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Baker KA, Lamichhane R, Lamichhane T, Rueda D, Cunningham PR. Protein-RNA Dynamics in the Central Junction Control 30S Ribosome Assembly. J Mol Biol 2016; 428:3615-31. [PMID: 27192112 DOI: 10.1016/j.jmb.2016.05.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 05/02/2016] [Accepted: 05/07/2016] [Indexed: 11/18/2022]
Abstract
Interactions between ribosomal proteins (rproteins) and ribosomal RNA (rRNA) facilitate the formation of functional ribosomes. S15 is a central domain primary binding protein that has been shown to trigger a cascade of conformational changes in 16S rRNA, forming the functional structure of the central domain. Previous biochemical and structural studies in vitro have revealed that S15 binds a three-way junction of helices 20, 21, and 22, including nucleotides 652-654 and 752-754. All junction nucleotides except 653 are highly conserved among the Bacteria. To identify functionally important motifs within the junction, we subjected nucleotides 652-654 and 752-754 to saturation mutagenesis and selected and analyzed functional mutants. Only 64 mutants with greater than 10% ribosome function in vivo were isolated. S15 overexpression complemented mutations in the junction loop in each of the partially active mutants, although mutations that produced inactive ribosomes were not complemented by overexpression of S15. Single-molecule Förster or fluorescence resonance energy transfer (smFRET) was used to study the Mg(2+)- and S15-induced conformational dynamics of selected junction mutants. Comparison of the structural dynamics of these mutants with the wild type in the presence and absence of S15 revealed specific sequence and structural motifs in the central junction that are important in ribosome function.
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MESH Headings
- DNA Mutational Analysis
- Escherichia coli/chemistry
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Fluorescence Resonance Energy Transfer
- Genetic Complementation Test
- Macromolecular Substances/metabolism
- Magnesium/metabolism
- Models, Biological
- Models, Molecular
- Protein Binding
- Protein Conformation
- Protein Interaction Maps
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- Ribosomal Proteins/metabolism
- Ribosome Subunits, Small, Bacterial/metabolism
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Affiliation(s)
- Kris Ann Baker
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | - Rajan Lamichhane
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
| | - Tek Lamichhane
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA; Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
| | - David Rueda
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA; Section of Virology, Department of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK; Single Molecule Imaging Group, MRC Clinical Sciences Centre (CSC), Du Cane Road, London W12 0NN, UK.
| | - Philip R Cunningham
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA.
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52
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Abid Ali F, Renault L, Gannon J, Gahlon HL, Kotecha A, Zhou JC, Rueda D, Costa A. Cryo-EM structures of the eukaryotic replicative helicase bound to a translocation substrate. Nat Commun 2016; 7:10708. [PMID: 26888060 PMCID: PMC4759635 DOI: 10.1038/ncomms10708] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 01/12/2016] [Indexed: 02/06/2023] Open
Abstract
The Cdc45-MCM-GINS (CMG) helicase unwinds DNA during the elongation step of eukaryotic genome duplication and this process depends on the MCM ATPase function. Whether CMG translocation occurs on single- or double-stranded DNA and how ATP hydrolysis drives DNA unwinding remain open questions. Here we use cryo-electron microscopy to describe two subnanometre resolution structures of the CMG helicase trapped on a DNA fork. In the predominant state, the ring-shaped C-terminal ATPase of MCM is compact and contacts single-stranded DNA, via a set of pre-sensor 1 hairpins that spiral around the translocation substrate. In the second state, the ATPase module is relaxed and apparently substrate free, while DNA intimately contacts the downstream amino-terminal tier of the MCM motor ring. These results, supported by single-molecule FRET measurements, lead us to suggest a replication fork unwinding mechanism whereby the N-terminal and AAA+ tiers of the MCM work in concert to translocate on single-stranded DNA.
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Affiliation(s)
- Ferdos Abid Ali
- Macromolecular Machines, Clare Hall Laboratory, The Francis Crick Institute, Blanche Lane, South Mimms EN6 3LD, UK
| | - Ludovic Renault
- Macromolecular Machines, Clare Hall Laboratory, The Francis Crick Institute, Blanche Lane, South Mimms EN6 3LD, UK
- National Institute for Biological Standards and Control, Microscopy and Imaging, Blanche Lane, South Mimms EN6 3QG, UK
| | - Julian Gannon
- Macromolecular Machines, Clare Hall Laboratory, The Francis Crick Institute, Blanche Lane, South Mimms EN6 3LD, UK
| | - Hailey L. Gahlon
- Section of Virology and Single Molecule Imaging Group, Department of Medicine, MRC Clinical Centre, Imperial College London, London W12 0NN, UK
| | - Abhay Kotecha
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Jin Chuan Zhou
- Macromolecular Machines, Clare Hall Laboratory, The Francis Crick Institute, Blanche Lane, South Mimms EN6 3LD, UK
| | - David Rueda
- Section of Virology and Single Molecule Imaging Group, Department of Medicine, MRC Clinical Centre, Imperial College London, London W12 0NN, UK
| | - Alessandro Costa
- Macromolecular Machines, Clare Hall Laboratory, The Francis Crick Institute, Blanche Lane, South Mimms EN6 3LD, UK
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53
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Recruitment, Duplex Unwinding and Protein-Mediated Inhibition of the Dead-Box RNA Helicase Dbp2 at Actively Transcribed Chromatin. J Mol Biol 2016; 428:1091-1106. [PMID: 26876600 DOI: 10.1016/j.jmb.2016.02.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 01/26/2016] [Accepted: 02/02/2016] [Indexed: 02/07/2023]
Abstract
RNA helicases play fundamental roles in modulating RNA structures and facilitating RNA-protein (RNP) complex assembly in vivo. Previously, our laboratory demonstrated that the DEAD-box RNA helicase Dbp2 in Saccharomyces cerevisiae is required to promote efficient assembly of the co-transcriptionally associated mRNA-binding proteins Yra1, Nab2, and Mex67 onto poly(A)(+)RNA. We also found that Yra1 associates directly with Dbp2 and functions as an inhibitor of Dbp2-dependent duplex unwinding, suggestive of a cycle of unwinding and inhibition by Dbp2. To test this, we undertook a series of experiments to shed light on the order of events for Dbp2 in co-transcriptional mRNP assembly. We now show that Dbp2 is recruited to chromatin via RNA and forms a large, RNA-dependent complex with Yra1 and Mex67. Moreover, single-molecule fluorescence resonance energy transfer and bulk biochemical assays show that Yra1 inhibits unwinding in a concentration-dependent manner by preventing the association of Dbp2 with single-stranded RNA. This inhibition prevents over-accumulation of Dbp2 on mRNA and stabilization of a subset of RNA polymerase II transcripts. We propose a model whereby Yra1 terminates a cycle of mRNP assembly by Dbp2.
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54
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Senavirathne G, Bertram JG, Jaszczur M, Chaurasiya KR, Pham P, Mak CH, Goodman MF, Rueda D. Activation-induced deoxycytidine deaminase (AID) co-transcriptional scanning at single-molecule resolution. Nat Commun 2015; 6:10209. [PMID: 26681117 PMCID: PMC4703863 DOI: 10.1038/ncomms10209] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 11/13/2015] [Indexed: 12/20/2022] Open
Abstract
Activation-induced deoxycytidine deaminase (AID) generates antibody diversity in B cells by initiating somatic hypermutation (SHM) and class-switch recombination (CSR) during transcription of immunoglobulin variable (IgV) and switch region (IgS) DNA. Using single-molecule FRET, we show that AID binds to transcribed dsDNA and translocates unidirectionally in concert with RNA polymerase (RNAP) on moving transcription bubbles, while increasing the fraction of stalled bubbles. AID scans randomly when constrained in an 8 nt model bubble. When unconstrained on single-stranded (ss) DNA, AID moves in random bidirectional short slides/hops over the entire molecule while remaining bound for ∼5 min. Our analysis distinguishes dynamic scanning from static ssDNA creasing. That AID alone can track along with RNAP during transcription and scan within stalled transcription bubbles suggests a mechanism by which AID can initiate SHM and CSR when properly regulated, yet when unregulated can access non-Ig genes and cause cancer. Activation-induced deoxycytidine deaminase (AID) induces somatic hypermutation and class-switch recombination during transcription of immunoglobulin genes. Here the authors use single-molecule FRET to show that AID translocates together with RNA polymerase and scans within stalled transcription bubbles.
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Affiliation(s)
- Gayan Senavirathne
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, USA
| | - Jeffrey G Bertram
- Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
| | - Malgorzata Jaszczur
- Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
| | - Kathy R Chaurasiya
- Department of Medicine, Section of Virology, Imperial College London, Du Cane Road, London W12 0NN, UK.,Single Molecule Imaging Group, MRC Clinical Sciences Center, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Phuong Pham
- Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
| | - Chi H Mak
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA.,Center for Applied Mathematical Science, University of Southern California, Los Angeles, California 90089, USA
| | - Myron F Goodman
- Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA.,Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - David Rueda
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, USA.,Department of Medicine, Section of Virology, Imperial College London, Du Cane Road, London W12 0NN, UK.,Single Molecule Imaging Group, MRC Clinical Sciences Center, Imperial College London, Du Cane Road, London W12 0NN, UK
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55
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Single-molecule view of basal activity and activation mechanisms of the G protein-coupled receptor β2AR. Proc Natl Acad Sci U S A 2015; 112:14254-9. [PMID: 26578769 DOI: 10.1073/pnas.1519626112] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Binding of extracellular ligands to G protein-coupled receptors (GPCRs) initiates transmembrane signaling by inducing conformational changes on the cytoplasmic receptor surface. Knowledge of this process provides a platform for the development of GPCR-targeting drugs. Here, using a site-specific Cy3 fluorescence probe in the human β2-adrenergic receptor (β2AR), we observed that individual receptor molecules in the native-like environment of phospholipid nanodiscs undergo spontaneous transitions between two distinct conformational states. These states are assigned to inactive and active-like receptor conformations. Individual receptor molecules in the apo form repeatedly sample both conformations, with a bias toward the inactive conformation. Experiments in the presence of drug ligands show that binding of the full agonist formoterol shifts the conformational distribution in favor of the active-like conformation, whereas binding of the inverse agonist ICI-118,551 favors the inactive conformation. Analysis of single-molecule dwell-time distributions for each state reveals that formoterol increases the frequency of activation transitions, while also reducing the frequency of deactivation events. In contrast, the inverse agonist increases the frequency of deactivation transitions. Our observations account for the high level of basal activity of this receptor and provide insights that help to rationalize, on the molecular level, the widely documented variability of the pharmacological efficacies among GPCR-targeting drugs.
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56
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Brenlla A, Rueda D, Romano LJ. Mechanism of aromatic amine carcinogen bypass by the Y-family polymerase, Dpo4. Nucleic Acids Res 2015; 43:9918-27. [PMID: 26481355 PMCID: PMC4787768 DOI: 10.1093/nar/gkv1067] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 10/05/2015] [Indexed: 01/16/2023] Open
Abstract
Bulky DNA damage inhibits DNA synthesis by replicative polymerases and often requires the action of error prone bypass polymerases. The exact mechanism governing adduct-induced mutagenesis and its dependence on the DNA sequence context remains unclear. In this work, we characterize Dpo4 binding conformations and activity with DNA templates modified with the carcinogenic DNA adducts, 2-aminofluoene (AF) or N-acetyl-2-aminofluorene (AAF), using single-molecule FRET (smFRET) analysis and DNA synthesis extension assays. We find that in the absence of dNTPs, both adducts alter polymerase binding as measured by smFRET, but the addition of dNTPs induces the formation of a ternary complex having what appears to be a conformation similar to the one observed with an unmodified DNA template. We also observe that the misincorporation pathways for each adduct present significant differences: while an AF adduct induces a structure consistent with the previously observed primer-template looped structure, its acetylated counterpart uses a different mechanism, one consistent with a dNTP-stabilized misalignment mechanism.
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Affiliation(s)
- Alfonso Brenlla
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
| | - David Rueda
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA Department of Medicine, Section of Virology, Imperial College London, London, UK Single Molecule Imaging Group, MRC Clinical Sciences Centre, Imperial College London, London, UK
| | - Louis J Romano
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
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57
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Kim JY, Kim C, Lee NK. Real-time submillisecond single-molecule FRET dynamics of freely diffusing molecules with liposome tethering. Nat Commun 2015; 6:6992. [PMID: 25908552 PMCID: PMC4421855 DOI: 10.1038/ncomms7992] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 03/23/2015] [Indexed: 01/15/2023] Open
Abstract
Single-molecule fluorescence resonance energy transfer (smFRET) is one of the powerful techniques for deciphering the dynamics of unsynchronized biomolecules. However, smFRET is limited in its temporal resolution for observing dynamics. Here, we report a novel method for observing real-time dynamics with submillisecond resolution by tethering molecules to freely diffusing 100-nm-sized liposomes. The observation time for a diffusing molecule is extended to 100 ms with a submillisecond resolution, which allows for direct analysis of the transition states from the FRET time trace using hidden Markov modelling. We measure transition rates of up to 1,500 s–1 between two conformers of a Holliday junction. The rapid diffusional migration of Deinococcus radiodurans single-stranded DNA-binding protein (SSB) on single-stranded DNA is resolved by FRET, faster than that of Escherichia coli SSB by an order of magnitude. Our approach is a powerful method for studying the dynamics and movements of biomolecules at submillisecond resolution. Single-molecule fluorescence resonance energy transfer is widely used to probe biomolecular dynamics, but is limited by its temporal resolution. Here, Kim et al. push the limit to submillisecond for the duration of tens of milliseconds by tethering target molecules to liposomes in buffer solutions.
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Affiliation(s)
- Jae-Yeol Kim
- Department of Physics, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Cheolhee Kim
- Department of Physics, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Nam Ki Lee
- 1] Department of Physics, Pohang University of Science and Technology, Pohang 790-784, Korea [2] School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang 790-784, Korea
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58
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Holmstrom ED, Polaski JT, Batey RT, Nesbitt DJ. Single-molecule conformational dynamics of a biologically functional hydroxocobalamin riboswitch. J Am Chem Soc 2014; 136:16832-43. [PMID: 25325398 PMCID: PMC4277777 DOI: 10.1021/ja5076184] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
![]()
Riboswitches
represent a family of highly structured regulatory
elements found primarily in the leader sequences of bacterial mRNAs.
They function as molecular switches capable of altering gene expression;
commonly, this occurs via a conformational change in a regulatory
element of a riboswitch that results from ligand binding in the aptamer
domain. Numerous studies have investigated the ligand binding process,
but little is known about the structural changes in the regulatory
element. A mechanistic description of both processes is essential
for deeply understanding how riboswitches modulate gene expression.
This task is greatly facilitated by studying all aspects of riboswitch
structure/dynamics/function in the same model system. To this end,
single-molecule fluorescence resonance energy transfer (smFRET) techniques
have been used to directly observe the conformational dynamics of
a hydroxocobalamin (HyCbl) binding riboswitch (env8HyCbl) with a known crystallographic structure.1 The single-molecule RNA construct studied in this work
is unique in that it contains all of the structural elements both
necessary and sufficient for regulation of gene expression in a biological
context. The results of this investigation reveal that the undocking
rate constant associated with the disruption of a long-range kissing-loop
(KL) interaction is substantially decreased when the ligand is bound
to the RNA, resulting in a preferential stabilization of the docked
conformation. Notably, the formation of this tertiary KL interaction
directly sequesters the Shine-Dalgarno sequence (i.e., the ribosome
binding site) via base-pairing, thus preventing translation initiation.
These results reveal that the conformational dynamics of this regulatory
switch are quantitatively described by a four-state kinetic model,
whereby ligand binding promotes formation of the KL interaction. The
results of complementary cell-based gene expression experiments conducted
in Escherichia coli are highly correlated
with the smFRET results, suggesting that KL formation is directly
responsible for regulating gene expression.
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Affiliation(s)
- Erik D Holmstrom
- JILA, University of Colorado and National Institute of Standards and Technology, and ‡Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80309-0440, United States
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59
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Fluorescence methods in the investigation of the DEAD-box helicase mechanism. ACTA ACUST UNITED AC 2014; 105:161-92. [PMID: 25095995 DOI: 10.1007/978-3-0348-0856-9_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
DEAD-box proteins catalyze the ATP-dependent unwinding of RNA duplexes and accompany RNA molecules throughout their cellular life. Conformational changes in the helicase core of DEAD-box proteins are intimately linked to duplex unwinding. In the absence of ligands, the two RecA domains of the helicase core are separated. ATP and RNA binding induces a closure of the cleft between the RecA domains that is coupled to the distortion of bound RNA, leading to duplex destabilization and dissociation of one RNA strand. Reopening of the helicase core occurs after ATP hydrolysis and is coupled to phosphate release and dissociation of the second RNA strand.Fluorescence spectroscopy provides an array of approaches to study intermolecular interactions, local structural rearrangements, or large conformational changes of biomolecules. The fluorescence intensity of a fluorophore reports on its environment, and fluorescence anisotropy reflects the size of the molecular entity the fluorophore is part of. Fluorescence intensity and anisotropy are therefore sensitive probes to report on binding and dissociation events. Fluorescence resonance energy transfer (FRET) reports on the distance between two fluorophores and thus on conformational changes. Single-molecule FRET experiments reveal the distribution of conformational states and the kinetics of their interconversion. This chapter summarizes fluorescence approaches for monitoring individual aspects of DEAD-box protein activity, from nucleotide and RNA binding and RNA unwinding to protein and RNA conformational changes in the catalytic cycle, and illustrates exemplarily how fluorescence-based methods have contributed to understanding the mechanism of DEAD-box helicase-catalyzed RNA unwinding.
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60
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Hohlbein J, Craggs TD, Cordes T. Alternating-laser excitation: single-molecule FRET and beyond. Chem Soc Rev 2014; 43:1156-71. [PMID: 24037326 DOI: 10.1039/c3cs60233h] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The alternating-laser excitation (ALEX) scheme continues to expand the possibilities of fluorescence-based assays to study biological entities and interactions. Especially the combination of ALEX and single-molecule Förster Resonance Energy Transfer (smFRET) has been very successful as ALEX enables the sorting of fluorescently labelled species based on the number and type of fluorophores present. ALEX also provides a convenient way of accessing the correction factors necessary for determining accurate molecular distances. Here, we provide a comprehensive overview of the concept and current applications of ALEX and we explicitly discuss how to obtain fully corrected distance information across the entire FRET range. We also present new ideas for applications of ALEX which will push the limits of smFRET-based experiments in terms of temporal and spatial resolution for the study of complex biological systems.
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Affiliation(s)
- Johannes Hohlbein
- Laboratory of Biophysics, Wageningen UR, Wageningen, The Netherlands.
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61
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Pulsed IR heating studies of single-molecule DNA duplex dissociation kinetics and thermodynamics. Biophys J 2014; 106:220-31. [PMID: 24411254 DOI: 10.1016/j.bpj.2013.11.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 10/19/2013] [Accepted: 11/04/2013] [Indexed: 01/10/2023] Open
Abstract
Single-molecule fluorescence spectroscopy is a powerful technique that makes it possible to observe the conformational dynamics associated with biomolecular processes. The addition of precise temperature control to these experiments can yield valuable thermodynamic information about equilibrium and kinetic rate constants. To accomplish this, we have developed a microscopy technique based on infrared laser overtone/combination band absorption to heat small (≈10(-11) liter) volumes of water. Detailed experimental characterization of this technique reveals three major advantages over conventional stage heating methods: 1), a larger range of steady-state temperatures (20-100°C); 2), substantially superior spatial (≤20 μm) control; and 3), substantially superior temporal (≈1 ms) control. The flexibility and breadth of this spatial and temporally resolved laser-heating approach is demonstrated in single-molecule fluorescence assays designed to probe the dissociation of a 21 bp DNA duplex. These studies are used to support a kinetic model based on nucleic acid end fraying that describes dissociation for both short (<10 bp) and long (>10 bp) DNA duplexes. These measurements have been extended to explore temperature-dependent kinetics for the 21 bp construct, which permit determination of single-molecule activation enthalpies and entropies for DNA duplex dissociation.
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62
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Affiliation(s)
- Vasudha Aggarwal
- Center for Biophysics and Computational Biology; University of Illinois Urbana Champaign; Urbana IL USA
| | - Taekjip Ha
- Center for Biophysics and Computational Biology; University of Illinois Urbana Champaign; Urbana IL USA
- Department of Physics; University of Illinois Urbana Champaign; Urbana IL USA
- Howard Hughes Medical Institute; Urbana IL USA
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63
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Paudel B, Rueda D. RNA folding dynamics using laser-assisted single-molecule refolding. Methods Mol Biol 2014; 1086:289-307. [PMID: 24136611 DOI: 10.1007/978-1-62703-667-2_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
RNA folding pathways can be complex and even include kinetic traps or misfolded intermediates that can be slow to resolve. Characterizing these pathways is critical to understanding how RNA molecules acquire their biological function. We have previously developed a novel approach to help characterize such misfolded intermediates. Laser-assisted single-molecule refolding (LASR) is a powerful technique that combines temperature-jump (T-jump) kinetics with single-molecule detection. In a typical LASR experiment, the temperature is rapidly increased and conformational dynamics are characterized, in real-time, at the single-molecule level using single-molecule fluorescence resonance energy transfer (smFRET). Here, we provide detailed protocols for performing LASR experiments including sample preparation, temperature calibration, and data analysis.
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Affiliation(s)
- Bishnu Paudel
- Department of Medicine, Section of Virology, Imperial College, London, UK
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64
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Chandradoss SD, Haagsma AC, Lee YK, Hwang JH, Nam JM, Joo C. Surface passivation for single-molecule protein studies. J Vis Exp 2014. [PMID: 24797261 PMCID: PMC4179479 DOI: 10.3791/50549] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Single-molecule fluorescence spectroscopy has proven to be instrumental in understanding a wide range of biological phenomena at the nanoscale. Important examples of what this technique can yield to biological sciences are the mechanistic insights on protein-protein and protein-nucleic acid interactions. When interactions of proteins are probed at the single-molecule level, the proteins or their substrates are often immobilized on a glass surface, which allows for a long-term observation. This immobilization scheme may introduce unwanted surface artifacts. Therefore, it is essential to passivate the glass surface to make it inert. Surface coating using polyethylene glycol (PEG) stands out for its high performance in preventing proteins from non-specifically interacting with a glass surface. However, the polymer coating procedure is difficult, due to the complication arising from a series of surface treatments and the stringent requirement that a surface needs to be free of any fluorescent molecules at the end of the procedure. Here, we provide a robust protocol with step-by-step instructions. It covers surface cleaning including piranha etching, surface functionalization with amine groups, and finally PEG coating. To obtain a high density of a PEG layer, we introduce a new strategy of treating the surface with PEG molecules over two rounds, which remarkably improves the quality of passivation. We provide representative results as well as practical advice for each critical step so that anyone can achieve the high quality surface passivation.
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Affiliation(s)
- Stanley D Chandradoss
- Kavli Institute of NanoScience, Department of BioNanoScience, Delft University of Technology
| | - Anna C Haagsma
- Kavli Institute of NanoScience, Department of BioNanoScience, Delft University of Technology
| | | | - Jae-Ho Hwang
- Department of Chemistry, Seoul National University
| | - Jwa-Min Nam
- Department of Chemistry, Seoul National University
| | - Chirlmin Joo
- Kavli Institute of NanoScience, Department of BioNanoScience, Delft University of Technology;
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65
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Movileanu L. Watching single proteins using engineered nanopores. Protein Pept Lett 2014; 21:235-46. [PMID: 24370252 PMCID: PMC3924890 DOI: 10.2174/09298665113209990078] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2012] [Revised: 11/03/2012] [Accepted: 11/10/2012] [Indexed: 12/22/2022]
Abstract
Recent studies in the area of single-molecule detection of proteins with nanopores show a great promise in fundamental science, bionanotechnology and proteomics. In this mini-review, I discuss a comprehensive array of examinations of protein detection and characterization using protein and solid-state nanopores. These investigations demonstrate the power of the single-molecule nanopore measurements to reveal a broad range of functional, structural, biochemical and biophysical features of proteins, such as their backbone flexibility, enzymatic activity, binding affinity as well as their concentration, size and folding state. Engineered nanopores in organic materials and in inorganic membranes coupled with surface modification and protein engineering might provide a new generation of sensing devices for molecular biomedical diagnostics.
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Affiliation(s)
- Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA.
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66
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Larson JD, Rodgers ML, Hoskins AA. Visualizing cellular machines with colocalization single molecule microscopy. Chem Soc Rev 2014; 43:1189-200. [PMID: 23970346 PMCID: PMC3946777 DOI: 10.1039/c3cs60208g] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Many of the cell's macromolecular machines contain multiple components that transiently associate with one another. This compositional and dynamic complexity presents a challenge for understanding how these machines are constructed and function. Colocalization single molecule spectroscopy enables simultaneous observation of individual components of these machines in real-time and grants a unique window into processes that are typically obscured in ensemble assays. Colocalization experiments can yield valuable information about assembly pathways, compositional heterogeneity, and kinetics that together contribute to the development of richly detailed reaction mechanisms. This review focuses on recent advances in colocalization single molecule spectroscopy and how this technique has been applied to enhance our understanding of transcription, RNA splicing, and translation.
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Affiliation(s)
- Joshua D Larson
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Dr., Madison, USA.
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67
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Kruss S, Landry MP, Vander Ende E, Lima BM, Reuel NF, Zhang J, Nelson J, Mu B, Hilmer A, Strano M. Neurotransmitter Detection Using Corona Phase Molecular Recognition on Fluorescent Single-Walled Carbon Nanotube Sensors. J Am Chem Soc 2014; 136:713-24. [DOI: 10.1021/ja410433b] [Citation(s) in RCA: 223] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Sebastian Kruss
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Markita P. Landry
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Emma Vander Ende
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Barbara M.A. Lima
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Nigel F. Reuel
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jingqing Zhang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Justin Nelson
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Bin Mu
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Andrew Hilmer
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Michael Strano
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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68
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The Power of Single-Molecule FRET Microscopy Applied to DNA Nanotechnology. NUCLEIC ACIDS AND MOLECULAR BIOLOGY 2014. [DOI: 10.1007/978-3-642-38815-6_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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69
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Orevi T, Lerner E, Rahamim G, Amir D, Haas E. Ensemble and single-molecule detected time-resolved FRET methods in studies of protein conformations and dynamics. Methods Mol Biol 2014; 1076:113-169. [PMID: 24108626 DOI: 10.1007/978-1-62703-649-8_7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Most proteins are nanomachines that are selected to execute specific functions and therefore should have some degree of flexibility. The driving force that excites specific motions of domains and smaller chain elements is the thermal fluctuations of the solvent bath which are channeled to selected modes of motions by the structural constraints. Consequently characterization of the ensembles of conformers of proteins and their dynamics should be expressed in statistical terms, i.e., determination of probability distributions of the various conformers. This can be achieved by measurements of time-resolved dynamic non-radiative excitation energy transfer (trFRET) within ensembles of site specifically labeled protein molecules. Distributions of intramolecular segmental end-to-end distances and their fast fluctuations can be determined, and fast and slow conformational transitions within selected sections of the molecule can be monitored and analyzed. Both ensemble and single-molecule detection methods can be applied for data collection. In combination with synchronization methods, time-resolved FRET was also used for studies of fast conformational transitions, in particular the folding/unfolding transitions.
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Affiliation(s)
- Tomer Orevi
- The Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan, Israel
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70
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Brenlla A, Markiewicz RP, Rueda D, Romano LJ. Nucleotide selection by the Y-family DNA polymerase Dpo4 involves template translocation and misalignment. Nucleic Acids Res 2013; 42:2555-63. [PMID: 24270793 PMCID: PMC3936744 DOI: 10.1093/nar/gkt1149] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Y-family DNA polymerases play a crucial role in translesion DNA synthesis. Here, we have characterized the binding kinetics and conformational dynamics of the Y-family polymerase Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) using single-molecule fluorescence. We find that in the absence of dNTPs, the binary complex shuttles between two different conformations within ∼1 s. These data are consistent with prior crystal structures in which the nucleotide binding site is either occupied by the terminal base pair (preinsertion conformation) or empty following Dpo4 translocation by 1 base pair (insertion conformation). Most interestingly, on dNTP binding, only the insertion conformation is observed and the correct dNTP stabilizes this complex compared with the binary complex, whereas incorrect dNTPs destabilize it. However, if the n+1 template base is complementary to the incoming dNTP, a structure consistent with a misaligned template conformation is observed, in which the template base at the n position loops out. This structure provides evidence for a Dpo4 mutagenesis pathway involving a transient misalignment mechanism.
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Affiliation(s)
- Alfonso Brenlla
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA, Department of Medicine, Section of Virology, Imperial College London, London W12 0NN, UK and Single Molecule Imaging, MRC Clinical Sciences Center, Imperial College London, London W12 0NN, UK
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71
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Single molecule FRET data analysis procedures for FRET efficiency determination: Probing the conformations of nucleic acid structures. Methods 2013; 64:36-42. [DOI: 10.1016/j.ymeth.2013.04.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 04/02/2013] [Accepted: 04/03/2013] [Indexed: 11/23/2022] Open
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72
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Vrtis KB, Markiewicz RP, Romano LJ, Rueda D. Carcinogenic adducts induce distinct DNA polymerase binding orientations. Nucleic Acids Res 2013; 41:7843-53. [PMID: 23814187 PMCID: PMC3763543 DOI: 10.1093/nar/gkt554] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Revised: 05/15/2013] [Accepted: 05/24/2013] [Indexed: 12/18/2022] Open
Abstract
DNA polymerases must accurately replicate DNA to maintain genome integrity. Carcinogenic adducts, such as 2-aminofluorene (AF) and N-acetyl-2-aminofluorene (AAF), covalently bind DNA bases and promote mutagenesis near the adduct site. The mechanism by which carcinogenic adducts inhibit DNA synthesis and cause mutagenesis remains unclear. Here, we measure interactions between a DNA polymerase and carcinogenic DNA adducts in real-time by single-molecule fluorescence. We find the degree to which an adduct affects polymerase binding to the DNA depends on the adduct location with respect to the primer terminus, the adduct structure and the nucleotides present in the solution. Not only do the adducts influence the polymerase dwell time on the DNA but also its binding position and orientation. Finally, we have directly observed an adduct- and mismatch-induced intermediate state, which may be an obligatory step in the DNA polymerase proofreading mechanism.
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Affiliation(s)
- Kyle B. Vrtis
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA and Department of Medicine, Section of Virology, Imperial College London, London W12 0NN, UK
| | - Radoslaw P. Markiewicz
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA and Department of Medicine, Section of Virology, Imperial College London, London W12 0NN, UK
| | - Louis J. Romano
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA and Department of Medicine, Section of Virology, Imperial College London, London W12 0NN, UK
| | - David Rueda
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA and Department of Medicine, Section of Virology, Imperial College London, London W12 0NN, UK
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73
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Detection of Target Proteins by Fluorescence Anisotropy. J Fluoresc 2013; 23:881-8. [DOI: 10.1007/s10895-013-1194-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 02/24/2013] [Indexed: 01/28/2023]
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74
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Lamichhane R, Berezhna SY, Gill JP, Van der Schans E, Millar DP. Dynamics of site switching in DNA polymerase. J Am Chem Soc 2013; 135:4735-42. [PMID: 23409810 DOI: 10.1021/ja311641b] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA polymerases replicate DNA by catalyzing the template-directed polymerization of deoxynucleoside triphosphate (dNTP) substrates onto the 3' end of a growing DNA primer strand. Many DNA polymerases also possess a separate 3'-5' exonuclease activity that is used to remove misincorporated nucleotides from the nascent DNA (proofreading). The polymerase (pol) and exonuclease (exo) activities are spatially separated in different enzyme domains, indicating that a mechanism must exist to transfer the growing primer terminus from one site to the other. Here we report a single-molecule Förster resonance energy transfer (smFRET) system that directly monitors the movement of a DNA substrate between the pol and exo sites of DNA polymerase I Klenow fragment (KF). FRET trajectories recorded during the encounter between single polymerase and DNA molecules reveal that DNA can channel between the pol and exo sites in both directions while remaining closely associated with the enzyme (intramolecular transfer). In addition, it is evident from the trajectories that DNA can also dissociate from one site and subsequently rebind at the other (intermolecular transfer). Rate constants for each pathway have been determined by dwell-time analysis, revealing that intramolecular transfer is the faster of the two pathways. Unexpectedly, a mispaired primer terminus accesses the exo site more frequently when dNTP substrates are also present in solution, which is expected to enhance proofreading. Together, these results explain how the separate pol and exo activities of KF are physically coordinated to achieve efficient proofreading.
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Affiliation(s)
- Rajan Lamichhane
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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75
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Müller-McNicoll M, Neugebauer KM. How cells get the message: dynamic assembly and function of mRNA-protein complexes. Nat Rev Genet 2013; 14:275-87. [PMID: 23478349 DOI: 10.1038/nrg3434] [Citation(s) in RCA: 299] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
mRNA is packaged into ribonucleoprotein particles called mRNPs. A multitude of RNA-binding proteins as well as a host of associated proteins participate in the fate of mRNA from transcription and processing in the nucleus to translation and decay in the cytoplasm. Methodological innovations in cell biology and genome-wide high-throughput approaches have revealed an unexpected diversity of mRNA-associated proteins and unforeseen interconnections between mRNA-processing steps. Recent insights into mRNP formation in vivo have also highlighted the importance of mRNP packaging, which can sort RNAs on the basis of their length and determine mRNA fate through alternative mRNP assembly, processing and export pathways.
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Affiliation(s)
- Michaela Müller-McNicoll
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany.
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76
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Krüger AC, Hildebrandt LL, Kragh SL, Birkedal V. Structural Dynamics of Nucleic Acids by Single-Molecule FRET. Methods Cell Biol 2013; 113:1-37. [DOI: 10.1016/b978-0-12-407239-8.00001-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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77
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König SLB, Liyanage PS, Sigel RKO, Rueda D. Helicase-mediated changes in RNA structure at the single-molecule level. RNA Biol 2013; 10:133-48. [PMID: 23353571 DOI: 10.4161/rna.23507] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
RNA helicases are a diverse group of RNA-dependent ATPases known to play a large number of biological roles inside the cell, such as RNA unwinding, remodeling, export and degradation. Understanding how helicases mediate changes in RNA structure is therefore of fundamental interest. The advent of single-molecule spectroscopic techniques has unveiled with unprecedented detail the interplay of RNA helicases with their substrates. In this review, we describe the characterization of helicase-RNA interactions by single-molecule approaches. State-of-the-art techniques are presented, followed by a discussion of recent advancements in this exciting field.
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78
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Le Reste L, Hohlbein J, Gryte K, Kapanidis AN. Characterization of dark quencher chromophores as nonfluorescent acceptors for single-molecule FRET. Biophys J 2012; 102:2658-68. [PMID: 22713582 DOI: 10.1016/j.bpj.2012.04.028] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 04/03/2012] [Accepted: 04/06/2012] [Indexed: 11/16/2022] Open
Abstract
Dark quenchers are chromophores that primarily relax from the excited state to the ground state nonradiatively (i.e., are dark). As a result, they can serve as acceptors for Förster resonance energy transfer experiments without contributing significantly to background in the donor-emission channel, even at high concentrations. Although the advantages of dark quenchers have been exploited for ensemble bioassays, no systematic single-molecule study of dark quenchers has been performed, and little is known about their photophysical properties. Here, we present the first systematic single-molecule study of dark quenchers in conjunction with fluorophores and demonstrate the use of dark quenchers for monitoring multiple interactions and distances in multichromophore systems. Specifically, using double-stranded DNA standards labeled with two fluorophores and a dark quencher (either QSY7 or QSY21), we show that the proximity of a fluorophore and dark quencher can be monitored using the stoichiometry ratio available from alternating laser excitation spectroscopy experiments, either for single molecules diffusing in solution (using a confocal fluorescence) or immobilized on surfaces (using total-internal-reflection fluorescence). The latter experiments allowed characterization of the dark-quencher photophysical properties at the single-molecule level. We also use dark-quenchers to study the affinity and kinetics of binding of DNA Polymerase I (Klenow fragment) to DNA. The measured properties are in excellent agreement with the results of ensemble assays, validating the use of dark quenchers. Because dark-quencher-labeled biomolecules can be used in total-internal-reflection fluorescence experiments at concentrations of 1 μM or more without introducing a significant background, the use of dark quenchers should permit single-molecule Förster resonance energy transfer measurements for the large number of biomolecules that participate in interactions of moderate-to-low affinity.
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Affiliation(s)
- Ludovic Le Reste
- Biological Physics Research Group, Department of Physics, University of Oxford, Oxford, United Kingdom.
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79
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Markiewicz RP, Vrtis KB, Rueda D, Romano LJ. Single-molecule microscopy reveals new insights into nucleotide selection by DNA polymerase I. Nucleic Acids Res 2012; 40:7975-84. [PMID: 22669904 PMCID: PMC3439913 DOI: 10.1093/nar/gks523] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The mechanism by which DNA polymerases achieve their extraordinary accuracy has been intensely studied because of the linkage between this process and mutagenesis and carcinogenesis. Here, we have used single-molecule fluorescence microscopy to study the process of nucleotide selection and exonuclease action. Our results show that the binding of Escherichia coli DNA polymerase I (Klenow fragment) to a primer-template is stabilized by the presence of the next correct dNTP, even in the presence of a large excess of the other dNTPs and rNTPs. These results are consistent with a model where nucleotide selection occurs in the open complex prior to the formation of a closed ternary complex. Our assay can also distinguish between primer binding to the polymerase or exonuclease domain and, contrary to ensemble-averaged studies, we find that stable exonuclease binding only occurs with a mismatched primer terminus.
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80
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Senavirathne G, Jaszczur M, Auerbach PA, Upton TG, Chelico L, Goodman MF, Rueda D. Single-stranded DNA scanning and deamination by APOBEC3G cytidine deaminase at single molecule resolution. J Biol Chem 2012; 287:15826-35. [PMID: 22362763 DOI: 10.1074/jbc.m112.342790] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
APOBEC3G (Apo3G) is a single-stranded (ss)DNA cytosine deaminase that eliminates HIV-1 infectivity by converting C → U in numerous small target motifs on the minus viral cDNA. Apo3G deaminates linear ssDNA in vitro with pronounced spatial asymmetry favoring the 3' → 5' direction. A similar polarity observed in vivo is believed responsible for initiating localized C → T mutational gradients that inactivate the virus. When compared with double-stranded (ds)DNA scanning enzymes, e.g. DNA glycosylases that excise rare aberrant bases, there is a paucity of mechanistic studies on ssDNA scanning enzymes. Here, we investigate ssDNA scanning and motif-targeting mechanisms for Apo3G using single molecule Förster resonance energy transfer. We address the specific issue of deamination asymmetry within the general context of ssDNA scanning mechanisms and show that Apo3G scanning trajectories, ssDNA contraction, and deamination efficiencies depend on motif sequence, location, and ionic strength. Notably, we observe the presence of bidirectional quasi-localized scanning of Apo3G occurring proximal to a 5' hot motif, a motif-dependent DNA contraction greatest for 5' hot > 3' hot > 5' cold motifs, and diminished mobility at low salt. We discuss the single molecule Förster resonance energy transfer data in terms of a model in which deamination polarity occurs as a consequence of Apo3G binding to ssDNA in two orientations, one that is catalytically favorable, with the other disfavorable.
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Affiliation(s)
- Gayan Senavirathne
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
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81
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Yao J, Sun Y, Yang M, Duan Y. Chemistry, physics and biology of graphene-based nanomaterials: new horizons for sensing, imaging and medicine. ACTA ACUST UNITED AC 2012. [DOI: 10.1039/c2jm31632c] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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82
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Cardo L, Karunatilaka KS, Rueda D, Sigel RKO. Single molecule FRET characterization of large ribozyme folding. Methods Mol Biol 2012; 848:227-51. [PMID: 22315073 DOI: 10.1007/978-1-61779-545-9_15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A procedure to investigate the folding of group II intron by single molecule Fluorescence Resonance Energy Transfer (smFRET) using total internal reflection fluorescence microscopy (TIRFM) is described in this chapter. Using our previous studies on the folding and dynamics of a large ribozyme in the presence of metal ions (i.e., Mg(2+) and Ca(2+)) and/or the DEAD-box protein Mss116 as an example, we here describe step-by-step procedures to perform experiments. smFRET allows the investigation of individual molecules, thus, providing kinetic and mechanistic information hidden in ensemble averaged experiments.
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Affiliation(s)
- Lucia Cardo
- Institute of Inorganic Chemistry, University of Zurich, Zurich, Switzerland
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83
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RNA methods: from sequence to structure and dynamics. Methods 2010; 52:123-4. [PMID: 20883944 DOI: 10.1016/j.ymeth.2010.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/06/2010] [Indexed: 11/21/2022] Open
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