Single-stranded nucleic acids (ssNAs) are ubiquitous in many key cellular functions. Their flexibility limits both the number of high-resolution structures available, leaving only a small number of protein–ssNA crystal structures, while forcing solution investigations to report ensemble averages. A description of the conformational distributions of ssNAs is essential to more fully characterize biologically relevant interactions. We combine small angle X-ray scattering (SAXS) with ensemble-optimization methods (EOM) to dynamically build and refine sets of ssNA structures. By constructing candidate chains in representative dinucleotide steps and refining the models against SAXS data, a broad array of structures can be obtained to match varying solution conditions and strand sequences. In addition to the distribution of large scale structural parameters, this approach reveals, for the first time, intricate details of the phosphate backbone and underlying strand conformations. Such information on unperturbed strands will critically inform a detailed understanding of an array of problems including protein–ssNA binding, RNA folding and the polymer nature of NAs. In addition, this scheme, which couples EOM selection with an iteratively refining pool to give confidence in the underlying structures, is likely extendable to the study of other flexible systems.

Single-stranded DNA (ssDNA) is notable for its interactions with ssDNA binding proteins (SSBs) during fundamentally important biological processes including DNA repair and replication. Previous work has begun to characterize the conformational and electrostatic properties of ssDNA in association with SSBs. However, the conformational distributions of free ssDNA have been difficult to determine. To capture the vast array of ssDNA conformations in solution, we pair small angle X-ray scattering with novel ensemble fitting methods, obtaining key parameters such as the size, shape and stacking character of strands with different sequences. Complementary ion counting measurements using inductively coupled plasma atomic emission spectroscopy are employed to determine the composition of the ion atmosphere at physiological ionic strength. Applying this combined approach to poly dA and poly dT, we find that the global properties of these sequences are very similar, despite having vastly different propensities for single-stranded helical stacking. These results suggest that a relatively simple mechanism for the binding of ssDNA to non-specific SSBs may be at play, which explains the disparity in binding affinities observed for these systems.

Disordered homopolymeric regions of single-stranded RNA, such as U or A tracts, are found within functional RNAs where they play distinct roles in defining molecular structure and facilitating recognition by partners. Despite this prominence, details of conformational and biophysical properties of these regions have not yet been resolved. We apply a number of experimental techniques to investigate the conformations of these biologically important motifs, and provide quantitative measurements of their ion atmospheres. Single strands of RNA display pronounced sequence dependent conformations that relate to the unique ion atmospheres each attracts. Chains of rU bases are relatively unstructured under all conditions, while chains of rA bases display distinct ordering, through stacking or clustering motifs, depending on the composition of the surrounding solution. These dramatic structural differences are consistent with the measured disparity in ion composition and atmospheres around each homopolymer, revealing a complex interplay of base, ion and single-strand ordering. The unique structural and ionic signatures of homopolymer ssRNAs explains their role(s) in folding structured RNAs, and may explain their distinct recognition by protein partners.

Remarkable new insight has emerged into the biological role of RNA in cells. RNA folding and dynamics enable many of these newly discovered functions, calling for an understanding of RNA self-assembly and conformational dynamics. Because RNAs pass through multiple structures as they fold, an ensemble perspective is required to visualize the flow through fleetingly populated sets of states. Here, we combine microfluidic mixing technology and small angle X-ray scattering (SAXS) to measure the Mg-induced folding of a small RNA domain, the tP5abc three helix junction. Our measurements are interpreted using ensemble optimization to select atomically detailed structures that recapitulate each experimental curve. Structural ensembles, derived at key stages in both time-resolved studies and equilibrium titrations, reproduce the features of known intermediates, and more importantly, offer a powerful new structural perspective on the time-progression of folding. Distinct collapse phases along the pathway appear to be orchestrated by specific interactions with Mg ions. These key interactions subsequently direct motions of the backbone that position the partners of tertiary contacts for later bonding, and demonstrate a remarkable synergy between Mg and RNA across numerous time-scales.

. (2016), Physical mechanisms responsible for the water-induced degradation of PC61BM P3HT photovoltaic thin films. J. Polym. Sci. B Polym. Phys., 54: 141-146, which has been published in final form at http://dx.doi.org/10.1002/polb.23902. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving (http://olabout.wiley.com/WileyCDA/Section/id-820227.html) eprints@whiterose.ac.uk https://eprints.whiterose.ac.uk/ Reuse Unless indicated otherwise, fulltext items are protected by copyright with all rights reserved. The copyright exception in section 29 of the Copyright, Designs and Patents Act 1988 allows the making of a single copy solely for the purpose of non-commercial research or private study within the limits of fair dealing. The publisher or other rights-holder may allow further reproduction and re-use of this version -refer to the White Rose Research Online record for this item. Where records identify the publisher as the copyright holder, users can verify any specific terms of use on the publisher's website. TakedownIf you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing eprints@whiterose.ac.uk including the URL of the record and the reason for the withdrawal request. This communication examines the effect of heating and cooling on the integrity of a well studied polymer solar cell blend system, that of P3HT:PC 61 BM. Our device architecture also used the hole transport layer PEDOT:PSS below the solar cell layer. We have examined this system when exposed to heating and cooling cycles of the kind that may be experienced during working operation out in the real world. In particular we examined the impact on the surface of this thin polymer film system. Our findings show that under humid conditions the swollen PEDT:PSS layer makes it possible for water droplets to condense on the blend film surface, evaporation of the water leaves behind microscale surface deformations. We also ABSTRACTWe show that [6,6]-phenyl-C61-butyric acid methyl ester (PC 61 BM) at the surface of thin film blends of poly(3-hexylthiophene) (P3HT):PC 61 BM can be patterned by water. Using a series of heating and cooling steps water droplets condense onto the blend film surface. This is possible due to the liquid like, water swollen layer of PEDOT:PSS. Breath pattern water deformation and subsequent drying on the film surface results in isolated PC 61 BM structures, showing that migration of PC 61 BM takes place. This was confirmed by selective wavelength illumination to spatially map the photoluminescence from the P3HT and PC 61 BM. Within a device redistribution of the surface PC 61 BM into aggregates would be catastrophic, as it would dramatically alter device performance. We also postulate that repeated volume change of the PEDOT:PSS layer by water swelling may be in part responsible for the delamination failure mechanism in thin film solar cells devices.2

Small-molecule aptamers are composed of RNA or DNA sequences with intricate secondary and tertiary structure allowing them to perform many functions, including ligand binding and catalytic events.

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bound form of the dye is enhanced 1100-fold. The crystal structure of the RNA-dye complex revealed a three-tiered G-quadruplex RNA structure, with the dye binding to one face of the G-quadruplex. Moreover, the folding of the aptamer is strongly coupled to the binding of the dye, thus making the dye fluorescence a direct reporter of the folding state of the G-quadruplex RNA. Previous studies by our lab of a DNA G-quadruplex, revealed that it changes conformation and eventually unfolds under high pressure. We find that pressure modifies the folding of RNA Mango-dye complex as well, and appears to significantly slow the folding reaction. In addition, it is known that potassium ions play a crucial role in stabilizing G-quadruplexes. High pressure fluorescence experiments on RNA Mango at different salt concentrations will be presented as well. These results help to better understand the folding mechanism of RNA G-quadruplexes.