Counterion Distribution around DNA Probed by Solution X-Ray Scattering

Das, Rhiju; Mills, Thalia T.; Kwok, Lisa W.; Maskel, Gregory S.; Millett, Ian S.; Doniach, Sebastian; Finkelstein, K. D.; Herschlag, Daniel; Pollack, Lois

doi:10.1103/physrevlett.90.188103

Cited by 204 publications

(229 citation statements)

References 36 publications

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“…Thus, the recent ability to decipher the shape of this atmosphere by anomalous small angle x-ray scattering provided an unusually direct experimental window into properties of the atmosphere [56,57]. Further, the contents of the atmosphere have recently been quantitatively dissected, by essentially counting the ions associated with a nucleic acid under a variety of ionic conditions.…”

Section: Simple Forces Underlying the Complex Behavior Of Rnamentioning

confidence: 99%

Unwinding RNA's secrets: advances in the biology, physics, and modeling of complex RNAs

Chu

Herschlag

2008

Current Opinion in Structural Biology

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SummaryThe rapid development of our understanding of the diverse biological roles fulfilled by non-coding RNA has motivated interest in the basic macromolecular behavior, structure, and function of RNA. We focus on two areas in the behavior of complex RNAs. First, we present advances in the understanding of how RNA folding is accomplished in vivo by presenting a mechanism for the action of DEAD-box proteins. Members of this family are intimately associated with almost all cellular processes involving RNA, mediating RNA structural rearrangements and chaperoning their folding. Next, we focus on advances in understanding and characterizing the basic biophysical forces that govern the folding of complex RNAs. Ultimately we expect that a confluence and synergy between these approaches will lead to profound understanding of RNA and its biology.The explosion in our knowledge about noncoding RNA (ncRNA) -RNA that is not translated into protein -has expanded interest in RNA beyond the traditional RNA community. Diverse ncRNAs include the recently-discovered riboswitches, whose novel gene-regulation function is induced by the binding of small metabolites [1]; most of the so-called "Human Accelerated Regions" (HAR) of the human genome, whose recent evolution may be linked to the emergence of the human brain [2]; and many ncRNAs of unknown function [3]. These discoveries underscore the need to understand the fundamental macromolecular behavior of RNA, its structure and dynamics, and how these RNAs are handled and exploited in biology.Study of catalytic RNAs, which allow detection of correct folding via activity measurements, has established basic thermodynamic and kinetic properties of RNA folding. Large catalytic RNAs such as the group I intron from Tetrahymena thermophila and the RNase P RNA from Bacillus subtilis fold at vastly different rates under different conditions upon addition of Mg 2+ and have been shown to fold via multiple parallel pathways, in which different molecules follow different routes with different rates and intermediates, to a common final folded structure [4,5]. These observations support the common view that RNAs traverse rugged energy landscapes as they fold [6,7]. However, little is known about the true shape of these

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Section: Simple Forces Underlying the Complex Behavior Of Rnamentioning

confidence: 99%

Unwinding RNA's secrets: advances in the biology, physics, and modeling of complex RNAs

Chu

Herschlag

2008

Current Opinion in Structural Biology

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“…DNA. 30,31 Popular theoretical models include counterion condensation 32,33 or Poisson-Boltzmann (PB) theories, 34,35 although PB results for duplex DNA are in poor agreement with results from dialysis-type experiments. 26 MD simulation can also provide atomic details and in principle can describe the ionic atmosphere with great accuracy.…”

Section: B Comparison To Other Methodsmentioning

confidence: 99%

Accurate small and wide angle x-ray scattering profiles from atomic models of proteins and nucleic acids

Nguyên

Pabit

Meisburger

et al. 2014

The Journal of Chemical Physics

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A new method is introduced to compute X-ray solution scattering profiles from atomic models of macromolecules. The three-dimensional version of the Reference Interaction Site Model (RISM) from liquid-state statistical mechanics is employed to compute the solvent distribution around the solute, including both water and ions. X-ray scattering profiles are computed from this distribution together with the solute geometry. We describe an efficient procedure for performing this calculation employing a Lebedev grid for the angular averaging. The intensity profiles (which involve no adjustable parameters) match experiment and molecular dynamics simulations up to wide angle for two proteins (lysozyme and myoglobin) in water, as well as the small-angle profiles for a dozen biomolecules taken from the BioIsis.net database. The RISM model is especially well-suited for studies of nucleic acids in salt solution. Use of fiber-diffraction models for the structure of duplex DNA in solution yields close agreement with the observed scattering profiles in both the small and wide angle scattering (SAXS and WAXS) regimes. In addition, computed profiles of anomalous SAXS signals (for Rb + and Sr 2+ ) emphasize the ionic contribution to scattering and are in reasonable agreement with experiment. In cases where an absolute calibration of the experimental data at q = 0 is available, one can extract a count of the excess number of waters and ions; computed values depend on the closure that is assumed in the solution of the Ornstein-Zernike equations, with results from the Kovalenko-Hirata closure being closest to experiment for the cases studied here. © 2014 AIP Publishing LLC. [http://dx

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“…This assumption is unlikely to hold for RNA because its polyelectrolyte nature results in a different constellation of associated ions at each Mg 2+ concentration and, in particular, for the unfolded state, a different ensemble of unfolded conformers. [23][24][25][26] This extrapolation gives an estimate for P4-P6 folding cooperativity of 4.6 ± 0.5 kcal/mol instead of the value of 3.2 ± 0.2 kcal/mol obtained herein (see Supporting Information). Indeed, some extrapolations of energetic effects from mutations have given calculated ΔΔG effects for single-point mutants of >10 kcal/mol (e.g., refs 21,23 ), values that likely greatly overestimate the actual energetic differences.…”

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confidence: 99%

Direct Measurement of Tertiary Contact Cooperativity in RNA Folding

et al. 2008

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Cooperativity is a central feature of the structure and function of biological macromolecules. It is observed in the folding of proteins to their functional states, in the sharp response of hemoglobin and other proteins to changes in ligand concentration, and in the assembly of macromolecular complexes.Cooperativity in domain formation during protein folding has evolved as a mechanism by which Nature overcomes the difficulty in selectively stabilizing a uniquely folded and functional structure (or small family of structures), among the vast number of partially folded and nonfunctional states that would likely dominate if each of the weak long-range domain contacts were to form independently. This thermodynamic scenario is well-documented for single domain proteins (e.g., refs 1-3 ) and is typically measured using double mutant cycles, analogous to the mutant cycle shown in Figure 1c.Despite its fundamental importance, cooperativity is not always employed in all aspects of protein folding. Regions of proteins often form and break up as units, and these units are sometimes referred to as domains. Further, the cooperativity between domains can vary, from high, for a protein with extensive interfaces and reinforcing interactions, 4 to nonexistent, for a protein like titin with individual domains that are noninteracting "beads on a string". 5 RNA, like proteins, must often fold to distinct three-dimensional structures to carry out biological functions. However, RNA forms stable secondary structure in the absence of tertiary structure, indicating some limits to cooperativity in RNA tertiary folding. Indeed, one might consider folding of an RNA from a preformed secondary structure to a functional tertiary structure as akin to folding of a multidomain protein. The fundamental question then arises: To what extent is there cooperativity in RNA folding?We determined the tertiary contact cooperativity for the independently folding P4-P6 domain derived from the T. thermophila group I intron 6 (Figure 1a,b) using a single molecule fluorescence energy transfer (smFRET) folding assay. The P4-P6 crystal structure in 1996 revealed, for the first time, the side-by-side packing of RNA helices. 7 These helices are connected by a junction (J5/5a) and joined by two regions of tertiary contact, the metal core/ metal core receptor (MC/MCR, Figure 1a, Figure 1a,b, magenta). [6][7][8][9][10] We refer to these regions as "tertiary contacts", and we quantitatively investigate the energetic crosstalk between these tertiary contacts.A thermodynamic scheme for determining the tertiary contact cooperativity in P4-P6 is shown in Figure 1c. The unfolded ensemble (U) comprises the large number of conformations with secondary structure but no tertiary contacts. The unfolded ensemble is in equilibrium with the fully folded state , which has both tertiary contacts formed, and this equilibrium is described by K fold . The two intermediate species, I TL and I MC , have only one tertiary contact formed. In I TL , the tetraloop/receptor contact is formed...

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Counterion Distribution around DNA Probed by Solution X-Ray Scattering

Cited by 204 publications

References 36 publications

Unwinding RNA's secrets: advances in the biology, physics, and modeling of complex RNAs

Unwinding RNA's secrets: advances in the biology, physics, and modeling of complex RNAs

Accurate small and wide angle x-ray scattering profiles from atomic models of proteins and nucleic acids

Direct Measurement of Tertiary Contact Cooperativity in RNA Folding

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