The problem of how ions influence the folding of RNA into specific tertiary structures is being addressed from both thermodynamic (by how much do different salts affect the free energy change of folding) and structural (how are ions arranged on or near an RNA and what kinds of environments do they occupy) points of view. The challenge is to link these different approaches in a theoretical framework that relates the energetics of ion-RNA interactions to the spatial distribution of ions. This review distinguishes three different kinds of ion environments that differ in the extent of direct ion-RNA contacts and the degree to which the ion hydration is perturbed, and summarizes the current understanding of the way each environment relates to the overall energetics of RNA folding.

RNA molecules in monovalent salt solutions generally adopt a set of partially folded conformations containing only secondary structure, the intermediate or I state. Addition of Mg2+ strongly stabilizes the native tertiary structure (N state) relative to the I state. In this paper, a combination of experimental and computational approaches is used to estimate the free energy of the interaction of Mg2+ with partially folded I state RNAs and to consider the possibility that Mg2+ favors "compaction" of the I state to a set of conformations with a higher average charge density. A sequence variant with a drastically destabilized tertiary structure was used as a mimic of I state RNA; as measured by small-angle X-ray scattering, it adopted a progressively more compact conformation over a wide Mg2+ concentration range. Average free energies of the interaction of Mg2+ with the I state mimic were obtained by a fluorescence titration method. To interpret these experimental data further, we generated molecular models of the I state and used them in calculations with the nonlinear Poisson-Boltzmann equation to estimate the change in Mg2+-RNA interaction free energy as the average I state dimensions decrease from expanded to compact. The same models were also used to reproduce quantitatively the experimental difference in excess Mg2+ between N and I states. On the basis of these experiments and calculations, I state compaction appears to enhance Mg2+-I state interaction free energies by 10-20%, but this enhancement is at most 5% of the overall Mg2+-associated stabilization free energy for this rRNA fragment.

Mg 2؉ ions are very effective at stabilizing tertiary structures in RNAs. In most cases, folding of an RNA is so strongly coupled to its interactions with Mg 2؉ that it is difficult to separate free energies of Mg 2؉ -RNA interactions from the intrinsic free energy of RNA folding. To devise quantitative models accounting for this phenomenon of Mg 2؉ -induced RNA folding, it is necessary to independently determine Mg 2؉ -RNA interaction free energies for folded and unfolded RNA forms. In this work, the energetics of Mg 2؉ -RNA interactions are derived from an assay that measures the effective concentration of Mg 2؉ in the presence of RNA. These measurements are used with other measures of RNA stability to develop an overall picture of the energetics of Mg 2؉ -induced RNA folding. Two different RNAs are discussed, a pseudoknot and an rRNA fragment. Both RNAs interact strongly with Mg 2؉ when partially unfolded, but the two folded RNAs differ dramatically in their inherent stability in the absence of Mg 2؉ and in the free energy of their interactions with Mg 2؉ . From these results, it appears that any comprehensive framework for understanding Mg 2؉ -induced stabilization of RNA will have to (i) take into account the interactions of ions with the partially unfolded RNAs and (ii) identify factors responsible for the widely different strengths with which folded tertiary structures interact with Mg 2؉ .cations ͉ ion interaction coefficients ͉ Wyman linkage relations M g 2ϩ ions strongly stabilize RNA tertiary structures under conditions that only weakly affect RNA secondary structure stability, a phenomenon first studied in the folding of transfer RNA (1, 2). Although the sensitivity of RNA folding to Mg 2ϩ has been amply documented for many RNAs, it is still unknown how this sensitivity is quantitatively related to the strengths of Mg 2ϩ -RNA interactions. Thus, for most RNAs, the magnitude of the intrinsic RNA instability is unknown, nor is it known how much more favorably Mg 2ϩ interacts with the native RNA structure than with structures from which folding takes place. Lacking this fundamental overview of Mg 2ϩ -RNA interaction free energies, it has not been possible to carry out extensive evaluations of theoretical models that seek to explain Mg 2ϩ -induced RNA folding in terms of the underlying physical interactions (3, 4).In this article, we parse the tertiary folding of two different RNAs into the intrinsic free energy of folding in the absence of Mg 2ϩ and the free energies of Mg 2ϩ interactions with folded and partially folded states. To obtain the relevant free energies, we devised a practical experimental method for measuring the effect of RNA on Mg 2ϩ ion activities and derived the equations necessary for extracting Mg 2ϩ -RNA interaction free energies from the experimental data. The two RNAs have vastly different stabilities in the absence of Mg 2ϩ and correspondingly large differences in the favorable interactions of the native RNA structures with Mg 2ϩ . Clearly, different RNAs use different strategies ...

The ionic composition of a solution strongly influences the folding of an RNA into its native structure; of particular importance, the stabilities of RNA tertiary structures are sharply dependent on the concentration of Mg2+. Most measurements of the extent of Mg2+ interaction with an RNA have relied on equilibrium dialysis or indirect measurements. Here we describe an approach, based on titrations in the presence of a fluorescent indicator dye, that accurately measures the excess Mg2+ ion neutralizing the charge of an RNA (the interaction or Donnan coefficient, Γ2+) and the total free energy of Mg2+ - RNA interactions (ΔGRNA-2+). Automated data collection with computer-controlled titrators enables the collection of much larger data sets in a short time, compared to equilibrium dialysis. Γ2+ and ΔGRNA-2+ are thermodynamically rigorous quantities that are directly comparable with the results of theoretical calculations and simulations. In the event that RNA folding is coupled to the addition of MgCl2, the method directly monitors the uptake of Mg2+ associated with the folding transition.

We report a target enrichment method to map nucleosomes of large genomes at unprecedented coverage and resolution by deeply sequencing locus-specific mononucleosomal DNA enriched via hybridization with bacterial artificial chromosomes. We achieved ∼10 000-fold enrichment of specific loci, which enabled sequencing nucleosomes at up to ∼500-fold higher coverage than has been reported in a mammalian genome. We demonstrate the advantages of generating high-sequencing coverage for mapping the center of discrete nucleosomes, and we show the use of the method by mapping nucleosomes during T cell differentiation using nuclei from effector T-cells differentiated from clonal, isogenic, naïve, primary murine CD4 and CD8 T lymphocytes. The analysis reveals that discrete nucleosomes exhibit cell type-specific occupancy and positioning depending on differentiation status and transcription. This method is widely applicable to mapping many features of chromatin and discerning its landscape in large genomes at unprecedented resolution.

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We study the hemolytic activity of a hemolysin protein (HpmA) secreted by the gram negative bacterium Proteus mirabilis. HpmA is the A component of a type Vb, or two‐partner, secretion pathway (TPS pathway). To cross the outer membrane, unfolded periplasmic HpmA is recognized, exported, and folded by its membrane bound cognate B component. Once secreted, HpmA displays cytotoxic activity against mammalian cells, including red blood cells. HpmA is comprised of 1577 amino acids and contains at least two functional domains – a TPS domain that targets the protein to the correct B component and a hemolytic domain. Less than 20% of the HpmA structure is known, and none of the hemolytic domain structure is known. To address this problem, we used quantitative hemolytic activity assays to determine the contributions to protein function made by different segments of the hemolytic domain. Our data show a reduction but not elimination of function as the protein is progressively truncated. We have developed two models that could explain these results – an Assembly model and an Association model that differ in the stoichiometry of HpmA needed to lyse a red blood cell. The applicability of these models to different HpmA truncations and the implications for HpmA biological structure and function are discussed.

The linear DNA in a human cell is compacted over a million fold, so much that, when compacted, 60,000 feet of DNA can fit on the tip of a needle. The first stage of compaction, nucleosome formation, is already known to impact gene regulation. The further compaction of nucleosomes into a chromatin fiber has also been shown to limit accessibility of DNA to DNA binding proteins. Despite the nucleosome crystal structure and decades of biochemical assays, the structure of this fiber is still a matter of debate. There are two competing structures proposed for the chromatin fiber: a two start and a one start model. A major difference between these models is the path of the linker DNA. Computational studies of chromatin structure suggest that details such as the length of linker DNA between nucleosomes can cause changes in the type of structure adopted by the fiber. Experiments using different linker lengths and different solution conditions support this claim and provide evidence in support of each model of the chromatin fiber. No study, however, has unambiguously accounted for the in vivo variability of linker lengths found in natural chromatin. We are developing a protocol that will allow us to assay the structure of chromatin in vivo using yeast DNA to account for the true variability of in vivo nucleosome spacing. We have shown our assay is sensitive to the structure of chromatin and are assaying how that structure differs at different genomic locations. We anticipate that the overall structure of the fiber at each genomic location is important for regulation. Our future aim is to explicitly test this prediction by first using our models to correlate changes in the fiber structure to differences in transcriptional regulation.