Structure and Dynamics of Nucleic Acids

Abstract

In this chapter we describe the application of CW and pulsed EPR methods for the investigation of structural and dynamical properties of RNA and DNA molecules and their interaction with small molecules and proteins. Special emphasis will be given to recent applications of dipolar spectroscopy on nucleic acids.

Distance determination from dysprosium induced relaxation enhancement: a case study on membrane-inserted WALP23 polypeptides

“…Nanometer range distance constraints obtained from dipolar electron paramagnetic resonance (EPR) spectroscopy are broadly used in studies of structure and conformational changes of large biomolecules [1][2][3][4][5][6][7][8][9][10][11]. The distance measurements by EPR can supplement other methods, like NMR [12] or crystallography [13], or can be used as a stand-alone technique [14][15][16].…”

EPR-aided approach for solution structure determination of large RNAs or protein–RNA complexes

“…For small RNAs (less than 30-50 nts), site-specific introduction of spin labels is typically achieved by chemical synthesis of RNAs containing modified nucleotides to which spin labels are subsequently attached 17 . A commonly used and experimentally simple way to introduce spin labels into structured RNA without significantly altering the double-stranded RNA structure 18 is the attachment of the flexible 3-(2-iodoacetamido)-proxyl (IA-proxyl) spin label to a 4-thiouridine residue 19 .…”

Conformational dynamics of nucleic acid molecules studied by PELDOR spectroscopy with rigid spin labels

“…Several reviews and textbooks exist which describe the method [17] [59] and its applications to macromolecular systems such as proteins [18] and nucleic acids [19,[60][61][62] in detail. Therefore, here we will concentrate only on how to obtain angular information from the method of using rigid spin labels incorporated into nucleic acid molecules.…”