Many RNAs undergo large conformational changes in response to the binding of proteins and small molecules. However, when RNA functional dynamics occur in the ns-μs time scale they become invisible to traditional solution NMR relaxation methods. Residual dipolar couplings methods have revealed the presence of extensive ns-μs domain motions in HIV-1 TAR RNA, but this technique lacks information on the rates of motions. We have used solid-state deuterium NMR to quantitatively describe trajectories of key residues in TAR by exploiting the sensitivity of this technique to motions that occur in the ns-μs regime. Deuterium lineshape and relaxation data were used to model motions of residues within the TAR binding interface. The resulting motional models indicate that two functionally essential bases within the single stranded bulge sample both the free and Tat-bound conformations on the microsecond timescale in the complete absence of the protein. Thus, our results strongly support a conformational capture mechanism for recognition: the protein does not induce a new RNA structure, but instead captures an already-populated conformation.

The essential role played by local and collective motions in RNA function has led to a growing interest in the characterization of RNA dynamics. Recent investigations have revealed that even relatively simple RNAs experience complex motions over multiple time scales covering the entire ms-ps motional range. In this work, we use deuterium solid-state NMR to systematically investigate motions in HIV-1 TAR RNA as a function of hydration. We probe dynamics at three uridine residues in different structural environments ranging from helical to completely unrestrained. We observe distinct and substantial changes in (2)H solid-state relaxation times and lineshapes at each site as hydration levels increase. By comparing solid-state and solution state (13)C relaxation measurements, we establish that ns-micros motions that may be indicative of collective dynamics suddenly arise in the RNA as hydration reaches a critical point coincident with the onset of bulk hydration. Beyond that point, we observe smaller changes in relaxation rates and lineshapes in these highly hydrated solid samples, compared to the dramatic activation of motion occurring at moderate hydration.

Solution and solid-state NMR measurements were used together to examine motion in three sites in the HIV-1 TAR RNA. We wished to investigate the dynamics facilitating the conformational rearrangements the TAR RNA must undergo for tat binding, and in particular to characterize the full range of motional timescales accessible to this RNA. Our results demonstrate that the dynamics in TAR involving residues essential to tat binding include not only the faster motions detected by solution relaxation measurements, but also a significant component in the μs-ns timescale. The HIV-1 transactivation response (TAR) RNA provides a classic example of adaptive protein-RNA recognition 1,2 and is of key importance for viral replication. Transcription of the HIV genome is dependent upon binding of the viral regulatory protein tat at a three-nucleotide bulge linking two short helices comprising the TAR hairpin 3 (Figure 1). The inherent flexibility of this bulge allows it to undergo a conformational transition upon binding of Tat protein or

Both solid state and solution NMR relaxation measurements are routinely used to quantify the internal dynamics of biomolecules, but in very few cases have these two techniques been applied to the same system and even fewer attempts have been made so far to describe the results obtained through these two methods through a common theoretical framework. We have previously collected both solution 13 C and solid state 2 H relaxation measurements for multiple nuclei within the furanose rings of several nucleotides of the DNA sequence recognized by HhaI methyltransferase. The data demonstrated that the furanose rings within the GCGC recognition sequence are very flexible, with the furanose rings of the cytidine which is the methylation target experiencing the most extensive motions. In order to interpret these experimental results quantitatively, we have developed a dynamic model of furanose rings based on the analysis of solid state 2 H line shapes. The motions are modeled by treating bond reorientations as Brownian excursions within a restoring potential. By applying this model, we are able to reproduce the rates of 2 H spin-lattice relaxation in the solid and 13 C spin-lattice relaxation in solution using comparable restoring force constants and internal diffusion coefficients. As expected, the 13 C relaxation rates in solution are less sensitive to motions that are slower than overall molecular tumbling than to the details of global molecular reorientation, but are somewhat more sensitive to motions in the immediate region of the Larmor frequency. Thus, we conclude that the local internal motions of this DNA oligomer in solution and in the hydrated solid state are virtually the same, and we validate an approach to the conjoint analysis of solution and solid state NMR relaxation and line shapes data, with wide applicability to many biophysical problems.

Functional RNA molecules are conformationally dynamic and sample a multitude of dynamic modes over a wide range of frequencies. Thus, a comprehensive description of RNA dynamics requires the inclusion of a broad range of motions across multiple dynamic rates which must be derived from multiple spectroscopies. Here we describe a slow conformational exchange theoretical approach to combining the description of local motions in RNA that occur in the ns-μs window and are detected by solid-state NMR with non-rigid rotational motion of the HIV-1 TAR RNA in solution as observed by solution NMR. This theoretical model unifies the experimental results generated by solution and solid-state NMR and provides a comprehensive view of the dynamics of HIV-1 TAR RNA, a well-known paradigm of an RNA where function requires extensive conformational rearrangements. This methodology provides a quantitative atomic level view of the amplitudes and rates of the local and collective displacements of the TAR RNA molecule, and provides directly motional parameters for the conformational capture hypothesis of this classical RNA-ligand interaction.

Electron spin relaxation dynamics in colloidal ZnO quantum dots containing additional delocalized conduction band electrons (n-type) have been studied using electron paramagnetic resonance (EPR) spectroscopy. Variation of the 67 Zn (I ) 5/2) nuclear isotope content within the quantum dots allows the effects of the electron-nuclear hyperfine interaction on spin-spin and spin-lattice relaxation dynamics to be explored. Long room-temperature spin-spin relaxation times of T 2 ) 87 ns are observed in ZnO quantum dots almost completely depleted of 67 Zn.

HighlightsAn adaptation of the classical Ross–Macdonald model for vector disease transmission to incorporate time-dependent medical and entomological control measures.Modeling both mass drug administration and indoor residual spraying campaigns, the synchronous deployment of both yields a synergy where the impact of a joint intervention exceeds that of isolated campaigns.Openmalaria simulations, separately run, indicate comparable intervention impacts to the Ross/Macdonald model variant.The vector reservoir of parasitemia is found to be labile, and this dictates the impacts of the medical and entomological interventions.A scaling-law level of analysis is performed that estimates the rebound of infections in a community after interventions expire, and not only do higher transmission environments bounce back to prevalent infections faster, communities with stronger interventions are shown to have a slower relapse to parasitemia.

Background Control programmes for high burden countries are tasked with charting effective multi-year strategies for malaria control within significant resource constraints. Synergies between different control tools, in which more than additive benefit accrues from interventions used together, are of interest because they may be used to obtain savings or to maximize health impact per expenditure. One commonly used intervention in sub-Saharan Africa is indoor residual spraying (IRS), typically deployed through a mass campaign. While possible synergies between IRS and long-lasting insecticide-treated nets (LLINs) have been investigated in multiple transmission settings, coordinated synergy between IRS and other mass medical distribution campaigns have not attracted much attention. Recently, a strong timing-dependent synergy between an IRS campaign and a mass drug administration (MDA) was theoretically quantified. These synergistic benefits likely differ across settings depending on transmission intensity and its overall seasonal pattern. Methods High coverage interventions are modelled in different transmission environments using two methods: a Ross–Macdonald model variant and openmalaria simulations. The impact of each intervention strategy was measured through its ability to prevent host infections over time, and the effects were compared to the baseline case of deploying interventions in isolation. Results By modelling IRS and MDA together and varying their deployment times, a strong synergy was found when the administered interventions overlapped. The added benefit of co-timed interventions was robust to differences in the models. In the Ross–Macdonald model, the impact compared was roughly double the sequential interventions in most transmission settings. Openmalaria simulations of this medical control augmentation of an IRS campaign show an even stronger response with the same timing relationship. Conclusions The strong synergies found for these control tools between the complementary interventions demonstrate a general feature of effective concurrent campaign-style vector and medical interventions. A mass treatment campaign is normally short-lived, especially in higher transmission settings. When co-timed, the rapid clearing of the host parasite reservoir via chemotherapy is protected from resurgence by the longer duration of the vector control. An effective synchronous treatment campaign has the potential to greatly augment the impact of indoor residual spraying. Mass screening and treatment (MSAT) with highly sensitive rapid diagnostic tests may demonstrate a comparable trend while mass LLIN campaigns may similarly coordinate with MDA/MSAT.