1
|
Nguyen TTV, Xie X, Xu J, Wu Y, Hong M, Liu X. Plasmonic bimetallic nanodisk arrays for DNA conformation sensing. NANOSCALE 2019; 11:19291-19296. [PMID: 31560008 DOI: 10.1039/c9nr06101k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The integration of large-scale 2D bimetallic Ag/Au nanodisk arrays with gold nanoparticles is developed for sensing DNA conformation with the assistance of 3D finite-difference time-domain simulation. The optimized system comprising Ag/Au nanodisk arrays and gold nanoparticles offers a more than 6-fold enhancement in surface plasmon resonance shift, enabling the feasibility for sensitive DNA detection with a detection limit down to 100 femtomolar. Importantly, owing to the distance-dependent nature of the surface plasmon signal, sensitive differentiation of DNA conformations can be achieved with a conventional optical measurement. This platform could provide new exciting capabilities for a reliable, reproducible, and label-free assay analysis for investigating the conformations of DNA and other biological molecules.
Collapse
Affiliation(s)
- Thanh Thi Van Nguyen
- Advanced Materials for Micro- and Nano-Systems Programme, Singapore-MIT Alliance, 117576, Singapore
| | - Xiaoji Xie
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543, Singapore.
| | - Jiahui Xu
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543, Singapore.
| | - Yiming Wu
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543, Singapore.
| | - Minghui Hong
- Department of Electrical and Computer Engineering, National University of Singapore, 117576, Singapore
| | - Xiaogang Liu
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543, Singapore. and The N.1 Institute for Health, National University of Singapore, 28 Medical Dr. #05-COR, 117456, Singapore and Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University, Fuzhou, 350207, P. R. China
| |
Collapse
|
2
|
Vámosi G, Rueda D. DNA Bends the Knee to Transcription Factors. Biophys J 2017; 114:2253-2254. [PMID: 29229184 DOI: 10.1016/j.bpj.2017.10.047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 10/11/2017] [Indexed: 11/25/2022] Open
Affiliation(s)
- György Vámosi
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.
| | - David Rueda
- Single Molecule Imaging Group, MRC London Institute of Medical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
| |
Collapse
|
3
|
Eisold U, Behrends N, Wessig P, Kumke MU. Rigid Rod-Based FRET Probes for Membrane Sensing Applications. J Phys Chem B 2016; 120:9935-43. [PMID: 27559760 DOI: 10.1021/acs.jpcb.6b07285] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Oligospirothioketal (OSTK) rods are presented as an adjustable scaffold for optical membrane probes. The OSTK rods are readily incorporated into lipid bilayers due to their hydrophobic backbones. Because of their high length-over-diameter aspect ratio, only a minimal disturbance of the lipid bilayer is caused. OSTK rods show outstanding rigidity and allow defined labeling with fluorescent dyes, yielding full control of the orientation between the dye and OSTK skeleton. This allows the construction of novel Förster resonance energy transfer probes with highly defined relative orientations of the transition dipole moments of the donor and acceptor dyes and makes the class of OSTK probes a powerful, flexible toolbox for optical biosensing applications. Data on steady-state and time-resolved fluorescence experiments investigating the incorporation of coumarin- and [1,3]dioxolo[4,5-f][1,3]benzo-dioxole-labeled OSTKs in large unilamellar vesicles are presented as a show case.
Collapse
Affiliation(s)
- Ursula Eisold
- Physical Chemistry and ‡Bioorganic Chemistry, University of Potsdam, Institute of Chemistry , Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Nicole Behrends
- Physical Chemistry and ‡Bioorganic Chemistry, University of Potsdam, Institute of Chemistry , Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Pablo Wessig
- Physical Chemistry and ‡Bioorganic Chemistry, University of Potsdam, Institute of Chemistry , Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Michael U Kumke
- Physical Chemistry and ‡Bioorganic Chemistry, University of Potsdam, Institute of Chemistry , Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Schreck JS, Ouldridge TE, Romano F, Louis AA, Doye JPK. Characterizing the bending and flexibility induced by bulges in DNA duplexes. J Chem Phys 2016; 142:165101. [PMID: 25933790 DOI: 10.1063/1.4917199] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Advances in DNA nanotechnology have stimulated the search for simple motifs that can be used to control the properties of DNA nanostructures. One such motif, which has been used extensively in structures such as polyhedral cages, two-dimensional arrays, and ribbons, is a bulged duplex, that is, two helical segments that connect at a bulge loop. We use a coarse-grained model of DNA to characterize such bulged duplexes. We find that this motif can adopt structures belonging to two main classes: one where the stacking of the helices at the center of the system is preserved, the geometry is roughly straight, and the bulge is on one side of the duplex and the other where the stacking at the center is broken, thus allowing this junction to act as a hinge and increasing flexibility. Small loops favor states where stacking at the center of the duplex is preserved, with loop bases either flipped out or incorporated into the duplex. Duplexes with longer loops show more of a tendency to unstack at the bulge and adopt an open structure. The unstacking probability, however, is highest for loops of intermediate lengths, when the rigidity of single-stranded DNA is significant and the loop resists compression. The properties of this basic structural motif clearly correlate with the structural behavior of certain nano-scale objects, where the enhanced flexibility associated with larger bulges has been used to tune the self-assembly product as well as the detailed geometry of the resulting nanostructures. We further demonstrate the role of bulges in determining the structure of a "Z-tile," a basic building block for nanostructures.
Collapse
Affiliation(s)
- John S Schreck
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Thomas E Ouldridge
- Rudolph Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, United Kingdom
| | - Flavio Romano
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Ard A Louis
- Rudolph Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, United Kingdom
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| |
Collapse
|
6
|
Crawford R, Kelly DJ, Kapanidis AN. A Protein Biosensor That Relies on Bending of Single DNA Molecules. Chemphyschem 2012; 13:918-22. [DOI: 10.1002/cphc.201100881] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Revised: 01/13/2012] [Indexed: 11/11/2022]
|
7
|
Malarkey CS, Bestwick M, Kuhlwilm JE, Shadel GS, Churchill MEA. Transcriptional activation by mitochondrial transcription factor A involves preferential distortion of promoter DNA. Nucleic Acids Res 2011; 40:614-24. [PMID: 21948790 PMCID: PMC3258160 DOI: 10.1093/nar/gkr787] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mitochondrial transcription factor A (mtTFA/TFAM) is a nucleus-encoded, high-mobility-group-box (HMG-box) protein that regulates transcription of the mitochondrial genome by specifically recognizing light-strand and heavy-strand promoters (LSP, HSP1). TFAM also binds mitochondrial DNA in a non-sequence specific (NSS) fashion and facilitates its packaging into nucleoid structures. However, the requirement and contribution of DNA-bending for these two different binding modes has not been addressed in detail, which prompted this comparison of binding and bending properties of TFAM on promoter and non-promoter DNA. Promoter DNA increased the stability of TFAM to a greater degree than non-promoter DNA. However, the thermodynamic properties of DNA binding for TFAM with promoter and non-specific (NS) DNA were similar to each other and to other NSS HMG-box proteins. Fluorescence resonance energy transfer assays showed that TFAM bends promoter DNA to a greater degree than NS DNA. In contrast, TFAM lacking the C-terminal tail distorted both promoter and non-promoter DNA to a significantly reduced degree, corresponding with markedly decreased transcriptional activation capacity at LSP and HSP1 in vitro. Thus, the enhanced bending of promoter DNA imparted by the C-terminal tail is a critical component of the ability of TFAM to activate promoter-specific initiation by the core mitochondrial transcription machinery.
Collapse
Affiliation(s)
- Christopher S Malarkey
- Department of Pharmacology, University of Colorado Denver, School of Medicine, 12801 E. 17th Ave, Aurora, CO 80045-0511, USA
| | | | | | | | | |
Collapse
|
8
|
Mustoe AM, Bailor MH, Teixeira RM, Brooks CL, Al-Hashimi HM. New insights into the fundamental role of topological constraints as a determinant of two-way junction conformation. Nucleic Acids Res 2011; 40:892-904. [PMID: 21937512 PMCID: PMC3258142 DOI: 10.1093/nar/gkr751] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Recent studies have shown that topological constraints encoded at the RNA secondary structure level involving basic steric and stereochemical forces can significantly restrict the orientations sampled by helices across two-way RNA junctions. Here, we formulate these topological constraints in greater quantitative detail and use this topological framework to rationalize long-standing but poorly understood observations regarding the basic behavior of RNA two-way junctions. Notably, we show that the asymmetric nature of the A-form helix and the finite length of a bulge provide a physical basis for the experimentally observed directionality and bulge-length amplitude dependence of bulge induced inter-helical bends. We also find that the topologically allowed space can be modulated by variations in sequence, particularly with the addition of non-canonical GU base pairs at the junction, and, surprisingly, by the length of the 5′ and 3′ helices. A survey of two-way RNA junctions in the protein data bank confirms that junction residues have a strong preference to adopt looped-in, non-canonically base-paired conformations, providing a route for extending our bulge-directed framework to internal loop motifs and implying a simplified link between secondary and tertiary structure. Finally, our results uncover a new simple mechanism for coupling junction-induced topological constraints with tertiary interactions.
Collapse
Affiliation(s)
- Anthony M Mustoe
- Departments of Chemistry & Biophysics, The University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109-1055, USA
| | | | | | | | | |
Collapse
|
9
|
Abendroth F, Bujotzek A, Shan M, Haag R, Weber M, Seitz O. DNA-controlled bivalent presentation of ligands for the estrogen receptor. Angew Chem Int Ed Engl 2011; 50:8592-6. [PMID: 21793134 DOI: 10.1002/anie.201101655] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Revised: 05/02/2011] [Indexed: 12/31/2022]
Affiliation(s)
- Frank Abendroth
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany
| | | | | | | | | | | |
Collapse
|
10
|
Abendroth F, Bujotzek A, Shan M, Haag R, Weber M, Seitz O. DNA-gesteuerte bivalente Präsentation von Liganden für den Östrogenrezeptor. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201101655] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
|
11
|
Todoroki K, Yoshida H, Hayama T, Itoyama M, Nohta H, Yamaguchi M. Highly sensitive and selective derivatization-LC method for biomolecules based on fluorescence interactions and fluorous separations. J Chromatogr B Analyt Technol Biomed Life Sci 2010; 879:1325-37. [PMID: 21190905 DOI: 10.1016/j.jchromb.2010.11.038] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Revised: 11/29/2010] [Accepted: 11/29/2010] [Indexed: 11/29/2022]
Abstract
A fluorescence derivatization LC method is a powerful tool for the analysis with high sensitivity and selectivity of biological compounds. In this review, we introduce new types of fluorescence derivatization LC analysis methods. These are (1) detection-selective derivatization methods based on fluorescence interactions generated from fluorescently labeled analytes: excimer fluorescence derivatization and fluorescence resonance energy transfer (FRET) derivatization; (2) separation-selective derivatization methods using the fluorous separation technique: fluorous derivatization, F-trap fluorescence derivatization, and fluorous scavenging derivatization (FSD).
Collapse
Affiliation(s)
- Kenichiro Todoroki
- Faculty of Pharmaceutical Sciences, Fukuoka University, Nanakuma, Johnan, Fukuoka 814-0180, Japan
| | | | | | | | | | | |
Collapse
|
12
|
|
13
|
Wang K, Tang Z, Yang C, Kim Y, Fang X, Li W, Wu Y, Medley C, Cao Z, Li J, Colon P, Lin H, Tan W. Molekulartechnische DNA-Modifizierung: Molecular Beacons. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200800370] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
|
14
|
Wang K, Tang Z, Yang CJ, Kim Y, Fang X, Li W, Wu Y, Medley CD, Cao Z, Li J, Colon P, Lin H, Tan W. Molecular engineering of DNA: molecular beacons. Angew Chem Int Ed Engl 2009; 48:856-70. [PMID: 19065690 PMCID: PMC2772660 DOI: 10.1002/anie.200800370] [Citation(s) in RCA: 492] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Molecular beacons (MBs) are specifically designed DNA hairpin structures that are widely used as fluorescent probes. Applications of MBs range from genetic screening, biosensor development, biochip construction, and the detection of single-nucleotide polymorphisms to mRNA monitoring in living cells. The inherent signal-transduction mechanism of MBs enables the analysis of target oligonucleotides without the separation of unbound probes. The MB stem-loop structure holds the fluorescence-donor and fluorescence-acceptor moieties in close proximity to one another, which results in resonant energy transfer. A spontaneous conformation change occurs upon hybridization to separate the two moieties and restore the fluorescence of the donor. Recent research has focused on the improvement of probe composition, intracellular gene quantitation, protein-DNA interaction studies, and protein recognition.
Collapse
Affiliation(s)
- Kemin Wang
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
- Biomedical Engineering Center, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 (P.R. China)
| | - Zhiwen Tang
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Chaoyong James Yang
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005 (P.R. China)
| | - Youngmi Kim
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Xiaohong Fang
- Institute of Chemistry, Chinese Academy of Sciences 2 Zhongguancun Beiyijie, Beijing 100190 (P.R. China)
| | - Wei Li
- Biomedical Engineering Center, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 (P.R. China)
| | - Yanrong Wu
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Colin D. Medley
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Zehui Cao
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Jun Li
- Biomedical Engineering Center, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 (P.R. China)
| | - Patrick Colon
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Hui Lin
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Weihong Tan
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
- Biomedical Engineering Center, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 (P.R. China)
| |
Collapse
|
15
|
Blouin S, Craggs TD, Lafontaine DA, Penedo JC. Functional studies of DNA-protein interactions using FRET techniques. Methods Mol Biol 2009; 543:475-502. [PMID: 19378182 DOI: 10.1007/978-1-60327-015-1_28] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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.
Collapse
Affiliation(s)
- Simon Blouin
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, 2500 boul. Université, Sherbrooke, QC, Canada, J1K 2R1
| | | | | | | |
Collapse
|
16
|
Browne SM, Al-Rubeai M. Selection Methods for High-Producing Mammalian Cell Lines. CELL ENGINEERING 2009. [DOI: 10.1007/978-90-481-2245-5_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
|
17
|
Abstract
We present advances in the use of single-molecule FRET measurements with flexibly linked dyes to derive full 3D structures of DNA constructs based on absolute distances. The resolution obtained by this single-molecule approach harbours the potential to study in detail also protein- or damage-induced DNA bending. If one is to generate a geometric structural model, distances between fixed positions are needed. These are usually not experimentally accessible because of unknown fluorophore-linker mobility effects that lead to a distribution of FRET efficiencies and distances. To solve this problem, we performed studies on DNA double-helices by systematically varying donor acceptor distances from 2 to 10 nm. Analysis of dye-dye quenching and fluorescence anisotropy measurements reveal slow positional and fast orientational fluorophore dynamics, that results in an isotropic average of the FRET efficiency. We use a nonlinear conversion function based on MD simulations that allows us to include this effect in the calculation of absolute FRET distances. To obtain unique structures, we performed a quantitative statistical analysis for the conformational search in full space based on triangulation, which uses the known helical nucleic acid features. Our higher accuracy allowed the detection of sequence-dependent DNA bending by 16 degrees . For DNA with bulged adenosines, we also quantified the kink angles introduced by the insertion of 1, 3 and 5 bases to be 32 degrees +/- 6 degrees , 56 degrees +/- 4 degrees and 73 +/- 2 degrees , respectively. Moreover, the rotation angles and shifts of the helices were calculated to describe the relative orientation of the two arms in detail.
Collapse
|
18
|
Vámosi G, Clegg RM. Helix−Coil Transition of a Four-Way DNA Junction Observed by Multiple Fluorescence Parameters. J Phys Chem B 2008; 112:13136-48. [DOI: 10.1021/jp8034055] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- György Vámosi
- Cell Biology and Signaling Research Group of the Hungarian Academy of Sciences, Department of Biophysics and Cell Biology, Medical and Health Science Center, University of Debrecen, Debrecen, Hungary HU H-4012, and Department of Physics, University of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801-3080
| | - Robert M. Clegg
- Cell Biology and Signaling Research Group of the Hungarian Academy of Sciences, Department of Biophysics and Cell Biology, Medical and Health Science Center, University of Debrecen, Debrecen, Hungary HU H-4012, and Department of Physics, University of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801-3080
| |
Collapse
|
19
|
Dragan AI, Privalov PL. Use of fluorescence resonance energy transfer (FRET) in studying protein-induced DNA bending. Methods Enzymol 2008; 450:185-99. [PMID: 19152861 DOI: 10.1016/s0076-6879(08)03409-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The specific association of many DNA-binding proteins with DNA frequently results in significant deformation of the DNA. Protein-induced DNA bends depend on the protein, the DNA sequence, the environmental conditions, and in some cases are very substantial, implying that DNA bending has important functional significance. The precise determination of the DNA deformation caused by proteins under various conditions is therefore of importance for understanding the biological role of the association. This review considers methods for the investigation of protein-induced DNA bending by measuring the change in fluorescence resonance energy transfer (FRET) between fluorophores placed at the ends of the target DNA duplex. This FRET technique is particularly efficient when the protein-induced bend in the DNA is considerable and results in a significant decrease in the distance between the DNA ends bearing the fluorophores. However, in the case of small bends the change of distance between the ends of short DNA duplexes, as typically used in protein binding experiments (about 16-20 bp), is too small to be detected accurately by FRET. In such cases the change of the distance between the fluorophores can be increased by using levers attached to the binding site, that is, using two bulges to construct a U-shaped DNA in which the central part contains the protein-binding site and the fluorophores are attached to the ends of the perpendicularly directed arms.
Collapse
Affiliation(s)
- Anatoly I Dragan
- Institute of Fluorescence, University of Maryland Biotechnology Institute, Columbus Center, Baltimore, Maryland, USA
| | | |
Collapse
|
20
|
McDonald RJ, Dragan AI, Kirk WR, Neff KL, Privalov PL, Maher LJ. DNA Bending by Charged Peptides: Electrophoretic and Spectroscopic Analyses. Biochemistry 2007; 46:2306-16. [PMID: 17279773 DOI: 10.1021/bi061921a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We are testing the idea that placement of fixed charges near one face of the DNA double helix can induce DNA bending by a purely electrostatic mechanism. If stretching forces between DNA phosphates are significant, fixed charges should induce DNA bending by asymmetrically modulating these forces. We have previously tested this hypothesis by adding charged residues to small bZIP DNA binding peptides and monitoring DNA bending using electrophoretic phasing assays. Our results were consistent with an electrostatic model of DNA bending in predicted directions. We now confirm these observations with fluorescence resonance energy transfer (FRET). Using a "U"-shaped DNA probe, we report that DNA bending by charged bZIP peptides is readily detected by FRET. We further show that charged bZIP peptides cause DNA bending rather than DNA twisting.
Collapse
Affiliation(s)
- Robert J McDonald
- Medical Scientist Training Program, Mayo Clinic College of Medicine, Rochester, Minnesota 55905, USA
| | | | | | | | | | | |
Collapse
|
21
|
Yoshitake M, Nohta H, Yoshida H, Yoshitake T, Todoroki K, Yamaguchi M. Selective Determination of Native Fluorescent Bioamines through Precolumn Derivatization and Liquid Chromatography Using Intramolecular Fluorescence Resonance Energy Transfer Detection. Anal Chem 2005; 78:920-7. [PMID: 16448069 DOI: 10.1021/ac051414j] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this paper, we introduce a novel approach for the highly selective and sensitive analysis of native fluorescent bioamines (indoleamines and catecholamines). This method is based on intramolecular fluorescence resonance energy transfer (FRET) detection in a liquid chromatography (LC) system following precolumn derivatization of the bioamines' amino groups. In this detection process, we monitored the FRET from the native fluorescent moieties (donor) to the derivatized fluorophore (acceptor). From a screening study involving 15 fluorescent reagents, we found that o-phthalaldehyde (OPA) generated the FRET most effectively. The OPA derivatives of the native fluorescent bioamines emitted OPA fluorescence (445 nm) through an intermolecular FRET process when they were excited at the excitation maximum wavelengths of the native fluorescent bioamines (280 nm). The generation of FRET was confirmed through comparison with the analysis of a nonfluorescent amine (isoleucine) performed using LC and a three-dimensional fluorescence detection system. We were able to separate the OPA derivatives of the indoleamines and catecholamines when performing LC on an ODS column. The detection limits (signal-to-noise ratio, 3) for the indoleamines and catecholamines, at a 20-muL injection volume, were 17-120 and 28-200 fmol, respectively. The sensitivity of the intramolecular FRET-forming derivatization method is higher than those of systems that take advantage of both native fluorescence detection (i.e., without derivatization) and the conventional detection of OPA derivatives. Furthermore, this method provides enough selectivity and sensitivity for the determination of the indoleamines present in the urine of healthy humans.
Collapse
Affiliation(s)
- Makoto Yoshitake
- Faculty of Pharmaceutical Sciences, Fukuoka University, Nanakuma, Johnan, Japan
| | | | | | | | | | | |
Collapse
|
22
|
Dragan AI, Liu Y, Makeyeva EN, Privalov PL. DNA-binding domain of GCN4 induces bending of both the ATF/CREB and AP-1 binding sites of DNA. Nucleic Acids Res 2004; 32:5192-7. [PMID: 15459288 PMCID: PMC521666 DOI: 10.1093/nar/gkh854] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The interaction of proteins with DNA results, in some cases, in DNA bending, and this might have functional importance. However, when the protein-induced bending of DNA is small, its measurement presents a problem. It is shown that the fluorescence resonance energy transfer between fluorophores placed on the ends of the specially designed U-shaped DNA, which contains the DNA-binding sites at its central part, can be successfully used for this purpose. The lever effect of the arms of such U-shaped DNA ensures that the distance between the fluorophores is very sensitive to bending of the central part. Using this technique, it was shown that (i) the AP-1 and ATF/CREB binding sites of GCN4 transcription factor are pre-bent to the same extent (approximately 12 degrees toward the major groove) and (ii) binding of the GCN4 DNA-binding domain (GCN4-bZIP) results in additional bending of both these target sites but to a greater extent at the ATF/CREB site. In total, in the complex with GCN4-bZIP, the ATF/CREB site is bent by (25 +/- 2) degrees and the AP-1 site by (20 +/- 2) degrees toward the minor groove.
Collapse
Affiliation(s)
- Anatoly I Dragan
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | | | | | | |
Collapse
|
23
|
Khrapunov S, Brenowitz M. Comparison of the effect of water release on the interaction of the Saccharomyces cerevisiae TATA binding protein (TBP) with "TATA Box" sequences composed of adenosine or inosine. Biophys J 2004; 86:371-83. [PMID: 14695279 PMCID: PMC1303802 DOI: 10.1016/s0006-3495(04)74113-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The formation of sequence-specific complexes of TATA binding protein (TBP) with the minor groove of DNA results in the burial of large nonpolar surfaces and the exclusion of water from these interfaces. The release of water is thus expected to provide a significant entropic driving force for formation of the transcription-preinitiated complexes mediated by the binding of TBP to specific sequences. In this article are described equilibrium-binding studies of Saccharomyces cerevisiae TBP to 14 bp oligonucleotides bearing either the tightly bound and efficiently transcribed adenovirus major late promoter (TATAAAAG) or its inosine-substituted derivative (TITIIIIG) as a function of neutral osmolyte concentration. These two DNA sequences present the same pattern of minor groove hydrogen-bond donors and acceptors to the protein. TBP-DNA complex formation was monitored by steady-state fluorescence resonance energy transfer measurements of the oligonucleotides end-labeled with fluorescein (donor) and TAMRA (acceptor). Correct interpretation of the results obtained with the inosine-substituted sequence required careful consideration of the optical properties of the dyes as a function of osmolyte concentration to demonstrate that the relative change in the end-to-end distances for TATAAAAG- and TITIIIIG-bearing oligonucleotides is the same upon TBP binding. Although the affinity of TBP is slightly greater for the adenosine compared with the inosine-substituted TATA sequence in the absence of osmolyte, the end-to-end distances of the bound DNA in complex with TBP, the enthalpic and electrostatic components of binding, are identical within experimental precision. However, approximately 18 additional molecules of water are released upon TBP binding the TATAAAAG as compared with the TITIIIIG sequence resulting in an entropic advantage to the binding of the natural promoter sequence. These results are considered with regard to differences in the flexibility and hydration of the two DNA sequences.
Collapse
Affiliation(s)
- Sergei Khrapunov
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA.
| | | |
Collapse
|
24
|
Wojtuszewski K, Mukerji I. HU binding to bent DNA: a fluorescence resonance energy transfer and anisotropy study. Biochemistry 2003; 42:3096-104. [PMID: 12627977 DOI: 10.1021/bi0264014] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
HU, an architectural DNA-binding protein, either stabilizes DNA in a bent conformation or induces a bend upon binding to give other proteins access to the DNA. In this study, HU binding affinity for a bent DNA sequence relative to a linear sequence was investigated using fluorescence anisotropy measurements. A static bend was achieved by the introduction of two phased A4T4 tracts in a 20 bp duplex. Binding affinity for 20 bp duplexes containing two phased A-tracts in either a 5'-3' or 3'-5' orientation was found to be almost 10-fold higher than HU binding to a random sequence 20 bp duplex (6.1 vs 0.68 microM(-1)). The fluorescence technique of resonance energy transfer was used to quantitatively determine the static bend of the DNA duplexes and the HU-induced bend. DNA molecules were 5'-end labeled with fluorescein as the donor or rhodamine as the acceptor. From the efficiency of energy transfer, the end-to-end distance of the DNA duplexes was calculated. The end-to-end distance relative to DNA contour length (R/R(C)) yields a bend angle for the A-tract duplex of 45 +/- 7 degrees in the absence of HU and 70 +/- 3 degrees in the presence of HU. The bend angle calculated for the T4A4 tract duplex was 62 +/- 4 degrees after binding two HU dimers. Fluorescence anisotropy measurements reveal that HU binds in a 1:1 stoichiometry to the A4T4 tract duplex but a 2:1 stoichiometry to the T4A4 tract and random sequence duplex. These findings suggest that HU binding and recognition of DNA may be governed by a structural mechanism.
Collapse
Affiliation(s)
- Kristi Wojtuszewski
- Molecular Biology and Biochemistry Department, Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut 06459-0175, USA
| | | |
Collapse
|
25
|
Proudnikov D, Yuferov V, Zhou Y, LaForge KS, Ho A, Kreek MJ. Optimizing primer--probe design for fluorescent PCR. J Neurosci Methods 2003; 123:31-45. [PMID: 12581847 DOI: 10.1016/s0165-0270(02)00325-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
TaqMan, a variation of fluorescent PCR, is a powerful tool for gene expression and polymorphism studies. Here we describe the design and evaluation of 27 new TaqMan primer-probe sets for rat genes that play a key role in neural signaling. These newly designed and synthesized probes were tested and then used for quantification of RNA isolated from rat brain. The usual length of common TaqMan probes is 25 bases or less. In these studies we constructed probes with lengths of 25-39 bases to span exon-exon junctions of nucleic acids to avoid the influence of DNA contamination upon the RNA quantification. The specific sequences at these positions required probes of these lengths to optimize hybridization. We found that the relocation of the quencher from the traditional 3' position to an internal one increases the sensitivity of probe up to 30 fold. Substitution of 6-carboxyfluorescein with Alexa Fluor 488 as fluorophore and TAMRA with non-fluorescent quencher dabcyl was also investigated. We also describe the evaluation of part of a newly designed set of 27 TaqMan primer-probes for the measurement of differences in gene expression levels in samples from the caudate putamen region of rat brain after 'binge' paradigm cocaine administration. Cocaine-induced alterations in expression of c-fos and preprodynorphin mRNAs measured by TaqMan were confirmed by ribonuclease protection assay.
Collapse
MESH Headings
- Animals
- Caudate Nucleus/chemistry
- Caudate Nucleus/drug effects
- Caudate Nucleus/metabolism
- Cocaine-Related Disorders/genetics
- Cocaine-Related Disorders/metabolism
- DNA Primers
- Fluorescent Dyes
- Gene Expression/drug effects
- Genes, fos/genetics
- Glyceraldehyde-3-Phosphate Dehydrogenases/biosynthesis
- Glyceraldehyde-3-Phosphate Dehydrogenases/genetics
- Male
- Neuropeptides/genetics
- Polymorphism, Genetic
- Putamen/chemistry
- Putamen/drug effects
- Putamen/metabolism
- RNA, Messenger/analysis
- RNA, Messenger/biosynthesis
- RNA, Ribosomal, 18S/analysis
- RNA, Ribosomal, 18S/metabolism
- Rats
- Receptors, Dopamine D2/genetics
- Receptors, Opioid/genetics
- Reference Standards
- Reproducibility of Results
- Reverse Transcriptase Polymerase Chain Reaction/methods
Collapse
Affiliation(s)
- Dmitri Proudnikov
- Laboratory of the Biology of Addictive Diseases, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.
| | | | | | | | | | | |
Collapse
|
26
|
Lorenz M, Hillisch A, Diekmann S. Fluorescence resonance energy transfer studies of U-shaped DNA molecules. J Biotechnol 2002; 82:197-209. [PMID: 11999690 DOI: 10.1016/s1389-0352(01)00038-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Fluorescence resonance energy transfer studies allow to determine global shape properties of nucleic acids and nucleoprotein complexes. In many DNA-protein complexes, the DNA is more or less bent and the degree of bending can be obtained by FRET. For example, the DNA in complex with the integration host factor (IHF) is kinked by approximately 160 degrees building a U-shaped structure. The two DNA helix ends come close to one another in space in a distance range easily measurable by FRET. The global DNA structure of this complex can be mimicked by introducing two regions with unpaired bases ('bulges') into the DNA each producing a sharp kink of approximately 80 degrees. These U-shaped DNA constructs were used to measure the electrostatic interaction of the two nearly parallel negatively charged DNA helix arms. The electrostatic repulsion between the helix arms, and as a consequence their distance, decreases with growing salt concentration of mono- or divalent cations. This experimental approach also allows the sensitive study of the local structure of DNA sequences positioned between the two bulges.
Collapse
Affiliation(s)
- Mike Lorenz
- Institut für Molekulare Biotechnologie, Jena, Germany
| | | | | |
Collapse
|
27
|
Lorenz M, Diekmann S. Quantitative distance information on protein-DNA complexes determined in polyacrylamide gels by fluorescence resonance energy transfer. Electrophoresis 2001; 22:990-8. [PMID: 11358153 DOI: 10.1002/1522-2683()22:6<990::aid-elps990>3.0.co;2-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
In polyacrylamide gels, we have quantitatively determined Forster transfer (fluorescense resonance energy transfer, FRET) between two fluorescent dyes attached to DNA in protein-DNA complexes. The donor-dye fluorescein labeled to DNA retains its free mobility in the polyacrylamide gel, however, its fluorescence properties change. The different quantum yield of fluorescein in the gel is found to be independent of the gel concentration and can thus be quantitatively taken into account by a reduced Forster distance R0 of 46 A compared to 50 A in solution. We have determined global structural properties of two proteins binding to double-labeled DNA using a novel gel-based fluorescence resonance energy transfer assay. In polyacrylamide gels we have analyzed the binding of integration host factor (IHF) and the high mobility group protein NHP6a to their substrate DNA. The measured Forster transfer efficiency allows us to deduce information on the overall shape and the DNA bending angle in the complex.
Collapse
Affiliation(s)
- M Lorenz
- Department of Molecular Biology, Institute for Molecular Biotechnology, Jena, Germany
| | | |
Collapse
|
28
|
Altenberg-Greulich B, Vriend G. Where to attach dye molecules to a protein: lessons from the computer program what if. J Mol Struct 2001. [DOI: 10.1016/s0022-2860(01)00798-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
29
|
Kapanidis AN, Ebright YW, Ludescher RD, Chan S, Ebright RH. Mean DNA bend angle and distribution of DNA bend angles in the CAP-DNA complex in solution. J Mol Biol 2001; 312:453-68. [PMID: 11563909 DOI: 10.1006/jmbi.2001.4976] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In order to define the mean DNA bend angle and distribution of DNA bend angles in the catabolite activator protein (CAP)-DNA complex in solution under standard transcription initiation conditions, we have performed nanosecond time-resolved fluorescence measurements quantifying energy transfer between a probe incorporated at a specific site in CAP, and a complementary probe incorporated at each of five specific sites in DNA. The results indicate that the mean DNA bend angle is 77(+/-3) degrees - consistent with the mean DNA bend angle observed in crystallographic structures (80(+/-12) degrees ). Lifetime-distribution analysis indicates that the distribution of DNA bend angles is relatively narrow, with <10 % of DNA bend angles exceeding 100 degrees. Millisecond time-resolved luminescence measurements using lanthanide-chelate probes provide independent evidence that the upper limit of the distribution of DNA bend angles is approximately 100 degrees. The methods used here will permit mutational analysis of CAP-induced DNA bending and the role of CAP-induced DNA bending in transcriptional activation.
Collapse
Affiliation(s)
- A N Kapanidis
- Howard Hughes Medical Institute, Waksman Institute and Department of Chemistry, Piscataway, NJ 08854, USA
| | | | | | | | | |
Collapse
|
30
|
Hillisch A, Lorenz M, Diekmann S. Recent advances in FRET: distance determination in protein-DNA complexes. Curr Opin Struct Biol 2001; 11:201-7. [PMID: 11297928 DOI: 10.1016/s0959-440x(00)00190-1] [Citation(s) in RCA: 128] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Fluorescence resonance energy transfer (FRET) provides information on the distance between a donor and an acceptor dye in the range 10 to 100 A. Knowledge of the exact positions of some dyes with respect to nucleic acids now enables us to translate these data into precise structural information using molecular modeling. Advances in the preparation of dye-labeled nucleic acid molecules and in new techniques, such as the measurement of FRET in polyacrylamide gels or in vivo, will lead to an increasingly important role of FRET in structural and molecular biology.
Collapse
Affiliation(s)
- A Hillisch
- EnTec GmbH, Adolf-Reichwein-Strasse 20, D-07745 Jena, Germany.
| | | | | |
Collapse
|