples for integration into biosensors. Several innovative strategies for ssDNA generation have been deployed, encompassing techniques, such as asymmetric PCR, Exonuclease-PCR, isothermal amplification, biotin-streptavidin PCR, transcription-reverse transcription, ssDNA overhang generation, and urea denaturation PAGE. These approaches have been seamlessly integrated with biosensors for biological sample analysis, ushering in a new era of disease detection and monitoring. This amalgamation of ssDNA generation techniques with biosensing applications holds significant promise, not only in improving the speed and accuracy of diagnostic processes but also in fortifying the global response to deadly diseases, thereby underlining the pivotal role of cutting-edge biotechnology in public health and disease prevention.
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Affiliation(s)
- David Septian Sumanto Marpaung
- Department of Biosystems Engineering, Institut Teknologi Sumatera, Jl. Terusan Ryacudu, Way Huwi, Kec. Jati Agung, Lampung Selatan, Lampung, 35365, Indonesia.
| | - Ayu Oshin Yap Sinaga
- Department of Biology, Institut Teknologi Sumatera, Jl. Terusan Ryacudu, Way Huwi, Kec. Jati Agung, Lampung Selatan, Lampung, 35365, Indonesia
| | - Damayanti Damayanti
- Department of Chemical Engineering, Institut Teknologi Sumatera, Jl. Terusan Ryacudu, Way Huwi, Kec. Jati Agung, Lampung Selatan, Lampung, 35365, Indonesia
| | - Taharuddin Taharuddin
- Department of Chemical Engineering, University of Lampung, Jl. Prof. Dr. Ir. Sumantri Brojonegoro No.1, Gedong Meneng, Kec. Rajabasa, Kota Bandar Lampung, Lampung, 35141, Indonesia
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2
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Ateiah M, Gandalipov ER, Rubel AA, Rubel MS, Kolpashchikov DM. DNA Nanomachine (DNM) Biplex Assay for Differentiating Bacillus cereus Species. Int J Mol Sci 2023; 24:ijms24054473. [PMID: 36901903 PMCID: PMC10003685 DOI: 10.3390/ijms24054473] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/16/2023] [Accepted: 02/21/2023] [Indexed: 03/12/2023] Open
Abstract
Conventional methods for the detection and differentiation of Bacillus cereus group species have drawbacks mostly due to the complexity of genetic discrimination between the Bacillus cereus species. Here, we describe a simple and straightforward assay based on the detected unamplified bacterial 16S rRNA by DNA nanomachine (DNM). The assay uses a universal fluorescent reporter and four all-DNA binding fragments, three of which are responsible for "opening up" the folded rRNA while the fourth stand is responsible for detecting single nucleotide variation (SNV) with high selectivity. Binding of the DNM to 16S rRNA results in the formation of the 10-23 deoxyribozyme catalytic core that cleaves the fluorescent reporter and produces a signal, which is amplified over time due to catalytic turnover. This developed biplex assay enables the detection of B. thuringiensis 16S rRNA at fluorescein and B. mycoides at Cy5 channels with a limit of detection of 30 × 103 and 35 × 103 CFU/mL, respectively, after 1.5 h with a hands-on time of ~10 min. The new assay may simplify the analysis of biological RNA samples and might be useful for environmental monitoring as a simple and inexpensive alternative to amplification-based nucleic acid analysis. The DNM proposed here may become an advantageous tool for detecting SNV in clinically significant DNA or RNA samples and can easily differentiate SNV under broadly variable experimental conditions and without prior amplification.
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Affiliation(s)
- Muhannad Ateiah
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, Lomonosova St. 9, St. Petersburg 191002, Russia; (M.A.); (E.R.G.); (M.S.R.)
| | - Erik R. Gandalipov
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, Lomonosova St. 9, St. Petersburg 191002, Russia; (M.A.); (E.R.G.); (M.S.R.)
| | - Aleksandr A. Rubel
- Laboratory of Amyloid Biology, St. Petersburg State University, Universitetskaya enb. 7-9, St. Petersburg 199034, Russia;
| | - Maria S. Rubel
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, Lomonosova St. 9, St. Petersburg 191002, Russia; (M.A.); (E.R.G.); (M.S.R.)
| | - Dmitry M. Kolpashchikov
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, Lomonosova St. 9, St. Petersburg 191002, Russia; (M.A.); (E.R.G.); (M.S.R.)
- Chemistry Department, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL 32816-2366, USA
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32816, USA
- Correspondence:
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3
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Sarkar S, Colón-Roura G, Pearse A, Armitage BA. Targeting a KRAS i-motif forming sequence by unmodified and gamma-modified peptide nucleic acid oligomers. Biopolymers 2023; 114:e23529. [PMID: 36573547 PMCID: PMC10078108 DOI: 10.1002/bip.23529] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 12/04/2022] [Accepted: 12/07/2022] [Indexed: 12/28/2022]
Abstract
Growing interest in i-motif DNA as a transcriptional regulatory element motivates development of synthetic molecules capable of targeting these structures. In this study, we designed unmodified peptide nucleic acid (PNA) and gamma-modified PNA (γPNA) oligomers complementary to an i-motif forming sequence derived from the promoter of the KRAS oncogene. Biophysical techniques such as circular dichroism (CD) spectroscopy, CD melting, and fluorescence spectroscopy demonstrated the successful invasion of the i-motif by PNA and γPNA. Both PNA and γPNA showed very strong binding to the target sequence with high thermal stability of the resulting heteroduplexes. Interestingly fluorescence and CD experiments indicated formation of an intermolecular i-motif structure via the overhangs of target-probe heteroduplexes formed by PNA/γPNA invasion of the intramolecular i-motif. Targeting promoter i-motif forming sequences with high-affinity oligonucleotide mimics like γPNAs may represent a new approach for inhibiting KRAS transcription, thereby representing a potentially useful anti-cancer strategy.
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Affiliation(s)
- Srijani Sarkar
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Gabriela Colón-Roura
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Alexander Pearse
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Bruce A Armitage
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
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4
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Shiekh S, Jack A, Saurabh A, Mustafa G, Kodikara S, Gyawali P, Hoque M, Pressé S, Yildiz A, Balci H. Shelterin reduces the accessibility of telomeric overhangs. Nucleic Acids Res 2022; 50:12885-12895. [PMID: 36511858 PMCID: PMC9825182 DOI: 10.1093/nar/gkac1176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/25/2022] [Accepted: 11/25/2022] [Indexed: 12/15/2022] Open
Abstract
Telomeres terminate with a 50-300 bases long single-stranded G-rich overhang, which can be misrecognized as a DNA damage repair site. Shelterin plays critical roles in maintaining and protecting telomere ends by regulating access of various physiological agents to telomeric DNA, but the underlying mechanism is not well understood. Here, we measure how shelterin affects the accessibility of long telomeric overhangs by monitoring transient binding events of a short complementary peptide nucleic acid (PNA) probe using FRET-PAINT in vitro. We observed that the POT1 subunit of shelterin reduces the accessibility of the PNA probe by ∼2.5-fold, indicating that POT1 effectively binds to and protects otherwise exposed telomeric sequences. In comparison, a four-component shelterin stabilizes POT1 binding to the overhang by tethering POT1 to the double-stranded telomeric DNA and reduces the accessibility of telomeric overhangs by ∼5-fold. This enhanced protection suggests shelterin restructures the junction between single and double-stranded telomere, which is otherwise the most accessible part of the telomeric overhang.
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Affiliation(s)
- Sajad Shiekh
- Department of Physics, Kent State University, Kent, OH 44242, USA
| | - Amanda Jack
- Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA
| | - Ayush Saurabh
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Golam Mustafa
- Department of Physics, Kent State University, Kent, OH 44242, USA
| | | | - Prabesh Gyawali
- Department of Physics, Kent State University, Kent, OH 44242, USA
| | - Mohammed Enamul Hoque
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Steve Pressé
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, AZ 85287, USA
- School of Molecular Science, Arizona State University, Tempe, AZ 85287, USA
| | - Ahmet Yildiz
- Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA
- Physics Department, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Hamza Balci
- Department of Physics, Kent State University, Kent, OH 44242, USA
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5
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Lu Z, Liu Y, Deng Y, Jia B, Ding X, Zheng P, Li Z. OaAEP1-mediated PNA-protein conjugation enables erasable imaging of membrane proteins. Chem Commun (Camb) 2022; 58:8448-8451. [PMID: 35797663 DOI: 10.1039/d2cc02153f] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the use of a protein ligase to covalently ligate a protein to a peptide nucleic acid (PNA). The rapid ligation demands only an N-terminal GL dipeptide in the target protein and a C-terminal NGL tripeptide in the PNA. We demonstrate the versatility of this approach by attaching a PNA strand to three different proteins. Lastly, we show that erasable imaging of EGFR on HEK293 cell membranes is achieved with DNA origami nanostructures and toehold-mediated strand displacement.
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Affiliation(s)
- Zhangwei Lu
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China. .,State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Yutong Liu
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Road, Nanjing, 210023, P. R. China.
| | - Yibing Deng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Road, Nanjing, 210023, P. R. China.
| | - Bin Jia
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China. .,State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Xuan Ding
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China. .,State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Road, Nanjing, 210023, P. R. China.
| | - Zhe Li
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China. .,State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
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Adjusting the Structure of a Peptide Nucleic Acid (PNA) Molecular Beacon and Promoting Its DNA Detection by a Hybrid with Quencher-Modified DNA. Processes (Basel) 2022. [DOI: 10.3390/pr10040722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
In this study, we performed an elaborate adjustment of the structure of peptide nucleic acid (PNA) molecular beacons as probes for detecting nucleic acids. We synthesized the PNA beacons with various numbers of Glu, Lys, and dabcyl (Dab) quenchers in them, and we investigated their fluorescence changes (F1/1/F0) with and without full-match DNA. As the numbers of Glu/Lys or Dab increased, the F1/1/F0 tended to decrease. Among the different beacons, the PNA beacon with one Glu and one Lys (P1Q1) showed the largest F1/1/F0. On the other hand, a relatively large F1/1/F0 was obtained when the number of Glu/Lys and the number of Dab were the same, and the balance between the numbers of Glu/Lys and Dab seemed to affect the F1/1/F0. We also investigated the DNA detection by the prehybrid of P1Q1, which consists of the T790M base sequence, [P1Q1(T790M)], with quencher-modified DNA (Q-DNA). We examined the DNA detection with single-base mismatch by P1Q1(T790M), and we clarified that there was difficulty in detecting the sequence with P1Q1 alone, but that the sequence was successfully detected by the prehybrid of P1Q1 with the Q-DNA.
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7
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Tan Y, Zhong W, Tang W, Fan J, Zhang X, Guo D, Wu X, Liu Y. Improvement of Molecular Diagnosis Using Domain-Level Single-Nucleotide Variants by Eliminating Unexpected Secondary Structures. Chemistry 2020; 26:16256-16260. [PMID: 32964533 DOI: 10.1002/chem.202003592] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Indexed: 01/06/2023]
Abstract
Identification of single-nucleotide variants (SNVs) is of great significance in molecular diagnosis. The problem that should not be ignored in the identification process is that the unexpected secondary structure of the target nucleic acid may greatly affect the detection accuracy. Herein, we proposed a conditional domain-level SNV diagnosis strategy, in which the subsequent SNV detection can only be carried out after eliminating the unexpected secondary structure of target DNA. Specifically, the target DNA is assembled into a rigid double strand, which makes folding the target DNA difficult and the unexpected secondary structure is eliminated. Based on this double-stranded structure, specially designed probes are used to detect double-stranded properties and report abundant domain-level oligonucleotide information to improve the effective information in the detection results and complete domain-level SNV diagnosis. If the unexpected secondary structure is not eliminated, the detector will first detect it and feed back to us, ensuring the accuracy of the subsequent detection results. With the occurrence (or not) of SNV and the change of the SNV site, in the proof-of-concept experiment, we successfully identified the four homologous sequences to be tested related to BRAF gene.
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Affiliation(s)
- Yun Tan
- College of Chemistry and Environmental Engineering, Shenzhen University, Nanhai Avenue 3688, Nanshan District, Shenzhen, Guangdong, CN, 518060, P. R. China
| | - Weiye Zhong
- College of Chemistry and Environmental Engineering, Shenzhen University, Nanhai Avenue 3688, Nanshan District, Shenzhen, Guangdong, CN, 518060, P. R. China
| | - Weiyang Tang
- College of Chemistry and Environmental Engineering, Shenzhen University, Nanhai Avenue 3688, Nanshan District, Shenzhen, Guangdong, CN, 518060, P. R. China
| | - Jin Fan
- College of Chemistry and Environmental Engineering, Shenzhen University, Nanhai Avenue 3688, Nanshan District, Shenzhen, Guangdong, CN, 518060, P. R. China
| | - Xiaohui Zhang
- College of Chemistry and Environmental Engineering, Shenzhen University, Nanhai Avenue 3688, Nanshan District, Shenzhen, Guangdong, CN, 518060, P. R. China
| | - Donghua Guo
- College of Chemistry and Environmental Engineering, Shenzhen University, Nanhai Avenue 3688, Nanshan District, Shenzhen, Guangdong, CN, 518060, P. R. China
| | - Xiaolong Wu
- College of Chemistry and Environmental Engineering, Shenzhen University, Nanhai Avenue 3688, Nanshan District, Shenzhen, Guangdong, CN, 518060, P. R. China
| | - Yizhen Liu
- College of Chemistry and Environmental Engineering, Shenzhen University, Nanhai Avenue 3688, Nanshan District, Shenzhen, Guangdong, CN, 518060, P. R. China
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8
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Li X, Pei Y, Zhang Y, Liu Y, Fu W, Li J, You H, Huang J. Single-Molecule Mechanical Unfolding of AT-Rich Chromosomal Fragile Site DNA Hairpins: Resolving the Thermodynamic and Kinetic Effects of a Single G-T Mismatch. J Phys Chem B 2020; 124:9365-9370. [PMID: 32970435 DOI: 10.1021/acs.jpcb.0c06954] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Chromosomal fragile sites (CFSs) contain AT-rich sequences that tend to form hairpins on lagging strands in DNA replication, making them hotspots for chromosomal rearrangements in cancers. Here, we investigate the structural stability of the AT-rich CFS DNA hairpins with a single non-AT base pair using magnetic tweezers. Strikingly, a single G-T mismatched base pair in the short CFS DNA hairpin gives a 38.7% reduction of the unfolding Gibbs free energy and a 100-fold increase of the transition kinetics compared to a single G-C matched base pair, which are deviated from the theoretical simulations. Our study reveals the unique features of CFSs to provide profound insights into chromosomal instability and structure-specific genome targeting therapeutics for genetic disorder-related diseases.
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Affiliation(s)
- Xiong Li
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Yufeng Pei
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yashuo Zhang
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yajun Liu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Wenhao Fu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Huijuan You
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jinqing Huang
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
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9
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Fitzpatrick CR, Lu-Irving P, Copeland J, Guttman DS, Wang PW, Baltrus DA, Dlugosch KM, Johnson MTJ. Chloroplast sequence variation and the efficacy of peptide nucleic acids for blocking host amplification in plant microbiome studies. MICROBIOME 2018; 6:144. [PMID: 30121081 PMCID: PMC6098832 DOI: 10.1186/s40168-018-0534-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 08/14/2018] [Indexed: 05/25/2023]
Abstract
BACKGROUND The ability to efficiently characterize microbial communities from host individuals can be limited by co-amplification of host organellar sequences (mitochondrial and/or plastid), which share a common ancestor and thus sequence similarity with extant bacterial lineages. One promising approach is the use of sequence-specific peptide nucleic acid (PNA) clamps, which bind to, and block amplification of, host-derived DNA. Universal PNA clamps have been proposed to block host plant-derived mitochondrial (mPNA) and plastid (pPNA) sequences at the V4 16S rRNA locus, but their efficacy across a wide range of host plant species has not been experimentally tested. RESULTS Using the universal PNA clamps, we amplified and sequenced root microbial communities from replicate individuals of 32 plant species with a most recent common ancestor inferred at 140 MYA. We found the average rate of host plastid contamination across plant species was 23%, however, particular lineages exhibited much higher rates (62-94%), with the highest levels of contamination occurring in the Asteraceae. We investigated chloroplast sequence variation at the V4 locus across 500 land plant species (Embryophyta) and found six lineages with mismatches between plastid and the universal pPNA sequence, including all species within the Asteraceae. Using a modified pPNA for the Asteraceae sequence, we found (1) host contamination in Asteraceae species was reduced from 65 to 23%; and (2) host contamination in non-Asteraceae species was increased from 12 to 69%. These results demonstrate that even single nucleotide mismatches can lead to drastic reductions in pPNA efficacy in blocking host amplification. Importantly, we found that pPNA type (universal or modified) had no effect on the detection of individual bacterial taxa, or estimates of within and between sample bacterial diversity, suggesting that our modification did not introduce bias against particular bacterial lineages. CONCLUSIONS When high similarity exists between host organellar DNA and PCR target sequences, PNA clamps are an important molecular tool to reduce host contamination during amplification. Here, we provide a validated framework to modify universal PNA clamps to accommodate host variation in organellar sequences.
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Affiliation(s)
- Connor R Fitzpatrick
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada.
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada.
| | - Patricia Lu-Irving
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Julia Copeland
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - David S Guttman
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Pauline W Wang
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - David A Baltrus
- School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Katrina M Dlugosch
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Marc T J Johnson
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
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10
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Patlolla PR, Mallajosyula SS, Datta B. Template-Free Self-Assembly of Dimeric Dicarbocyanine Dyes. ChemistrySelect 2017. [DOI: 10.1002/slct.201702045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Prathap Reddy Patlolla
- Department of Chemistry; Indian Institute of Technology Gandhinagar; Palaj, Gandhinagar 382355 India, Phone: 079-2395-2073, Fax: 079-2397-2622
| | - Sairam S. Mallajosyula
- Department of Chemistry; Indian Institute of Technology Gandhinagar; Palaj, Gandhinagar 382355 India, Phone: 079-2395-2073, Fax: 079-2397-2622
| | - Bhaskar Datta
- Department of Chemistry; Indian Institute of Technology Gandhinagar; Palaj, Gandhinagar 382355 India, Phone: 079-2395-2073, Fax: 079-2397-2622
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11
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Peracchi A. Dissecting the hybridization of oligonucleotides to structured complementary sequences. Biochim Biophys Acta Gen Subj 2016; 1860:1107-17. [PMID: 26876643 DOI: 10.1016/j.bbagen.2016.02.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 01/18/2016] [Accepted: 02/08/2016] [Indexed: 01/03/2023]
Abstract
BACKGROUND When oligonucleotides hybridize to long target molecules, the process is slowed by the secondary structure in the targets. The phenomenon has been analyzed in several previous studies, but many details remain poorly understood. METHODS I used a spectrofluorometric strategy, focusing on the formation/breaking of individual base pairs, to study the kinetics of association between a DNA hairpin and >20 complementary oligonucleotides ('antisenses'). RESULTS Hybridization rates differed by over three orders of magnitude. Association was toehold-mediated, both for antisenses binding to the target's ends and for those designed to interact with the loop. Binding of these latter, besides being consistently slower, was affected to variable, non-uniform extents by the asymmetric loop structure. Divalent metal ions accelerated hybridization, more pronouncedly when nucleation occurred at the loop. Incorporation of locked nucleic acid (LNA) residues in the antisenses substantially improved the kinetics only when LNAs participated to the earliest hybridization steps. The effects of individual LNAs placed along the antisense indicated that the reaction transition state occurred after invading at least the first base pair of the stem. CONCLUSIONS The experimental approach helps dissect hybridization reactions involving structured nucleic acids. Toehold-dependent, nucleation-invasion models appear fully appropriate for describing such reactions. Estimating the stability of nucleation complexes formed at internal toeholds is the major hurdle for the quantitative prediction of hybridization rates. GENERAL SIGNIFICANCE While analyzing the mechanisms of a fundamental biochemical process (hybridization), this work also provides suggestions for the improvement of technologies that rely on such process.
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Affiliation(s)
- Alessio Peracchi
- Department of Life Sciences, Laboratory of Biochemistry, Molecular Biology and Bioinformatics, University of Parma, 43124 Parma, Italy.
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12
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Wang C, Bae JH, Zhang DY. Native characterization of nucleic acid motif thermodynamics via non-covalent catalysis. Nat Commun 2016; 7:10319. [PMID: 26782977 PMCID: PMC4735651 DOI: 10.1038/ncomms10319] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 11/27/2015] [Indexed: 12/12/2022] Open
Abstract
DNA hybridization thermodynamics is critical for accurate design of oligonucleotides for biotechnology and nanotechnology applications, but parameters currently in use are inaccurately extrapolated based on limited quantitative understanding of thermal behaviours. Here, we present a method to measure the ΔG° of DNA motifs at temperatures and buffer conditions of interest, with significantly better accuracy (6- to 14-fold lower s.e.) than prior methods. The equilibrium constant of a reaction with thermodynamics closely approximating that of a desired motif is numerically calculated from directly observed reactant and product equilibrium concentrations; a DNA catalyst is designed to accelerate equilibration. We measured the ΔG° of terminal fluorophores, single-nucleotide dangles and multinucleotide dangles, in temperatures ranging from 10 to 45 °C. DNA hybridisation thermodynamics parameters underlie rational design of oligonucleotides for diagnostics and nanotechnology. Here, the authors present an accurate method to measure the free energy of a given DNA structure at specific temperature and buffer conditions.
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Affiliation(s)
- Chunyan Wang
- Department of Bioengineering, Rice University, Houston, Texas 77030, USA
| | - Jin H Bae
- Department of Bioengineering, Rice University, Houston, Texas 77030, USA
| | - David Yu Zhang
- Department of Bioengineering, Rice University, Houston, Texas 77030, USA.,Systems, Synthetic, and Physical Biology, Rice University, Houston, Texas 77030, USA
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13
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Exploitation of a very small peptide nucleic acid as a new inhibitor of miR-509-3p involved in the regulation of cystic fibrosis disease-gene expression. BIOMED RESEARCH INTERNATIONAL 2014; 2014:610718. [PMID: 24829907 PMCID: PMC4009323 DOI: 10.1155/2014/610718] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 03/18/2014] [Indexed: 12/13/2022]
Abstract
Computational techniques, and in particular molecular dynamics (MD) simulations, have been successfully used as a complementary technique to predict and analyse the structural behaviour of nucleic acids, including peptide nucleic acid- (PNA-) RNA hybrids. This study shows that a 7-base long PNA complementary to the seed region of miR-509-3p, one of the miRNAs involved in the posttranscriptional regulation of the CFTR disease-gene of Cystic Fibrosis, and bearing suitable functionalization at its N- and C-ends aimed at improving its resistance to nucleases and cellular uptake, is able to revert the expression of the luciferase gene containing the 3′UTR of the gene in A549 human lung cancer cells, in agreement with the MD results that pointed at the formation of a stable RNA/PNA heteroduplex notwithstanding the short sequence of the latter. The here reported results widen the interest towards the use of small PNAs as effective anti-miRNA agents.
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14
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Zhang Z, Revyakin A, Grimm JB, Lavis LD, Tjian R. Single-molecule tracking of the transcription cycle by sub-second RNA detection. eLife 2014; 3:e01775. [PMID: 24473079 PMCID: PMC3901038 DOI: 10.7554/elife.01775] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Transcription is an inherently stochastic, noisy, and multi-step process, in which fluctuations at every step can cause variations in RNA synthesis, and affect physiology and differentiation decisions in otherwise identical cells. However, it has been an experimental challenge to directly link the stochastic events at the promoter to transcript production. Here we established a fast fluorescence in situ hybridization (fastFISH) method that takes advantage of intrinsically unstructured nucleic acid sequences to achieve exceptionally fast rates of specific hybridization (∼10e7 M−1s−1), and allows deterministic detection of single nascent transcripts. Using a prototypical RNA polymerase, we demonstrated the use of fastFISH to measure the kinetic rates of promoter escape, elongation, and termination in one assay at the single-molecule level, at sub-second temporal resolution. The principles of fastFISH design can be used to study stochasticity in gene regulation, to select targets for gene silencing, and to design nucleic acid nanostructures. DOI:http://dx.doi.org/10.7554/eLife.01775.001 The body produces proteins by transcribing DNA (genes) to make messenger RNA, which is then translated to make a protein. Transcription begins when an enzyme called RNA polymerase binds to the DNA and catalyzes the process by which genetic information from the double helix is copied to a complementary RNA transcript, which subsequently becomes the messenger RNA. Because a living cell usually contains only one or a few copies (alleles) of a given gene, molecular fluctuations play a crucial role in cellular transcription. Therefore, studying transcription kinetics at the level of single molecules may provide critical insights into how cells deal with—or even take advantage of—molecular fluctuations. A number of different single-molecule techniques can be used to follow transcription, but these techniques are often relatively slow compared to transcription in living cells, or they suffer from other problems such as only being able to study one step in the transcription process. Now, Zhang, Revyakin et al. have systematically devised a technique called ‘fastFISH’ that is fast enough to track the production of single RNA molecules directly and instantaneously. FastFISH builds on an existing technique called FISH—short for fluorescence in situ hybridization—in which fluorescent molecules are attached to single strands of DNA or RNA. These single strands pair with specific regions of complementary DNA or RNA molecules, and they can be visualized with a fluorescence microscope. However, conventional FISH is a ‘snap-shot’ technique that is not suitable for making real-time observations under physiological conditions. FastFISH relies on single strands of fluorescently labeled DNA and RNA that bind to complementary strands of DNA or RNA extremely quickly, even under physiological conditions, because they contain only three of the four ‘regular’ nucleotides that make up DNA or RNA. As a proof of principle, Zhang, Revyakin et al. used fastFISH to study the kinetics of transcription by the bacteriophage T7 RNA polymerase and were able to measure multiple stages of the transcription cycle in a single-molecule experimental setup. By allowing each stage of transcription to be tracked in real-time at the level of single-molecules, fastFISH will permit a more in-depth analysis of the factors that regulate how genes are expressed as proteins in our cells. Moreover, the ability to design single-strand probes that bind rapidly to DNA and RNA targets could have many additional applications, including new strategies for more efficient gene silencing. DOI:http://dx.doi.org/10.7554/eLife.01775.002
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Affiliation(s)
- Zhengjian Zhang
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, United States
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15
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Amato F, Tomaiuolo R, Borbone N, Elce A, Amato J, D'Errico S, De Rosa G, Mayol L, Piccialli G, Oliviero G, Castaldo G. Design, synthesis and biochemical investigation, by in vitro luciferase reporter system, of peptide nucleic acids as new inhibitors of miR-509-3p involved in the regulation of cystic fibrosis disease-gene expression. MEDCHEMCOMM 2014. [DOI: 10.1039/c3md00257h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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16
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Shimada H, Sakurai T, Kitamura Y, Matsuura H, Ihara T. Metallo-regulation of the bimolecular triplex formation of a peptide nucleic acid. Dalton Trans 2013; 42:16006-13. [PMID: 23897510 DOI: 10.1039/c3dt51386f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Peptide nucleic acid (PNA) conjugates incorporating a bipyridine unit were prepared. The bipyridine was built into the loop moiety of PNAs that were designed to specifically form a hairpin and a PNA/DNA bimolecular triplex. While the thermal stability of the hairpin structure was only minimally affected by Cu(2+) addition, the PNA/DNA bimolecular triplex structure was significantly destabilized by complexation with Cu(2+). The melting temperature of the bimolecular triplex decreased by 17.4 °C in the presence of Cu(2+). This corresponds to more than a 1000 fold decrease in the binding constant for bimolecular triplex formation. Upon complexation, the bipyridine unit underwent a drastic conformational change which accounts for the observed differences in the thermal stabilities of the triplex upon binding. The bipyridine-PNA conjugate may be useful as an allosteric DNA carrier that releases the DNA in response to a certain metal ion concentration.
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Affiliation(s)
- Hiroshi Shimada
- Department of Applied Chemistry and Biochemistry, Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan.
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17
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Wang W, Yuan X, Zhang W, Gao Q, Qi H, Zhang C. Cascade signal amplification for ultra-sensitive impedimetric detection of DNA hybridization using a hairpin DNA as probe. Electrochim Acta 2012. [DOI: 10.1016/j.electacta.2012.06.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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18
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Kundu LM, Tsukada H, Matsuoka Y, Kanayama N, Takarada T, Maeda M. Estimation of binding constants of peptide nucleic acid and secondary-structured DNA by affinity capillary electrophoresis. Anal Chem 2012; 84:5204-9. [PMID: 22624952 DOI: 10.1021/ac301025m] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
An affinity capillary electrophoresis method was developed to determine a binding constant between a peptide nucleic acid (PNA) and a hairpin-structured DNA. A diblock copolymer composed of PNA and polyethylene glycol (PEG) was synthesized as a novel affinity probe. The base sequence of the probe's PNA segment was complementary to a hairpin-structured region of a 60-base single-stranded DNA (ssDNA). Upon applying a voltage, the DNA hairpin migrated slowly compared to a random sequence ssDNA in the presence of the PNA probe. This retardation was induced by strand invasion of the PNA into the DNA hairpin to form a hybridized complex, where the PEG segment received a large amount of hydrodynamic friction during electrophoresis. The binding constant between the PNA probe and the DNA hairpin was easily determined by mobility analysis. This simple method would be potentially beneficial in studying binding behaviors of various artificial nucleotides to natural DNA or RNA.
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Affiliation(s)
- Lal Mohan Kundu
- Bioengineering Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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19
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Lomzov AA, Pyshnyi DV. Considering the oligonucleotide secondary structures in thermodynamic and kinetic analysis of DNA duplex formation. Biophysics (Nagoya-shi) 2012. [DOI: 10.1134/s0006350912010137] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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20
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Li J, Qi XJ, Du YY, Fu HE, Chen GN, Yang HH. Efficient detection of secondary structure folded nucleic acids related to Alzheimer's disease based on junction probes. Biosens Bioelectron 2012; 36:142-6. [PMID: 22560436 DOI: 10.1016/j.bios.2012.04.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2011] [Revised: 03/15/2012] [Accepted: 04/09/2012] [Indexed: 11/28/2022]
Abstract
Single stranded DNA often forms stable secondary structures under physiological conditions. These DNA secondary structures play important physiological roles. However, the analysis of such secondary structure folded DNA is often complicated because of its high thermodynamic stability and slow hybridization kinetics. In this article, we demonstrate that Y-shaped junction probes could be used for rapid and highly efficient detection of secondary structure folded DNA. Our approach contained a molecular beacon (MB) probe and an assistant probe. In the absence of target, the MB probe failed to hybridize with the assistant probe. Whereas, the MB probe and the assistant probe could cooperatively unwind the secondary structure folded DNA target to form a ternary Y-shaped junction structure. In this condition, the MB probe was also opened, resulting in separating the fluorophores from the quenching moiety and emitting the fluorescence signal. This approach allowed for the highly sensitive detection of secondary structure folded DNA target, such as a tau specific DNA fragment related to Alzheimer's disease in this case. Additionally, this approach showed strong SNPs identifying capability. Furthermore, it was noteworthy that this newly proposed approach was capable of detecting secondary structure folded DNA target in cell lysate samples.
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Affiliation(s)
- Juan Li
- The Key Laboratory of Analysis and Detection Technology for Food Safety of the MOE, College of Chemistry and Chemical Engineering, Fuzhou University, Fuzhou 350002, PR China
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21
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Low–medium resolution HLA-DQ2/DQ8 typing for coeliac disease predisposition analysis by colorimetric assay. Anal Bioanal Chem 2012; 403:807-19. [DOI: 10.1007/s00216-012-5898-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Revised: 02/20/2012] [Accepted: 02/22/2012] [Indexed: 10/28/2022]
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22
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Nguyen C, Grimes J, Gerasimova YV, Kolpashchikov DM. Molecular-beacon-based tricomponent probe for SNP analysis in folded nucleic acids. Chemistry 2011; 17:13052-8. [PMID: 21956816 PMCID: PMC3221966 DOI: 10.1002/chem.201101987] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Indexed: 01/13/2023]
Abstract
Hybridization probes are often inefficient in the analysis of single-stranded DNA or RNA that are folded in stable secondary structures. A molecular beacon (MB) probe is a short DNA hairpin with a fluorophore and a quencher attached to opposite sides of the oligonucleotide. The probe is widely used in real-time analysis of specific DNA and RNA sequences. This study demonstrates how a conventional MB probe can be used for the analysis of nucleic acids that form very stable (T(m) > 80 °C) hairpin structures. Here we demonstrate that the MB probe is not efficient in direct analysis of secondary structure-folded analytes, whereas a MB-based tricomponent probe is suitable for these purposes. The tricomponent probe takes advantage of two oligonucleotide adaptor strands f and m. Each adaptor strand contains a fragment complementary to the analyte and a fragment complementary to a MB probe. In the presence of a specific analyte, the two adaptor strands hybridize to the analyte and the MB probe, thus forming a quadripartite complex. DNA strand f binds to the analyte with high affinity and unwinds its secondary structure. Strand m forms a stable complex only with the fully complementary analyte. The MB probe fluorescently reports the formation of the quadripartite associate. It was demonstrated that the DNA analytes folded in hairpin structures with stems containing 5, 6, 7, 8, 9, 11, or 13 base pairs can be detected in real time with the limit of detection (LOD) lying in the nanomolar range. The stability of the stem region in the DNA analyte did not affect the LOD. Analytes containing single base substitutions in the stem or in the loop positions were discriminated from the fully complementary DNA at room temperature. The tricomponent probe promises to simplify nucleic acid analysis at ambient temperatures in such applications as in vivo RNA monitoring, detection of pathogens, and single nucleotide polymorphism (SNP) genotyping by DNA microarrays.
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Affiliation(s)
- Camha Nguyen
- Camha Nguyen, Jeffrey Grimes, Dr. Y. V. Gerasimova, Dr. D. M. Kolpashchikov Chemistry Department University of Central Florida 4000 Central Florida Blvd., Orlando, FL 32816, USA
| | - Jeffrey Grimes
- Camha Nguyen, Jeffrey Grimes, Dr. Y. V. Gerasimova, Dr. D. M. Kolpashchikov Chemistry Department University of Central Florida 4000 Central Florida Blvd., Orlando, FL 32816, USA
| | - Yulia V. Gerasimova
- Camha Nguyen, Jeffrey Grimes, Dr. Y. V. Gerasimova, Dr. D. M. Kolpashchikov Chemistry Department University of Central Florida 4000 Central Florida Blvd., Orlando, FL 32816, USA
| | - Dmitry M. Kolpashchikov
- Camha Nguyen, Jeffrey Grimes, Dr. Y. V. Gerasimova, Dr. D. M. Kolpashchikov Chemistry Department University of Central Florida 4000 Central Florida Blvd., Orlando, FL 32816, USA
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23
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Avila-Figueroa A, Cattie D, Delaney S. A small unstructured nucleic acid disrupts a trinucleotide repeat hairpin. Biochem Biophys Res Commun 2011; 413:532-6. [PMID: 21924238 DOI: 10.1016/j.bbrc.2011.08.130] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Accepted: 08/30/2011] [Indexed: 10/17/2022]
Abstract
A variety of neurodegenerative disorders are associated with the expansion of trinucleotide repeat (TNR) sequences. These repetitive sequences are prone to adopting non-canonical structures, such as intrastrand stem-loop hairpins. Indeed, the formation and persistence of these hairpins during DNA replication and/or repair have been proposed as factors that facilitate TNR expansion. Given this proposed contribution of TNR hairpins to the expansion mechanism, disruption of such structures via strand invasion offers a potential means to negate the disease-initiating expansion. In this work, we investigated the strand invading abilities of a (CTG)(3) unstructured nucleic acid on a (CAG)(10) TNR hairpin. Using fluorescence, optical, and electrophoretic methods, instantaneous disruption of the (CAG)(10) hairpin by (CTG)(3) was observed at low temperatures. Additionally, we have identified three distinct duplex-like species that form between (CAG)(10) and (CTG)(3); these include 1, 2, or 3 (CTG)(3) sequences hybridized to (CAG)(10). The results presented here showcase (CTG)(3) as an invader of a TNR hairpin and suggest that unstructured nucleic acids could serve as a scaffold to design agents to prevent TNR expansion.
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Affiliation(s)
- Amalia Avila-Figueroa
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, RI 02912, United States
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24
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Amato J, Pagano B, Borbone N, Oliviero G, Gabelica V, Pauw ED, D'Errico S, Piccialli V, Varra M, Giancola C, Piccialli G, Mayol L. Targeting G-quadruplex structure in the human c-Kit promoter with short PNA sequences. Bioconjug Chem 2011; 22:654-63. [PMID: 21410246 DOI: 10.1021/bc100444v] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The cKit87up sequence d((5')AGGGAGGGCGCTGGGAGGAGGG(3')) can form a unique G-quadruplex structure in the promoter region of the human c-kit protooncogene. It provides a peculiar platform for the design of selective quadruplex-binding agents, which could potentially repress the protooncogene transcription. In this study, we examined the binding of a small library of PNA probes (P1-P5) targeting cKit87up quadruplex in either K(+)- or NH(4)(+)-containing solutions by using a combination of UV, CD, PAGE, ITC, and ESI-MS methodologies. Our results showed that (1) P1-P4 interact with the cKit87up quadruplex, and (2) the binding mode depends on the quadruplex stability. In K(+) buffer, P1-P4 bind the ckit87up quadruplex structure as "quadruplex-binding agents". The same holds for P1 in NH(4)(+) solution. On the contrary, in NH(4)(+) solution, P2-P4 overcome the quadruplex structure by forming PNA/DNA hybrid complexes, thus acting as "quadruplex openers".
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Affiliation(s)
- Jussara Amato
- Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli Federico II , via D. Montesano 49, 80131, Napoli, Italy
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25
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Grimes J, Gerasimova YV, Kolpashchikov DM. Real-time SNP analysis in secondary-structure-folded nucleic acids. Angew Chem Int Ed Engl 2011; 49:8950-3. [PMID: 20963740 DOI: 10.1002/anie.201004475] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Jeffrey Grimes
- Chemistry Department, University of Central Florida, 4000 Central Blvd, Orlando, FL 32816, USA
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26
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Abstract
Absorption spectroscopy is one of the most widely used techniques employed for determining the concentrations of absorbing species (chromophores) in solutions. It is a nondestructive technique which biologists and biochemists and now systems biologists use to quantify the cellular components and characteristic parameters of functional molecules. This quantification is most relevant in the context of systems biology. For creating a quantitative depiction of a metabolic pathway, a number of parameters and variables are important and these need to be determined experimentally. This chapter describes the UV-visible absorption spectroscopy used to produce experimental data for bottom-up modeling approaches of systems biology which uses concentrations and kinetic parameters (K(m) and V(max)) of enzymes of metabolic/signaling pathways, intracellular concentrations of metabolites and fluxes. It also briefly describes the application of this technique for quantification of biomolecules and investigating biomolecular interactions.
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Affiliation(s)
- Sanjay M Nilapwar
- Manchester Interdisciplinary Biocentre, The University of Manchester, Manchester, United Kingdom
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27
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Dave N, Liu J. Fast molecular beacon hybridization in organic solvents with improved target specificity. J Phys Chem B 2010; 114:15694-9. [PMID: 21062084 DOI: 10.1021/jp106754k] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA hybridization is of tremendous importance in biology, bionanotechnology, and biophysics. Molecular beacons are engineered DNA hairpins with a fluorophore and a quencher labeled on each of the two ends. A target DNA can open the hairpin to give an increased fluorescence signal. To date, the majority of molecular beacon detections have been performed only in aqueous buffers. We describe herein DNA detection in nine different organic solvents, methanol, ethanol, isopropanol, acetonitrile, formamide, dimethylformamide (DMF), dimethyl sulfoxide (DMSO), ethylene glycol, and glycerol, varying each up to 75% (v/v). In comparison with detection in water, the detection in organic solvents showed several important features. First, the molecular beacon hybridizes to its target DNA in the presence of all nine solvents up to a certain percentage. Second, the rate of this hybridization was significantly faster in most organic solvents compared with water. For example, in 56% ethanol, the beacon showed a 70-fold rate enhancement. Third, the ability of the molecular beacon to discriminate single-base mismatch is still maintained. Lastly, the DNA melting temperature in the organic solvents showed a solvent concentration-dependent decrease. This study suggests that molecular beacons can be used for applications where organic solvents must be involved or organic solvents can be intentionally added to improve the molecular beacon performance.
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Affiliation(s)
- Neeshma Dave
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
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28
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Grimes J, Gerasimova YV, Kolpashchikov DM. Real-Time SNP Analysis in Secondary-Structure-Folded Nucleic Acids. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201004475] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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29
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Avila Figueroa A, Delaney S. Mechanistic studies of hairpin to duplex conversion for trinucleotide repeat sequences. J Biol Chem 2010; 285:14648-57. [PMID: 20228068 DOI: 10.1074/jbc.m109.061853] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The expansion of a trinucleotide repeat sequence, such as CAG/CTG, has been pinpointed as the molecular basis for a number of neurodegenerative disorders. It has been proposed that as part of the expansion process, these repetitive sequences adopt non-B conformations such as hairpins. However, the prevalence of these hairpins and their contributions to the DNA expansion have not been well defined. In this work, we utilized a molecular beacon strategy to examine the stability of the (CAG)(10) hairpin and also its behavior in the presence of the complementary (CTG)(10) hairpin. We find that the two hairpins represent kinetically trapped species that can coexist but irreversibly convert to duplex upon thermal induction. Furthermore, as monitored by fluorescence and optical analysis, modifications to the base composition of either the loop or stem region have a profound effect on the ability of the trinucleotide repeat hairpins to convert to duplex. Additionally, the rate of duplex formation is also reduced with these loop and stem-modified hairpins. These results demonstrate that the trinucleotide repeat hairpins can convert to duplex via two independent mechanisms as follows: the loop-loop interactions found in kissing hairpins or the stem-stem interactions of a cruciform.
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30
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Xiao Y, Lou X, Uzawa T, Plakos KJI, Plaxco KW, Soh HT. An electrochemical sensor for single nucleotide polymorphism detection in serum based on a triple-stem DNA probe. J Am Chem Soc 2010; 131:15311-6. [PMID: 19807078 DOI: 10.1021/ja905068s] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We report here an electrochemical approach that offers, for the first time, single-step, room-temperature single nucleotide polymorphism (SNP) detection directly in complex samples (such as blood serum) without the need for target modification, postwashing, or the addition of exogenous reagents. This sensor, which is sensitive, stable, and reusable, is comprised of a single, self-complementary, methylene blue-labeled DNA probe possessing a triple-stem structure. This probe takes advantage of the large thermodynamic changes in enthalpy and entropy that result from major conformational rearrangements that occur upon binding a perfectly matched target, resulting in a large-scale change in the faradaic current. As a result, the discrimination capabilities of this sensor greatly exceed those of earlier single- and double-stem electrochemical sensors and support rapid (minutes), single-step, reagentless, room-temperature detection of single nucleotide substitutions. To elucidate the theoretical basis of the sensor's selectivity, we present a comparative thermodynamic analysis among single-, double-, and triple-stem probes.
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Affiliation(s)
- Yi Xiao
- Materials Department, University of California, Santa Barbara, California 93106, USA.
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31
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Filippov NS, Lomzov AA, Pyshnyi DV. Thermodynamic description of oligonucleotide self-association in DNA concatamer structures. Biophysics (Nagoya-shi) 2009. [DOI: 10.1134/s0006350909030038] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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32
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Miranda-Castro R, de-los-Santos-Álvarez N, Lobo-Castañón M, Miranda-Ordieres A, Tuñón-Blanco P. Structured Nucleic Acid Probes for Electrochemical Devices. ELECTROANAL 2009. [DOI: 10.1002/elan.200904653] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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33
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Xiao Y, Plakos KJI, Lou X, White RJ, Qian J, Plaxco KW, Soh HT. Fluorescence detection of single-nucleotide polymorphisms with a single, self-complementary, triple-stem DNA probe. Angew Chem Int Ed Engl 2009; 48:4354-8. [PMID: 19431180 DOI: 10.1002/anie.200900369] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Singled out for its singularity: In a single-step, single-component, fluorescence-based method for the detection of single-nucleotide polymorphisms at room temperature, the sensor is comprised of a single, self-complementary DNA strand that forms a triple-stem structure. The large conformational change that occurs upon binding to perfectly matched (PM) targets results in a significant increase in fluorescence (see picture; F = fluorophore, Q = quencher).
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Affiliation(s)
- Yi Xiao
- Materials Department, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
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34
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Ali MM, Li Y. Colorimetric sensing by using allosteric-DNAzyme-coupled rolling circle amplification and a peptide nucleic acid-organic dye probe. Angew Chem Int Ed Engl 2009; 48:3512-5. [PMID: 19360817 DOI: 10.1002/anie.200805966] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Target detection by the naked eye: The action of an RNA-cleaving allosteric DNAzyme in response to ligand binding was coupled to a rolling circle amplification process to generate long single-stranded DNA molecules for colorimetric sensing (see scheme). Upon hybridization of the resulting DNA with a complementary PNA sequence in the presence of a duplex-binding dye, the color of the dye changed from blue to purple.
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Affiliation(s)
- M Monsur Ali
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, ON L8N 3Z5, Canada
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35
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Xiao Y, Plakos K, Lou X, White R, Qian J, Plaxco K, Soh H. Fluorescence Detection of Single-Nucleotide Polymorphisms with a Single, Self-Complementary, Triple-Stem DNA Probe. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200900369] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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36
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Jo JJ, Kim MJ, Son JT, Kim J, Shin JS. Single-fluorophore monitoring of DNA hybridization for investigating the effect of secondary structure on the nucleation step. Biochem Biophys Res Commun 2009; 385:88-93. [PMID: 19422793 DOI: 10.1016/j.bbrc.2009.04.140] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Accepted: 04/28/2009] [Indexed: 11/17/2022]
Abstract
Nucleic acid hybridization is one of the essential biological processes involved in storage and transmission of genetic information. Here we quantitatively determined the effect of secondary structure on the hybridization activation energy using structurally defined oligonucleotides. It turned out that activation energy is linearly proportional to the length of a single-stranded region flanking a nucleation site, generating a 0.18 kcal/mol energy barrier per nucleotide. Based on this result, we propose that the presence of single-stranded segments available for non-productive base pairing with a nucleation counterpart extends the searching process for nucleation sites to find a perfect match. This result may provide insights into rational selection of a target mRNA site for siRNA and antisense gene silencing.
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Affiliation(s)
- Joon-Jung Jo
- Department of Biotechnology, Yonsei University, Shinchon-Dong 134, Seodaemun-Gu, Seoul 120-749, South Korea
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37
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Ali M, Li Y. Colorimetric Sensing by Using Allosteric-DNAzyme-Coupled Rolling Circle Amplification and a Peptide Nucleic Acid-Organic Dye Probe. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200805966] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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38
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Lubin AA, Vander Stoep Hunt B, White RJ, Plaxco KW. Effects of Probe Length, Probe Geometry, and Redox-Tag Placement on the Performance of the Electrochemical E-DNA Sensor. Anal Chem 2009; 81:2150-8. [DOI: 10.1021/ac802317k] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Arica A. Lubin
- Department of Chemistry and Biochemistry and Biomolecular Science and Engineering Program, University of California, Santa Barbara, California 93106
| | - Brook Vander Stoep Hunt
- Department of Chemistry and Biochemistry and Biomolecular Science and Engineering Program, University of California, Santa Barbara, California 93106
| | - Ryan J. White
- Department of Chemistry and Biochemistry and Biomolecular Science and Engineering Program, University of California, Santa Barbara, California 93106
| | - Kevin W. Plaxco
- Department of Chemistry and Biochemistry and Biomolecular Science and Engineering Program, University of California, Santa Barbara, California 93106
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39
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Lahoud G, Timoshchuk V, Lebedev A, Arar K, Hou YM, Gamper H. Properties of pseudo-complementary DNA substituted with weakly pairing analogs of guanine or cytosine. Nucleic Acids Res 2008; 36:6999-7008. [PMID: 18987000 PMCID: PMC2602760 DOI: 10.1093/nar/gkn797] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A straightforward enzymatic protocol for converting regular DNA into pseudo-complementary DNA could improve the performance of oligonucleotide microarrays by generating readily hybridizable structure-free targets. Here we screened several highly destabilizing analogs of G and C for one that could be used with 2-aminoadenine (nA) and 2-thiothymine (sT) to generate structure-free DNA that is fully accessible to complementary probes. The analogs, which included bioactive bases such as 6-thioguanine (sG), 5-nitrocytosine (NitroC), 2-pyrimidinone (P; the free base of zebularine) and 6-methylfuranopyrimidinone (MefP), were prepared as dNTPs and evaluated as substrates for T7 and Phi29 DNA polymerases that lacked editor function. Pairing properties of the analogs were characterized by solution hybridization assays using modified oligonucleotides or primer extension products. P and MeP did not support robust primer extension whereas sG and NitroC did. In hybridization assays, however, sG lacked discrimination and NitroC paired too strongly to C. The dNTPs of two other base analogs, 7-nitro-7-deazahypoxanthine (NitrocH) and 2-thiocytosine (sC), exhibited the greatest promise. Either analog could be used with nA and sT to generate DNA that was nearly structure-free. Hybridization of probes to these modified DNAs will require the development of base analogs that pair strongly to NitrocH or sC.
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Affiliation(s)
- Georges Lahoud
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
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40
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Lahoud G, Timoshchuk V, Lebedev A, de Vega M, Salas M, Arar K, Hou YM, Gamper H. Enzymatic synthesis of structure-free DNA with pseudo-complementary properties. Nucleic Acids Res 2008; 36:3409-19. [PMID: 18448471 PMCID: PMC2425472 DOI: 10.1093/nar/gkn209] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Long single-stranded DNAs and RNAs possess considerable secondary structure under conditions that support stable hybrid formation with oligonucleotides. Consequently, different oligomeric probes can hybridize to the same target with efficiencies that vary by several orders of magnitude. The ability to enzymatically generate structure-free single-stranded copies of any nucleic acid without impairing Watson–Crick base pairing to short probes would eliminate this problem and significantly improve the performance of many oligonucleotide-based applications. Synthetic nucleic acids that exhibit these properties are defined as pseudo-complementary. Previously, we described a pseudo-complementary A-T couple consisting of 2-aminoadenine (nA) and 2-thiothymine (sT) bases. The nA-sT couple is a mismatch even though nA-T and A-sT are stable base pairs. Here we show that 7-alkyl-7-deazaguanine and N4-alkylcytosine (where alkyl = methyl or ethyl) can be used in conjunction with nA and sT to render DNA largely structure-free and pseudo-complementary. The deoxynucleoside triphosphates (dNTPs) of these bases are incorporated into DNA by selected mesophilic and thermophilic DNA polymerases and the resulting primer extension products hybridize with good specificity and stability to oligonucleotide probes composed of the standard bases. Further optimization and characterization of the synthesis and properties of pseudo-complementary DNA should lead to an ideal target for use with oligonucleotide probes that are <25 nt in length.
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Affiliation(s)
- Georges Lahoud
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
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41
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Chen C, Wang W, Wang Z, Wei F, Zhao XS. Influence of secondary structure on kinetics and reaction mechanism of DNA hybridization. Nucleic Acids Res 2007; 35:2875-84. [PMID: 17430963 PMCID: PMC1888818 DOI: 10.1093/nar/gkm177] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Hybridization of nucleic acids with secondary structure is involved in many biological processes and technological applications. To gain more insight into its mechanism, we have investigated the kinetics of DNA hybridization/denaturation via fluorescence resonance energy transfer (FRET) on perfectly matched and single-base-mismatched DNA strands. DNA hybridization shows non-Arrhenius behavior. At high temperature, the apparent activation energies of DNA hybridization are negative and independent of secondary structure. In contrast, when temperature decreases, the apparent activation energies of DNA hybridization change to positive and become structure dependent. The large unfavorable enthalpy of secondary structure melting is compensated for by concomitant duplex formation. Based on our results, we propose a reaction mechanism about how the melting of secondary structure influences the hybridization process. A significant point in the mechanism is that the rate-limiting step switches along with temperature variation in the hybridization process of structured DNA, because the free energy profile of hybridization in structured DNA varies with the variation in temperature.
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Affiliation(s)
| | | | | | | | - Xin Sheng Zhao
- *To whom correspondence should be addressed. +86-10-62751727+86-10-62751708
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42
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Liu J, Tiefenauer L, Tian S, Nielsen PE, Knoll W. PNA-DNA hybridization study using labeled streptavidin by voltammetry and surface plasmon fluorescence spectroscopy. Anal Chem 2007; 78:470-6. [PMID: 16408929 DOI: 10.1021/ac051299c] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Using ferrocene-streptavidin conjugates as amplifiers, we recently have demonstrated the simultaneous detection of DNA hybridization to peptide nucleic acid (PNA)-modified gold surfaces at the femtomole level by electrochemical and surface plasmon resonance techniques (Liu, J.; Tian, S.; Tiefenauer, L.; Nielsen, P. E.; Knoll, W. Anal. Chem. 2005, 77, 2756-2761). In this paper, a detailed study of the binding behavior of PNA-DNA is presented by square wave voltammetry and surface plasmon field-enhanced fluorescence spectroscopy (SPFS). The different binding constants for fully matched and single-mismatched DNA were obtained. The effect of the buffer concentration on the PNA-DNA hybrids was investigated using labeled streptavidin by cyclic voltammetry (CV) and SPFS. At high ionic strength, both the CV and SPFS signals were restrained dramatically, which is most probably due to a conformational change of the short-strand PNA-DNA helices on the surface. We conclude that the combination of electrochemical techniques with SPFS is very useful for the study of short DNA structure transformation.
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Affiliation(s)
- Jianyun Liu
- Max-Planck-Institute for Polymer Research, Ackermannweg 10, D-55128, Mainz, Germany.
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43
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Panyutin IG, Panyutin IV, Demidov VV. Targeting linear duplex DNA with mixed-base peptide nucleic acid oligomers facilitated by bisPNA openers. Anal Biochem 2006; 362:145-7. [PMID: 17184722 DOI: 10.1016/j.ab.2006.11.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2006] [Accepted: 11/08/2006] [Indexed: 11/30/2022]
Affiliation(s)
- Igor G Panyutin
- Department of Nuclear Medicine, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
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44
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Gao Y, Wolf LK, Georgiadis RM. Secondary structure effects on DNA hybridization kinetics: a solution versus surface comparison. Nucleic Acids Res 2006; 34:3370-7. [PMID: 16822858 PMCID: PMC1488884 DOI: 10.1093/nar/gkl422] [Citation(s) in RCA: 240] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The hybridization kinetics for a series of designed 25mer probe–target pairs having varying degrees of secondary structure have been measured by UV absorbance and surface plasmon resonance (SPR) spectroscopy in solution and on the surface, respectively. Kinetic rate constants derived from the resultant data decrease with increasing probe and target secondary structure similarly in both solution and surface environments. Specifically, addition of three intramolecular base pairs in the probe and target structure slow hybridization by a factor of two. For individual strands containing four or more intramolecular base pairs, hybridization cannot be described by a traditional two-state model in solution-phase nor on the surface. Surface hybridization rates are also 20- to 40-fold slower than solution-phase rates for identical sequences and conditions. These quantitative findings may have implications for the design of better biosensors, particularly those using probes with deliberate secondary structure.
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Affiliation(s)
| | | | - Rosina M. Georgiadis
- To whom correspondence should be addressed. Tel: +1 617 353 2500; Fax: +1 617 353 6466;
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45
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Gamper HB, Arar K, Gewirtz A, Hou YM. Unrestricted Hybridization of Oligonucleotides to Structure-Free DNA. Biochemistry 2006; 45:6978-86. [PMID: 16734433 DOI: 10.1021/bi0600392] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The existence of secondary structure in long single-stranded DNA and RNA is a serious obstacle to the practical use of short oligonucleotide probes (<20-mers). Here, we show that replication of a highly structured DNA in the presence of a unique set of dNTP analogues leads to synthesis of daughter DNA with a significantly reduced level of secondary structure. This replicated DNA, composed of 2-aminoadenine, 2-thiothymine, 7-deazaguanine, and cytosine bases, was readily accessible to tiled 8-mer LNA and 15-mer DNA probes, whereas an unmodified version of the same DNA was inaccessible. Importantly, while the base analogues enhanced probe-target stability, they did not significantly reduce the specificity of base pairing. The availability of structure-free DNA targets should facilitate the use of short oligonucleotide probes and promote development of generic oligonucleotide microarrays.
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Affiliation(s)
- Howard B Gamper
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA.
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46
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Xu Y, Yang L, Ye X, He P, Fang Y. Impedance-Based DNA Biosensor Employing Molecular Beacon DNA as Probe and Thionine as Charge Neutralizer. ELECTROANAL 2006. [DOI: 10.1002/elan.200503465] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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47
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Cai J, Li X, Taylor JS. Improved nucleic acid triggered probe activation through the use of a 5-thiomethyluracil peptide nucleic acid building block. Org Lett 2005; 7:751-4. [PMID: 15727432 DOI: 10.1021/ol0478382] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To improve the efficiency of a nucleic acid triggered probe activation (NATPA) system a 5-thiomethyluracil peptide nucleic acid (PNA) building block has been synthesized. Attachment of imidazole and a coumarin ester to uracils at the ends of two PNAs resulted in a 550 000-fold acceleration of DNA-triggered coumarin release relative to imidazole and a 6-fold increase in k(cat) relative to a system which had these groups attached to the amino and carboxy ends of PNAs. [structure: see text]
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Affiliation(s)
- Jianfeng Cai
- Department of Chemistry, Washington University, One Brookings Drive, St. Louis, MO 63130, USA
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48
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Lu L, Rininsland FH, Wittenburg SK, Achyuthan KE, McBranch DW, Whitten DG. Biocidal activity of a light-absorbing fluorescent conjugated polyelectrolyte. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2005; 21:10154-9. [PMID: 16229539 DOI: 10.1021/la046987q] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Herein we describe studies that indicate a cationic conjugated polyelectrolyte shows biocidal activity against gram-negative bacteria (Escherichia coli, E. coli, BL21, with plasmids for Azurin and ampicillin resistance) and gram-positive bacterial spores (Bacillus anthracis, Sterne, B. anthracis, Sterne). These studies were carried out with aqueous suspensions of the conjugated polyelectrolyte, with the polyelectrolyte in supported formats and with samples in which the conjugated polyelectrolyte was coated on the bacteria. The results are interesting in that the biocidal activity is light-induced and appears effective due to the ability of the conjugated polyelectrolyte to form a surface coating on both types of bacteria. The effects observed here should be general and suggest that a range of conjugated polyelectrolytes in different formulations may provide a useful new class of biocides for both dark and light-activated applications.
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Affiliation(s)
- Liangde Lu
- QTL Biosystems, 2778 Agua Fria, Santa Fe, New Mexico 87507-5491, USA
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49
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Smolina IV, Demidov VV, Soldatenkov VA, Chasovskikh SG, Frank-Kamenetskii MD. End invasion of peptide nucleic acids (PNAs) with mixed-base composition into linear DNA duplexes. Nucleic Acids Res 2005; 33:e146. [PMID: 16204449 PMCID: PMC1243805 DOI: 10.1093/nar/gni151] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Peptide nucleic acid (PNA) is a synthetic DNA mimic with valuable properties and a rapidly growing scope of applications. With the exception of recently introduced pseudocomplementary PNAs, binding of common PNA oligomers to target sites located inside linear double-stranded DNAs (dsDNAs) is essentially restricted to homopurine-homopyrimidine sequence motifs, which significantly hampers some of the PNA applications. Here, we suggest an approach to bypass this limitation of common PNAs. We demonstrate that PNA with mixed composition of ordinary nucleobases is capable of sequence-specific targeting of complementary dsDNA sites if they are located at the very termini of DNA duplex. We then show that such targeting makes it possible to perform capturing of designated dsDNA fragments via the DNA-bound biotinylated PNA as well as to signal the presence of a specific dsDNA sequence, in the case a PNA beacon is employed. We also examine the PNA-DNA conjugate and prove that it can initiate the primer-extension reaction starting from the duplex DNA termini when a DNA polymerase with the strand-displacement ability is used. We thus conclude that recognition of duplex DNA by mixed-base PNAs via the end invasion has a promising potential for site-specific and sequence-unrestricted DNA manipulation and detection.
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Affiliation(s)
- Irina V Smolina
- Center for Advanced Biotechnology, Boston University, 36 Cummington Street, Boston, MA 02215, USA.
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50
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Kierzek E, Ciesielska A, Pasternak K, Mathews DH, Turner DH, Kierzek R. The influence of locked nucleic acid residues on the thermodynamic properties of 2'-O-methyl RNA/RNA heteroduplexes. Nucleic Acids Res 2005; 33:5082-93. [PMID: 16155181 PMCID: PMC1201327 DOI: 10.1093/nar/gki789] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2005] [Revised: 08/08/2005] [Accepted: 08/08/2005] [Indexed: 11/28/2022] Open
Abstract
The influence of locked nucleic acid (LNA) residues on the thermodynamic properties of 2'-O-methyl RNA/RNA heteroduplexes is reported. Optical melting studies indicate that LNA incorporated into an otherwise 2'-O-methyl RNA oligonucleotide usually, but not always, enhances the stabilities of complementary duplexes formed with RNA. Several trends are apparent, including: (i) a 3' terminal U LNA and 5' terminal LNAs are less stabilizing than interior and other 3' terminal LNAs; (ii) most of the stability enhancement is achieved when LNA nucleotides are separated by at least one 2'-O-methyl nucleotide; and (iii) the effects of LNA substitutions are approximately additive when the LNA nucleotides are separated by at least one 2'-O-methyl nucleotide. An equation is proposed to approximate the stabilities of complementary duplexes formed with RNA when at least one 2'-O-methyl nucleotide separates LNA nucleotides. The sequence dependence of 2'-O-methyl RNA/RNA duplexes appears to be similar to that of RNA/RNA duplexes, and preliminary nearest-neighbor free energy increments at 37 degrees C are presented for 2'-O-methyl RNA/RNA duplexes. Internal mismatches with LNA nucleotides significantly destabilize duplexes with RNA.
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Affiliation(s)
- Elzbieta Kierzek
- Department of Chemistry and Department of Pediatrics, University of RochesterRC Box 270216, Rochester, NY 14627-0216, USA
- Institute of Bioorganic Chemistry, Polish Academy of Sciences60-714 Poznan, Noskowskiego 12/14, Poland
| | - Anna Ciesielska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences60-714 Poznan, Noskowskiego 12/14, Poland
| | - Karol Pasternak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences60-714 Poznan, Noskowskiego 12/14, Poland
| | - David H. Mathews
- Center for Molecular Pediatric Research, University of Rochester School of Medicine and DentistryRochester, New York, 14642, USA
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and DentistryRochester, New York, 14642, USA
| | - Douglas H. Turner
- Department of Chemistry and Department of Pediatrics, University of RochesterRC Box 270216, Rochester, NY 14627-0216, USA
- Center for Molecular Pediatric Research, University of Rochester School of Medicine and DentistryRochester, New York, 14642, USA
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences60-714 Poznan, Noskowskiego 12/14, Poland
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