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  1. Article: Site-directed spin labeling studies on nucleic acid structure and dynamics.

    Sowa, Glenna Z / Qin, Peter Z

    Progress in nucleic acid research and molecular biology

    2008  Volume 82, Page(s) 147–197

    MeSH term(s) Binding Sites ; Crystallography, X-Ray ; DNA/chemistry ; DNA/drug effects ; Deoxyribose/chemistry ; Electron Spin Resonance Spectroscopy ; Models, Molecular ; Nucleic Acid Conformation ; Nucleic Acids/chemistry ; Nucleic Acids/drug effects ; RNA/chemistry ; RNA/drug effects ; Ribose/chemistry ; Sensitivity and Specificity ; Spin Labels
    Chemical Substances Nucleic Acids ; Spin Labels ; Deoxyribose (533-67-5) ; RNA (63231-63-0) ; Ribose (681HV46001) ; DNA (9007-49-2)
    Language English
    Publishing date 2008-10-11
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
    ZDB-ID 209326-1
    ISSN 0079-6603 ; 0091-4886
    ISSN 0079-6603 ; 0091-4886
    DOI 10.1016/S0079-6603(08)00005-6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Global structure of a three-way junction in a phi29 packaging RNA dimer determined using site-directed spin labeling.

    Zhang, Xiaojun / Tung, Chang-Shung / Sowa, Glenna Z / Hatmal, Ma'mon M / Haworth, Ian S / Qin, Peter Z

    Journal of the American Chemical Society

    2012  Volume 134, Issue 5, Page(s) 2644–2652

    Abstract: The condensation of bacteriophage phi29 genomic DNA into its preformed procapsid requires the DNA packaging motor, which is the strongest known biological motor. The packaging motor is an intricate ring-shaped protein/RNA complex, and its function ... ...

    Abstract The condensation of bacteriophage phi29 genomic DNA into its preformed procapsid requires the DNA packaging motor, which is the strongest known biological motor. The packaging motor is an intricate ring-shaped protein/RNA complex, and its function requires an RNA component called packaging RNA (pRNA). Current structural information on pRNA is limited, which hinders studies of motor function. Here, we used site-directed spin labeling to map the conformation of a pRNA three-way junction that bridges binding sites for the motor ATPase and the procapsid. The studies were carried out on a pRNA dimer, which is the simplest ring-shaped pRNA complex and serves as a functional intermediate during motor assembly. Using a nucleotide-independent labeling scheme, stable nitroxide radicals were attached to eight specific pRNA sites without perturbing RNA folding and dimer formation, and a total of 17 internitroxide distances spanning the three-way junction were measured using Double Electron-Electron Resonance spectroscopy. The measured distances, together with steric chemical constraints, were used to select 3662 viable three-way junction models from a pool of 65 billion. The results reveal a similar conformation among the viable models, with two of the helices (H(T) and H(L)) adopting an acute bend. This is in contrast to a recently reported pRNA tetramer crystal structure, in which H(T) and H(L) stack onto each other linearly. The studies establish a new method for mapping global structures of complex RNA molecules, and provide information on pRNA conformation that aids investigations of phi29 packaging motor and developments of pRNA-based nanomedicine and nanomaterial.
    MeSH term(s) Bacteriophages/chemistry ; Dimerization ; Models, Molecular ; Nucleic Acid Conformation ; RNA, Viral/chemistry ; Spin Labels
    Chemical Substances RNA, Viral ; Spin Labels
    Language English
    Publishing date 2012-01-27
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 3155-0
    ISSN 1520-5126 ; 0002-7863
    ISSN (online) 1520-5126
    ISSN 0002-7863
    DOI 10.1021/ja2093647
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Polyamine-induced bundling of F-actin.

    Sowa, Glenna Z / Cannell, David S / Liu, Andrea J / Reisler, Emil

    The journal of physical chemistry. B

    2006  Volume 110, Issue 44, Page(s) 22279–22284

    Abstract: To better understand the mechanism of actin filament (F-actin) bundling by polyamines, we have measured the onset of bundling as a function of polyamine concentration. Samples were centrifuged at low speeds to separate bundles from unbundled actin, and ... ...

    Abstract To better understand the mechanism of actin filament (F-actin) bundling by polyamines, we have measured the onset of bundling as a function of polyamine concentration. Samples were centrifuged at low speeds to separate bundles from unbundled actin, and the relative amounts of actin in the pellet and supernatant were determined via gel electrophoresis, yielding a description of the bundling transition as a function of actin and polyamine concentrations. These experiments were carried out for two different polyamines, spermine (tetravalent) and spermidine (trivalent). We found that the threshold concentration of polyamine needed to bundle actin is independent of both actin concentration and Mg2+ concentration over a wide range in Mg2+ concentration. We also find that spermine in F-actin bundles is essentially invisible in solution-phase proton NMR, suggesting that it is bound so tightly to F-actin that it is immobilized.
    MeSH term(s) Actin Cytoskeleton/metabolism ; Actins/isolation & purification ; Magnesium/pharmacology ; Polyamines/pharmacology ; Protein Binding/drug effects ; Spermidine/pharmacology ; Spermine/pharmacology
    Chemical Substances Actins ; Polyamines ; Spermine (2FZ7Y3VOQX) ; Magnesium (I38ZP9992A) ; Spermidine (U87FK77H25)
    Language English
    Publishing date 2006-11-09
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 1520-6106
    ISSN 1520-6106
    DOI 10.1021/jp063371w
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Global Structure of a Three-Way Junction in a Phi29 Packaging RNA Dimer Determined Using Site-Directed Spin Labeling

    Zhang, Xiaojun / Hatmal Ma’mon M / Haworth Ian S / Qin Peter Z / Sowa Glenna Z / Tung Chang-Shung

    Journal of the American Chemical Society. 2012 Feb. 08, v. 134, no. 5

    2012  

    Abstract: The condensation of bacteriophage phi29 genomic DNA into its preformed procapsid requires the DNA packaging motor, which is the strongest known biological motor. The packaging motor is an intricate ring-shaped protein/RNA complex, and its function ... ...

    Abstract The condensation of bacteriophage phi29 genomic DNA into its preformed procapsid requires the DNA packaging motor, which is the strongest known biological motor. The packaging motor is an intricate ring-shaped protein/RNA complex, and its function requires an RNA component called packaging RNA (pRNA). Current structural information on pRNA is limited, which hinders studies of motor function. Here, we used site-directed spin labeling to map the conformation of a pRNA three-way junction that bridges binding sites for the motor ATPase and the procapsid. The studies were carried out on a pRNA dimer, which is the simplest ring-shaped pRNA complex and serves as a functional intermediate during motor assembly. Using a nucleotide-independent labeling scheme, stable nitroxide radicals were attached to eight specific pRNA sites without perturbing RNA folding and dimer formation, and a total of 17 internitroxide distances spanning the three-way junction were measured using Double Electron–Electron Resonance spectroscopy. The measured distances, together with steric chemical constraints, were used to select 3662 viable three-way junction models from a pool of 65 billion. The results reveal a similar conformation among the viable models, with two of the helices (HT and HL) adopting an acute bend. This is in contrast to a recently reported pRNA tetramer crystal structure, in which HT and HL stack onto each other linearly. The studies establish a new method for mapping global structures of complex RNA molecules, and provide information on pRNA conformation that aids investigations of phi29 packaging motor and developments of pRNA-based nanomedicine and nanomaterial.
    Keywords adenosinetriphosphatase ; bacteriophages ; binding sites ; crystal structure ; DNA ; DNA packaging ; electron paramagnetic resonance spectroscopy ; free radicals ; models ; nanomaterials ; nanomedicine ; RNA ; RNA folding
    Language English
    Dates of publication 2012-0208
    Size p. 2644-2652.
    Publishing place American Chemical Society
    Document type Article
    ZDB-ID 3155-0
    ISSN 1520-5126 ; 0002-7863
    ISSN (online) 1520-5126
    ISSN 0002-7863
    DOI 10.1021%2Fja2093647
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

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  5. Article ; Online: Measuring nanometer distances in nucleic acids using a sequence-independent nitroxide probe.

    Qin, Peter Z / Haworth, Ian S / Cai, Qi / Kusnetzow, Ana K / Grant, Gian Paola G / Price, Eric A / Sowa, Glenna Z / Popova, Anna / Herreros, Bruno / He, Honghang

    Nature protocols

    2007  Volume 2, Issue 10, Page(s) 2354–2365

    Abstract: This protocol describes the procedures for measuring nanometer distances in nucleic acids using a nitroxide probe that can be attached to any nucleotide within a given sequence. Two nitroxides are attached to phosphorothioates that are chemically ... ...

    Abstract This protocol describes the procedures for measuring nanometer distances in nucleic acids using a nitroxide probe that can be attached to any nucleotide within a given sequence. Two nitroxides are attached to phosphorothioates that are chemically substituted at specific sites of DNA or RNA. Inter-nitroxide distances are measured using a four-pulse double electron-electron resonance technique, and the measured distances are correlated to the parent structures using a Web-accessible computer program. Four to five days are needed for sample labeling, purification and distance measurement. The procedures described herein provide a method for probing global structures and studying conformational changes of nucleic acids and protein/nucleic acid complexes.
    MeSH term(s) Chromatography, High Pressure Liquid ; DNA/chemistry ; Electron Spin Resonance Spectroscopy/methods ; Molecular Probe Techniques ; Nitrogen Oxides/chemistry ; RNA/chemistry ; Software ; Spin Labels
    Chemical Substances Nitrogen Oxides ; Spin Labels ; RNA (63231-63-0) ; DNA (9007-49-2) ; nitroxyl (GFQ4MMS07W)
    Language English
    Publishing date 2007-10-18
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2244966-8
    ISSN 1750-2799 ; 1754-2189
    ISSN (online) 1750-2799
    ISSN 1754-2189
    DOI 10.1038/nprot.2007.308
    Database MEDical Literature Analysis and Retrieval System OnLINE

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