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Browsing by Subject "Kjarnsýrur"

Browsing by Subject "Kjarnsýrur"

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  • Saha, Subham (University of Iceland, School of Engineering and Natural Sciences, Faculty of Physical Sciences, 2017-06)
    Electron paramagnetic resonance (EPR) spectroscopy is routinely used to study the structure and dynamics of nucleic acids, to obtain information about their functions. A prerequisite for most EPR studies of nucleic acids is the incorporation of ...
  • Júlíusson, Haraldur Yngvi (University of Iceland, School of Engineering and Natural Sciences, Faculty of Physical Sciences, 2020-02-01)
    Rafeindasegullitrófsgreiningu (e. Electron Paramagnetic Resonance, EPR) er reglubundið beitt í rannsóknum á byggingu og hreyfingu kjarnsýra til að fá upplýsingar um starfsemi þeirra og hlutverk. Innleiðing meðseglandi kjarna á ákveðinn stað í kjarnsýrum ...
  • Jagtap, Anil P.; Geiger, Michel-Andreas; Stöppler, Daniel; Orwick-Rydmark, Marcella; Oschkinat, Hartmut; Sigurdsson, Snorri (Royal Society of Chemistry (RSC), 2016)
    Dynamic nuclear polarization (DNP) is an efficient method to overcome the inherent low sensitivity of magic-angle spinning (MAS) solid-state NMR. We report a new polarizing agent (bcTol), designed for biological applications, that yielded an enhancement ...
  • Gophane, Dnyaneshwar B.; Endeward, Burkhard; Prisner, Thomas F.; Sigurdsson, Snorri (Wiley, 2014-10-08)
    Three structurally related isoindoline-derived spin labels that have different mobilities were incorporated into duplex DNA to systematically study the effect of motion on orientation-dependent pulsed electron-electron double resonance (PELDOR) ...
  • Grytz, C. M.; Kazemi, S.; Marko, A.; Cekan, P.; Güntert, P.; Sigurdsson, Snorri; Prisner, Thomas F. (Royal Society of Chemistry (RSC), 2017)
    Distance measurements are performed between a pair of spin labels attached to nucleic acids using Pulsed Electron–Electron Double Resonance (PELDOR, also called DEER) spectroscopy which is a complementary tool to other structure determination methods ...
  • Kaminker, Ilia; Bye, Morgan; Mendelman, Natanel; Gislason, Kristmann; Sigurdsson, Snorri; Goldfarb, Daniella (Royal Society of Chemistry (RSC), 2015)
    Mn2+ localization in hairpin 92 of the 23S ribosomal RNA (HP92) was obtained using W-band (95 GHz) DEER (double electron-electron resonance) distance measurements between the Mn2+ ion and nitroxide spin labels on the RNA. It was found to be preferably ...
  • Gränz, Markus; Erlenbach, Nicole; Spindler, Philipp; Gophane, Dnyaneshwar B.; Stelzl, Lukas S.; Sigurdsson, Snorri; Prisner, Thomas F. (Wiley, 2018-08-13)
    The investigation of the structure and conformational dynamics of biomolecules under physiological conditions is challenging for structural biology. Although pulsed electron paramagnetic resonance (like PELDOR) techniques provide long‐range distance ...
  • Grytz, C. M.; Marko, A.; Cekan, P.; Sigurdsson, Snorri; Prisner, Thomas F. (Royal Society of Chemistry (RSC), 2016)
    The cocaine aptamer is a DNA three-way junction that binds cocaine at its helical junction. We studied the global conformation and overall flexibility of the aptamer in the absence and presence of cocaine by pulsed electron-electron double resonance ...
  • Heinz, Marcel; Erlenbach, Nicole; Stelzl, Lukas S; Thierolf, Grace; Kamble, Nilesh Ramesh; Sigurdsson, Snorri; Prisner, Thomas F.; Hummer, Gerhard (Oxford University Press (OUP), 2019-11-28)
    Pulsed electron paramagnetic resonance (EPR) experiments, among them most prominently pulsed electron-electron double resonance experiments (PELDOR/DEER), resolve the conformational dynamics of nucleic acids with high resolution. The wide application ...
  • Hetzke, Thilo; Vogel, Marc; Gophane, Dnyaneshwar B.; Weigand, Julia E.; Suess, Beatrix; Sigurdsson, Snorri; Prisner, Thomas F. (Cold Spring Harbor Laboratory, 2018-10-18)
    The tetracycline-binding RNA aptamer (TC-aptamer) is a synthetic riboswitch that binds the antibiotic tetracycline (TC) with exceptionally high affinity. Although a crystal structure exists of the TC-bound state, little is known about the conformational ...
  • Gutmann, Torsten; Liu, Jiquan; Rothermel, Niels; Xu, Yeping; Jaumann, Eva; Werner, Mayke; Breitzke, Hergen; Sigurdsson, Snorri; Buntkowsky, Gerd (Wiley, 2015-01-23)
    A novel heterogeneous dirhodium catalyst has been synthesized. This stable catalyst is constructed from dirhodium acetate dimer (Rh2(OAc)4) units, which are covalently linked to amine‐ and carboxyl‐bifunctionalized mesoporous silica (SBA‐15NH2COOH). ...
  • Shelke, Sandip; Sandholt, Gunnar Birgir; Sigurdsson, Snorri (Royal Society of Chemistry (RSC), 2014)
    Non-covalent and site-directed spin labeling gives easy access to spin-labeled nucleic acids for the study of their structure and dynamics by electron paramagnetic resonance (EPR) spectroscopy. In a search for improved spin labels for non-covalent ...
  • Kamble, Nilesh Ramesh; Gränz, Markus; Prisner, Thomas F.; Sigurdsson, Snorri (Royal Society of Chemistry (RSC), 2016)
    An isoindoline-nitroxide derivative of guanine (G, "G-spin") was shown to bind specifically and effectively to abasic sites in duplex RNAs. Distance measurements on a G-labeled duplex RNA with PELDOR (DEER) showed a strong orientation dependence. Thus, ...
  • Saha, Subham; Hetzke, Thilo; Prisner, Thomas F.; Sigurdsson, Snorri (Royal Society of Chemistry (RSC), 2018)
    In the first example of site-directed spin-labeling of unmodified RNA, a pyrrolidine-nitroxide derivative of tetramethylrosamine (TMR) was shown to bind with high affinity to the malachite green (MG) aptamer, as determined by continuous-wave (CW) ...
  • Kamble, Nilesh Ramesh; Wolfrum, Manpreet; Halbritter, Thomas; Sigurdsson, Snorri; Richert, Clemens (Wiley, 2020-01-21)
    Studying nucleic acids often requires labeling. Many labeling approaches require covalent bonds between the nucleic acid and the label, which complicates experimental procedures. Noncovalent labeling avoids the need for highly specific reagents and ...
  • Mandal, Sucharita; Sigurdsson, Snorri (Wiley, 2020-05-12)
    1,3‐Bis(diphenylene)‐2‐phenylallyl (BDPA)‐based radicals are of interest as polarizing agents for dynamic nuclear polarization (DNP). For this purpose, a BDPA‐nitroxide biradical, employing a phosphodiester linkage, was synthesized. Contrary to what ...
  • Kamble, Nilesh Ramesh (University of Iceland, School of Engineering and Natural Sciences, Faculty of Physical Sciences, 2017-12-21)
    Electron paramagnetic resonance (EPR) spectroscopy is a well known technique that is routinely used to investigate the structure and dynamics of nucleic acids. EPR requires incorporation of paramagnetic centers at specific sites, called site-directed ...
  • Jinga, Viorel; Csiki, Irma Eva; Manolescu, Andrei; Iordache, Paul; Mates, Ioan Nicolae; Radavoi, Daniel; Rascu, Stefan; Badescu, Daniel; Badea, Paula; Mates, Dana (Wiley, 2016-01-15)
    Prostate cancer is the third‐most common form of cancer in men in Romania. The Romanian unscreened population represents a good sample to study common genetic risk variants. However, a comprehensive analysis has not been conducted yet. Here, we report ...
  • Gophane, Dnyaneshwar B.; Endeward, Burkhard; Prisner, Thomas F.; Sigurdsson, Snorri (Royal Society of Chemistry (RSC), 2018)
    A new isoindoline-derived benzimidazole nitroxide spin label, ImUm, was synthesized and incorporated into RNA oligoribonucleotides. ImUm is the first example of a conformationally unambiguous spin label for RNA, in which the nitroxide N–O bond lies on ...
  • Saha, Subham; Jagtap, Anil P.; Sigurdsson, Snorri (Royal Society of Chemistry (RSC), 2015)
    Two aromatic isothiocyanates, derived from isoindoline nitroxides, were synthesized and selectively reacted with 2′-amino groups in RNA. The spin labels displayed limited mobility in RNA, making them promising candidates for distance measurements by ...