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  • 1
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    Unraveling the electronic structure of individual photosynthetic pigment-protein complexes (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-07-20
    Description: Low-temperature single-molecule spectroscopic techniques were applied to a light-harvesting pigment-protein complex (LH2) from purple photosynthetic bacteria. The properties of the electronically excited states of the two circular assemblies (B800 and B850) of bacteriochlorophyll a (BChl a) pigment molecules in the individual complexes were revealed, without ensemble averaging. The results show that the excited states of the B800 ring of pigments are mainly localized on individual BChl a molecules. In contrast, the absorption of a photon by the B850 ring can be consistently described in terms of an excitation that is completely delocalized over the ring. This property may contribute to the high efficiency of energy transfer in these photosynthetic complexes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉van Oijen AM -- Ketelaars -- Kohler -- Aartsma -- Schmidt -- New York, N.Y. -- Science. 1999 Jul 16;285(5426):400-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for the Study of Excited States of Molecules, Department of Biophysics, Huygens Laboratory, Leiden University, Post Office Box 9504, 2300 RA Leiden, Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10411501" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    Dynamics of DNA replication loops reveal temporal control of lagging-strand synthesis (2008)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2008-11-26
    Description: In all organisms, the protein machinery responsible for the replication of DNA, the replisome, is faced with a directionality problem. The antiparallel nature of duplex DNA permits the leading-strand polymerase to advance in a continuous fashion, but forces the lagging-strand polymerase to synthesize in the opposite direction. By extending RNA primers, the lagging-strand polymerase restarts at short intervals and produces Okazaki fragments. At least in prokaryotic systems, this directionality problem is solved by the formation of a loop in the lagging strand of the replication fork to reorient the lagging-strand DNA polymerase so that it advances in parallel with the leading-strand polymerase. The replication loop grows and shrinks during each cycle of Okazaki fragment synthesis. Here we use single-molecule techniques to visualize, in real time, the formation and release of replication loops by individual replisomes of bacteriophage T7 supporting coordinated DNA replication. Analysis of the distributions of loop sizes and lag times between loops reveals that initiation of primer synthesis and the completion of an Okazaki fragment each serve as a trigger for loop release. The presence of two triggers may represent a fail-safe mechanism ensuring the timely reset of the replisome after the synthesis of every Okazaki fragment.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2651468/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2651468/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hamdan, Samir M -- Loparo, Joseph J -- Takahashi, Masateru -- Richardson, Charles C -- van Oijen, Antoine M -- GM-077248/GM/NIGMS NIH HHS/ -- GM-54397/GM/NIGMS NIH HHS/ -- R01 GM077248/GM/NIGMS NIH HHS/ -- R01 GM077248-02/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Jan 15;457(7227):336-9. doi: 10.1038/nature07512. Epub 2008 Nov 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19029884" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriophage T7/*metabolism ; Bacteriophage lambda/genetics ; DNA Replication/*physiology ; DNA, Viral/analysis/*biosynthesis ; DNA-Directed DNA Polymerase/metabolism ; Microscopy, Fluorescence ; Multienzyme Complexes/metabolism ; Time Factors
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 3
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    Biochemistry. Nudging through a nucleosome (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-08-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Otterstrom, Jason J -- van Oijen, Antoine M -- R01 GM077248/GM/NIGMS NIH HHS/ -- R01 GM077248-03/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2009 Jul 31;325(5940):547-8. doi: 10.1126/science.1177311.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19644099" target="_blank"〉PubMed〈/a〉
    Keywords: Base Pairing ; Base Sequence ; Catalytic Domain ; DNA/chemistry/*metabolism ; Diffusion ; Nucleosomes/*metabolism ; Optical Tweezers ; RNA Polymerase II/chemistry/*metabolism ; RNA, Messenger/metabolism ; Templates, Genetic ; *Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
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    Single-molecule kinetics of lambda exonuclease reveal base dependence and dynamic disorder (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-08-30
    Description: We used a multiplexed approach based on flow-stretched DNA to monitor the enzymatic digestion of lambda-phage DNA by individual bacteriophage lambda exonuclease molecules. Statistical analyses of multiple single-molecule trajectories observed simultaneously reveal that the catalytic rate is dependent on the local base content of the substrate DNA. By relating single-molecule kinetics to the free energies of hydrogen bonding and base stacking, we establish that the melting of a base from the DNA is the rate-limiting step in the catalytic cycle. The catalytic rate also exhibits large fluctuations independent of the sequence, which we attribute to conformational changes of the enzyme-DNA complex.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉van Oijen, Antoine M -- Blainey, Paul C -- Crampton, Donald J -- Richardson, Charles C -- Ellenberger, Tom -- Xie, X Sunney -- 5R01GM61577-03/GM/NIGMS NIH HHS/ -- R01GM55390-07/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Aug 29;301(5637):1235-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12947199" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriophage lambda/*enzymology ; Base Composition ; Base Sequence ; Binding Sites ; Catalysis ; DNA, Single-Stranded/chemistry/*metabolism ; DNA, Viral/chemistry/*metabolism ; Exodeoxyribonucleases/chemistry/*metabolism ; Hydrogen Bonding ; Hydrolysis ; Kinetics ; Nucleic Acid Conformation ; Protein Conformation ; Thermodynamics ; Viral Proteins
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 5
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    Unsynchronised subunit motion in single trimeric sodium-coupled aspartate transporters (2013)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2013-10-05
    Description: Excitatory amino acid transporters (EAATs) are secondary transport proteins that mediate the uptake of glutamate and other amino acids. EAATs fulfil an important role in neuronal signal transmission by clearing the excitatory neurotransmitters from the synaptic cleft after depolarization of the postsynaptic neuron. An intensively studied model system for understanding the transport mechanism of EAATs is the archaeal aspartate transporter GltPh. Each subunit in the homotrimeric GltPh supports the coupled translocation of one aspartate molecule and three Na(+) ions as well as an uncoupled flux of Cl(-) ions. Recent crystal structures of GltPh revealed three possible conformations for the subunits, but it is unclear whether the motions of individual subunits are coordinated to support transport. Here, we report the direct observation of conformational dynamics in individual GltPh trimers embedded in the membrane by applying single-molecule fluorescence resonance energy transfer (FRET). By analysing the transporters in a lipid bilayer instead of commonly used detergent micelles, we achieve conditions that approximate the physiologically relevant ones. From the kinetics of FRET level transitions we conclude that the three GltPh subunits undergo conformational changes stochastically and independently of each other.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Erkens, Guus B -- Hanelt, Inga -- Goudsmits, Joris M H -- Slotboom, Dirk Jan -- van Oijen, Antoine M -- England -- Nature. 2013 Oct 3;502(7469):119-23. doi: 10.1038/nature12538.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24091978" target="_blank"〉PubMed〈/a〉
    Keywords: Aspartic Acid/*chemistry/*metabolism ; Fluorescence Resonance Energy Transfer ; Glutamate Plasma Membrane Transport Proteins/*chemistry/metabolism ; Lipid Bilayers/metabolism ; *Models, Molecular ; Protein Structure, Tertiary ; Pyrococcus horikoshii/chemistry/metabolism ; Sodium/*chemistry
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 6
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    Bypass of a protein barrier by a replicative DNA helicase (2012)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2012-12-04
    Description: Replicative DNA helicases generally unwind DNA as a single hexamer that encircles and translocates along one strand of the duplex while excluding the complementary strand (known as steric exclusion). By contrast, large T antigen, the replicative DNA helicase of the simian virus 40 (SV40), is reported to function as a pair of stacked hexamers that pumps double-stranded DNA through its central channel while laterally extruding single-stranded DNA. Here we use single-molecule and ensemble assays to show that large T antigen assembled on the SV40 origin unwinds DNA efficiently as a single hexamer that translocates on single-stranded DNA in the 3'-to-5' direction. Unexpectedly, large T antigen unwinds DNA past a DNA-protein crosslink on the translocation strand, suggesting that the large T antigen ring can open to bypass bulky adducts. Together, our data underscore the profound conservation among replicative helicase mechanisms, and reveal a new level of plasticity in the interactions of replicative helicases with DNA damage.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3521859/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3521859/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yardimci, Hasan -- Wang, Xindan -- Loveland, Anna B -- Tappin, Inger -- Rudner, David Z -- Hurwitz, Jerard -- van Oijen, Antoine M -- Walter, Johannes C -- 5 R01 GM034559/GM/NIGMS NIH HHS/ -- GM077248/GM/NIGMS NIH HHS/ -- GM086466/GM/NIGMS NIH HHS/ -- GM62267/GM/NIGMS NIH HHS/ -- HL098316/HL/NHLBI NIH HHS/ -- R01 GM062267/GM/NIGMS NIH HHS/ -- R01 HL098316/HL/NHLBI NIH HHS/ -- England -- Nature. 2012 Dec 13;492(7428):205-9. doi: 10.1038/nature11730. Epub 2012 Nov 28.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23201686" target="_blank"〉PubMed〈/a〉
    Keywords: Antigens, Viral, Tumor/metabolism ; DNA Helicases/*metabolism ; DNA Replication ; DNA, Single-Stranded/metabolism ; DNA, Viral/metabolism ; Replication Origin/physiology ; Simian virus 40/*enzymology ; Viral Proteins/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 7
    Electronic Resource
    Electronic Resource
    Single-molecule fluorescence autocorrelation experiments on pentacene: The dependence of intersystem crossing on isotopic composition (1999)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 110 (1999), S. 9151-9159 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Single pentacene molecules containing 13C or 1H in a pentacene-d14 doped p-terphenyl crystal have been studied by fluorescence autocorrelation. The triplet dynamics has been analyzed and a systematic dependence of the S1→T1 intersystem crossing rate on isotopic composition was found. This variation is discussed in terms of a modulation of the near resonance of the first excited singlet state S1 and vibrational levels of an intermediating triplet state T3 which results from the distinct isotope dependence of the zero-point energy of both electronic states. © 1999 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.478837
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  • 8
    Electronic Resource
    Electronic Resource
    Continuous-wave two-photon excitation of individual CdS nanocrystallites (2001)
    Woodbury, NY : American Institute of Physics (AIP)
    Applied Physics Letters 79 (2001), S. 830-832 
    Details
    ISSN: 1077-3118
    Source: AIP Digital Archive
    Topics: Physics
    Notes: By use of low-temperature confocal microscopy, continuous-wave two-photon fluorescence images are obtained of individual CdS nanocrystallites embedded in a polymer matrix. The quadratic dependence of the emission rate on the applied laser power proves that the observed fluorescence originates from the simultaneous absorption of two photons. From the experimental data the two-photon absorption cross-section σ(2) could be determined, resulting in a value smaller than that known from literature. The work presented is a first step towards high-resolution fluorescence-excitation spectroscopy on the electronic states in the band edge, inaccessible by conventional one-photon spectroscopy. © 2001 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.1391231
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  • 9
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    Sequence-dependent sliding kinetics of p53 (2012)
    National Academy of Sciences
    Details
    Publication Date: 2012-09-25
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 10
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    How DNA-repair proteins find their targets (2012)
    National Academy of Sciences
    Details
    Publication Date: 2012-10-29
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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