1
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An Y, Xu D, Wen X, Chen C, Liu G, Lu Z. Internal Light Sources-Mediated Photodynamic Therapy Nanoplatforms: Hope for the Resolution of the Traditional Penetration Problem. Adv Healthc Mater 2024; 13:e2301326. [PMID: 37413664 DOI: 10.1002/adhm.202301326] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/21/2023] [Accepted: 06/29/2023] [Indexed: 07/08/2023]
Abstract
Photodynamic therapy (PDT) is an alternative cancer treatment technique with a noninvasive nature, high selectivity, and minimal adverse effects. The indispensable light source used in PDT is a critical factor in determining the energy conversion of photosensitizers (PSs). Traditional light sources are primarily concentrated in the visible light region, severely limiting their penetration depth and making them prone to scattering and absorption when applied to biological tissues. For that reason, its efficacy in treating deep-seated lesions is often inadequate. Self-exciting PDT, also known as auto-PDT (APDT), is an attractive option for circumventing the limited penetration depth of traditional PDT and has acquired significant attention. APDT employs depth-independent internal light sources to excite PSs through resonance or radiative energy transfer. APDT has considerable potential for treating deep-tissue malignancies. To facilitate many researchers' comprehension of the latest research progress in this field and inspire the emergence of more novel research results. This review introduces internal light generation mechanisms and characteristics and provides an overview of current research progress based on the recently reported APDT nanoplatforms. The current challenges and possible solutions of APDT nanoplatforms are also presented and provide insights for future research in the final section of this article.
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Affiliation(s)
- Yibo An
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics & Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Dazhuang Xu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics & Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Xiaofei Wen
- Department of Interventional Radiology, The First Affilited Hospital of Xiamen University, Xiamen, 361000, China
| | - Chuan Chen
- Department of Pharmacy, Xiamen Medical College, Xiamen, 361023, China
| | - Gang Liu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics & Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Zhixiang Lu
- School of Pharmaceutical Sciences, Xiamen University, Xiamen, 361102, China
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2
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Sorour MI, Kistler KA, Marcus AH, Matsika S. Accurate Modeling of Excitonic Coupling in Cyanine Dye Cy3. J Phys Chem A 2021; 125:7852-7866. [PMID: 34494437 DOI: 10.1021/acs.jpca.1c05556] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Accurate modeling of excitonic coupling in molecules is of great importance for inferring the structures and dynamics of coupled systems. Cy3 is a cyanine dye that is widely used in molecular spectroscopy. Its well-separated excitation bands, high sensitivity to the surroundings, and the high energy transfer efficiency make it a perfect choice for excitonic coupling experiments. Many methods have been used to model the excitonic coupling in molecules with varying degrees of accuracy. The atomic transition charge model offers a high-accuracy and cost-effective way to calculating the excitonic coupling. The main focus of this work is to generate high-quality atomic transition charges that can accurately model the Cy3 dye's transition density. The transition density of the excitation of the ground to first excited state is calculated using configuration-interaction singles and time-dependent density functional theory and is benchmarked against the algebraic diagrammatic construction method. Using the transition density we derived the atomic transition charges using two approaches: Mulliken population analysis and charges fitted to the transition electrostatic potential. The quality of the charges is examined, and their ability to accurately calculate the excitonic coupling is assessed via comparison to experimental data of an artificial biscyanine construct. Theoretical comparisons to the supermolecule ab initio couplings and the widely used point-dipole approximation are also made. Results show that using the transition electrostatic potential is a reliable approach for generating the transition atomic charges. A high-quality set of charges, that can be used to model the Cy3 dye dimer excitonic coupling with high-accuracy and a reasonable computational cost, is obtained.
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Affiliation(s)
- Mohammed I Sorour
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Kurt A Kistler
- Department of Chemistry, Brandywine Campus, The Pennsylvania State University, Media, Pennsylvania 19063, United States
| | - Andrew H Marcus
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403, United States
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
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3
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Bartels K, Lasitza‐Male T, Hofmann H, Löw C. Single-Molecule FRET of Membrane Transport Proteins. Chembiochem 2021; 22:2657-2671. [PMID: 33945656 PMCID: PMC8453700 DOI: 10.1002/cbic.202100106] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/03/2021] [Indexed: 12/31/2022]
Abstract
Uncovering the structure and function of biomolecules is a fundamental goal in structural biology. Membrane-embedded transport proteins are ubiquitous in all kingdoms of life. Despite structural flexibility, their mechanisms are typically studied by ensemble biochemical methods or by static high-resolution structures, which complicate a detailed understanding of their dynamics. Here, we review the recent progress of single molecule Förster Resonance Energy Transfer (smFRET) in determining mechanisms and timescales of substrate transport across membranes. These studies do not only demonstrate the versatility and suitability of state-of-the-art smFRET tools for studying membrane transport proteins but they also highlight the importance of membrane mimicking environments in preserving the function of these proteins. The current achievements advance our understanding of transport mechanisms and have the potential to facilitate future progress in drug design.
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Affiliation(s)
- Kim Bartels
- Centre for Structural Systems Biology (CSSB)DESY and European Molecular Biology Laboratory HamburgNotkestrasse 8522607HamburgGermany
| | - Tanya Lasitza‐Male
- Department of Structural BiologyWeizmann Institute of ScienceHerzl St. 2347610001RehovotIsrael
| | - Hagen Hofmann
- Department of Structural BiologyWeizmann Institute of ScienceHerzl St. 2347610001RehovotIsrael
| | - Christian Löw
- Centre for Structural Systems Biology (CSSB)DESY and European Molecular Biology Laboratory HamburgNotkestrasse 8522607HamburgGermany
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4
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Liu J, Liu S, Liu C, Zhang Y, Pan Y, Wang Z, Wang J, Wen T, Deng L. Nabe: an energetic database of amino acid mutations in protein-nucleic acid binding interfaces. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021; 2021:6352208. [PMID: 34389843 PMCID: PMC8363842 DOI: 10.1093/database/baab050] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 07/23/2021] [Accepted: 07/29/2021] [Indexed: 12/17/2022]
Abstract
Protein–nucleic acid complexes play essential roles in regulating transcription, translation, DNA replication, repair and recombination, RNA processing and translocation. Site-directed mutagenesis has been extremely useful in understanding the principles of protein–DNA and protein–RNA interactions, and experimentally determined mutagenesis data are prerequisites for designing effective algorithms for predicting the binding affinity change upon mutation. However, a vital challenge in this area is the lack of sufficient public experimentally recognized mutation data, which leads to difficulties in developing computational prediction methods. In this article, we present Nabe, an integrated database of amino acid mutations and their effects on the binding free energy in protein–DNA and protein–RNA interactions for which binding affinities have been experimentally determined. Compared with existing databases and data sets, Nabe is the largest protein–nucleic acid mutation database, containing 2506 mutations in 473 protein–DNA and protein–RNA complexes, and of that 1751 are alanine mutations in 405 protein–nucleic acid complexes. For researchers to conveniently utilize the data, Nabe assembles protein–DNA and protein–RNA benchmark databases by adopting the data-processing procedures in the majority of models. To further facilitate users to query data, Nabe provides a searchable and graphical web page. Database URL: http://nabe.denglab.org
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Affiliation(s)
- Junyi Liu
- School of Computer Science and Engineering, Central South University, 22 Shaoshan South Road, Changsha 410075, China.,Viterbi School of Engineering, University of Southern California, 3650 McClintock Ave. OHE 106, Los Angeles, CA 90089, USA
| | - Siyu Liu
- School of Computer Science and Engineering, Central South University, 22 Shaoshan South Road, Changsha 410075, China
| | - Chenzhe Liu
- School of Computer Science and Engineering, Central South University, 22 Shaoshan South Road, Changsha 410075, China
| | - Yaping Zhang
- School of Computer Science and Engineering, Central South University, 22 Shaoshan South Road, Changsha 410075, China
| | - Yuliang Pan
- School of Computer Science and Engineering, Central South University, 22 Shaoshan South Road, Changsha 410075, China
| | - Zixiang Wang
- School of Computer Science and Engineering, Central South University, 22 Shaoshan South Road, Changsha 410075, China
| | - Jiacheng Wang
- School of Computer Science and Engineering, Central South University, 22 Shaoshan South Road, Changsha 410075, China
| | - Ting Wen
- School of Computer Science and Engineering, Central South University, 22 Shaoshan South Road, Changsha 410075, China
| | - Lei Deng
- School of Computer Science and Engineering, Central South University, 22 Shaoshan South Road, Changsha 410075, China
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5
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Jiang Y, Liu HF, Liu R. Systematic comparison and prediction of the effects of missense mutations on protein-DNA and protein-RNA interactions. PLoS Comput Biol 2021; 17:e1008951. [PMID: 33872313 PMCID: PMC8084330 DOI: 10.1371/journal.pcbi.1008951] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 04/29/2021] [Accepted: 04/08/2021] [Indexed: 12/30/2022] Open
Abstract
The binding affinities of protein-nucleic acid interactions could be altered due to missense mutations occurring in DNA- or RNA-binding proteins, therefore resulting in various diseases. Unfortunately, a systematic comparison and prediction of the effects of mutations on protein-DNA and protein-RNA interactions (these two mutation classes are termed MPDs and MPRs, respectively) is still lacking. Here, we demonstrated that these two classes of mutations could generate similar or different tendencies for binding free energy changes in terms of the properties of mutated residues. We then developed regression algorithms separately for MPDs and MPRs by introducing novel geometric partition-based energy features and interface-based structural features. Through feature selection and ensemble learning, similar computational frameworks that integrated energy- and nonenergy-based models were established to estimate the binding affinity changes resulting from MPDs and MPRs, but the selected features for the final models were different and therefore reflected the specificity of these two mutation classes. Furthermore, the proposed methodology was extended to the identification of mutations that significantly decreased the binding affinities. Extensive validations indicated that our algorithm generally performed better than the state-of-the-art methods on both the regression and classification tasks. The webserver and software are freely available at http://liulab.hzau.edu.cn/PEMPNI and https://github.com/hzau-liulab/PEMPNI. Protein-nucleic acid interactions play important roles in various cellular processes. Missense mutations occurring in DNA- or RNA-binding proteins (termed MPDs and MPRs, respectively) could change the binding affinities of these interactions. Previous studies have compared protein-DNA and protein-RNA interactions from multifaceted viewpoints, but less attention has been given to the similarities and specific differences between the effects of MPDs and MPRs and between the methodologies for predicting the affinity changes induced by the two mutation classes. Therefore, we systematically compared their impacts and demonstrated that MPDs and MPRs could have specific preferences for binding affinity changes. These observations motivated us to construct regression models separately for MPDs and MPRs by introducing novel energy and nonenergy descriptors. Although similar frameworks were developed to estimate these two categories of mutation effects, different descriptors were selected in the regression models and further revealed the specificity of mutation classes. The interplay between the energy and nonenergy modules effectively improved prediction performance. Our algorithm can also be adopted to disentangle mutations significantly decreasing binding affinities from other mutations.
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Affiliation(s)
- Yao Jiang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, P. R. China
| | - Hui-Fang Liu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, P. R. China
| | - Rong Liu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, P. R. China
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6
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Fatima U, Ameen F, Soleja N, Khan P, Almansob A, Ahmad A. A Fluorescence Resonance Energy Transfer-Based Analytical Tool for Nitrate Quantification in Living Cells. ACS OMEGA 2020; 5:30306-30314. [PMID: 33251465 PMCID: PMC7689916 DOI: 10.1021/acsomega.0c04868] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 11/02/2020] [Indexed: 05/11/2023]
Abstract
Nitrate (NO3 -) is a critical source of nitrogen (N) available to microorganisms and plants. Nitrate sensing activates signaling pathways in the plant system that impinges upon, developmental, molecular, metabolic, and physiological responses locally, and globally. To sustain, the high crop productivity and high nutritional value along with the sustainable environment, the study of rate-controlling steps of a metabolic network of N assimilation through fluxomics becomes an attractive strategy. To monitor the flux of nitrate, we developed a non-invasive genetically encoded fluorescence resonance energy transfer (FRET)-based tool named "FLIP-NT" that monitors the real-time uptake of nitrate in the living cells. The developed nanosensor is suitable for real-time monitoring of nitrate flux in living cells at subcellular compartments with high spatio-temporal resolution. The developed FLIP-NT nanosensor was not affected by the pH change and have specificity for nitrate with an affinity constant (K d) of ∼5 μM. A series of affinity mutants have also been generated to expand the physiological detection range of the sensor protein with varying K d values. It has been found that this sensor successfully detects the dynamics of nitrate fluctuations in bacteria and yeast, without the disruption of cellular organization. This FLIP-NT nanosensor could be a very important tool that will help us to advance the understanding of nitrate signaling.
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Affiliation(s)
- Urooj Fatima
- Department
of Botany, Faculty of Life Sciences, Aligarh
Muslim University, Aligarh 202002, India
| | - Fuad Ameen
- Department
of Botany & Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Neha Soleja
- Department
of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Parvez Khan
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Abobakr Almansob
- Department
of Botany & Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Altaf Ahmad
- Department
of Botany, Faculty of Life Sciences, Aligarh
Muslim University, Aligarh 202002, India
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7
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Shaw RA, Johnston-Wood T, Ambrose B, Craggs TD, Hill JG. CHARMM-DYES: Parameterization of Fluorescent Dyes for Use with the CHARMM Force Field. J Chem Theory Comput 2020; 16:7817-7824. [DOI: 10.1021/acs.jctc.0c00721] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Robert A. Shaw
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF, U.K
- Present address: ARC Centre of Excellence in Exciton Science, School of Science, RMIT University, Melbourne, VIC 3000, Australia
| | - Tristan Johnston-Wood
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF, U.K
- Present address: Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, U.K
| | - Benjamin Ambrose
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF, U.K
| | - Timothy D. Craggs
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF, U.K
| | - J. Grant Hill
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF, U.K
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8
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Pan Y, Zhou S, Guan J. Computationally identifying hot spots in protein-DNA binding interfaces using an ensemble approach. BMC Bioinformatics 2020; 21:384. [PMID: 32938375 PMCID: PMC7495898 DOI: 10.1186/s12859-020-03675-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Protein-DNA interaction governs a large number of cellular processes, and it can be altered by a small fraction of interface residues, i.e., the so-called hot spots, which account for most of the interface binding free energy. Accurate prediction of hot spots is critical to understand the principle of protein-DNA interactions. There are already some computational methods that can accurately and efficiently predict a large number of hot residues. However, the insufficiency of experimentally validated hot-spot residues in protein-DNA complexes and the low diversity of the employed features limit the performance of existing methods. RESULTS Here, we report a new computational method for effectively predicting hot spots in protein-DNA binding interfaces. This method, called PreHots (the abbreviation of Predicting Hotspots), adopts an ensemble stacking classifier that integrates different machine learning classifiers to generate a robust model with 19 features selected by a sequential backward feature selection algorithm. To this end, we constructed two new and reliable datasets (one benchmark for model training and one independent dataset for validation), which totally consist of 123 hot spots and 137 non-hot spots from 89 protein-DNA complexes. The data were manually collected from the literature and existing databases with a strict process of redundancy removal. Our method achieves a sensitivity of 0.813 and an AUC score of 0.868 in 10-fold cross-validation on the benchmark dataset, and a sensitivity of 0.818 and an AUC score of 0.820 on the independent test dataset. The results show that our approach outperforms the existing ones. CONCLUSIONS PreHots, which is based on stack ensemble of boosting algorithms, can reliably predict hot spots at the protein-DNA binding interface on a large scale. Compared with the existing methods, PreHots can achieve better prediction performance. Both the webserver of PreHots and the datasets are freely available at: http://dmb.tongji.edu.cn/tools/PreHots/ .
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Affiliation(s)
- Yuliang Pan
- Department of Computer Science and Technology, Tongji University, No. 4800 Caoan Road, Shanghai, 201804, China
| | - Shuigeng Zhou
- Shanghai Key Laboratory of Intelligent Information Processing, and School of Computer Science, Fudan University, No. 220 Handan Road, Shanghai, 200433, China
| | - Jihong Guan
- Department of Computer Science and Technology, Tongji University, No. 4800 Caoan Road, Shanghai, 201804, China.
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9
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Jana P, Šupljika F, Schmuck C, Piantanida I. Naphthalene diimide bis-guanidinio-carbonyl-pyrrole as a pH-switchable threading DNA intercalator. Beilstein J Org Chem 2020; 16:2201-2211. [PMID: 32983268 PMCID: PMC7492691 DOI: 10.3762/bjoc.16.185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 08/26/2020] [Indexed: 12/16/2022] Open
Abstract
A novel naphthalene diimde analogue (NDI) equipped at the imide positions with two guanidinio-carbonyl-pyrrole (GCP) pendant arms interacted significantly stronger with ds-DNA at pH 5 than at pH 7, due to reversible protonation of the GCP arms. This was consequence of a pH-switchable threading intercalation into ds-DNAs only at pH 5, while at neutral conditions (pH 7) NDI-GCP2 switched to the DNA minor groove binding. Intriguingly, NDI-GCP2 was at both pH values studied bound to the ds-RNA major groove, still showing a higher affinity and thermal denaturation effect at pH 5 due to GCP protonation. At excess over the DNA/RNA conjugate NDI-GCP2 showed also aggregation along the ds-polynucleotide and AFM and DLS demonstrated that NDI-GCP2 has pronounced ds-DNA condensation ability.
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Affiliation(s)
- Poulami Jana
- Institute for Organic Chemistry, University of Duisburg-Essen, Universitässtrasse 7, 45141 Essen, Germany.,Integrated Science Education & Research Centre, Siksha-Bhavana, Visva-Bharati, Santiniketan-731235, India
| | - Filip Šupljika
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, P. O. Box 180, HR-10002 Zagreb, Croatia.,Laboratory for Physical Chemistry and Corrosion, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Croatia
| | - Carsten Schmuck
- Institute for Organic Chemistry, University of Duisburg-Essen, Universitässtrasse 7, 45141 Essen, Germany
| | - Ivo Piantanida
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, P. O. Box 180, HR-10002 Zagreb, Croatia
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10
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Botti V, Cesaretti A, Ban Ž, Crnolatac I, Consiglio G, Elisei F, Piantanida I. Fine structural tuning of styryl-based dyes for fluorescence and CD-based sensing of various ds-DNA/RNA sequences. Org Biomol Chem 2019; 17:8243-8258. [PMID: 31464340 DOI: 10.1039/c9ob01186b] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A set of styryl- and bis-styryl dyes, varying in length, aromatic surface, net positive charge and steric positioning or bulkiness of substituents, was tested for interactions with various ds-DNA or ds-RNA. Most of the compounds showed strong affinity toward ds-DNA/RNA, directly correlated to the synergistic contribution of the aromatic-conjugated surface and net positive charge. The volume or positioning of terminal aromatic substituents directly controlled the binding mode of the core structure, shifting between DNA/RNA groove binding or DNA/RNA intercalation. Consequently, upon binding to DNA/RNA the fluorimetric and induced CD (ICD) response varied for different compounds, for instance one derivative showed specific fluorescence increase with AT-DNA, while another derivative showed specific ICD response with AU-RNA. Preliminary screening on human tumour cell lines revealed an efficient cellular uptake for all dyes. Only mono-styryl-quinoline derivatives showed a strong antiproliferative activity combined with efficient fluorescent localisation, thus showing promising theragnostic potential, while other compounds were negligibly cytotoxic but still efficient fluorescent markers of cytoplasmic organelles.
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Affiliation(s)
- Valentina Botti
- Department of Chemistry, Biology and Biotechnology and Centro di Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN) University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy.
| | - Alessio Cesaretti
- Department of Chemistry, Biology and Biotechnology and Centro di Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN) University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy.
| | - Željka Ban
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10002 Zagreb, Croatia.
| | - Ivo Crnolatac
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10002 Zagreb, Croatia.
| | - Giuseppe Consiglio
- Department of Chemical Sciences, University of Catania, viale Andrea Doria 6, 95125 Catania, Italy
| | - Fausto Elisei
- Department of Chemistry, Biology and Biotechnology and Centro di Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN) University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy.
| | - Ivo Piantanida
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10002 Zagreb, Croatia.
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11
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Velmurugu Y, Vivas P, Connolly M, Kuznetsov SV, Rice PA, Ansari A. Two-step interrogation then recognition of DNA binding site by Integration Host Factor: an architectural DNA-bending protein. Nucleic Acids Res 2019; 46:1741-1755. [PMID: 29267885 PMCID: PMC5829579 DOI: 10.1093/nar/gkx1215] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 12/08/2017] [Indexed: 12/23/2022] Open
Abstract
The dynamics and mechanism of how site-specific DNA-bending proteins initially interrogate potential binding sites prior to recognition have remained elusive for most systems. Here we present these dynamics for Integration Host factor (IHF), a nucleoid-associated architectural protein, using a μs-resolved T-jump approach. Our studies show two distinct DNA-bending steps during site recognition by IHF. While the faster (∼100 μs) step is unaffected by changes in DNA or protein sequence that alter affinity by >100-fold, the slower (1–10 ms) step is accelerated ∼5-fold when mismatches are introduced at DNA sites that are sharply kinked in the specific complex. The amplitudes of the fast phase increase when the specific complex is destabilized and decrease with increasing [salt], which increases specificity. Taken together, these results indicate that the fast phase is non-specific DNA bending while the slow phase, which responds only to changes in DNA flexibility at the kink sites, is specific DNA kinking during site recognition. Notably, the timescales for the fast phase overlap with one-dimensional diffusion times measured for several proteins on DNA, suggesting that these dynamics reflect partial DNA bending during interrogation of potential binding sites by IHF as it scans DNA.
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Affiliation(s)
- Yogambigai Velmurugu
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Paula Vivas
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Mitchell Connolly
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Serguei V Kuznetsov
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Phoebe A Rice
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Anjum Ansari
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA.,Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
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12
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PremPDI estimates and interprets the effects of missense mutations on protein-DNA interactions. PLoS Comput Biol 2018; 14:e1006615. [PMID: 30533007 PMCID: PMC6303081 DOI: 10.1371/journal.pcbi.1006615] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 12/21/2018] [Accepted: 11/01/2018] [Indexed: 01/01/2023] Open
Abstract
Protein-DNA interactions play important roles in regulations of many vital cellular processes, including transcription, translation, DNA replication and recombination. Sequence variants occurring in these DNA binding proteins that alter protein-DNA interactions may cause significant perturbations or complete abolishment of function, potentially leading to diseases. Developing a mechanistic understanding of impacts of variants on protein-DNA interactions becomes a persistent need. To address this need we introduce a new computational method PremPDI that predicts the effect of single missense mutation in the protein on the protein-DNA interaction and calculates the quantitative binding affinity change. The PremPDI method is based on molecular mechanics force fields and fast side-chain optimization algorithms with parameters optimized on experimental sets of 219 mutations from 49 protein-DNA complexes. PremPDI yields a very good agreement between predicted and experimental values with Pearson correlation coefficient of 0.71 and root-mean-square error of 0.86 kcal mol-1. The PremPDI server could map mutations on a structural protein-DNA complex, calculate the associated changes in binding affinity, determine the deleterious effect of a mutation, and produce a mutant structural model for download. PremPDI can be applied to many tasks, such as determination of potential damaging mutations in cancer and other diseases. PremPDI is available at http://lilab.jysw.suda.edu.cn/research/PremPDI/. Developing methods for accurate prediction of effects of amino acid substitutions on protein-DNA interactions is important for a wide range of biomedical applications such as understanding disease-causing mechanism of missense mutations and guiding protein engineering. Very few methods have been developed for predicting the effects of mutations on protein-DNA binding affinity. Here we report a new computational method, PRedicts the Effects of single Mutations on Protein-DNA Interactions (PremPDI). The core of the PremPDI method is based on molecular mechanics force fields and fast side-chain optimization algorithms that makes the PremPDI algorithm efficient and being fast enough to handle large number of cases. The performance of the PremPDI protocol was tested against experimentally determined binding free energy changes of 219 mutations from 49 protein-DNA complexes and yields very good correlation coefficient. The PremPDI webserver is available to the community at http://lilab.jysw.suda.edu.cn/research/PremPDI/.
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13
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Peng Y, Sun L, Jia Z, Li L, Alexov E. Predicting protein-DNA binding free energy change upon missense mutations using modified MM/PBSA approach: SAMPDI webserver. Bioinformatics 2018; 34:779-786. [PMID: 29091991 DOI: 10.1093/bioinformatics/btx698] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 10/27/2017] [Indexed: 12/28/2022] Open
Abstract
Motivation Protein-DNA interactions are essential for regulating many cellular processes, such as transcription, replication, recombination and translation. Amino acid mutations occurring in DNA-binding proteins have profound effects on protein-DNA binding and are linked with many diseases. Hence, accurate and fast predictions of the effects of mutations on protein-DNA binding affinity are essential for understanding disease-causing mechanisms and guiding plausible treatments. Results Here we report a new method Single Amino acid Mutation binding free energy change of Protein-DNA Interaction (SAMPDI). The method utilizes modified Molecular Mechanics Poisson-Boltzmann Surface Area (MM/PBSA) approach along with an additional set of knowledge-based terms delivered from investigations of the physicochemical properties of protein-DNA complexes. The method is benchmarked against experimentally determined binding free energy changes caused by 105 mutations in 13 proteins (compiled ProNIT database and data from recent references), and results in correlation coefficient of 0.72. Availability and implementation http://compbio.clemson.edu/SAMPDI. Contact ealexov@clemson.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yunhui Peng
- Department of Physics and Astronomy, Clemson University, Clemson SC 29634, USA
| | - Lexuan Sun
- Department of Physics and Astronomy, Clemson University, Clemson SC 29634, USA
| | - Zhe Jia
- Department of Physics and Astronomy, Clemson University, Clemson SC 29634, USA
| | - Lin Li
- Department of Physics and Astronomy, Clemson University, Clemson SC 29634, USA
| | - Emil Alexov
- Department of Physics and Astronomy, Clemson University, Clemson SC 29634, USA
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14
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Teunissen AJP, Pérez-Medina C, Meijerink A, Mulder WJM. Investigating supramolecular systems using Förster resonance energy transfer. Chem Soc Rev 2018; 47:7027-7044. [PMID: 30091770 PMCID: PMC6441672 DOI: 10.1039/c8cs00278a] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Supramolecular systems have applications in areas as diverse as materials science, biochemistry, analytical chemistry, and nanomedicine. However, analyzing such systems can be challenging due to the wide range of time scales, binding strengths, distances, and concentrations at which non-covalent phenomena take place. Due to their versatility and sensitivity, Förster resonance energy transfer (FRET)-based techniques are excellently suited to meet such challenges. Here, we detail the ways in which FRET has been used to study non-covalent interactions in both synthetic and biological supramolecular systems. Among other topics, we examine methods to measure molecular forces, determine protein conformations, monitor assembly kinetics, and visualize in vivo drug release from nanoparticles. Furthermore, we highlight multiplex FRET techniques, discuss the field's limitations, and provide a perspective on new developments.
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Affiliation(s)
- Abraham J. P. Teunissen
- Translational and Molecular Imaging Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
| | - Carlos Pérez-Medina
- Translational and Molecular Imaging Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
| | - Andries Meijerink
- Department of Chemistry, Utrecht University, Princetonplein 1, 3584 CC Utrecht, The Netherlands
| | - Willem J. M. Mulder
- Translational and Molecular Imaging Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
- Department of Medical Biochemistry, Academic Medical Center, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- Laboratory of Chemical biology, Department of Biomedical Engineering and Institute for Complex Molecular systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, The Netherlands
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15
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Shiraogawa T, Candel G, Fukuda R, Ciofini I, Adamo C, Okamoto A, Ehara M. Photophysical properties of fluorescent imaging biological probes of nucleic acids: SAC-CI and TD-DFT Study. J Comput Chem 2018; 40:127-134. [PMID: 30144120 DOI: 10.1002/jcc.25553] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 07/13/2018] [Indexed: 01/06/2023]
Abstract
Recently, exciton-controlled hybridization-sensitive fluorescent oligonucleotide (ECHO) probe, which shows strong emission in the near-infrared region via hybridization to the target DNA and/or RNA strand, has been developed. In this work, photophysical properties of the chromophores of these probes and the fluorescent mechanism have been investigated by the SAC-CI and TD-DFT calculations. Three fluorescent cyanine chromophores whose excitation is challenging for TD-DFT methods, have been examined regarding the photo-absorption and emission spectra. The SAC-CI method well reproduces the experimental values with respect to transition energies, while the quantitative prediction by TD-DFT calculations is difficult for these chromophores. Some stable structures of H-aggregate system were computationally located and two of the configurations were examined for the photo-absorption. The present results support for the assumption based on experimental measurement in which strong fluorescence is due to the monomer unit in nearly planar structure and its suppression of probes is to the H-aggregates of two exciton units. Stokes shifts of these three chromophores were qualitatively reproduced by the theoretical calculations, while the energy splitting due to H-aggregate in the hybridized probe was slightly overestimated. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Takafumi Shiraogawa
- SOKENDAI, The Graduate University for Advanced Studies, Nishigonaka, Myodaiji, Okazaki, 444-8585, Japan
| | - G Candel
- Institut de Recherche de Chimie Paris, PSL Research University, CNRS, Chimie ParisTech, 11 rue Pierre et Marie Curie, Paris, F-75005, France
| | - Ryoichi Fukuda
- Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Kyoto, 615-8245, Japan.,Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto, 615-8520, Japan
| | - Ilaria Ciofini
- Institut de Recherche de Chimie Paris, PSL Research University, CNRS, Chimie ParisTech, 11 rue Pierre et Marie Curie, Paris, F-75005, France
| | - Carlo Adamo
- Institut de Recherche de Chimie Paris, PSL Research University, CNRS, Chimie ParisTech, 11 rue Pierre et Marie Curie, Paris, F-75005, France.,Institut Universitaire de France, 103 Boulevard Saint Michel, F-75005, Paris, France
| | - Akimitsu Okamoto
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan.,Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Masahiro Ehara
- SOKENDAI, The Graduate University for Advanced Studies, Nishigonaka, Myodaiji, Okazaki, 444-8585, Japan.,Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Kyoto, 615-8245, Japan.,Institute for Molecular Science and Research Center for Computational Science, Nishigonaka, Myodaiji, Okazaki, 444-8585, Japan
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16
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Otto JP, Wang L, Pochorovski I, Blau SM, Aspuru-Guzik A, Bao Z, Engel GS, Chiu M. Disentanglement of excited-state dynamics with implications for FRET measurements: two-dimensional electronic spectroscopy of a BODIPY-functionalized cavitand. Chem Sci 2018; 9:3694-3703. [PMID: 29780500 PMCID: PMC5935064 DOI: 10.1039/c8sc00818c] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 03/15/2018] [Indexed: 12/14/2022] Open
Abstract
Two-dimensional electronic spectroscopy of energy transfer and competing dynamics highlights how conformational changes create issues with lifetime-based FRET measurements.
Förster Resonance Energy Transfer (FRET) is the incoherent transfer of an electronic excitation from a donor fluorophore to a nearby acceptor. FRET has been applied as a probe of local chromophore environments and distances on the nanoscale by extrapolating transfer efficiencies from standard experimental parameters, such as fluorescence intensities or lifetimes. Competition from nonradiative relaxation processes is often assumed to be constant in these extrapolations, but in actuality, this competition depends on the donor and acceptor environments and can, therefore, be affected by conformational changes. To study the effects of nonradiative relaxation on FRET dynamics, we perform two-dimensional electronic spectroscopy (2DES) on a pair of azaboraindacene (BODIPY) dyes, attached to opposite arms of a resorcin[4]arene cavitand. Temperature-induced switching between two equilibrium conformations, vase at 294 K to kite at 193 K, increases the donor–acceptor distance from 0.5 nm to 3 nm, affecting both FRET efficiency and nonradiative relaxation. By disentangling different dynamics based on lifetimes extracted from a series of 2D spectra, we independently observe nonradiative relaxation, FRET, and residual fluorescence from the donor in both vase to kite conformations. We observe changes in both FRET rate and nonradiative relaxation when the molecule switches from vase to kite, and measure a significantly greater difference in transfer efficiency between conformations than would be determined by standard lifetime-based measurements. These observations show that changes in competing nonradiative processes must be taken into account when highly accurate measurements of FRET efficiency are desired.
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Affiliation(s)
- John P Otto
- Department of Chemistry , University of Chicago , Chicago , IL 60637 , USA .
| | - Lili Wang
- Department of Chemistry , University of Chicago , Chicago , IL 60637 , USA .
| | - Igor Pochorovski
- Department of Chemical Engineering , Stanford University , Stanford , CA 94305 , USA . ;
| | - Samuel M Blau
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , MA 02138 , USA
| | - Alán Aspuru-Guzik
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , MA 02138 , USA.,Senior Fellow , Canadian Institute for Advanced Research , Toronto , Ontario M5G 1Z8 , Canada
| | - Zhenan Bao
- Department of Chemical Engineering , Stanford University , Stanford , CA 94305 , USA . ;
| | - Gregory S Engel
- Department of Chemistry , University of Chicago , Chicago , IL 60637 , USA .
| | - Melanie Chiu
- Department of Chemical Engineering , Stanford University , Stanford , CA 94305 , USA . ;
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17
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Pokhrel N, Origanti S, Davenport EP, Gandhi D, Kaniecki K, Mehl RA, Greene EC, Dockendorff C, Antony E. Monitoring Replication Protein A (RPA) dynamics in homologous recombination through site-specific incorporation of non-canonical amino acids. Nucleic Acids Res 2017; 45:9413-9426. [PMID: 28934470 PMCID: PMC5766198 DOI: 10.1093/nar/gkx598] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 07/09/2017] [Indexed: 12/23/2022] Open
Abstract
An essential coordinator of all DNA metabolic processes is Replication Protein A (RPA). RPA orchestrates these processes by binding to single-stranded DNA (ssDNA) and interacting with several other DNA binding proteins. Determining the real-time kinetics of single players such as RPA in the presence of multiple DNA processors to better understand the associated mechanistic events is technically challenging. To overcome this hurdle, we utilized non-canonical amino acids and bio-orthogonal chemistry to site-specifically incorporate a chemical fluorophore onto a single subunit of heterotrimeric RPA. Upon binding to ssDNA, this fluorescent RPA (RPAf) generates a quantifiable change in fluorescence, thus serving as a reporter of its dynamics on DNA in the presence of multiple other DNA binding proteins. Using RPAf, we describe the kinetics of facilitated self-exchange and exchange by Rad51 and mediator proteins during various stages in homologous recombination. RPAf is widely applicable to investigate its mechanism of action in processes such as DNA replication, repair and telomere maintenance.
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Affiliation(s)
- Nilisha Pokhrel
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA
| | - Sofia Origanti
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA
| | | | - Disha Gandhi
- Department of Chemistry, Marquette University, Milwaukee, WI 53201, USA
| | - Kyle Kaniecki
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.,Department of Genetics and Development, Columbia University, New York, NY 10032, USA
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Eric C Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Chris Dockendorff
- Department of Chemistry, Marquette University, Milwaukee, WI 53201, USA
| | - Edwin Antony
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA
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18
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Bulushev RD, Marion S, Petrova E, Davis SJ, Maerkl SJ, Radenovic A. Single Molecule Localization and Discrimination of DNA-Protein Complexes by Controlled Translocation Through Nanocapillaries. NANO LETTERS 2016; 16:7882-7890. [PMID: 27960483 DOI: 10.1021/acs.nanolett.6b04165] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Through the use of optical tweezers we performed controlled translocations of DNA-protein complexes through nanocapillaries. We used RNA polymerase (RNAP) with two binding sites on a 7.2 kbp DNA fragment and a dCas9 protein tailored to have five binding sites on λ-DNA (48.5 kbp). Measured localization of binding sites showed a shift from the expected positions on the DNA that we explained using both analytical fitting and a stochastic model. From the measured force versus stage curves we extracted the nonequilibrium work done during the translocation of a DNA-protein complex and used it to obtain an estimate of the effective charge of the complex. In combination with conductivity measurements, we provided a proof of concept for discrimination between different DNA-protein complexes simultaneous to the localization of their binding sites.
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Affiliation(s)
- Roman D Bulushev
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL , 1015 Lausanne, Switzerland
| | - Sanjin Marion
- Institute of Physics , Bijenička cesta 46, HR-10000 Zagreb, Croatia
| | - Ekaterina Petrova
- Laboratory of Biological Network Characterization, Institute of Bioengineering, School of Engineering, EPFL , 1015 Lausanne, Switzerland
| | - Sebastian J Davis
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL , 1015 Lausanne, Switzerland
| | - Sebastian J Maerkl
- Laboratory of Biological Network Characterization, Institute of Bioengineering, School of Engineering, EPFL , 1015 Lausanne, Switzerland
| | - Aleksandra Radenovic
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL , 1015 Lausanne, Switzerland
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19
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Liu Q, Wang W, Zhan C, Yang T, Kohane DS. Enhanced Precision of Nanoparticle Phototargeting in Vivo at a Safe Irradiance. NANO LETTERS 2016; 16:4516-4520. [PMID: 27310596 DOI: 10.1021/acs.nanolett.6b01730] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A large proportion of the payload delivered by nanoparticulate therapies is deposited not in the desired target destination but in off-target locations such as the liver and spleen. Here, we demonstrate that phototargeting can improve the specific targeting of nanoparticles to tumors. The combination of efficient triplet-triplet annihilation upconversion (TTA-UC) and Förster resonance energy transfer (FRET) processes allowed in vivo phototargeting at a safe irradiance (200 mW/cm(2)) over a short period (5 min) using green light.
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Affiliation(s)
- Qian Liu
- Laboratory for Biomaterials and Drug Delivery, Department of Anesthesiology, Division of Critical Care Medicine, Boston Children's Hospital, Harvard Medical School , 300 Longwood Avenue, Boston, Massachusetts 02115, United States
| | - Weiping Wang
- Laboratory for Biomaterials and Drug Delivery, Department of Anesthesiology, Division of Critical Care Medicine, Boston Children's Hospital, Harvard Medical School , 300 Longwood Avenue, Boston, Massachusetts 02115, United States
| | - Changyou Zhan
- Laboratory for Biomaterials and Drug Delivery, Department of Anesthesiology, Division of Critical Care Medicine, Boston Children's Hospital, Harvard Medical School , 300 Longwood Avenue, Boston, Massachusetts 02115, United States
| | - Tianshe Yang
- Laboratory for Biomaterials and Drug Delivery, Department of Anesthesiology, Division of Critical Care Medicine, Boston Children's Hospital, Harvard Medical School , 300 Longwood Avenue, Boston, Massachusetts 02115, United States
- Institute of Advanced Materials, School of Materials Science & Engineering, Nanjing University of Posts and Telecommunications , 9 Wenyuan Road, Nanjing 210023, P. R. China
| | - Daniel S Kohane
- Laboratory for Biomaterials and Drug Delivery, Department of Anesthesiology, Division of Critical Care Medicine, Boston Children's Hospital, Harvard Medical School , 300 Longwood Avenue, Boston, Massachusetts 02115, United States
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20
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Superresolution imaging of telomeres with continuous wave stimulated emission depletion (STED) microscope. Sci China Chem 2016. [DOI: 10.1007/s11426-016-0020-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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21
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Blouin S, Craggs TD, Lafontaine DA, Penedo JC. Functional Studies of DNA-Protein Interactions Using FRET Techniques. Methods Mol Biol 2016; 1334:115-41. [PMID: 26404147 DOI: 10.1007/978-1-4939-2877-4_8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Protein-DNA interactions underpin life and play key roles in all cellular processes and functions including DNA transcription, packaging, replication, and repair. Identifying and examining the nature of these interactions is therefore a crucial prerequisite to understand the molecular basis of how these fundamental processes take place. The application of fluorescence techniques and in particular fluorescence resonance energy transfer (FRET) to provide structural and kinetic information has experienced a stunning growth during the past decade. This has been mostly promoted by new advances in the preparation of dye-labeled nucleic acids and proteins and in optical sensitivity, where its implementation at the level of individual molecules has opened a new biophysical frontier. Nowadays, the application of FRET-based techniques to the analysis of protein-DNA interactions spans from the classical steady-state and time-resolved methods averaging over large ensembles to the analysis of distances, conformational changes, and enzymatic reactions in individual protein-DNA complexes. This chapter introduces the practical aspects of applying these methods for the study of protein-DNA interactions.
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Affiliation(s)
- Simon Blouin
- Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | | | - Daniel A Lafontaine
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, 2500 Boulevard de L'Université, Sherbrooke, QC, Canada, J1K 2R1.
| | - J Carlos Penedo
- School of Physics and Astronomy, University of St. Andrews, St. Andrews, UK
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22
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Kumar Verma R, Takei F, Nakatani K. Synthesis and Photophysical Properties of Fluorescence Molecular Probe for Turn-ON-Type Detection of Cytosine Bulge DNA. Org Lett 2016; 18:3170-3. [DOI: 10.1021/acs.orglett.6b01378] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Rajiv Kumar Verma
- Department
of Regulatory Bioorganic Chemistry, The Institute of Scientific and
Industrial Research, Osaka University, Mihogaoka, 8-1,
Ibaraki, Osaka 567-0047, Japan
| | - Fumie Takei
- National Defense Medical College, Namiki, 3-2, Tokorozawa, Saitama 359-8513, Japan
| | - Kazuhiko Nakatani
- Department
of Regulatory Bioorganic Chemistry, The Institute of Scientific and
Industrial Research, Osaka University, Mihogaoka, 8-1,
Ibaraki, Osaka 567-0047, Japan
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23
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Venditti V, Egner TK, Clore GM. Hybrid Approaches to Structural Characterization of Conformational Ensembles of Complex Macromolecular Systems Combining NMR Residual Dipolar Couplings and Solution X-ray Scattering. Chem Rev 2016; 116:6305-22. [PMID: 26739383 PMCID: PMC5590664 DOI: 10.1021/acs.chemrev.5b00592] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Solving structures or structural ensembles of large macromolecular systems in solution poses a challenging problem. While NMR provides structural information at atomic resolution, increased spectral complexity, chemical shift overlap, and short transverse relaxation times (associated with slow tumbling) render application of the usual techniques that have been so successful for medium sized systems (<50 kDa) difficult. Solution X-ray scattering, on the other hand, is not limited by molecular weight but only provides low resolution structural information related to the overall shape and size of the system under investigation. Here we review how combining atomic resolution structures of smaller domains with sparse experimental data afforded by NMR residual dipolar couplings (which yield both orientational and shape information) and solution X-ray scattering data in rigid-body simulated annealing calculations provides a powerful approach for investigating the structural aspects of conformational dynamics in large multidomain proteins. The application of this hybrid methodology is illustrated for the 128 kDa dimer of bacterial Enzyme I which exists in a variety of open and closed states that are sampled at various points in the catalytic cycles, and for the capsid protein of the human immunodeficiency virus.
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Affiliation(s)
- Vincenzo Venditti
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Timothy K. Egner
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - G. Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
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24
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Raja A, Montoya Castillo A, Zultak J, Zhang XX, Ye Z, Roquelet C, Chenet DA, van der Zande AM, Huang P, Jockusch S, Hone J, Reichman DR, Brus LE, Heinz TF. Energy Transfer from Quantum Dots to Graphene and MoS2: The Role of Absorption and Screening in Two-Dimensional Materials. NANO LETTERS 2016; 16:2328-33. [PMID: 26928675 DOI: 10.1021/acs.nanolett.5b05012] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We report efficient nonradiative energy transfer (NRET) from core-shell, semiconducting quantum dots to adjacent two-dimensional sheets of graphene and MoS2 of single- and few-layer thickness. We observe quenching of the photoluminescence (PL) from individual quantum dots and enhanced PL decay rates in time-resolved PL, corresponding to energy transfer rates of 1-10 ns(-1). Our measurements reveal contrasting trends in the NRET rate from the quantum dot to the van der Waals material as a function of thickness. The rate increases significantly with increasing layer thickness of graphene, but decreases with increasing thickness of MoS2 layers. A classical electromagnetic theory accounts for both the trends and absolute rates observed for the NRET. The countervailing trends arise from the competition between screening and absorption of the electric field of the quantum dot dipole inside the acceptor layers. We extend our analysis to predict the type of NRET behavior for the near-field coupling of a chromophore to a range of semiconducting and metallic thin film materials.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Tony F Heinz
- Departments of Applied Physics and Photon Science, Stanford University , Stanford, California 94305, United States
- SLAC National Accelerator Laboratory , Menlo Park, California 94025, United States
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25
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Soltani N, Manzoori J, Amjadi M, Lotfipour F, Jouyban A. Development and Validation of A Spectrofluorimetric Determination of Calf Thymus DNA Using a Terbium-Danofloxacin Probe. PHARMACEUTICAL SCIENCES 2016. [DOI: 10.15171/ps.2016.02] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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26
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Okamoto A. Thiazole Orange-Tethered Nucleic Acids and ECHO Probes for Fluorometric Detection of Nucleic Acids. MODIFIED NUCLEIC ACIDS 2016. [DOI: 10.1007/978-3-319-27111-8_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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27
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A new trend to determine biochemical parameters by quantitative FRET assays. Acta Pharmacol Sin 2015; 36:1408-15. [PMID: 26567729 DOI: 10.1038/aps.2015.82] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 08/26/2015] [Indexed: 01/15/2023] Open
Abstract
Förster resonance energy transfer (FRET) has been widely used in biological and biomedical research because it can determine molecule or particle interactions within a range of 1-10 nm. The sensitivity and efficiency of FRET strongly depend on the distance between the FRET donor and acceptor. Historically, FRET assays have been used to quantitatively deduce molecular distances. However, another major potential application of the FRET assay has not been fully exploited, that is, the use of FRET signals to quantitatively describe molecular interactive events. In this review, we discuss the use of quantitative FRET assays for the determination of biochemical parameters, such as the protein interaction dissociation constant (K(d)), enzymatic velocity (k(cat)) and K(m). We also describe fluorescent microscopy-based quantitative FRET assays for protein interaction affinity determination in cells as well as fluorimeter-based quantitative FRET assays for protein interaction and enzymatic parameter determination in solution.
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28
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Bulushev RD, Marion S, Radenovic A. Relevance of the Drag Force during Controlled Translocation of a DNA-Protein Complex through a Glass Nanocapillary. NANO LETTERS 2015; 15:7118-25. [PMID: 26393370 DOI: 10.1021/acs.nanolett.5b03264] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Combination of glass nanocapillaries with optical tweezers allowed us to detect DNA-protein complexes in physiological conditions. In this system, a protein bound to DNA is characterized by a simultaneous change of the force and ionic current signals from the level observed for the bare DNA. Controlled displacement of the protein away from the nanocapillary opening revealed decay in the values of the force and ionic current. Negatively charged proteins EcoRI, RecA, and RNA polymerase formed complexes with DNA that experienced electrophoretic force lower than the bare DNA inside nanocapillaries. Force profiles obtained for DNA-RecA in our system were different than those in the system with nanopores in membranes and optical tweezers. We suggest that such behavior is due to the dominant impact of the drag force comparing to the electrostatic force acting on a DNA-protein complex inside nanocapillaries. We explained our results using a stochastic model taking into account the conical shape of glass nanocapillaries.
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Affiliation(s)
- Roman D Bulushev
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL , 1015 Lausanne, Switzerland
| | - Sanjin Marion
- Institute of Physics , Bijenicka cesta 46, HR-10000 Zagreb, Croatia
| | - Aleksandra Radenovic
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL , 1015 Lausanne, Switzerland
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29
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Radić Stojković M, Piotrowski P, Schmuck C, Piantanida I. A short, rigid linker between pyrene and guanidiniocarbonyl-pyrrole induced a new set of spectroscopic responses to the ds-DNA secondary structure. Org Biomol Chem 2015; 13:1629-33. [PMID: 25502619 DOI: 10.1039/c4ob02169j] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel pyrene-guanidiniocarbonyl-pyrrole dye, characterised by a short, rigid linker between the two chromophores, interacts strongly with ds-DNA but only negligibly with ds-RNA. Under neutral conditions the dye shows strong selectivity toward AT-DNA (with respect to GC-DNA). Binding is accompanied by a specific ICD band at 350 nm and fluorescence quenching for all DNAs/RNAs studied. At pH 5 the affinity of the dye is reversed, now favouring GC-DNA over AT-DNA. A strong emission increase for AT-DNA is observed but with quenching for GC-DNA.
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Affiliation(s)
- Marijana Radić Stojković
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, P. O. Box 180, HR-10002 Zagreb, Croatia.
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Zhang X, Daaboul GG, Spuhler PS, Freedman DS, Yurt A, Ahn S, Avci O, Ünlü MS. Nanoscale characterization of DNA conformation using dual-color fluorescence axial localization and label-free biosensing. Analyst 2015; 139:6440-9. [PMID: 25340741 DOI: 10.1039/c4an01425a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Quantitative determination of the density and conformation of DNA molecules tethered to the surface can help optimize and understand DNA nanosensors and nanodevices, which use conformational or motional changes of surface-immobilized DNA for detection or actuation. We present an interferometric sensing platform that combines (i) dual-color fluorescence spectroscopy for precise axial co-localization of two fluorophores attached at different nucleotides of surface-immobilized DNA molecules and (ii) independent label-free quantification of biomolecule surface density at the same site. Using this platform, we examined the conformation of DNA molecules immobilized on a three-dimensional polymeric surface and demonstrated simultaneous detection of DNA conformational change and binding in real-time. These results demonstrate that independent quantification of both surface density and molecular nanoscale conformation constitutes a versatile approach for nanoscale solid-biochemical interface investigations and molecular binding assays.
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Affiliation(s)
- Xirui Zhang
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215, USA.
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31
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Huang YC, Yu HZ, Sen D. DNA mechatronic devices switched by K+and by Sr2+are structurally, topologically, and electronically distinct. Biopolymers 2015; 103:460-8. [DOI: 10.1002/bip.22595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 11/17/2014] [Accepted: 11/18/2014] [Indexed: 01/22/2023]
Affiliation(s)
- Yu Chuan Huang
- Department of Molecular Biology & Biochemistry; Simon Fraser University; Burnaby B C V5A 1S6 Canada
| | - Hua-Zhong Yu
- Department of Molecular Biology & Biochemistry; Simon Fraser University; Burnaby B C V5A 1S6 Canada
- Department of Chemistry; Simon Fraser University; Burnaby British Columbia V5A 1S6 Canada
| | - Dipankar Sen
- Department of Molecular Biology & Biochemistry; Simon Fraser University; Burnaby B C V5A 1S6 Canada
- Department of Chemistry; Simon Fraser University; Burnaby British Columbia V5A 1S6 Canada
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32
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Higgins NP, Vologodskii AV. Topological Behavior of Plasmid DNA. Microbiol Spectr 2015; 3:10.1128/microbiolspec.PLAS-0036-2014. [PMID: 26104708 PMCID: PMC4480603 DOI: 10.1128/microbiolspec.plas-0036-2014] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Indexed: 11/20/2022] Open
Abstract
The discovery of the B-form structure of DNA by Watson and Crick led to an explosion of research on nucleic acids in the fields of biochemistry, biophysics, and genetics. Powerful techniques were developed to reveal a myriad of different structural conformations that change B-DNA as it is transcribed, replicated, and recombined and as sister chromosomes are moved into new daughter cell compartments during cell division. This article links the original discoveries of superhelical structure and molecular topology to non-B form DNA structure and contemporary biochemical and biophysical techniques. The emphasis is on the power of plasmids for studying DNA structure and function. The conditions that trigger the formation of alternative DNA structures such as left-handed Z-DNA, inter- and intra-molecular triplexes, triple-stranded DNA, and linked catenanes and hemicatenanes are explained. The DNA dynamics and topological issues are detailed for stalled replication forks and for torsional and structural changes on DNA in front of and behind a transcription complex and a replisome. The complex and interconnected roles of topoisomerases and abundant small nucleoid association proteins are explained. And methods are described for comparing in vivo and in vitro reactions to probe and understand the temporal pathways of DNA and chromosome chemistry that occur inside living cells.
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Affiliation(s)
- N Patrick Higgins
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294
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33
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34
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Abstract
Myriad biological processes proceed through states that defy characterization by conventional atomic-resolution structural biological methods. The invisibility of these 'dark' states can arise from their transient nature, low equilibrium population, large molecular weight, and/or heterogeneity. Although they are invisible, these dark states underlie a range of processes, acting as encounter complexes between proteins and as intermediates in protein folding and aggregation. New methods have made these states accessible to high-resolution analysis by nuclear magnetic resonance (NMR) spectroscopy, as long as the dark state is in dynamic equilibrium with an NMR-visible species. These methods - paramagnetic NMR, relaxation dispersion, saturation transfer, lifetime line broadening, and hydrogen exchange - allow the exploration of otherwise invisible states in exchange with a visible species over a range of timescales, each taking advantage of some unique property of the dark state to amplify its effect on a particular NMR observable. In this review, we introduce these methods and explore two specific techniques - paramagnetic relaxation enhancement and dark state exchange saturation transfer - in greater detail.
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Affiliation(s)
- Nicholas J. Anthis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
| | - G. Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
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35
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Blackstock D, Chen W. Halo-tag mediated self-labeling of fluorescent proteins to molecular beacons for nucleic acid detection. Chem Commun (Camb) 2014; 50:13735-8. [DOI: 10.1039/c4cc07118b] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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36
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Vivas P, Velmurugu Y, Kuznetsov SV, Rice PA, Ansari A. Global analysis of ion dependence unveils hidden steps in DNA binding and bending by integration host factor. J Chem Phys 2014; 139:121927. [PMID: 24089739 DOI: 10.1063/1.4818596] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Proteins that recognize and bind to specific sites on DNA often distort the DNA at these sites. The rates at which these DNA distortions occur are considered to be important in the ability of these proteins to discriminate between specific and nonspecific sites. These rates have proven difficult to measure for most protein-DNA complexes in part because of the difficulty in separating the kinetics of unimolecular conformational rearrangements (DNA bending and kinking) from the kinetics of bimolecular complex association and dissociation. A notable exception is the Integration Host Factor (IHF), a eubacterial architectural protein involved in chromosomal compaction and DNA recombination, which binds with subnanomolar affinity to specific DNA sites and bends them into sharp U-turns. The unimolecular DNA bending kinetics has been resolved using both stopped-flow and laser temperature-jump perturbation. Here we expand our investigation by presenting a global analysis of the ionic strength dependence of specific binding affinity and relaxation kinetics of an IHF-DNA complex. This analysis enables us to obtain each of the underlying elementary rates (DNA bending/unbending and protein-DNA association/dissociation), and their ionic strength dependence, even under conditions where the two processes are coupled. Our analysis indicates interesting differences in the ionic strength dependence of the bi- versus unimolecular steps. At moderate [KCl] (100-500 mM), nearly all the ionic strength dependence to the overall equilibrium binding affinity appears in the bimolecular association/dissociation of an initial, presumably weakly bent, encounter complex, with a slope SK(bi) ≈ 8 describing the loglog-dependence of the equilibrium constant to form this complex on [KCl]. In contrast, the unimolecular equilibrium constant to form the fully wrapped specific complex from the initial complex is nearly independent of [KCl], with SK(uni) < 0.5. This result is counterintuitive because there are at least twice as many ionic protein-DNA contacts in the fully wrapped complex than in the weakly bent intermediate. The following picture emerges from this analysis: in the bimolecular step, the observed [KCl]-dependence is consistent with the number of DNA counterions expected to be released when IHF binds nonspecifically to DNA whereas in the unimolecular reorganization step, the weak [KCl]-dependence suggests that two effects cancel one another. On one hand, formation of additional protein-DNA contacts in the fully wrapped complex releases bound counterions into bulk solution, which is entropically favored by decreasing [salt]. On the other hand, formation of the fully wrapped complex also releases tightly bound water molecules, which is osmotically favored by increasing [salt]. More generally, our global analysis strategy is applicable to other protein-DNA complexes, and opens up the possibility of measuring DNA bending rates in complexes where the unimolecular and bimolecular steps are not easily separable.
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Affiliation(s)
- Paula Vivas
- Department of Physics, University of Illinois at Chicago, Chicago, Illinois 60607, USA
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37
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Malik-Chaudhry HK, Saavedra A, Liao J. A linker strategy for trans-FRET assay to determine activation intermediate of NEDDylation cascade. Biotechnol Bioeng 2014; 111:1288-95. [PMID: 24415255 DOI: 10.1002/bit.25183] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 12/27/2013] [Accepted: 01/03/2014] [Indexed: 11/10/2022]
Abstract
Förster resonance energy transfer (FRET) technology has been widely used in biological and biomedical research and is a valuable tool for elucidating molecular interactions in vitro and in vivo. Quantitative FRET analysis is a powerful method for determining biochemical parameters and molecular distances at nanometer levels. Recently, we reported theoretical developments and experimental procedures for determining the dissociation constant, Kd and enzymatic kinetics parameters, Kcat and KM, of protein interactions with the engineered FRET pair, CyPet and YPet. The strong FRET signal from this pair made these developments possible. However, the direct link of fluorescent proteins with proteins of interests may interfere with the folding of some fusion proteins. Here, we report a new protein engineering strategy for improving FRET signals by adding a linker between the fluorescent protein and the targeted protein. This improvement allowed us to follow the covalent conjugation of NEDD8 to its E2 ligase in the presence of E1 and ATP, which was difficult to determine without linker. Three linkers, LAEAAAKEAA, TSGSPGLQEFGT, and LAAALAAA, which are alpha helix or random coil, all significantly improved the FRET signals. Our results show a general methodology for improving trans-FRET signals to effectively determine biochemical reaction intermediates.
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Affiliation(s)
- Harbani Kaur Malik-Chaudhry
- Department of Bioengineering, Center for Bioengineering Research, Bourns College of Engineering, 900 University Avenue, Riverside, California, 92521
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Crnolatac I, Tumir LM, Lesev NY, Vasilev AA, Deligeorgiev TG, Mišković K, Glavaš-Obrovac L, Vugrek O, Piantanida I. Probing the structural properties of DNA/RNA grooves with sterically restricted phosphonium dyes: screening of dye cytotoxicity and uptake. ChemMedChem 2013; 8:1093-103. [PMID: 23729313 DOI: 10.1002/cmdc.201300085] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 04/24/2013] [Indexed: 11/10/2022]
Abstract
To explore in greater detail the recently reported rare kinetic differentiation between homo-polymeric and alternating AT-DNA sequences by using sterically restricted phosphonium dyes that form dimers within the DNA minor groove, new analogues were prepared in which the quinolone phosphonium moiety was kept constant, while the size and hydrogen bonding properties of the rest of the molecule were varied. Structure-activity relationship studies revealed that a slight increase in length by an additional methylene unit results in loss of kinetic AT selectivity, but yielded an AT-selective fluorescence response. These DNA/RNA-groove-bound dyes combine very low cytotoxicity with efficient cellular uptake and intriguingly specific fluorescent marking of mitochondria. In contrast to longer analogues, a decrease in length (by methylene unit removal) and rearrangement of positive charge resulted in dyes that had switched to the intercalative binding mode to GC DNA/dsRNA but that still form dimers in the minor groove of AT sequences, consequently yielding a significantly different chiro-optical response. The latter dyes also revealed strongly selective antiproliferative activity toward HeLa cancer cells.
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Affiliation(s)
- Ivo Crnolatac
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, PO Box 180, 10002 Zagreb, Croatia
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39
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Wang Z, Zhang K, Shen Y, Smith J, Bloch S, Achilefu S, Wooley KL, Taylor JS. Imaging mRNA expression levels in living cells with PNA·DNA binary FRET probes delivered by cationic shell-crosslinked nanoparticles. Org Biomol Chem 2013; 11:3159-67. [PMID: 23538604 PMCID: PMC3687806 DOI: 10.1039/c3ob26923j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Optical imaging of gene expression through the use of fluorescent antisense probes targeted to the mRNA has been an area of great interest. The main obstacles to developing highly sensitive antisense fluorescent imaging agents have been the inefficient intracellular delivery of the probes and high background signal from unbound probes. Binary antisense probes have shown great promise as mRNA imaging agents because a signal can only occur if both probes are bound simultaneously to the mRNA target site. Selecting an accessible binding site is made difficult by RNA folding and protein binding in vivo and the need to bind two probes. Even more problematic, has been a lack of methods for efficient cytoplasmic delivery of the probes that would be suitable for eventual applications in vivo in animals. Herein we report the imaging of iNOS mRNA expression in live mouse macrophage cells with PNA·DNA binary FRET probes delivered by a cationic shell crosslinked knedel-like nanoparticle (cSCK). We first demonstrate that FRET can be observed on in vitro transcribed mRNA with both the PNA probes and the PNA·DNA hybrid probes. We then demonstrate that the FRET signal can be observed in live cells when the hybrid probes are transfected with the cSCK, and that the strength of the FRET signal is sequence specific and depends on the mRNA expression level.
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Affiliation(s)
- Zhenghui Wang
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
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40
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Yu X, Wu X, Bermejo GA, Brooks BR, Taraska JW. Accurate high-throughput structure mapping and prediction with transition metal ion FRET. Structure 2012; 21:9-19. [PMID: 23273426 DOI: 10.1016/j.str.2012.11.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 11/15/2012] [Accepted: 11/17/2012] [Indexed: 11/28/2022]
Abstract
Mapping the landscape of a protein's conformational space is essential to understanding its functions and regulation. The limitations of many structural methods have made this process challenging for most proteins. Here, we report that transition metal ion FRET (tmFRET) can be used in a rapid, highly parallel screen, to determine distances from multiple locations within a protein at extremely low concentrations. The distances generated through this screen for the protein maltose binding protein (MBP) match distances from the crystal structure to within a few angstroms. Furthermore, energy transfer accurately detects structural changes during ligand binding. Finally, fluorescence-derived distances can be used to guide molecular simulations to find low energy states. Our results open the door to rapid, accurate mapping and prediction of protein structures at low concentrations, in large complex systems, and in living cells.
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Affiliation(s)
- Xiaozhen Yu
- Laboratory of Molecular Biophysics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xiongwu Wu
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Guillermo A Bermejo
- Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Justin W Taraska
- Laboratory of Molecular Biophysics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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41
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Chen NT, Cheng SH, Liu CP, Souris JS, Chen CT, Mou CY, Lo LW. Recent advances in nanoparticle-based Förster resonance energy transfer for biosensing, molecular imaging and drug release profiling. Int J Mol Sci 2012; 13:16598-623. [PMID: 23443121 PMCID: PMC3546710 DOI: 10.3390/ijms131216598] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Revised: 11/15/2012] [Accepted: 11/16/2012] [Indexed: 01/10/2023] Open
Abstract
Förster resonance energy transfer (FRET) may be regarded as a "smart" technology in the design of fluorescence probes for biological sensing and imaging. Recently, a variety of nanoparticles that include quantum dots, gold nanoparticles, polymer, mesoporous silica nanoparticles and upconversion nanoparticles have been employed to modulate FRET. Researchers have developed a number of "visible" and "activatable" FRET probes sensitive to specific changes in the biological environment that are especially attractive from the biomedical point of view. This article reviews recent progress in bringing these nanoparticle-modulated energy transfer schemes to fruition for applications in biosensing, molecular imaging and drug delivery.
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Affiliation(s)
- Nai-Tzu Chen
- Division of Medical Engineering Research, National Health Research Institutes, Zhunan 35053, Miaoli County, Taiwan; E-Mails: (N.-T.C.); (S.-H.C.); (C.-P.L.)
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan; E-Mail:
| | - Shih-Hsun Cheng
- Division of Medical Engineering Research, National Health Research Institutes, Zhunan 35053, Miaoli County, Taiwan; E-Mails: (N.-T.C.); (S.-H.C.); (C.-P.L.)
- Department of Radiology, The University of Chicago, Chicago, IL 60637, USA; E-Mails: (J.S.S.); (C.-T.C.)
| | - Ching-Ping Liu
- Division of Medical Engineering Research, National Health Research Institutes, Zhunan 35053, Miaoli County, Taiwan; E-Mails: (N.-T.C.); (S.-H.C.); (C.-P.L.)
| | - Jeffrey S. Souris
- Department of Radiology, The University of Chicago, Chicago, IL 60637, USA; E-Mails: (J.S.S.); (C.-T.C.)
| | - Chen-Tu Chen
- Department of Radiology, The University of Chicago, Chicago, IL 60637, USA; E-Mails: (J.S.S.); (C.-T.C.)
| | - Chung-Yuan Mou
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan; E-Mail:
| | - Leu-Wei Lo
- Division of Medical Engineering Research, National Health Research Institutes, Zhunan 35053, Miaoli County, Taiwan; E-Mails: (N.-T.C.); (S.-H.C.); (C.-P.L.)
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42
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Liu Y, Hu Y, Guo Y, Ma H, Li J, Jiang C. Targeted imaging of activated caspase-3 in the central nervous system by a dual functional nano-device. J Control Release 2012; 163:203-10. [DOI: 10.1016/j.jconrel.2012.09.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2012] [Revised: 06/20/2012] [Accepted: 09/02/2012] [Indexed: 12/21/2022]
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43
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Ai X, Niu L, Li Y, Yang F, Su X. A novel β-Cyclodextrin-QDs optical biosensor for the determination of amantadine and its application in cell imaging. Talanta 2012; 99:409-14. [DOI: 10.1016/j.talanta.2012.05.072] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 05/31/2012] [Accepted: 05/31/2012] [Indexed: 12/20/2022]
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Reginsson GW, Shelke SA, Rouillon C, White MF, Sigurdsson ST, Schiemann O. Protein-induced changes in DNA structure and dynamics observed with noncovalent site-directed spin labeling and PELDOR. Nucleic Acids Res 2012; 41:e11. [PMID: 22941643 PMCID: PMC3592447 DOI: 10.1093/nar/gks817] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Site-directed spin labeling and pulsed electron-electron double resonance (PELDOR or DEER) have previously been applied successfully to study the structure and dynamics of nucleic acids. Spin labeling nucleic acids at specific sites requires the covalent attachment of spin labels, which involves rather complicated and laborious chemical synthesis. Here, we use a noncovalent label strategy that bypasses the covalent labeling chemistry and show that the binding specificity and efficiency are large enough to enable PELDOR or DEER measurements in DNA duplexes and a DNA duplex bound to the Lac repressor protein. In addition, the rigidity of the label not only allows resolution of the structure and dynamics of oligonucleotides but also the determination of label orientation and protein-induced conformational changes. The results prove that this labeling strategy in combination with PELDOR has a great potential for studying both structure and dynamics of oligonucleotides and their complexes with various ligands.
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Affiliation(s)
- Gunnar W Reginsson
- Biomedical Sciences Research Complex, Centre of Magnetic Resonance, University of St Andrews, St Andrews KY16 9ST, UK
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45
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Jang S, Cheng YC. Resonance energy flow dynamics of coherently delocalized excitons in biological and macromolecular systems: Recent theoretical advances and open issues. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2012. [DOI: 10.1002/wcms.1111] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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46
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Battle CH, Jayawickramarajah J. Supramolecular Approaches for Inhibition of Protein-Protein and Protein-DNA Interactions. Supramol Chem 2012. [DOI: 10.1002/9780470661345.smc181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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47
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Brutzer H, Schwarz FW, Seidel R. Scanning evanescent fields using a pointlike light source and a nanomechanical DNA gear. NANO LETTERS 2012; 12:473-478. [PMID: 22148854 DOI: 10.1021/nl203876w] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The characterization of three-dimensional inhomogeneous illumination fields is a challenge in modern microscopy. Here we use a four-arm DNA junction as a nanomechanical translation stage to move a single fluorescent quantum dot through an exponentially decaying evanescent field. Recording the emission of the quantum dot within the evanescent field as well as under homogeneous illumination allows one to directly obtain the intensity distribution of the excitation field without additional deconvolution. Our method will allow the characterization of a broad range of illumination fields and to study near-field effects between small optical probes.
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Affiliation(s)
- Hergen Brutzer
- Biotechnology Center, Technische Universität Dresden, Dresden 01062, Germany
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48
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Xie F, Zhu J, Deng C, Huang G, Mitchelson K, Cheng J. General and reliable quantitative measurement of fluorescence resonance energy transfer using three fluorescence channels. Analyst 2012; 137:1013-9. [PMID: 22234659 DOI: 10.1039/c2an15902c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this paper, we describe a comprehensive general system adapted for quantitative fluorescence resonance energy transfer (FRET) measurement using signals from three channels of a fluorescence instrument. The general FRET measurement system involves two established methods, as well as two novel approaches. Unlike the previous measurements, which can be taken correctly only when the quantity of the acceptor is greater than or equal to that of the donor, one of our novel methods can overcome this obstacle and take quantitative FRET measurements when the donor is in excess of the acceptor. Hence the general FRET measurement system allowed one to determine the exact distance when the donor and acceptor were present in different quantities, and integrated the methods for quantitative FRET measurements. The uniformity of measured values and utility of each method were validated using molecular standards based on DNA oligonucleotide rulers. We also discussed and validated the use of a novel method for estimating the relative quantities of the donor and acceptor fluorophores when they were not known before an appropriate method of this system can be selected.
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Affiliation(s)
- Fengbo Xie
- Medical Systems Biology Research Center, Tsinghua University School of Medicine, Haidian District, Beijing, 100084, China
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49
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Schuler B, Müller-Späth S, Soranno A, Nettels D. Application of confocal single-molecule FRET to intrinsically disordered proteins. Methods Mol Biol 2012; 896:21-45. [PMID: 22821515 DOI: 10.1007/978-1-4614-3704-8_2] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Intrinsically disordered proteins (IDPs) are characterized by a large degree of conformational heterogeneity. In such cases, classical experimental methods often yield only mean values, averaged over the entire ensemble of molecules. The microscopic distributions of conformations, trajectories, or sequences of events often remain unknown, and with them the underlying molecular mechanisms. Signal averaging can be avoided by observing individual molecules. A particularly versatile method is highly sensitive fluorescence detection. In combination with Förster resonance energy transfer (FRET), distances and conformational dynamics can be investigated in single molecules. This chapter introduces the practical aspects of applying confocal single-molecule FRET experiments to the study of IDPs.
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Affiliation(s)
- Benjamin Schuler
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
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50
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Kupstat A, Ritschel T, Kumke MU. Oxazine dye-conjugated dna oligonucleotides: Förster resonance energy transfer in view of molecular dye-DNA interactions. Bioconjug Chem 2011; 22:2546-57. [PMID: 22073970 DOI: 10.1021/bc200379y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In this work, the photophysical properties of two oxazine dyes (ATTO 610 and ATTO 680) covalently attached via a C6-amino linker to the 5'-end of short single-stranded as well as double-stranded DNA (ssDNA and dsDNA, respectively) of different lengths were investigated. The two oxazine dyes were chosen because of the excellent spectral overlap, the high extinction coefficients, and the high fluorescence quantum yield of ATTO 610, making them an attractive Förster resonance energy transfer (FRET) pair for bioanalytical applications in the far-red spectral range. To identify possible molecular dye-DNA interactions that cause photophysical alterations, we performed a detailed spectroscopic study, including time-resolved fluorescence anisotropy and fluorescence correlation spectroscopy measurements. As an effect of the DNA conjugation, the absorption and fluorescence maxima of both dyes were bathochromically shifted and the fluorescence decay times were increased. Moreover, the absorption of conjugated ATTO 610 was spectrally broadened, and a dual fluorescence emission was observed. Steric interactions with ssDNA as well as dsDNA were found for both dyes. The dye-DNA interactions were strengthened from ssDNA to dsDNA conjugates, pointing toward interactions with specific dsDNA domains (such as the top of the double helix). Although these interactions partially blocked the dye-linker rotation, a free (unhindered) rotational mobility of at least one dye facilitated the appropriate alignment of the transition dipole moments in doubly labeled ATTO 610/ATTO 680-dsDNA conjugates for the performance of successful FRET. Considering the high linker flexibility for the determination of the donor-acceptor distances, good accordance between theoretical and experimental FRET parameters was obtained. The considerably large Förster distance of ~7 nm recommends the application of this FRET pair not only for the detection of binding reactions between nucleic acids in living cells but also for monitoring interactions of larger biomolecules such as proteins.
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Affiliation(s)
- Annette Kupstat
- Universität Potsdam , Institut für Chemie, Physikalische Chemie, Potsdam-Golm, Germany
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