These are the sources and citations used to research RNA dynamics. This bibliography was generated on Cite This For Me on

  • Journal

    Al-Hashimi, H. M.

    Dynamics-Based Amplification of RNA Function and Its Characterization by Using NMR Spectroscopy

    2005 - ChemBioChem

    In-text: (Al-Hashimi 1506-1519)

    Your Bibliography: Al-Hashimi, Hashim M. "Dynamics-Based Amplification Of RNA Function And Its Characterization By Using NMR Spectroscopy." ChemBioChem 6.9 (2005): 1506-1519. Web.

  • Journal

    Buck, J., Furtig, B., Noeske, J., Wohnert, J. and Schwalbe, H.

    Time-resolved NMR methods resolving ligand-induced RNA folding at atomic resolution

    2007 - Proceedings of the National Academy of Sciences

    In-text: (Buck et al. 15699-15704)

    Your Bibliography: Buck, J. et al. "Time-Resolved NMR Methods Resolving Ligand-Induced RNA Folding At Atomic Resolution." Proceedings of the National Academy of Sciences 104.40 (2007): 15699-15704. Web.

  • Journal

    Cao, S., Fürtig, B., Schwalbe, H. and Chen, S.

    Folding Kinetics for the Conformational Switch between Alternative RNA Structures

    2010 - The Journal of Physical Chemistry B

    Transitions between different conformational states, so-called conformational switching, are intrinsic to RNA catalytic and regulatory functions. Often, conformational switching occurs on time scales of several seconds. In combination with the recent real-time NMR experiments (Wenter et al. Angew. Chem. Int. Ed. 2005, 44, 2600; Wenter et al. ChemBioChem 2006, 7, 417) for the transitions between bistable RNA conformations, we combine the master equation method with the kinetic cluster method to investigate the detailed kinetic mechanism and the factors that govern the folding kinetics. We propose that heat capacity change (ΔCp) upon RNA folding may be important for RNA folding kinetics. In addition, we find that, for tetraloop hairpins, noncanonical (tertiary) intraloop interactions are important to determine the folding kinetics. Furthermore, through theory-experiment comparisons, we find that the different rate models for the fundamental steps (i.e., formation/disruption of a base pair or stack) can cause contrasting results in the theoretical predictions

    In-text: (Cao et al. 13609-13615)

    Your Bibliography: Cao, Song et al. "Folding Kinetics For The Conformational Switch Between Alternative RNA Structures." The Journal of Physical Chemistry B 114.42 (2010): 13609-13615. Web.

  • Journal

    Clay, M. C., Ganser, L. R., Merriman, D. K. and Al-Hashimi, H. M.

    Resolving sugar puckers in RNA excited states exposes slow modes of repuckering dynamics

    2017 - Nucleic Acids Research

    Recent studies have shown that RNAs exist in dynamic equilibrium with short-lived low-abundance ‘excited states’ that form by reshuffling base pairs in and around non-canonical motifs. These conformational states are proposed to be rich in non-canonical motifs and to play roles in the folding and regulatory functions of non-coding RNAs but their structure proves difficult to characterize given their transient nature. Here, we describe an approach for determining sugar pucker conformation in RNA excited states through nuclear magnetic resonance measurements of C1΄ and C4΄ rotating frame spin relaxation (R1ρ) in uniformly 13C/15N labeled RNA samples. Application to HIV-1 TAR exposed slow modes of sugar repuckering dynamics at the μs and ms timescale accompanying transitions between non-helical (C2΄-endo) to helical (C3΄-endo) conformations during formation of two distinct excited states. In contrast, we did not obtain any evidence for slow sugar repuckering dynamics for nucleotides in a variety of structural contexts that do not undergo non-helical to helical transitions. Our results outline a route for significantly improving the conformational characterization of RNA excited states and suggest that slow modes of repuckering dynamics gated by transient changes in secondary structure are quite common in RNA.

    In-text: (Clay et al. e134-e134)

    Your Bibliography: Clay, Mary C. et al. "Resolving Sugar Puckers In RNA Excited States Exposes Slow Modes Of Repuckering Dynamics." Nucleic Acids Research 45 (2017): e134-e134. Web.

  • Journal

    Cordero, P. and Das, R.

    Rich RNA Structure Landscapes Revealed by Mutate-and-Map Analysis

    2015 - PLOS Computational Biology

    Landscapes exhibiting multiple secondary structures arise in natural RNA molecules that modulate gene expression, protein synthesis, and viral infection [corrected]. We report herein that high-throughput chemical experiments can isolate an RNA's multiple alternative secondary structures as they are stabilized by systematic mutagenesis (mutate-and-map, M2) and that a computational algorithm, REEFFIT, enables unbiased reconstruction of these states' structures and populations. In an in silico benchmark on non-coding RNAs with complex landscapes, M2-REEFFIT recovers 95% of RNA helices present with at least 25% population while maintaining a low false discovery rate (10%) and conservative error estimates. In experimental benchmarks, M2-REEFFIT recovers the structure landscapes of a 35-nt MedLoop hairpin, a 110-nt 16S rRNA four-way junction with an excited state, a 25-nt bistable hairpin, and a 112-nt three-state adenine riboswitch with its expression platform, molecules whose characterization previously required expert mutational analysis and specialized NMR or chemical mapping experiments. With this validation, M2-REEFFIT enabled tests of whether artificial RNA sequences might exhibit complex landscapes in the absence of explicit design. An artificial flavin mononucleotide riboswitch and a randomly generated RNA sequence are found to interconvert between three or more states, including structures for which there was no design, but that could be stabilized through mutations. These results highlight the likely pervasiveness of rich landscapes with multiple secondary structures in both natural and artificial RNAs and demonstrate an automated chemical/computational route for their empirical characterization.

    In-text: (Cordero and Das e1004473)

    Your Bibliography: Cordero, Pablo, and Rhiju Das. "Rich RNA Structure Landscapes Revealed By Mutate-And-Map Analysis." PLOS Computational Biology 11.11 (2015): e1004473. Web.

  • Journal

    Coveney, P. V. and Wan, S.

    On the calculation of equilibrium thermodynamic properties from molecular dynamics

    2016 - Physical Chemistry Chemical Physics

    The purpose of statistical mechanics is to provide a route to the calculation of macroscopic properties of matter from their constituent microscopic components. It is well known that the macrostates emerge as ensemble averages of microstates. However, this is more often stated than implemented in computer simulation studies. Here we consider foundational aspects of statistical mechanics which are overlooked in most textbooks and research articles that purport to compute macroscopic behaviour from microscopic descriptions based on classical mechanics and show how due attention to these issues leads in directions which have not been widely appreciated in the field of molecular dynamics simulation.

    In-text: (Coveney and Wan 30236-30240)

    Your Bibliography: Coveney, Peter V., and Shunzhou Wan. "On The Calculation Of Equilibrium Thermodynamic Properties From Molecular Dynamics." Physical Chemistry Chemical Physics 18.44 (2016): 30236-30240. Web.

  • Journal

    Cruz, J. A. and Westhof, E.

    The Dynamic Landscapes of RNA Architecture

    2009 - Cell

    In-text: (Cruz and Westhof 604-609)

    Your Bibliography: Cruz, José Almeida, and Eric Westhof. "The Dynamic Landscapes Of RNA Architecture." Cell 136 (2009): 604-609. Web.

  • Journal

    Cruz, J. A. and Westhof, E.

    The Dynamic Landscapes of RNA Architecture

    2009 - Cell

    Cited in connection with importance of NMR for nucleic acids

    In-text: (Cruz and Westhof 604-609)

    Your Bibliography: Cruz, José Almeida, and Eric Westhof. "The Dynamic Landscapes Of RNA Architecture." Cell 136.4 (2009): 604-609. Web.

  • Journal

    Dagenais, P., Girard, N., Bonneau, E. and Legault, P.

    Insights into RNA structure and dynamics from recent NMR and X-ray studies of the Neurospora Varkud satellite ribozyme

    2017 - Wiley Interdisciplinary Reviews: RNA

    Despite the large number of noncoding RNAs and their importance in several biological processes, our understanding of RNA structure and dynamics at atomic resolution is still very limited. Like many other RNAs, the Neurospora Varkud satellite (VS) ribozyme performs its functions through dynamic exchange of multiple conformational states. More specifically, the VS ribozyme recognizes and cleaves its stem-loop substrate via a mechanism that involves several structural transitions within its stem-loop substrate. The recent publications of high-resolution structures of the VS ribozyme, obtained by NMR spectroscopy and X-ray crystallography, offer an opportunity to integrate the data and closely examine the structural and dynamic properties of this model RNA system. Notably, these investigations provide a valuable example of the divide-and-conquer strategy for structural and dynamic characterization of a large RNA, based on NMR structures of several individual subdomains. The success of this divide-and-conquer approach reflects the modularity of RNA architecture and the great care taken in identifying the independently-folding modules. Together with previous biochemical and biophysical characterizations, the recent NMR and X-ray studies provide a coherent picture into how the VS ribozyme recognizes its stem-loop substrate. Such in-depth characterization of this RNA enzyme will serve as a model for future structural and engineering studies of dynamic RNAs and may be particularly useful in planning divide-and-conquer investigations. WIREs RNA 2017, 8:e1421. doi: 10.1002/wrna.1421 For further resources related to this article, please visit the WIREs website.

    In-text: (Dagenais et al. e1421)

    Your Bibliography: Dagenais, Pierre et al. "Insights Into RNA Structure And Dynamics From Recent NMR And X-Ray Studies Of The Neurospora Varkud Satellite Ribozyme." Wiley Interdisciplinary Reviews: RNA 8.5 (2017): e1421. Web.

  • Journal

    Dethoff, E. A., Chugh, J., Mustoe, A. M. and Al-Hashimi, H. M.

    Functional complexity and regulation through RNA dynamics

    2012 - Nature

    In-text: (Dethoff et al. 322-330)

    Your Bibliography: Dethoff, Elizabeth A. et al. "Functional Complexity And Regulation Through RNA Dynamics." Nature 482 (2012): 322-330. Web.

  • Journal

    Eichhorn, C. D. and Al-Hashimi, H. M.

    Structural dynamics of a single-stranded RNA-helix junction using NMR

    2014 - RNA

    Many regulatory RNAs contain long single strands (ssRNA) that adjoin secondary structural elements. Here, we use NMR spectroscopy to study the dynamic properties of a 12-nucleotide (nt) ssRNA tail derived from the prequeuosine riboswitch linked to the 3' end of a 48-nt hairpin. Analysis of chemical shifts, NOE connectivity, (13)C spin relaxation, and residual dipolar coupling data suggests that the first two residues (A25 and U26) in the ssRNA tail stack onto the adjacent helix and assume an ordered conformation. The following U26-A27 step marks the beginning of an A6-tract and forms an acute pivot point for substantial motions within the tail, which increase toward the terminal end. Despite substantial internal motions, the ssRNA tail adopts, on average, an A-form helical conformation that is coaxial with the helix. Our results reveal a surprising degree of structural and dynamic complexity at the ssRNA-helix junction, which involves a fine balance between order and disorder that may facilitate efficient pseudoknot formation on ligand recognition.

    In-text: (Eichhorn and Al-Hashimi 782-791)

    Your Bibliography: Eichhorn, C. D., and H. M. Al-Hashimi. "Structural Dynamics Of A Single-Stranded RNA-Helix Junction Using NMR." RNA 20.6 (2014): 782-791. Web.

  • Journal

    Eichhorn, C. D. and Al-Hashimi, H. M.

    Structural dynamics of a single-stranded RNA-helix junction using NMR

    2014 - RNA

    In-text: (Eichhorn and Al-Hashimi 782-791)

    Your Bibliography: Eichhorn, C. D., and H. M. Al-Hashimi. "Structural Dynamics Of A Single-Stranded RNA-Helix Junction Using NMR." RNA 20.6 (2014): 782-791. Web.

  • Journal

    Eichhorn, C. D. and Al-Hashimi, H. M.

    Structural dynamics of a single-stranded RNA-helix junction using NMR

    2014 - RNA

    In-text: (Eichhorn and Al-Hashimi 782-791)

    Your Bibliography: Eichhorn, C. D., and H. M. Al-Hashimi. "Structural Dynamics Of A Single-Stranded RNA-Helix Junction Using NMR." RNA 20.6 (2014): 782-791. Web.

  • Journal

    Fürtig, B., Reining, A., Sochor, F., Oberhauser, E. M., Heckel, A. and Schwalbe, H.

    Characterization of Conformational Dynamics of Bistable RNA by Equilibrium and Non-Equilibrium NMR

    2013 - Current Protocols in Nucleic Acid Chemistry

    In-text: (Fürtig et al. 11.13.1-11.13.16)

    Your Bibliography: Fürtig, Boris et al. "Characterization Of Conformational Dynamics Of Bistable RNA By Equilibrium And Non-Equilibrium NMR." Current Protocols in Nucleic Acid Chemistry 55.1 (2013): 11.13.1-11.13.16. Web.

  • Journal

    Fürtig, B., Wenter, P., Reymond, L., Richter, C., Pitsch, S. and Schwalbe, H.

    Conformational Dynamics of Bistable RNAs Studied by Time-Resolved NMR Spectroscopy

    2007 - Journal of the American Chemical Society

    The structural transition between two alternate conformations of bistable RNAs has been characterized by time-resolved NMR spectroscopy. The mechanism, kinetics, and thermodynamics underlying the global structural transition of bistable RNAs were delineated. Both bistable RNA conformations and a partial unstructured RNA of identical sequence could be trapped using photolabile protecting groups. This trapping allowed for an investigation of the initial folding from an unfolded RNA to one of the preferred conformations of the bistable RNA and of the structural transitions involved. Folding of the secondary structure elements occurs rapidly, while the global structural transition of the bistable RNA occurs on a time scale of minutes and shows marked temperature dependence. Comparison of these results with bistable systems previously investigated leads to the prediction of activation enthalpies (ΔH⧧) associated with global structural transitions in RNA.

    In-text: (Fürtig et al. 16222-16229)

    Your Bibliography: Fürtig, Boris et al. "Conformational Dynamics Of Bistable Rnas Studied By Time-Resolved NMR Spectroscopy." Journal of the American Chemical Society 129.51 (2007): 16222-16229. Web.

  • Journal

    Fürtig, B., Buck, J., Manoharan, V., Bermel, W., Jäschke, A., Wenter, P., Pitsch, S. and Schwalbe, H.

    Time-resolved NMR studies of RNA folding

    2007 - Biopolymers

    The application of real-time NMR experiments to the study of RNA folding, as reviewed in this article, is relatively new. For many RNA folding events, current investigations suggest that the time scales are in the second to minute regime. In addition, the initial investigations suggest that different folding rates are observed for one structural transition may be due to the hierarchical folding units of RNA. Many of the experiments developed in the field of NMR of protein folding cannot directly be transferred to RNA: hydrogen exchange experiments outside the spectrometer cannot be applied since the intrinsic exchange rates are too fast in RNA, relaxation dispersion experiments on the other require faster structural transitions than those observed in RNA. On the other hand, information derived from time-resolved NMR experiments, namely the acquisition of native chemical shifts, can be readily interpreted in light of formation of a single long-range hydrogen bonding interaction. Together with mutational data that can readily be obtained for RNA and new ligation technologies that enhance site resolution even further, time-resolved NMR may become a powerful tool to decipher RNA folding. Such understanding will be of importance to understand the functions of coding and non-coding RNAs in cells. # 2007 Wiley Periodicals, Inc. Biopolymers 86: 360–383, 2007. Keywords: NMR spectroscopy; RNA folding; time-resolved NMR; photolabile caged compounds

    In-text: (Fürtig et al. 360-383)

    Your Bibliography: Fürtig, Boris et al. "Time-Resolved NMR Studies Of RNA Folding." Biopolymers 86.5-6 (2007): 360-383. Web.

  • Journal

    Fürtig, B., Buck, J., Manoharan, V., Bermel, W., Jäschke, A., Wenter, P., Pitsch, S. and Schwalbe, H.

    Time-resolved NMR studies of RNA folding

    2007 - Biopolymers

    Cite in connection with NMR spectroscopy as major source of structura and dynamical information on nucleic acids in solution.

    In-text: (Fürtig et al. 360-383)

    Your Bibliography: Fürtig, Boris et al. "Time-Resolved NMR Studies Of RNA Folding." Biopolymers 86.5-6 (2007): 360-383. Web.

  • Journal

    Getz, M., Sun, X., Casiano-Negroni, A., Zhang, Q. and Al-Hashimi, H. M.

    Review NMR studies of RNA dynamics and structural plasticity using NMR residual dipolar couplings

    2007 - Biopolymers

    An increasing number of RNAs are being discovered that perform their functions by undergoing large changes in conformation in response to a variety of cellular signals, including recognition of proteins and small molecular targets, changes in temperature, and RNA synthesis itself. The measurement of NMR residual dipolar couplings (RDCs) in partially aligned systems is providing new insights into the structural plasticity of RNA through combined characterization of large-amplitude collective helix motions and local flexibility in noncanonical regions over a wide window of biologically relevant timescales (<milliseconds). Here, we review RDC methodology for studying RNA structural dynamics and survey what has been learnt thus far from application of these methods. Future methodological challenges are also identified.

    In-text: (Getz et al. 384-402)

    Your Bibliography: Getz, Melissa et al. "Review NMR Studies Of RNA Dynamics And Structural Plasticity Using NMR Residual Dipolar Couplings." Biopolymers 86.5-6 (2007): 384-402. Web.

  • Journal

    Marušič, M., Schlagnitweit, J. and Petzold, K.

    Front Cover: RNA Dynamics by NMR Spectroscopy (ChemBioChem 21/2019)

    2019 - ChemBioChem

    An ever-increasing number of functional RNAs require a mechanistic understanding. RNA function relies on changes in its structure, so-called dynamics. To reveal dynamic processes and higher energy structures, new NMR methods have been developed to elucidate these dynamics in RNA with atomic resolution. In this Review, we provide an introduction to dynamics novices and an overview of methods that access most dynamic timescales, from picoseconds to hours. Examples are provided as well as insight into theory, data acquisition and analysis for these different methods. Using this broad spectrum of methodology, unprecedented detail and invisible structures have been obtained and are reviewed here. RNA, though often more complicated and therefore neglected, also provides a great system to study structural changes, as these RNA structural changes are more easily defined—Lego like—than in proteins, hence the numerous revelations of RNA excited states.

    In-text: (Marušič, Schlagnitweit and Petzold 2683-2683)

    Your Bibliography: Marušič, Maja, Judith Schlagnitweit, and Katja Petzold. "Front Cover: RNA Dynamics By NMR Spectroscopy (Chembiochem 21/2019)." ChemBioChem 20.21 (2019): 2683-2683. Web.

  • Journal

    Mouzakis, K., Dethoff, E., Tonelli, M., Al-Hashimi, H. and Butcher, S.

    Dynamic Motions of the HIV-1 Frameshift Site RNA

    2015 - Biophysical Journal

    The HIV-1 frameshift site (FS) plays a critical role in viral replication. During translation, the HIV-1 FS transitions from a 3-helix to a 2-helix junction RNA secondary structure. The 2-helix junction structure contains a GGA bulge, and purine-rich bulges are common motifs in RNA secondary structure. Here, we investigate the dynamics of the HIV-1 FS 2-helix junction RNA. Interhelical motions were studied under different ionic conditions using NMR order tensor analysis of residual dipolar couplings. In 150 mM potassium, the RNA adopts a 43°(±4°) interhelical bend angle (β) and displays large amplitude, anisotropic interhelical motions characterized by a 0.52(±0.04) internal generalized degree of order (GDOint) and distinct order tensor asymmetries for its two helices (η = 0.26(±0.04) and 0.5(±0.1)). These motions are effectively quenched by addition of 2 mM magnesium (GDOint = 0.87(±0.06)), which promotes a near-coaxial conformation (β = 15°(±6°)) of the two helices. Base stacking in the bulge was investigated using the fluorescent purine analog 2-aminopurine. These results indicate that magnesium stabilizes extrahelical conformations of the bulge nucleotides, thereby promoting coaxial stacking of helices. These results are highly similar to previous studies of the HIV transactivation response RNA, despite a complete lack of sequence similarity between the two RNAs. Thus, the conformational space of these RNAs is largely determined by the topology of their interhelical junctions.

    In-text: (Mouzakis et al. 644-654)

    Your Bibliography: Mouzakis, Kathryn D. et al. "Dynamic Motions Of The HIV-1 Frameshift Site RNA." Biophysical Journal 108 (2015): 644-654. Web.

  • Journal

    Mustoe, A. M., Brooks, C. L. and Al-Hashimi, H. M.

    Hierarchy of RNA Functional Dynamics

    2014 - Annual Review of Biochemistry

    In-text: (Mustoe, Brooks and Al-Hashimi 441-466)

    Your Bibliography: Mustoe, Anthony M., Charles L. Brooks, and Hashim M. Al-Hashimi. "Hierarchy Of RNA Functional Dynamics." Annual Review of Biochemistry 83 (2014): 441-466. Web.

  • Journal

    Plumridge, A., Katz, A. M., Calvey, G. D., Elber, R., Kirmizialtin, S. and Pollack, L.

    Time-Resolved SAXS and Ensemble Modelling Reveal Magnesium Orchestration across an RNA Folding Landscape

    2018 - Biophysical Journal

    In-text: (Plumridge et al. 433a)

    Your Bibliography: Plumridge, Alex et al. "Time-Resolved SAXS And Ensemble Modelling Reveal Magnesium Orchestration Across An RNA Folding Landscape." Biophysical Journal 114.3 (2018): 433a. Web.

  • Journal

    Rinnenthal, J., Buck, J., Ferner, J., Wacker, A., FÜrtig, B. and Schwalbe, H.

    Mapping the Landscape of RNA Dynamics with NMR Spectroscopy

    2011 - Accounts of Chemical Research

    In-text: (Rinnenthal et al. 1292-1301)

    Your Bibliography: Rinnenthal, Jörg et al. "Mapping The Landscape Of RNA Dynamics With NMR Spectroscopy." Accounts of Chemical Research 44.12 (2011): 1292-1301. Web.

  • Journal

    Rinnenthal, J., Buck, J., Ferner, J., Wacker, A., FÜrtig, B. and Schwalbe, H.

    Mapping the Landscape of RNA Dynamics with NMR Spectroscopy

    2011 - Accounts of Chemical Research

    Cite in connection with importance of NMR for nucleic acids

    In-text: (Rinnenthal et al. 1292-1301)

    Your Bibliography: Rinnenthal, Jörg et al. "Mapping The Landscape Of RNA Dynamics With NMR Spectroscopy." Accounts of Chemical Research 44.12 (2011): 1292-1301. Web.

  • Journal

    Salmon, L., Yang, S. and Al-Hashimi, H. M.

    Advances in the Determination of Nucleic Acid Conformational Ensembles

    2014 - Annual Review of Physical Chemistry

    Conformational changes in nucleic acids play a key role in the way genetic information is stored, transferred, and processed in living cells. Here, we describe new approaches that employ a broad range of experimental data, including NMR-derived chemical shifts and residual dipolar couplings, small-angle X-ray scattering, and computational approaches such as molecular dynamics simulations to determine ensembles of DNA and RNA at atomic resolution. We review the complementary information that can be obtained from diverse sets of data and the various methods that have been developed to combine these data with computational methods to construct ensembles and assess their uncertainty. We conclude by surveying RNA and DNA ensembles determined using these methods, highlighting the unique physical and functional insights obtained so far.

    In-text: (Salmon, Yang and Al-Hashimi 293-316)

    Your Bibliography: Salmon, Loïc, Shan Yang, and Hashim M. Al-Hashimi. "Advances In The Determination Of Nucleic Acid Conformational Ensembles." Annual Review of Physical Chemistry 65 (2014): 293-316. Web.

  • Journal

    Sattler, M.

    Dynamic RNA world

    2015 - RNA

    In-text: (Sattler 727-728)

    Your Bibliography: Sattler, Michael. "Dynamic RNA World." RNA 21.4 (2015): 727-728. Web.

  • Journal

    SCHROEDER, K. T.

    NMR spectroscopy of RNA duplexes containing pseudouridine in supercooled water

    2005 - RNA

    In-text: (SCHROEDER 1012-1016)

    Your Bibliography: SCHROEDER, K. T. "NMR Spectroscopy Of RNA Duplexes Containing Pseudouridine In Supercooled Water." RNA 11.7 (2005): 1012-1016. Web.

  • Journal

    Schroeder, S. J.

    Challenges and approaches to predicting RNA with multiple functional structures

    2018 - RNA

    The revolution in sequencing technology demands new tools to interpret the genetic code. As in vivo transcriptome-wide chemical probing techniques advance, new challenges emerge in the RNA folding problem. The emphasis on one sequence folding into a single minimum free energy structure is fading as a new focus develops on generating RNA structural ensembles and identifying functional structural features in ensembles. This review describes an efficient combinatorially complete method and three free energy minimization approaches to predicting RNA structures with more than one functional fold, as well as two methods for analysis of a thermodynamics-based Boltzmann ensemble of structures. The review then highlights two examples of viral RNA 3'-UTR regions that fold into more than one conformation and have been characterized by single molecule fluorescence energy resonance transfer or NMR spectroscopy. These examples highlight the different approaches and challenges in predicting structure and function from sequence for RNA with multiple biological roles and folds. More well-defined examples and new metrics for measuring differences in RNA structures will guide future improvements in prediction of RNA structure and function from sequence.

    In-text: (Schroeder 1615-1624)

    Your Bibliography: Schroeder, Susan J. "Challenges And Approaches To Predicting RNA With Multiple Functional Structures." RNA 24.12 (2018): 1615-1624. Web.

  • Journal

    Tsukanov, R., Tomov, T. E., Masoud, R., Drory, H., Plavner, N., Liber, M. and Nir, E.

    Detailed Study of DNA Hairpin Dynamics Using Single-Molecule Fluorescence Assisted by DNA Origami

    2013 - The Journal of Physical Chemistry B

    The dynamics of two DNA hairpins (5′-TCGCCT-A31-AGGCGA-3′ and 5′-TCGCCG-A31-CGGCGA-3′) were studied using immobilization-based and diffusion-based single-molecule fluorescence techniques. The techniques enabled separated and detailed investigation of the states and of the transition reactions. Only two states, open and closed, were identified from analysis of the FRET histograms; metastable states with lifetimes longer than the technique resolution (0.3 ms) were not observed. The opening and closing reaction rates were determined directly from the FRET time trajectories, and the Gibbs free energies of these states and of the transition state were calculated using the Kramer theory. The rates, which are undoubtedly of transitions between the fully closed and the fully open states and ranged from 2 to 90 s–1, were lower (∼10-fold) than the rates previously determined from fluorescence correlation spectroscopy. The heights of the barriers for closing were almost identical for the two hairpins. The barrier for opening the hairpin with the stronger stem was higher (4.3 kJ/mol) than that for the hairpin with the weaker stem, in very good agreement with the difference in stability calculated by the nearest-neighbor method. The barrier for closing the hairpin decreased (∼8 kJ/mol) and the barrier for opening increased (∼4 kJ/mol) with increasing NaCl concentration (10–100 mM), indicating that higher ionic strength stabilizes the folded state with respect to the transition state and stabilizes the transition state relative to the unfolded state. The very good agreements in the dynamics measured for free hairpins, for hairpins anchored to origami, and for hairpins anchored to the coverslip and the very good agreement between the two single-molecule techniques demonstrate that neither the origami nor the coverslip influence the hairpin dynamics, supporting a previous demonstration that origami can serve as a platform for biophysical investigations

    In-text: (Tsukanov et al. 11932-11942)

    Your Bibliography: Tsukanov, Roman et al. "Detailed Study Of DNA Hairpin Dynamics Using Single-Molecule Fluorescence Assisted By DNA Origami." The Journal of Physical Chemistry B 117.40 (2013): 11932-11942. Web.

  • Journal

    Villada-Balbuena, M. and Carbajal-Tinoco, M. D.

    One-Bead Coarse-Grained Model for RNA 3D Structure with Non-Canonical Interactions

    2019 - Biophysical Journal

    In-text: (Villada-Balbuena and Carbajal-Tinoco 353a)

    Your Bibliography: Villada-Balbuena, Mario, and Mauricio D. Carbajal-Tinoco. "One-Bead Coarse-Grained Model For RNA 3D Structure With Non-Canonical Interactions." Biophysical Journal 116.3 (2019): 353a. Web.

  • Journal

    Zhang, Q. and Al-Hashimi, H. M.

    Domain-elongation NMR spectroscopy yields new insights into RNA dynamics and adaptive recognition

    2009 - RNA

    In-text: (Zhang and Al-Hashimi 1941-1948)

    Your Bibliography: Zhang, Q., and H. M. Al-Hashimi. "Domain-Elongation NMR Spectroscopy Yields New Insights Into RNA Dynamics And Adaptive Recognition." RNA 15.11 (2009): 1941-1948. Web.

  • Journal

    Zhang, T., Faraggi, E. and Zhou, Y.

    Fluctuations of backbone torsion angles obtained from NMR-determined structures and their prediction

    2010 - Proteins: Structure, Function, and Bioinformatics

    In-text: (Zhang, Faraggi and Zhou 3353-3362)

    Your Bibliography: Zhang, Tuo, Eshel Faraggi, and Yaoqi Zhou. "Fluctuations Of Backbone Torsion Angles Obtained From NMR-Determined Structures And Their Prediction." Proteins: Structure, Function, and Bioinformatics 78 (2010): 3353-3362. Web.

  • Journal

    Zhang, T., Faraggi, E. and Zhou, Y.

    Fluctuations of backbone torsion angles obtained from NMR-determined structures and their prediction

    2010 - Proteins: Structure, Function, and Bioinformatics

    In-text: (Zhang, Faraggi and Zhou 3353-3362)

    Your Bibliography: Zhang, Tuo, Eshel Faraggi, and Yaoqi Zhou. "Fluctuations Of Backbone Torsion Angles Obtained From NMR-Determined Structures And Their Prediction." Proteins: Structure, Function, and Bioinformatics 78 (2010): 3353-3362. Web.

  • Journal

    Zhao, C. and Pyle, A. M.

    Structural Insights into the Mechanism of Group II Intron Splicing

    2017 - Trends in Biochemical Sciences

    While the major architectural features and active-site components of group II introns have been known for almost a decade, information on the individual stages of splicing has been lacking. Recent advances in crystallography and cryo-electron microscopy (cryo-EM) have provided major new insights into the structure of intact lariat introns. Conformational changes that mediate the steps of splicing and retrotransposition are being elucidated, revealing the dynamic, highly coordinated motions that are required for group II intron activity. Finally, these ribozymes can now be viewed in their larger, more natural context as components of holoenzymes that include encoded maturase proteins. These studies expand our understanding of group II intron structural diversity and evolution, while setting the stage for rigorous mechanistic analysis of RNA splicing machines

    In-text: (Zhao and Pyle 470-482)

    Your Bibliography: Zhao, Chen, and Anna Marie Pyle. "Structural Insights Into The Mechanism Of Group II Intron Splicing." Trends in Biochemical Sciences 42.6 (2017): 470-482. Web.

  • Journal

    Zhao, L. and Xia, T.

    Probing RNA conformational dynamics and heterogeneity using femtosecond time-resolved fluorescence spectroscopy

    2009 - Methods

    In-text: (Zhao and Xia 128-135)

    Your Bibliography: Zhao, Liang, and Tianbing Xia. "Probing RNA Conformational Dynamics And Heterogeneity Using Femtosecond Time-Resolved Fluorescence Spectroscopy." Methods 49.2 (2009): 128-135. Web.

Click here to start building your own bibliography
Keep on Citing!
Cite This For Me:
The Easiest Tool to Create your Bibliographies Online
Join Us!

Save Time and Improve Your Marks with Cite This For Me

10,587 students joined last month!

  • ✔ Save your bibliographies for longer
  • ✔ Super fast and accurate citation program
  • ✔ Save time when referencing
  • ✔ Make your student life easy and fun
  • ✔ Pay only once with our Forever plan
  • ✔ Use plagiarism checker
  • ✔ Create and edit multiple bibliographies
Join