Towards Structural Genomics of RNA: Rapid NMR Resonance Assignment and Simultaneous RNA Tertiary Structure Determination Using Residual Dipolar Couplings

Characterizing the relative orientation and dynamics of RNA A-form helices using NMR residual dipolar couplings

“…2a). Not only are these assignments the easiest to establish in nucleic acids using conventional methods [27][28][29] , there are possibilities for integrating RDC measurements into the assignment process thereby enhancing the efficiency and robustness of application even further 30,31 . Second, the conformation of Watson-Crick (WC) base pairs in helical stems does not need to be determined-rather it is modeled a priori using the idealized A-form geometry 32,33 taking into account parameterized structural deviations 23 .…”

“…Second, the conformation of Watson-Crick (WC) base pairs in helical stems does not need to be determined-rather it is modeled a priori using the idealized A-form geometry 32,33 taking into account parameterized structural deviations 23 . Third, computational methods are available for interpreting RDCs in a semi-automated manner 23,31,[34][35][36] (Fig. 2b).…”

Resolution-optimized NMR measurement of 1DCH, 1DCC and 2DCH residual dipolar couplings in nucleic acid bases

“…RDCs are particularly useful in nucleic acids, where the number of NOE restraints is typically relatively low, especially those involving long-range contacts. The fact that dipolar restraints provide information on internuclear bond vectors relative to a single axis system, that of the alignment tensor, allows for the study of global properties such as helix bending or relative helix orientations in multi-subunit molecules (Tjandra et al, 2000;Vermeulen et al, 2000;Al-Hashimi et al, 2002;Bondensgaard et al, 2002;MacDonald and Lu, 2002;Barbic et al, 2003;Lukavsky et al, 2003;Stefl et al, 2004). However, most applications have relied on a relatively small number of couplings per nucleotide, far fewer than the number of variable torsion angles.…”

Structure and Dynamics of Proteins from Nuclear Magnetic Resonance Spectroscopy

“…They may also be acquired very rapidly and accurately by a number of techniques including, direct measurement of splittings in coupled heteronuclear single quantum coherence spectra (HSQC) (Bax et al, 1994;Bodenhausen & Ruben, 1980;Cavanagh et al, 1995;Tolman & Prestegard, 1996). RDCs provide structural (Bax et al, 2001;Cornilescu et al, 1999;Delaglio et al, 2000) and motional (Al-Hashimi et al, 2002b;Bax, 2003;Bernardo & Blackledge, 2004a, 2004bBlackledge, 2005;Clore & Schwieters, 2003;O'Neil-Cabello et al, 2004;Tolman, 2001;Yi et al, 2004) information in a biologically relevant timescale and have been used in studies of carbohydrates (Adeyeye et al, 2003;Tian et al, 2001a), nucleic acids (Al-Hashimi et al, 2000a, 2002a, 2002bTjandra et al, 2000;Vermeulen et al, 2000) and proteins (Andrec et al, 2001;Assfalg et al, 2003;Bertini et al, 2003;Clore & Bewley, 2002;Cornilescu et al, 1999;Fowler et al, 2000;Tian et al, 2001b). The use of RDCs as the main source of structural information has led to a significant reduction in data collection and analysis, while providing the possibility of simultaneous resonance assignment, structure determination, and identification of dynamical regions (Bernado & Blackledge, 2004b;Prestegard et al, 2005;Shealy et al, 2011;Tian et al, 2001b;…”