1
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Cadden G, Wilken S, Magennis S. A single CAA interrupt in a DNA three-way junction containing a CAG repeat hairpin results in parity-dependent trapping. Nucleic Acids Res 2024; 52:9317-9327. [PMID: 39041420 PMCID: PMC11347167 DOI: 10.1093/nar/gkae644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/04/2024] [Accepted: 07/14/2024] [Indexed: 07/24/2024] Open
Abstract
An increasing number of human disorders are attributed to genomic expansions of short tandem repeats (STRs). Secondary DNA structures formed by STRs are believed to play an important role in expansion, while the presence of nucleotide interruptions within the pure repeat sequence is known to delay the onset and progression of disease. We have used two single-molecule fluorescence techniques to analyse the structure and dynamics of DNA three-way junctions (3WJs) containing CAG repeat hairpin slipouts, with and without a single CAA interrupt. For a 3WJ with a (CAG)10 slipout, the CAA interrupt is preferentially located in the hairpin loop, and the branch migration dynamics are 4-fold slower than for the 3WJ with a pure (CAG)10, and 3-fold slower than a 3WJ with a pure (CAG)40 repeat. The (CAG)11 3WJ with CAA interrupt adopts a conformation that places the interrupt in or near the hairpin loop, with similar dynamics to the pure (CAG)10 and (CAG)11 3WJs. We have shown that changing a single nucleotide (G to A) in a pure repeat can have a large impact on 3WJ structure and dynamics, which may be important for the protective role of interrupts in repeat expansion diseases.
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Affiliation(s)
- Gillian M Cadden
- School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, Glasgow G12 8QQ, UK
| | - Svea J Wilken
- School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, Glasgow G12 8QQ, UK
| | - Steven W Magennis
- School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, Glasgow G12 8QQ, UK
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2
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Lauzon D, Vallée-Bélisle A. Design and Thermodynamics Principles to Program the Cooperativity of Molecular Assemblies. Angew Chem Int Ed Engl 2024; 63:e202313944. [PMID: 37975629 DOI: 10.1002/anie.202313944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/10/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
Most functional nanosystems in living organisms are constructed using multimeric assemblies that provide multiple advantages over their monomeric counterparts such as cooperative or anti-cooperative responses, integration of multiple signals and self-regulation. Inspired by these natural nanosystems, chemists have been synthesizing self-assembled supramolecular systems over the last 50 years with increasing complexity with applications ranging from biosensing, drug delivery, synthetic biology, and system chemistry. Although many advances have been made concerning the design principles of novel molecular architectures and chemistries, little is still known, however, about how to program their dynamic of assembly so that they can assemble at the required concentration and with the right sensitivity. Here, we used synthetic DNA assemblies and double-mutant cycle analysis to explore the thermodynamic basis to program the cooperativity of molecular assemblies. The results presented here exemplify how programmable molecular assemblies can be efficiently built by fusing interacting domains and optimizing their compaction. They may also provide the rational basis for understanding the thermodynamic and mechanistic principles driving the evolution of multimeric biological complexes.
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Affiliation(s)
- Dominic Lauzon
- Laboratory of Biosensors & Nanomachines, Department of Chemistry, Université de Montréal, Montréal, H2V 0B3, QC, Canada
| | - Alexis Vallée-Bélisle
- Laboratory of Biosensors & Nanomachines, Department of Chemistry, Université de Montréal, Montréal, H2V 0B3, QC, Canada
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3
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Zhao F, Frandsen M, Capodaglio S, Sleiman HF. DNA-Mediated Peptide Assembly into Protein Mimics. J Am Chem Soc 2024; 146:1946-1956. [PMID: 38226787 DOI: 10.1021/jacs.3c08984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Abstract
The design of new protein structures is challenging due to their vast sequence space and the complexity of protein folding. Here, we report a new modular DNA-templated strategy to construct protein mimics. We achieve the spatial control of multiple peptide units by conjugation with DNA and hybridization to a branched DNA trimer template followed by covalent stapling of the preorganized peptides into a single unit. A library of protein mimics with different lengths, sequences, and heptad registers has been efficiently constructed. DNA-templated protein mimics show an α-helix or coiled-coil motif formation even when they are constructed from weakly interacting peptide units. Their attached DNA handles can be used to exert dynamic control over the protein mimics' secondary and tertiary structures. This modular strategy will facilitate the development of DNA-encoded protein libraries for the rapid discovery of new therapeutics, enzymes, and antibody mimics.
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Affiliation(s)
- Fangzhou Zhao
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC H3A0B8, Canada
| | - Martin Frandsen
- Department of Chemistry and Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus C, Aarhus 8000, Denmark
| | - Sabrina Capodaglio
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, Parma I-43124, Italy
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC H3A0B8, Canada
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4
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Malina J, Kostrhunova H, Scott P, Brabec V. Metallohelices stabilize DNA three-way junctions and induce DNA damage in cancer cells. Nucleic Acids Res 2023; 51:7174-7183. [PMID: 37351627 PMCID: PMC10415117 DOI: 10.1093/nar/gkad536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/31/2023] [Accepted: 06/08/2023] [Indexed: 06/24/2023] Open
Abstract
DNA three-way junctions (3WJ) represent one of the simplest supramolecular DNA structures arising as intermediates in homologous recombination in the absence of replication. They are also formed transiently during DNA replication. Here we examine the ability of Fe(II)-based metallohelices to act as DNA 3WJ binders and induce DNA damage in cells. We investigated the interaction of eight pairs of enantiomerically pure Fe(II) metallohelices with four different DNA junctions using biophysical and molecular biology methods. The results show that the metallohelices stabilize all types of tested DNA junctions, with the highest selectivity for the Y-shaped 3WJ and minimal selectivity for the 4WJ. The potential of the best stabilizer of DNA junctions and, at the same time, the most selective 3WJ binder investigated in this work to induce DNA damage was determined in human colon cancer HCT116 cells. These metallohelices proved to be efficient in killing cancer cells and triggering DNA damage that could yield therapeutic benefits.
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Affiliation(s)
- Jaroslav Malina
- Czech Academy of Sciences, Institute of Biophysics, Brno, CZ-61200, Czech Republic
| | - Hana Kostrhunova
- Czech Academy of Sciences, Institute of Biophysics, Brno, CZ-61200, Czech Republic
| | - Peter Scott
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Viktor Brabec
- Czech Academy of Sciences, Institute of Biophysics, Brno, CZ-61200, Czech Republic
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5
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Heterogeneous migration routes of DNA triplet repeat slip-outs. BIOPHYSICAL REPORTS 2022; 2:None. [PMID: 36299495 PMCID: PMC9586884 DOI: 10.1016/j.bpr.2022.100070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/08/2022] [Indexed: 12/02/2022]
Abstract
It is unclear how the length of a repetitive DNA tract determines the onset and progression of repeat expansion diseases, but the dynamics of secondary DNA structures formed by repeat sequences are believed to play an important role. It was recently shown that three-way DNA junctions containing slip-out hairpins of CAG or CTG repeats and contiguous triplet repeats in the adjacent duplex displayed single-molecule FRET (smFRET) dynamics that were ascribed to both local conformational motions and longer-range branch migration. Here we explore these so-called "mobile" slip-out structures through a detailed kinetic analysis of smFRET trajectories and coarse-grained modeling. Despite the apparent structural simplicity, with six FRET states resolvable, most smFRET states displayed biexponential dwell-time distributions, attributed to structural heterogeneity and overlapping FRET states. Coarse-grained modeling for a (GAC)10 repeat slip-out included trajectories that corresponded to a complete round of branch migration; the structured free energy landscape between slippage events supports the dynamical complexity observed by smFRET. A hairpin slip-out with 40 CAG repeats, which is above the repeat length required for disease in several triplet repeat disorders, displayed smFRET dwell times that were on average double those of 3WJs with 10 repeats. The rate of secondary-structure rearrangement via branch migration, relative to particular DNA processing pathways, may be an important factor in the expansion of triplet repeat expansion diseases.
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6
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Conformational and migrational dynamics of slipped-strand DNA three-way junctions containing trinucleotide repeats. Nat Commun 2021; 12:204. [PMID: 33420051 PMCID: PMC7794359 DOI: 10.1038/s41467-020-20426-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 11/30/2020] [Indexed: 12/18/2022] Open
Abstract
Expansions of CAG/CTG trinucleotide repeats in DNA are the cause of at least 17 degenerative human disorders, including Huntington’s Disease. Repeat instability is thought to occur via the formation of intrastrand hairpins during replication, repair, recombination, and transcription though relatively little is known about their structure and dynamics. We use single-molecule Förster resonance energy transfer to study DNA three-way junctions (3WJs) containing slip-outs composed of CAG or CTG repeats. 3WJs that only have repeats in the slip-out show two-state behavior, which we attribute to conformational flexibility at the 3WJ branchpoint. When the triplet repeats extend into the adjacent duplex, additional dynamics are observed, which we assign to interconversion of positional isomers. We propose a branchpoint migration model that involves conformational rearrangement, strand exchange, and bulge-loop movement. This migration has implications for how repeat slip-outs are processed by the cellular machinery, disease progression, and their development as drug targets. DNA three-way junctions are branched structures formed during replication, repair, and recombination, and are involved in models of repeat expansion. Here the authors use single-molecule Förster resonance energy transfer to reveal the dynamics of DNA three-way junctions containing slip-outs composed of CAG or CTG repeats.
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7
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Wang X, Tao Z. Expanding the analytical applications of nucleic acid hybridization using junction probes. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:4931-4938. [PMID: 33043948 DOI: 10.1039/d0ay01605e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Nucleic acid hybridization is crucial in target recognition with respect to in vitro and in vivo nucleic acid biosensing. Conventional linear probes and molecular beacons encounter challenges in multiplexing and specific recognition of intractable nucleic acids. Advances in nucleic acid nanotechnologies have resulted in a set of novel structural probes: junction probes (JPs), which make full use of the advantages of specificity, stability, programmability and predictability of Watson-Crick base pairing. In recent years, junction probes have been regularly implemented in constructing systems related to biosensing, synthetic biology and gene regulation. Herein, we summarize the latest advances in JP designs as potential nucleic acid biosensing systems and their expansive applications, and provide some general guidelines for developing JP based sensing strategies for implementation of such systems.
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Affiliation(s)
- Xuchu Wang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Zhejiang University, Hangzhou, China.
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8
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Integration of logic gates to CRISPR/Cas12a system for rapid and sensitive detection of pathogenic bacterial genes. Anal Chim Acta 2020; 1125:162-168. [DOI: 10.1016/j.aca.2020.05.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/24/2020] [Accepted: 05/04/2020] [Indexed: 12/26/2022]
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9
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Dong Y, Yao C, Zhu Y, Yang L, Luo D, Yang D. DNA Functional Materials Assembled from Branched DNA: Design, Synthesis, and Applications. Chem Rev 2020; 120:9420-9481. [DOI: 10.1021/acs.chemrev.0c00294] [Citation(s) in RCA: 168] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Yuhang Dong
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Chi Yao
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Yi Zhu
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Lu Yang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Dan Luo
- Department of Biological & Environmental Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Dayong Yang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
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10
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Zhu J, Haynes CJE, Kieffer M, Greenfield JL, Greenhalgh RD, Nitschke JR, Keyser UF. Fe II4L 4 Tetrahedron Binds to Nonpaired DNA Bases. J Am Chem Soc 2019; 141:11358-11362. [PMID: 31283214 PMCID: PMC7007224 DOI: 10.1021/jacs.9b03566] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A water-soluble self-assembled supramolecular FeII4L4 tetrahedron binds to single stranded DNA, mismatched DNA base pairs, and three-way DNA junctions. Binding of the coordination cage quenches fluorescent labels on the DNA strand, which provides an optical means to detect the interaction and allows the position of the binding site to be gauged with respect to the fluorescent label. Utilizing the quenching and binding properties of the coordination cage, we developed a simple and rapid detection method based on fluorescence quenching to detect unpaired bases in double-stranded DNA.
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Affiliation(s)
- Jinbo Zhu
- Cavendish Laboratory, University of Cambridge , JJ Thomson Avenue , Cambridge CB3 0HE , United Kingdom
| | - Cally J E Haynes
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Marion Kieffer
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Jake L Greenfield
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Ryan D Greenhalgh
- Cavendish Laboratory, University of Cambridge , JJ Thomson Avenue , Cambridge CB3 0HE , United Kingdom
| | - Jonathan R Nitschke
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge , JJ Thomson Avenue , Cambridge CB3 0HE , United Kingdom
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11
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Leveille MP, Tran T, Dingillo G, Cannon B. Detection of Mg 2+-dependent, coaxial stacking rearrangements in a bulged three-way DNA junction by single-molecule FRET. Biophys Chem 2018; 245:25-33. [PMID: 30551070 DOI: 10.1016/j.bpc.2018.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 11/30/2018] [Accepted: 12/01/2018] [Indexed: 12/15/2022]
Abstract
Three-way helical junctions (3WJs) arise in genetic processing, and they have architectural and functional roles in structured nucleic acids. An internal bulge at the junction core allows the helical domains to become oriented into two possible, coaxially stacked conformers. Here, the helical stacking arrangements for a series of bulged, DNA 3WJs were examined using ensemble fluorescence resonance energy transfer (FRET) and single-molecule FRET (smFRET) approaches. The 3WJs varied according to the GC content and sequence of the junction core as well as the pyrimidine content of the internal bulge. Mg2+ titration experiments by ensemble FRET show that both stacking conformations have similar Mg2+ requirements for folding. Strikingly, smFRET experiments reveal that a specific junction sequence can populate both conformers and that this junction undergoes continual interconversion between the two stacked conformers. These findings will support the development of folding principles for the rational design of functional DNA nanostructures.
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Affiliation(s)
| | - Thao Tran
- Department of Physics, Loyola University Chicago, Chicago, IL, USA
| | - Gianna Dingillo
- Department of Physics, Loyola University Chicago, Chicago, IL, USA
| | - Brian Cannon
- Department of Physics, Loyola University Chicago, Chicago, IL, USA.
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12
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Ma L, Sun N, Meng Y, Tu C, Cao X, Wei Y, Chu L, Diao A. Harnessing the affinity of magnetic nanoparticles toward dye-labeled DNA and developing it as an universal aptasensor revealed by lipopolysaccharide detection. Anal Chim Acta 2018; 1036:107-114. [PMID: 30253820 DOI: 10.1016/j.aca.2018.06.060] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Revised: 06/15/2018] [Accepted: 06/21/2018] [Indexed: 12/20/2022]
Abstract
In current study, we have found that several magnetic nanoparticles (MNPs) are able to absorb DNA molecules, and surface engineering would be beneficial to tune such interaction. We then have focused on the assembly of polyethylenimine (PEI) coated MNPs (PEI-MNPs) with ssDNA (single-stranded DNA) and found this assembly is mediated by two forces, namely the electrostatic interactions of surface charges of MNPs and the phosphate backbones of DNA; as well as the coordination of exterior iron ions (especially Fe3+) of MNPs and DNA phosphate backbones. The fluorescence of dye-labeled DNA is significantly quenched when being complexed with PEI-MNPs, which is proved to be caused by static quenching. This PEI-MNPs interact with DNA, which could be harnessed for devising a novel type of aptasensor. This has been examplified by the selective and sensitive detection of lipopolysaccharide (LPS). The LOD (limit of detection) is ∼35 ng/mL and the linear range from 50 ng/mL to 10 μg/mL. Compared with widely used graphene oxide (GO)‒ssDNA aptamer sensors, we also have demonstrated that the PEI-MNPs based sensor is able to better avoid non-specific DNA displacement by interfering proteins, generating more satisfactory signal-to-background ratio. Our proposed sensor could be a supplement to classic GO‒DNA sensors. In summary, our work provides fundamental understanding of MNPs‒DNA interactions and also paves the way for developing novel MNPs based sensing approaches, which would contribute to nano‒bio interface and DNA-assisted bio-analysis, DNA-coordinated nano-materials and DNA-directed assembly.
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Affiliation(s)
- Long Ma
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, School of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China; Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China; State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin, 300457, China.
| | - Nana Sun
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, School of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China; Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Yuanyuan Meng
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, School of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China; Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Chunhao Tu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, School of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China; Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Xiuqi Cao
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, School of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China; Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Yongchang Wei
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, School of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China; Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Liqiang Chu
- College of Chemical Engineering and Materials Science, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Aipo Diao
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, School of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China; Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China; State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin, 300457, China.
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13
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Baltierra-Jasso LE, Morten MJ, Magennis SW. Sub-Ensemble Monitoring of DNA Strand Displacement Using Multiparameter Single-Molecule FRET. Chemphyschem 2018; 19:551-555. [PMID: 29316151 DOI: 10.1002/cphc.201800012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Indexed: 11/09/2022]
Abstract
Non-enzymatic DNA strand displacement is an important mechanism in dynamic DNA nanotechnology. Here, we show that the large parameter space that is accessible by single-molecule FRET is ideal for the simultaneous monitoring of multiple reactants and products of DNA strand exchange reactions. We monitored the strand displacement from double-stranded DNA (dsDNA) by single-stranded DNA (ssDNA) at 37 °C; the data were modelled as a second-order reaction approaching equilibrium, with a rate constant of 10 m-1 s-1 . We also followed the displacement from a DNA three-way junction (3WJ) by ssDNA. The presence of three internal mismatched bases in the middle of the invading strand did not prevent displacement from the 3WJ, but reduced the second-order rate constant by about 50 %. We attribute strand exchange in the dsDNA and 3WJ to a zero-toehold pathway from the blunt-ended duplex arms. The single-molecule approach demonstrated here will be useful for studying complex DNA networks.
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Affiliation(s)
- Laura E Baltierra-Jasso
- WestCHEM School of Chemistry, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
| | - Michael J Morten
- WestCHEM School of Chemistry, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
| | - Steven W Magennis
- WestCHEM School of Chemistry, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
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14
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Smith DA, Holroyd LF, van Mourik T, Jones AC. A DFT study of 2-aminopurine-containing dinucleotides: prediction of stacked conformations with B-DNA structure. Phys Chem Chem Phys 2017; 18:14691-700. [PMID: 27186599 DOI: 10.1039/c5cp07816d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The fluorescence properties of dinucleotides incorporating 2-aminopurine (2AP) suggest that the simplest oligonucleotides adopt conformations similar to those found in duplex DNA. However, there is a lack of structural data for these systems. We report a density functional theory (DFT) study of the structures of 2AP-containing dinucleotides (deoxydinucleoside monophosphates), including full geometry optimisation of the sugar-phosphate backbone. Our DFT calculations employ the M06-2X functional for reliable treatment of dispersion interactions and include implicit aqueous solvation. Dinucleotides with 2AP in the 5'-position and each of the natural bases in the 3'-position are examined, together with the analogous 5'-adenine-containing systems. Computed structures are compared in detail with typical B-DNA base-step parameters, backbone torsional angles and sugar pucker, derived from crystallographic data. We find that 2AP-containing dinucleotides adopt structures that closely conform to B-DNA in all characteristic parameters. The structures of 2AP-containing dinucleotides closely resemble those of their adenine-containing counterparts, demonstrating the fidelity of 2AP as a mimic of the natural base. As a first step towards exploring the conformational heterogeneity of dinucleotides, we also characterise an imperfectly stacked conformation and one in which the bases are completely unstacked.
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Affiliation(s)
- Darren A Smith
- EaStCHEM School of Chemistry, The University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, UK.
| | - Leo F Holroyd
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK
| | - Tanja van Mourik
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK
| | - Anita C Jones
- EaStCHEM School of Chemistry, The University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, UK.
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15
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Toulmin A, Baltierra-Jasso LE, Morten MJ, Sabir T, McGlynn P, Schröder GF, Smith BO, Magennis SW. Conformational Heterogeneity in a Fully Complementary DNA Three-Way Junction with a GC-Rich Branchpoint. Biochemistry 2017; 56:4985-4991. [PMID: 28820590 DOI: 10.1021/acs.biochem.7b00677] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA three-way junctions (3WJs) are branched structures that serve as important biological intermediates and as components in DNA nanostructures. We recently derived the global structure of a fully complementary 3WJ and found that it contained unpaired bases at the branchpoint, which is consistent with previous observations of branch flexibility and branchpoint reactivity. By combining high-resolution single-molecule Förster resonance energy transfer, molecular modeling, time-resolved ensemble fluorescence spectroscopy, and the first 19F nuclear magnetic resonance observations of fully complementary 3WJs, we now show that the 3WJ structure can adopt multiple distinct conformations depending upon the sequence at the branchpoint. A 3WJ with a GC-rich branchpoint adopts an open conformation with unpaired bases at the branch and at least one additional conformation with an increased number of base interactions at the branchpoint. This structural diversity has implications for branch interactions and processing in vivo and for technological applications.
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Affiliation(s)
- Anita Toulmin
- The School of Chemistry, The University of Manchester , Oxford Road, Manchester M13 9PL, U.K.,The Photon Science Institute, The University of Manchester , Alan Turing Building, Oxford Road, Manchester M13 9PL, U.K
| | - Laura E Baltierra-Jasso
- The School of Chemistry, The University of Manchester , Oxford Road, Manchester M13 9PL, U.K.,The Photon Science Institute, The University of Manchester , Alan Turing Building, Oxford Road, Manchester M13 9PL, U.K.,School of Chemistry, WestCHEM, University of Glasgow , Joseph Black Building, University Avenue, Glasgow G12 8QQ, U.K
| | - Michael J Morten
- School of Chemistry, WestCHEM, University of Glasgow , Joseph Black Building, University Avenue, Glasgow G12 8QQ, U.K
| | - Tara Sabir
- The School of Chemistry, The University of Manchester , Oxford Road, Manchester M13 9PL, U.K.,The Photon Science Institute, The University of Manchester , Alan Turing Building, Oxford Road, Manchester M13 9PL, U.K
| | - Peter McGlynn
- Department of Biology, University of York , Wentworth Way, York YO10 5DD, U.K
| | - Gunnar F Schröder
- Institute of Complex Systems (ICS-6), Forschungszentrum Jülich , 52425 Jülich, Germany.,Physics Department, Heinrich-Heine Universität Düsseldorf , Düsseldorf, Germany
| | - Brian O Smith
- Institute of Molecular, Cell and Systems Biology, University of Glasgow , Glasgow G12 8QQ, U.K
| | - Steven W Magennis
- School of Chemistry, WestCHEM, University of Glasgow , Joseph Black Building, University Avenue, Glasgow G12 8QQ, U.K
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16
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Brown KE, Singh APN, Wu YL, Mishra AK, Zhou J, Lewis FD, Young RM, Wasielewski MR. Tracking Hole Transport in DNA Hairpins Using a Phenylethynylguanine Nucleobase. J Am Chem Soc 2017; 139:12084-12092. [DOI: 10.1021/jacs.7b06998] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Kristen E. Brown
- Department of Chemistry,
Argonne-Northwestern Solar Energy Research (ANSER) Center, and Institute
for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Arunoday P. N. Singh
- Department of Chemistry,
Argonne-Northwestern Solar Energy Research (ANSER) Center, and Institute
for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Yi-Lin Wu
- Department of Chemistry,
Argonne-Northwestern Solar Energy Research (ANSER) Center, and Institute
for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Ashutosh Kumar Mishra
- Department of Chemistry,
Argonne-Northwestern Solar Energy Research (ANSER) Center, and Institute
for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Jiawang Zhou
- Department of Chemistry,
Argonne-Northwestern Solar Energy Research (ANSER) Center, and Institute
for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Frederick D. Lewis
- Department of Chemistry,
Argonne-Northwestern Solar Energy Research (ANSER) Center, and Institute
for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Ryan M. Young
- Department of Chemistry,
Argonne-Northwestern Solar Energy Research (ANSER) Center, and Institute
for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Michael R. Wasielewski
- Department of Chemistry,
Argonne-Northwestern Solar Energy Research (ANSER) Center, and Institute
for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
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17
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Sun F, You Y, Liu J, Song Q, Shen X, Na N, Ouyang J. DNA Three-Way Junction for Differentiation of Single-Nucleotide Polymorphisms with Fluorescent Copper Nanoparticles. Chemistry 2017; 23:6979-6982. [DOI: 10.1002/chem.201701361] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Feifei Sun
- Key Laboratory of Theoretical and Computational Photochemistry; Ministry of Education; College of Chemistry; Beijing Normal University; Beijing 100875 P. R. China
| | - Ying You
- Key Laboratory of Theoretical and Computational Photochemistry; Ministry of Education; College of Chemistry; Beijing Normal University; Beijing 100875 P. R. China
- High School Affiliated to Southwest University; Chongqing 400700 P. R. China
| | - Jie Liu
- Department of Chemistry; Tsinghua University; Beijing 100084 P. R. China
| | - Quanwei Song
- State Key Laboratory of Petroleum Pollution Control; Beijing 102206 P. R. China
- CNPC Research Institute of Safety and Environmental Technology; Beijing 102206 P. R. China
| | - Xiaotong Shen
- Key Laboratory of Theoretical and Computational Photochemistry; Ministry of Education; College of Chemistry; Beijing Normal University; Beijing 100875 P. R. China
| | - Na Na
- Key Laboratory of Theoretical and Computational Photochemistry; Ministry of Education; College of Chemistry; Beijing Normal University; Beijing 100875 P. R. China
| | - Jin Ouyang
- Key Laboratory of Theoretical and Computational Photochemistry; Ministry of Education; College of Chemistry; Beijing Normal University; Beijing 100875 P. R. China
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18
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Ma L, Sun N, Tu C, Zhang Q, Diao A. Design of an aptamer – based fluorescence displacement biosensor for selective and sensitive detection of kanamycin in aqueous samples. RSC Adv 2017. [DOI: 10.1039/c7ra07052g] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
A label-free detection method for kanamycin A using an aptamer-based displacement biosensor has been developed.
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Affiliation(s)
- Long Ma
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
| | - Nana Sun
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
| | - Chunhao Tu
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
| | - Qian Zhang
- College of Chemical Engineering and Materials Science
- Tianjin University of Science & Technology
- Tianjin 300457
- China
| | - Aipo Diao
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
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19
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Bacteriophage T5 gene D10 encodes a branch-migration protein. Sci Rep 2016; 6:39414. [PMID: 28009009 PMCID: PMC5180179 DOI: 10.1038/srep39414] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 11/22/2016] [Indexed: 11/21/2022] Open
Abstract
Helicases catalyze the unwinding of double-stranded nucleic acids where structure and phosphate backbone contacts, rather than nucleobase sequence, usually determines substrate specificity. We have expressed and purified a putative helicase encoded by the D10 gene of bacteriophage T5. Here we report that this hitherto uncharacterized protein possesses branch migration and DNA unwinding activity. The initiation of substrate unwinding showed some sequence dependency, while DNA binding and DNA-dependent ATPase activity did not. DNA footprinting and purine-base interference assays demonstrated that D10 engages these substrates with a defined polarity that may be established by protein-nucleobase contacts. Bioinformatic analysis of the nucleotide databases revealed genes predicted to encode proteins related to D10 in archaebacteria, bacteriophages and in viruses known to infect a range of eukaryotic organisms.
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20
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DNA Three Way Junction Core Decorated with Amino Acids-Like Residues-Synthesis and Characterization. Molecules 2016; 21:molecules21091082. [PMID: 27563857 PMCID: PMC6274049 DOI: 10.3390/molecules21091082] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 08/08/2016] [Accepted: 08/10/2016] [Indexed: 11/17/2022] Open
Abstract
Construction and physico-chemical behavior of DNA three way junction (3WJ) functionalized by protein-like residues (imidazole, alcohol and carboxylic acid) at unpaired positions at the core is described. One 5'-C(S)-propargyl-thymidine nucleotide was specifically incorporated on each strand to react through a post synthetic CuACC reaction with either protected imidazolyl-, hydroxyl- or carboxyl-azide. Structural impacts of 5'-C(S)-functionalization were investigated to evaluate how 3WJ flexibility/stability is affected.
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21
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Moiseeva ED, Bazhulina NP, Gursky YG, Grokhovsky SL, Surovaya AN, Gursky GV. Targeting Holliday junctions by origin DNA-binding protein of herpes simplex virus type 1. J Biomol Struct Dyn 2016; 35:704-723. [PMID: 26987269 DOI: 10.1080/07391102.2016.1161561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
In the present paper, the interactions of the origin binding protein (OBP) of herpes simplex virus type 1 (HSV1) with synthetic four-way Holliday junctions (HJs) were studied using electrophoresis mobility shift assay and the FRET method and compared with the interactions of the protein with duplex and single-stranded DNAs. It has been found that OBP exhibits a strong preference for binding to four-way and three-way DNA junctions and possesses much lower affinities to duplex and single-stranded DNAs. The protein forms three types of complexes with HJs. It forms complexes I and II which are reminiscent of the tetramer and octamer complexes with four-way junction of HJ-specific protein RuvA of Escherichia coli. The binding approaches saturation level when two OBP dimers are bound per junction. In the presence of Mg2+ ions (≥2 mM) OBP also interacts with HJ in the stacked arm form (complex III). In the presence of 5 mM ATP and 10 mM Mg2+ ions OBP catalyzes processing of the HJ in which one of the annealed oligonucleotides has a 3'-terminal tail containing 20 unpaired thymine residues. The observed preference of OBP for binding to the four-way DNA junctions provides a basis for suggestion that OBP induces large DNA structural changes upon binding to Box I and Box II sites in OriS. These changes involve the bending and partial melting of the DNA at A+T-rich spacer and also include the formation of HJ containing Box I and Box II inverted repeats and flanking DNA sequences.
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Affiliation(s)
- E D Moiseeva
- a Engelhardt Institute of Molecular Biology , Russian Academy of Sciences , ul. Vavilova 32, 119991 Moscow , Russia
| | - N P Bazhulina
- a Engelhardt Institute of Molecular Biology , Russian Academy of Sciences , ul. Vavilova 32, 119991 Moscow , Russia
| | - Y G Gursky
- b Russian Cardiology Research-and-Production Complex , 3ya Cherepkovskaya ul. 15a, 121552 Moscow , Russia
| | - S L Grokhovsky
- a Engelhardt Institute of Molecular Biology , Russian Academy of Sciences , ul. Vavilova 32, 119991 Moscow , Russia
| | - A N Surovaya
- a Engelhardt Institute of Molecular Biology , Russian Academy of Sciences , ul. Vavilova 32, 119991 Moscow , Russia
| | - G V Gursky
- a Engelhardt Institute of Molecular Biology , Russian Academy of Sciences , ul. Vavilova 32, 119991 Moscow , Russia
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22
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Ma L, Li Y, Meng L, Deng H, Li Y, Zhang Q, Diao A. Biological fluorination from the sea: discovery of a SAM-dependent nucleophilic fluorinating enzyme from the marine-derived bacterium Streptomyces xinghaiensis NRRL B24674. RSC Adv 2016. [DOI: 10.1039/c6ra00100a] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The first ever marine originated fluorinating enzyme, which promises to be useful in biotransformation and synthetic biology, is described.
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Affiliation(s)
- Long Ma
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
| | - Yufeng Li
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
| | - Lingpei Meng
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
| | - Hai Deng
- Marine Biodiscovery Centre
- Department of Chemistry
- University of Aberdeen
- Aberdeen AB24 3UE
- UK
| | - Yuyin Li
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
| | - Qiang Zhang
- Tianjin 3rd Center Hospital
- Tianjin 300170
- China
| | - Aipo Diao
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
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23
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Ma L, Liu H, Wu G, Sun N, Meng L, Li Y, Liu Z, Diao A. A dual-channel detection of mercuric ions using a label free G-quadruplex-based DNAzyme molecule. Analyst 2016; 141:3997-4000. [DOI: 10.1039/c6an00795c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have constructed a ‘turn-off’ and label free bio-sensor using a DNAzyme molecule.
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Affiliation(s)
- Long Ma
- Biomolecular Sciences Research Complex
- EaStCHEM School of Chemistry
- University of St Andrews
- Fife KY16 9ST
- UK
| | - Haiyan Liu
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
| | - Guanrong Wu
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
| | - Nana Sun
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
| | - Lingpei Meng
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
| | - Yuyin Li
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
| | - Zhenxing Liu
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
| | - Aipo Diao
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
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24
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Ma L, Wu G, Li Y, Qin P, Meng L, Liu H, Li Y, Diao A. A reversible metal ion fueled DNA three-way junction molecular device for "turn-on and -off" fluorescence detection of mercury ions (II) and biothiols respectively with high selectivity and sensitivity. NANOSCALE 2015; 7:18044-18048. [PMID: 26487480 DOI: 10.1039/c5nr04688b] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We constructed a reversible molecular device in the nanoscale based on a DNA three-way junction (3WJ) fueled by Hg(2+) binding and sequestration. It is highly responsive to external stimuli, which brings about optically detectable global structural changes. Such a DNA device can serve as a novel "turn-on and -off" fluorescent sensor for Hg(2+) and biothiol detection with high selectivity and sensitivity.
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Affiliation(s)
- Long Ma
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, School of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China. and Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Guanrong Wu
- Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China and Biomolecular Sciences Research Complex, EaStCHEM School of Chemistry, University of St Andrews, Fife KY16 9ST, UK.
| | - Yufeng Li
- Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China and Biomolecular Sciences Research Complex, EaStCHEM School of Chemistry, University of St Andrews, Fife KY16 9ST, UK.
| | - Ping Qin
- Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China and Biomolecular Sciences Research Complex, EaStCHEM School of Chemistry, University of St Andrews, Fife KY16 9ST, UK.
| | - Lingpei Meng
- Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China and Biomolecular Sciences Research Complex, EaStCHEM School of Chemistry, University of St Andrews, Fife KY16 9ST, UK.
| | - Haiyan Liu
- Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China and Biomolecular Sciences Research Complex, EaStCHEM School of Chemistry, University of St Andrews, Fife KY16 9ST, UK.
| | - Yuyin Li
- Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China and Biomolecular Sciences Research Complex, EaStCHEM School of Chemistry, University of St Andrews, Fife KY16 9ST, UK.
| | - Aipo Diao
- Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China and Biomolecular Sciences Research Complex, EaStCHEM School of Chemistry, University of St Andrews, Fife KY16 9ST, UK.
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25
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Zhang Y, Young RM, Thazhathveetil AK, Singh APN, Liu C, Berlin YA, Grozema FC, Lewis FD, Ratner MA, Renaud N, Siriwong K, Voityuk AA, Wasielewski MR, Beratan DN. Conformationally Gated Charge Transfer in DNA Three-Way Junctions. J Phys Chem Lett 2015; 6:2434-2438. [PMID: 26266714 DOI: 10.1021/acs.jpclett.5b00863] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Molecular structures that direct charge transport in two or three dimensions possess some of the essential functionality of electrical switches and gates. We use theory, modeling, and simulation to explore the conformational dynamics of DNA three-way junctions (TWJs) that may control the flow of charge through these structures. Molecular dynamics simulations and quantum calculations indicate that DNA TWJs undergo dynamic interconversion among "well stacked" conformations on the time scale of nanoseconds, a feature that makes the junctions very different from linear DNA duplexes. The studies further indicate that this conformational gating would control charge flow through these TWJs, distinguishing them from conventional (larger size scale) gated devices. Simulations also find that structures with polyethylene glycol linking groups ("extenders") lock conformations that favor CT for 25 ns or more. The simulations explain the kinetics observed experimentally in TWJs and rationalize their transport properties compared with double-stranded DNA.
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Affiliation(s)
- Yuqi Zhang
- †Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Ryan M Young
- ‡Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- §Argonne-Northwestern Solar Energy Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208, United States
| | - Arun K Thazhathveetil
- ‡Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Arunoday P N Singh
- ‡Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Chaoren Liu
- †Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Yuri A Berlin
- ‡Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Ferdinand C Grozema
- ∥DelftChemTech, Delft University of Technology, Julianalaan 136, 2628 BL Delft, The Netherlands
| | - Frederick D Lewis
- ‡Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Mark A Ratner
- ‡Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Nicolas Renaud
- ∥DelftChemTech, Delft University of Technology, Julianalaan 136, 2628 BL Delft, The Netherlands
| | - Khatcharin Siriwong
- ⊥Materials Chemistry Research Center, Department of Chemistry and Center for Innovation in Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Alexander A Voityuk
- #Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain, Institut de Química Computacional, Universitat de Girona, 17071 Girona, Spain
| | - Michael R Wasielewski
- ‡Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- §Argonne-Northwestern Solar Energy Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208, United States
| | - David N Beratan
- †Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
- ▽Departments of Biochemistry and Physics, Duke University, Durham, North Carolina 27708, United States
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26
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2-aminopurine as a fluorescent probe of DNA conformation and the DNA–enzyme interface. Q Rev Biophys 2015; 48:244-79. [DOI: 10.1017/s0033583514000158] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
AbstractNearly 50 years since its potential as a fluorescent base analogue was first recognized, 2-aminopurine (2AP) continues to be the most widely used fluorescent probe of DNA structure and the perturbation of that structure by interaction with enzymes and other molecules. In this review, we begin by considering the origin of the dramatic and intriguing difference in photophysical properties between 2AP and its structural isomer, adenine; although 2AP differs from the natural base only in the position of the exocyclic amine group, its fluorescence intensity is one thousand times greater. We then discuss the mechanism of interbase quenching of 2AP fluorescence in DNA, which is the basis of its use as a conformational probe but remains imperfectly understood. There are hundreds of examples in the literature of the use of changes in the fluorescence intensity of 2AP as the basis of assays of conformational change; however, in this review we will consider in detail only a few intensity-based studies. Our primary aim is to highlight the use of time-resolved fluorescence measurements, and the interpretation of fluorescence decay parameters, to explore the structure and dynamics of DNA. We discuss the salient features of the fluorescence decay of 2AP when incorporated in DNA and review the use of decay measurements in studying duplexes, single strands and other structures. We survey the use of 2AP as a probe of DNA-enzyme interaction and enzyme-induced distortion, focusing particularly on its use to study base flipping and the enhanced mechanistic insights that can be gained by a detailed analysis of the decay parameters, rather than merely monitoring changes in fluorescence intensity. Finally we reflect on the merits and shortcomings of 2AP and the prospects for its wider adoption as a fluorescence-decay-based probe.
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27
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Young RM, Singh APN, Thazhathveetil AK, Cho VY, Zhang Y, Renaud N, Grozema FC, Beratan DN, Ratner MA, Schatz GC, Berlin YA, Lewis FD, Wasielewski MR. Charge Transport across DNA-Based Three-Way Junctions. J Am Chem Soc 2015; 137:5113-22. [DOI: 10.1021/jacs.5b00931] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Ryan M. Young
- Department
of Chemistry, Northwestern University
, Evanston, Illinois
60208-3113, United States
- Argonne-Northwestern
Solar Energy Research (ANSER) Center, Northwestern University
, Evanston, Illinois
60208-3113, United States
| | - Arunoday P. N. Singh
- Department
of Chemistry, Northwestern University
, Evanston, Illinois
60208-3113, United States
| | - Arun K. Thazhathveetil
- Department
of Chemistry, Northwestern University
, Evanston, Illinois
60208-3113, United States
| | - Vincent Y. Cho
- Department
of Chemistry, Northwestern University
, Evanston, Illinois
60208-3113, United States
| | - Yuqi Zhang
- Departments
of Chemistry, Biochemistry, and Physics, Duke University
, Durham, North Carolina
27708, United States
| | - Nicolas Renaud
- DelftChemTech, Delft University of Technology
, Julianalaan 136, 2628 BL
Delft, The Netherlands
| | - Ferdinand C. Grozema
- DelftChemTech, Delft University of Technology
, Julianalaan 136, 2628 BL
Delft, The Netherlands
| | - David N. Beratan
- Departments
of Chemistry, Biochemistry, and Physics, Duke University
, Durham, North Carolina
27708, United States
| | - Mark A. Ratner
- Department
of Chemistry, Northwestern University
, Evanston, Illinois
60208-3113, United States
| | - George C. Schatz
- Department
of Chemistry, Northwestern University
, Evanston, Illinois
60208-3113, United States
| | - Yuri A. Berlin
- Department
of Chemistry, Northwestern University
, Evanston, Illinois
60208-3113, United States
| | - Frederick D. Lewis
- Department
of Chemistry, Northwestern University
, Evanston, Illinois
60208-3113, United States
| | - Michael R. Wasielewski
- Department
of Chemistry, Northwestern University
, Evanston, Illinois
60208-3113, United States
- Argonne-Northwestern
Solar Energy Research (ANSER) Center, Northwestern University
, Evanston, Illinois
60208-3113, United States
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28
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Liu S, Gong H, Sun X, Liu T, Wang L. A programmable Y-shaped junction scaffold-mediated modular and cascade amplification strategy for the one-step, isothermal and ultrasensitive detection of target DNA. Chem Commun (Camb) 2015; 51:17756-9. [DOI: 10.1039/c5cc07659e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A programmable Y-shaped junction probe-mediated modular and cascade amplification strategy was proposed for the one-pot, isothermal and ultrasensitive detection of target DNA.
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Affiliation(s)
- Shufeng Liu
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Hongwei Gong
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Xinya Sun
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Tao Liu
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Li Wang
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
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29
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Barros SA, Chenoweth DM. Recognition of nucleic acid junctions using triptycene-based molecules. Angew Chem Int Ed Engl 2014; 53:13746-50. [PMID: 25257803 DOI: 10.1002/anie.201407061] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 10/09/2014] [Indexed: 12/24/2022]
Abstract
The modulation of nucleic acids by small molecules is an essential process across the kingdoms of life. Targeting nucleic acids with small molecules represents a significant challenge at the forefront of chemical biology. Nucleic acid junctions are ubiquitous structural motifs in nature and in designed materials. Herein, we describe a new class of structure-specific nucleic acid junction stabilizers based on a triptycene scaffold. Triptycenes provide significant stabilization of DNA and RNA three-way junctions, providing a new scaffold for the development of nucleic acid junction binders with enhanced recognition properties. Additionally, we report cytotoxicity and cell uptake data in two human ovarian carcinoma cell lines.
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Affiliation(s)
- Stephanie A Barros
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104 (USA)
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30
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Barros SA, Chenoweth DM. Recognition of Nucleic Acid Junctions Using Triptycene-Based Molecules. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201407061] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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31
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Stubinitzky C, Bijeljanin A, Antusch L, Ebeling D, Hölscher H, Wagenknecht HA. Bifunctional DNA architectonics: three-way junctions with sticky perylene bisimide caps and a central metal lock. Chemistry 2014; 20:12009-14. [PMID: 25098549 DOI: 10.1002/chem.201402956] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Indexed: 12/23/2022]
Abstract
A new type of a bifunctional DNA architecture based on a three way junction is developed that combines the structural motif of sticky perylene bisimide caps with a tris-bipyridyl metal ion lock in the center part. A clear stabilizing effect was observed in the presence of Fe(3+), Ni(2+) and Zn(2+) by the formation of corresponding bipyridyl complexes in the branching part of the DNA three way junctions. The dimerization of the 5'-terminally attached perylene diimides (PDI) chromophores by hydrophobic interactions can be followed by significant changes in the UV/Vis absorption and steady-state fluorescence. The PDI-mediated DNA assembly occurs at temperatures below the melting temperature and is not influenced by the metal-ion bipyridyl locks in the central part. The corresponding AFM images revealed the formation of higher-ordered structures as the result of DNA assemblies mediated by the PDI interactions.
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Affiliation(s)
- Claudia Stubinitzky
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe (Germany), Fax: (+49)-721-608-44825
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32
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Probst M, Langenegger SM, Häner R. A modular LHC built on the DNA three-way junction. Chem Commun (Camb) 2014; 50:159-61. [PMID: 24177922 DOI: 10.1039/c3cc47490a] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A light-harvesting complex composed of a π-stacked multichromophoric array in a DNA three-way junction is described. The modular design allows for a ready exchange of non-covalently attached energy acceptors.
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Affiliation(s)
- Markus Probst
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
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33
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TAKANASHI K, KATO T. Sequence-selective Modification of DNA Cytosine by Using Junction-forming DNA Probes and Its Application to the Detection of Single Cytosine Methylation. ANAL SCI 2014; 30:371-6. [DOI: 10.2116/analsci.30.371] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Kenta TAKANASHI
- Graduate School of Bionics, Computer and Media Sciences, Tokyo University of Technology
| | - Teru KATO
- Graduate School of Bionics, Computer and Media Sciences, Tokyo University of Technology
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34
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Im K, Jeong D, Hur J, Kim SJ, Hwang S, Jin KS, Park N, Kim K. Robust analysis of synthetic label-free DNA junctions in solution by X-ray scattering and molecular simulation. Sci Rep 2013; 3:3226. [PMID: 24233055 PMCID: PMC3828567 DOI: 10.1038/srep03226] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 10/30/2013] [Indexed: 12/02/2022] Open
Abstract
Structural analysis of branched DNA molecules (BDM) is important as model systems for DNA junctions and also as building units for DNA assembly. Although there have been efforts to study the structures of BDM, label-free solution structures have not been well determined yet. Here, we used a combination of synchrotron-based experimental tools and computational simulation to study the global structures of label-free BDM in solution. Overall structures of 3-arm and 4-arm BDM were revealed as an asymmetric T(or Y)-shape and a distorted X-shape, respectively. The internal structures of the DNA double helix were shown to have a canonical B-form for both the BDM. We also reconstructed the thermal denaturation process of BDM by determining the transient global structures over a wide range of temperatures. The proposed high-resolution structures of BDM are expected to provide fundamental information for studies of the biological function of junction DNAs and DNA assembly.
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Affiliation(s)
- Kyuhyun Im
- 1] Frontier Research Laboratory, Samsung Advanced Institute of Technology, Samsung Electronics, Yongin, Gyeonggi-do 446-712, South Korea [2]
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35
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Addressable and unidirectional energy transfer along a DNA three-way junction programmed by pyrrole-imidazole polyamides. Sci Rep 2013; 3:1883. [PMID: 23703234 PMCID: PMC3662969 DOI: 10.1038/srep01883] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 05/10/2013] [Indexed: 11/23/2022] Open
Abstract
We describe a photonic waveguide where FRET is routed uni-directionally along a double-stranded DNA track. The efficiency of FRET is modulated by the supramolecular control of fluorophores along double-stranded DNA using fluorophore-tethered Pyrrole-Imidazole polyamides (PAs). We show that uni-directional FRET is enhanced by the complete assembly of each of the constituent parts, resulting in the selective routing of light along simple DNA duplexes as well as a three-way junction (3WJ).
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36
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Finger LD, Patel N, Beddows A, Ma L, Exell JC, Jardine E, Jones AC, Grasby JA. Observation of unpaired substrate DNA in the flap endonuclease-1 active site. Nucleic Acids Res 2013; 41:9839-47. [PMID: 23975198 PMCID: PMC3834815 DOI: 10.1093/nar/gkt737] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The structure- and strand-specific phosphodiesterase flap endonuclease-1 (FEN1), the prototypical 5′-nuclease, catalyzes the essential removal of 5′-single-stranded flaps during replication and repair. FEN1 achieves this by selectively catalyzing hydrolysis one nucleotide into the duplex region of substrates, always targeting the 5′-strand. This specificity is proposed to arise by unpairing the 5′-end of duplex to permit the scissile phosphate diester to contact catalytic divalent metal ions. Providing the first direct evidence for this, we detected changes induced by human FEN1 (hFEN1) in the low-energy CD spectra and fluorescence lifetimes of 2-aminopurine in substrates and products that were indicative of unpairing. Divalent metal ions were essential for unpairing. However, although 5′-nuclease superfamily-conserved active-site residues K93 and R100 were required to produce unpaired product, they were not necessary to unpair substrates. Nevertheless, a unique arrangement of protein residues around the unpaired DNA was detected only with wild-type protein, suggesting a cooperative assembly of active-site residues that may be triggered by unpaired DNA. The general principles of FEN1 strand and reaction-site selection, which depend on the ability of juxtaposed divalent metal ions to unpair the end of duplex DNA, may also apply more widely to other structure- and strand-specific nucleases.
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Affiliation(s)
- L David Finger
- Department of Chemistry, Centre for Chemical Biology, Krebs Institute, University of Sheffield, Sheffield, S3 7HF, UK and EaStCHEM School of Chemistry and Collaborative Optical Spectroscopy, Micromanipulation and Imaging Centre, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, UK
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37
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Paredes E, Zhang X, Ghodke H, Yadavalli VK, Das SR. Backbone-branched DNA building blocks for facile angular control in nanostructures. ACS NANO 2013; 7:3953-3961. [PMID: 23600590 DOI: 10.1021/nn305787m] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Nanotechnology based on the highly specific pairing of nucleobases in DNA has been used to generate a wide variety of well-defined two- and three-dimensional assemblies, both static and dynamic. However, control over the junction angles to achieve them has been limited. To achieve higher order assemblies, the strands of the DNA duplex are typically made to deviate at junctions with configurations based on crossovers or non-DNA moieties. Such strand crossovers tend to be intrinsically unstructured with the overall structural rigidity determined by the architecture of the nanoassembly, rather than the junction itself. Specific approaches to define nanoassembly junction angles are based either on the cooperative twist- and strain-promoted tuning of DNA persistence length leading to bent DNA rods for fairly large nano-objects, or de novo synthesis of individual junction inserts that are typically non-DNA and based on small organic molecules or metal-coordinating ligand moieties. Here, we describe a general strategy for direct control of junction angles in DNA nanostructures that are completely tunable about the DNA helix. This approach is used to define angular vertices through readily accessible backbone-branched DNAs (bbDNAs). We demonstrate how such bbDNAs can be used as a new building block in DNA nanoconstruction to obtain well-defined nanostructures. Angular control through readily accessible bbDNA building block provides a general and versatile approach for incorporating well-defined junctions in nanoconstructs and expands the toolkit toward achieving strain free, highly size- and shape-tunable DNA based architectures.
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Affiliation(s)
- Eduardo Paredes
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
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Slean MM, Reddy K, Wu B, Nichol Edamura K, Kekis M, Nelissen FHT, Aspers RLEG, Tessari M, Schärer OD, Wijmenga SS, Pearson CE. Interconverting conformations of slipped-DNA junctions formed by trinucleotide repeats affect repair outcome. Biochemistry 2013; 52:773-85. [PMID: 23339280 PMCID: PMC3566650 DOI: 10.1021/bi301369b] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Expansions of (CTG)·(CAG) repeated DNAs are the mutagenic cause of 14 neurological diseases, likely arising through the formation and processing of slipped-strand DNAs. These transient intermediates of repeat length mutations are formed by out-of-register mispairing of repeat units on complementary strands. The three-way slipped-DNA junction, at which the excess repeats slip out from the duplex, is a poorly understood feature common to these mutagenic intermediates. Here, we reveal that slipped junctions can assume a surprising number of interconverting conformations where the strand opposite the slip-out either is fully base paired or has one or two unpaired nucleotides. These unpaired nucleotides can also arise opposite either of the nonslipped junction arms. Junction conformation can affect binding by various structure-specific DNA repair proteins and can also alter correct nick-directed repair levels. Junctions that have the potential to contain unpaired nucleotides are repaired with a significantly higher efficiency than constrained fully paired junctions. Surprisingly, certain junction conformations are aberrantly repaired to expansion mutations: misdirection of repair to the non-nicked strand opposite the slip-out leads to integration of the excess slipped-out repeats rather than their excision. Thus, slipped-junction structure can determine whether repair attempts lead to correction or expansion mutations.
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Affiliation(s)
- Meghan M Slean
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
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Su X, Xiao X, Zhang C, Zhao M. Nucleic acid fluorescent probes for biological sensing. APPLIED SPECTROSCOPY 2012; 66:1249-1262. [PMID: 23146180 DOI: 10.1366/12-06803] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Nucleic acid fluorescent probes are playing increasingly important roles in biological sensing in recent years. In addition to the conventional functions of single-stranded DNA/RNA to hybridize with their complementary strands, affinity nucleic acids (aptamers) with specific target binding properties have also been developed, which has greatly broadened the application of nucleic acid fluorescent probes to the detection of a large variety of analytes, including small molecules, proteins, ions, and even whole cells. Another chemical property of nucleic acids is to act as substrates for various nucleic acid enzymes. This property can be utilized not only to detect those enzymes and screen their inhibitors, but also employed to develop effective signal amplification systems, which implies extensive applications. This review mainly covers the biosensing methods based on the above three types of nucleic acid fluorescent probes. The most widely used intensity-based biosensing assays are covered first, including nucleic acid probe-based signal amplification methods. Then fluorescence lifetime, fluorescence anisotropy, and fluorescence correlation spectroscopy assays are introduced, respectively. As a rapidly developing field, fluorescence imaging approaches are also briefly summarized.
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Affiliation(s)
- Xin Su
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, China
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40
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Preus S, Wilhelmsson LM. Advances in quantitative FRET-based methods for studying nucleic acids. Chembiochem 2012; 13:1990-2001. [PMID: 22936620 DOI: 10.1002/cbic.201200400] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Indexed: 01/02/2023]
Abstract
Förster resonance energy transfer (FRET) is a powerful tool for monitoring molecular distances and interactions at the nanoscale level. The strong dependence of transfer efficiency on probe separation makes FRET perfectly suited for "on/off" experiments. To use FRET to obtain quantitative distances and three-dimensional structures, however, is more challenging. This review summarises recent studies and technological advances that have improved FRET as a quantitative molecular ruler in nucleic acid systems, both at the ensemble and at the single-molecule levels.
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Affiliation(s)
- Søren Preus
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
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