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  1. Book ; Online ; Thesis: FRAND-Bedingungen bei SEP – Die Lizenzbereitschaftserklärung und das Problem der Bestimmung einer angemessenen Lizenzgebühr

    Heitkamp, Sara Isabell [Verfasser]

    2020  

    Author's details Sara Isabell Heitkamp
    Keywords Recht ; Law
    Subject code sg340
    Language German
    Publisher Peter Lang GmbH, Internationaler Verlag der Wissenschaften
    Publishing place Frankfurt a.M.
    Document type Book ; Online ; Thesis
    ISBN 978-3-631-80432-2 ; 3-631-80432-6
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  2. Article: Fluorescence-Detected Conformational Changes in Duplex DNA in Open Complex Formation by Escherichia coli RNA Polymerase: Upstream Wrapping and Downstream Bending Precede Clamp Opening and Insertion of the Downstream Duplex

    Sreenivasan, Raashi / Shkel, Irina A / Chhabra, Munish / Drennan, Amanda / Heitkamp, Sara / Wang, Hao-Che / Sridevi, Malavika A / Plaskon, Dylan / McNerney, Christina / Callies, Katelyn / Cimperman, Clare K / Record, M. Thomas

    Biochemistry. 2020 Mar. 27, v. 59, no. 16

    2020  

    Abstract: FRET (fluorescence resonance energy transfer) between far-upstream (−100) and downstream (+14) cyanine dyes (Cy3, Cy5) showed extensive bending and wrapping of λPR promoter DNA on Escherichia coli RNA polymerase (RNAP) in closed and open complexes (CC ... ...

    Abstract FRET (fluorescence resonance energy transfer) between far-upstream (−100) and downstream (+14) cyanine dyes (Cy3, Cy5) showed extensive bending and wrapping of λPR promoter DNA on Escherichia coli RNA polymerase (RNAP) in closed and open complexes (CC and OC, respectively). Here we determine the kinetics and mechanism of DNA bending and wrapping by FRET and of formation of RNAP contacts with −100 and +14 DNA by single-dye protein-induced fluorescence enhancement (PIFE). FRET and PIFE kinetics exhibit two phases: rapidly reversible steps forming a CC ensemble ({CC}) of four intermediates [initial (RPC), early (I₁E), mid (I₁M), and late (I₁L)], followed by conversion of {CC} to OC via I₁L. FRET and PIFE are first observed for I₁E, not RPc. FRET and PIFE together reveal large-scale bending and wrapping of upstream and downstream DNA as RPC advances to I₁E, decreasing the Cy3−Cy5 distance to ∼75 Å and making RNAP–DNA contacts at −100 and +14. We propose that far-upstream DNA wraps on the upper β′-clamp while downstream DNA contacts the top of the β-pincer in I₁E. Converting I₁E to I₁M (∼1 s time scale) reduces FRET efficiency with little change in −100 or +14 PIFE, interpreted as clamp opening that moves far-upstream DNA (on β′) away from downstream DNA (on β) to increase the Cy3−Cy5 distance by ∼14 Å. FRET increases greatly in converting I₁M to I₁L, indicating bending of downstream duplex DNA into the clamp and clamp closing to reduce the Cy3−Cy5 distance by ∼21 Å. In the subsequent rate-determining DNA-opening step, in which the clamp may also open, I₁L is converted to the initial unstable OC (I₂). Implications for facilitation of CC-to-OC isomerization by upstream DNA and upstream binding, DNA-bending transcription activators are discussed.
    Keywords DNA ; DNA-directed RNA polymerase ; Escherichia coli ; energy transfer ; fluorescence ; isomerization
    Language English
    Dates of publication 2020-0327
    Size p. 1565-1581.
    Publishing place American Chemical Society
    Document type Article
    Note NAL-AP-2-clean
    ZDB-ID 1108-3
    ISSN 1520-4995 ; 0006-2960
    ISSN (online) 1520-4995
    ISSN 0006-2960
    DOI 10.1021/acs.biochem.0c00098
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  3. Article ; Online: Fluorescence-Detected Conformational Changes in Duplex DNA in Open Complex Formation by

    Sreenivasan, Raashi / Shkel, Irina A / Chhabra, Munish / Drennan, Amanda / Heitkamp, Sara / Wang, Hao-Che / Sridevi, Malavika A / Plaskon, Dylan / McNerney, Christina / Callies, Katelyn / Cimperman, Clare K / Record, M Thomas

    Biochemistry

    2020  Volume 59, Issue 16, Page(s) 1565–1581

    Abstract: FRET (fluorescence resonance energy transfer) between far-upstream (-100) and downstream (+14) cyanine dyes (Cy3, Cy5) showed extensive bending and wrapping of ... ...

    Abstract FRET (fluorescence resonance energy transfer) between far-upstream (-100) and downstream (+14) cyanine dyes (Cy3, Cy5) showed extensive bending and wrapping of λP
    MeSH term(s) Carbocyanines/chemistry ; DNA/chemistry ; DNA/genetics ; DNA/metabolism ; DNA-Directed RNA Polymerases/chemistry ; DNA-Directed RNA Polymerases/metabolism ; Escherichia coli/enzymology ; Escherichia coli Proteins/chemistry ; Escherichia coli Proteins/metabolism ; Fluorescence ; Fluorescence Resonance Energy Transfer ; Fluorescent Dyes/chemistry ; Kinetics ; Nucleic Acid Conformation ; Promoter Regions, Genetic ; Protein Binding
    Chemical Substances Carbocyanines ; Escherichia coli Proteins ; Fluorescent Dyes ; cyanine dye 3 ; cyanine dye 5 ; DNA (9007-49-2) ; DNA-Directed RNA Polymerases (EC 2.7.7.6)
    Language English
    Publishing date 2020-04-07
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1108-3
    ISSN 1520-4995 ; 0006-2960
    ISSN (online) 1520-4995
    ISSN 0006-2960
    DOI 10.1021/acs.biochem.0c00098
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    Zs.A 217: Show issues Location:
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  4. Article: Fluorescence Resonance Energy Transfer Characterization of DNA Wrapping in Closed and Open Escherichia coli RNA Polymerase−λPR Promoter Complexes

    Sreenivasan, Raashi / Heitkamp Sara / Chhabra Munish / Saecker Ruth / Lingeman Emily / Poulos Mikaela / McCaslin Darrell / Capp Michael W / Artsimovitch Irina / Record M. Thomas

    Biochemistry. 2016 Apr. 12, v. 55, no. 14

    2016  

    Abstract: Initial recognition of promoter DNA by RNA polymerase (RNAP) is proposed to trigger a series of conformational changes beginning with bending and wrapping of the 40–50 bp of DNA immediately upstream of the −35 region. Kinetic studies demonstrated ... ...

    Abstract Initial recognition of promoter DNA by RNA polymerase (RNAP) is proposed to trigger a series of conformational changes beginning with bending and wrapping of the 40–50 bp of DNA immediately upstream of the −35 region. Kinetic studies demonstrated that the presence of upstream DNA facilitates bending and entry of the downstream duplex (to +20) into the active site cleft to form an advanced closed complex (CC), prior to melting of ∼13 bp (−11 to +2), including the transcription start site (+1). Atomic force microscopy and footprinting revealed that the stable open complex (OC) is also highly wrapped (−60 to +20). To test the proposed bent-wrapped model of duplex DNA in an advanced RNAP−λPR CC and compare wrapping in the CC and OC, we use fluorescence resonance energy transfer (FRET) between cyanine dyes at far-upstream (−100) and downstream (+14) positions of promoter DNA. Similarly large intrinsic FRET efficiencies are observed for the CC (0.30 ± 0.07) and the OC (0.32 ± 0.11) for both probe orientations. Fluorescence enhancements at +14 are observed in the single-dye-labeled CC and OC. These results demonstrate that upstream DNA is extensively wrapped and the start site region is bent into the cleft in the advanced CC, reducing the distance between positions −100 and +14 on promoter DNA from >300 to <100 Å. The proximity of upstream DNA to the downstream cleft in the advanced CC is consistent with the proposed mechanism for facilitation of OC formation by upstream DNA.
    Keywords DNA ; DNA-directed RNA polymerase ; Escherichia coli ; RNA ; active sites ; atomic force microscopy ; dyes ; energy transfer ; fluorescence ; melting ; models
    Language English
    Dates of publication 2016-0412
    Size p. 2174-2186.
    Publishing place American Chemical Society
    Document type Article
    ZDB-ID 1108-3
    ISSN 1520-4995 ; 0006-2960
    ISSN (online) 1520-4995
    ISSN 0006-2960
    DOI 10.1021%2Facs.biochem.6b00125
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    Zs.A 217: Show issues Location:
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  5. Article ; Online: Fluorescence Resonance Energy Transfer Characterization of DNA Wrapping in Closed and Open Escherichia coli RNA Polymerase-λP(R) Promoter Complexes.

    Sreenivasan, Raashi / Heitkamp, Sara / Chhabra, Munish / Saecker, Ruth / Lingeman, Emily / Poulos, Mikaela / McCaslin, Darrell / Capp, Michael W / Artsimovitch, Irina / Record, M Thomas

    Biochemistry

    2016  Volume 55, Issue 14, Page(s) 2174–2186

    Abstract: Initial recognition of promoter DNA by RNA polymerase (RNAP) is proposed to trigger a series of conformational changes beginning with bending and wrapping of the 40-50 bp of DNA immediately upstream of the -35 region. Kinetic studies demonstrated that ... ...

    Abstract Initial recognition of promoter DNA by RNA polymerase (RNAP) is proposed to trigger a series of conformational changes beginning with bending and wrapping of the 40-50 bp of DNA immediately upstream of the -35 region. Kinetic studies demonstrated that the presence of upstream DNA facilitates bending and entry of the downstream duplex (to +20) into the active site cleft to form an advanced closed complex (CC), prior to melting of ∼13 bp (-11 to +2), including the transcription start site (+1). Atomic force microscopy and footprinting revealed that the stable open complex (OC) is also highly wrapped (-60 to +20). To test the proposed bent-wrapped model of duplex DNA in an advanced RNAP-λP(R) CC and compare wrapping in the CC and OC, we use fluorescence resonance energy transfer (FRET) between cyanine dyes at far-upstream (-100) and downstream (+14) positions of promoter DNA. Similarly large intrinsic FRET efficiencies are observed for the CC (0.30 ± 0.07) and the OC (0.32 ± 0.11) for both probe orientations. Fluorescence enhancements at +14 are observed in the single-dye-labeled CC and OC. These results demonstrate that upstream DNA is extensively wrapped and the start site region is bent into the cleft in the advanced CC, reducing the distance between positions -100 and +14 on promoter DNA from >300 to <100 Å. The proximity of upstream DNA to the downstream cleft in the advanced CC is consistent with the proposed mechanism for facilitation of OC formation by upstream DNA.
    MeSH term(s) Bacterial Proteins/chemistry ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Bacteriophage lambda/metabolism ; Catalytic Domain ; DNA, Viral/chemistry ; DNA, Viral/metabolism ; DNA-Directed RNA Polymerases/chemistry ; DNA-Directed RNA Polymerases/genetics ; DNA-Directed RNA Polymerases/metabolism ; Escherichia coli/enzymology ; Escherichia coli Proteins/chemistry ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/metabolism ; Fluorescence Resonance Energy Transfer ; Fluorescent Dyes/chemistry ; Holoenzymes/chemistry ; Holoenzymes/genetics ; Holoenzymes/metabolism ; Kinetics ; Models, Molecular ; Molecular Conformation ; Promoter Regions, Genetic ; Protein Stability ; Protein Subunits/chemistry ; Protein Subunits/genetics ; Protein Subunits/metabolism ; Protein Unfolding ; Recombinant Proteins/chemistry ; Recombinant Proteins/metabolism ; Structural Homology, Protein ; Thermus thermophilus/enzymology
    Chemical Substances Bacterial Proteins ; DNA, Viral ; Escherichia coli Proteins ; Fluorescent Dyes ; Holoenzymes ; Protein Subunits ; Recombinant Proteins ; DNA-Directed RNA Polymerases (EC 2.7.7.6)
    Language English
    Publishing date 2016-04-12
    Publishing country United States
    Document type Comparative Study ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1108-3
    ISSN 1520-4995 ; 0006-2960
    ISSN (online) 1520-4995
    ISSN 0006-2960
    DOI 10.1021/acs.biochem.6b00125
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  6. Article: Pathway of ATP utilization and duplex rRNA unwinding by the DEAD-box helicase, DbpA

    Henn, Arnon / Cao, Wenxiang / Licciardello, Nicholas / Heitkamp, Sara E / Hackney, David D / De La Cruz, Enrique M

    Proceedings of the National Academy of Sciences of the United States of America. 2010 Mar. 2, v. 107, no. 9

    2010  

    Abstract: DEAD-box RNA helicase proteins use the energy of ATP hydrolysis to drive the unwinding of duplex RNA. However, the mechanism that couples ATP utilization to duplex RNA unwinding is unknown. We measured ATP utilization and duplex RNA unwinding by DbpA, a ... ...

    Abstract DEAD-box RNA helicase proteins use the energy of ATP hydrolysis to drive the unwinding of duplex RNA. However, the mechanism that couples ATP utilization to duplex RNA unwinding is unknown. We measured ATP utilization and duplex RNA unwinding by DbpA, a non-processive bacterial DEAD-box RNA helicase specifically activated by the peptidyl transferase center (PTC) of 23S rRNA. Consumption of a single ATP molecule is sufficient to unwind and displace an 8 base pair rRNA strand annealed to a 32 base pair PTC-RNA "mother strand" fragment. Strand displacement occurs after ATP binding and hydrolysis but before Pi product release. Pi release weakens binding to rRNA, thereby facilitating the release of the unwound rRNA mother strand and the recycling of DbpA for additional rounds of unwinding. This work explains how ATPase activity of DEAD-box helicases is linked to RNA unwinding.
    Keywords DEAD-box RNA helicases ; adenosine triphosphate ; adenosinetriphosphatase ; energy ; hydrolysis ; proteins ; recycling ; ribosomal RNA
    Language English
    Dates of publication 2010-0302
    Size p. 4046-4050.
    Publishing place National Academy of Sciences
    Document type Article
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.0913081107
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  7. Article ; Online: Pathway of ATP utilization and duplex rRNA unwinding by the DEAD-box helicase, DbpA.

    Henn, Arnon / Cao, Wenxiang / Licciardello, Nicholas / Heitkamp, Sara E / Hackney, David D / De La Cruz, Enrique M

    Proceedings of the National Academy of Sciences of the United States of America

    2010  Volume 107, Issue 9, Page(s) 4046–4050

    Abstract: DEAD-box RNA helicase proteins use the energy of ATP hydrolysis to drive the unwinding of duplex RNA. However, the mechanism that couples ATP utilization to duplex RNA unwinding is unknown. We measured ATP utilization and duplex RNA unwinding by DbpA, a ... ...

    Abstract DEAD-box RNA helicase proteins use the energy of ATP hydrolysis to drive the unwinding of duplex RNA. However, the mechanism that couples ATP utilization to duplex RNA unwinding is unknown. We measured ATP utilization and duplex RNA unwinding by DbpA, a non-processive bacterial DEAD-box RNA helicase specifically activated by the peptidyl transferase center (PTC) of 23S rRNA. Consumption of a single ATP molecule is sufficient to unwind and displace an 8 base pair rRNA strand annealed to a 32 base pair PTC-RNA "mother strand" fragment. Strand displacement occurs after ATP binding and hydrolysis but before P(i) product release. P(i) release weakens binding to rRNA, thereby facilitating the release of the unwound rRNA mother strand and the recycling of DbpA for additional rounds of unwinding. This work explains how ATPase activity of DEAD-box helicases is linked to RNA unwinding.
    MeSH term(s) Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/metabolism ; DEAD-box RNA Helicases/metabolism ; Escherichia coli Proteins/metabolism ; Hydrolysis ; Nucleic Acid Denaturation ; RNA, Ribosomal/chemistry ; RNA, Ribosomal/metabolism ; Recombinant Proteins/metabolism
    Chemical Substances Escherichia coli Proteins ; RNA, Ribosomal ; Recombinant Proteins ; Adenosine Diphosphate (61D2G4IYVH) ; Adenosine Triphosphate (8L70Q75FXE) ; dbpA protein, E coli (EC 3.6.1.-) ; DEAD-box RNA Helicases (EC 3.6.4.13)
    Language English
    Publishing date 2010-02-16
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.0913081107
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    Zs.A 1148: Show issues Location:
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