High-throughput dissection of the thermodynamic and conformational properties of a ubiquitous class of RNA tertiary contact motifs

Despite RNA’s diverse secondary and tertiary structures and its complex conformational changes, nature utilizes a limited set of structural “motifs”—helices, junctions, and tertiary contact modules—to build diverse functional RNAs. Thus, in-depth descriptions of a relatively small universe of RNA motifs may lead to predictive models of RNA tertiary conformational landscapes. Motifs may have different properties depending on sequence and secondary structure, giving rise to subclasses that expand the universe of RNA building blocks. Yet we know very little about motif subclasses, given the challenges in mapping conformational properties in high throughput. Previously, we used “RNA on a massively parallel array” (RNA-MaP), a quantitative, high-throughput technique, to study thousands of helices and two-way junctions. Here, we adapt RNA-MaP to study the thermodynamic and conformational properties of tetraloop/tetraloop receptor (TL/TLR) tertiary contact motifs, analyzing 1,493 TLR sequences from different classes. Clustering analyses revealed variability in TL specificity, stability, and conformational behavior. Nevertheless, natural GAAA/11ntR TL/TLRs, while varying in tertiary stability by ∼2.5 kcal/mol, exhibited conserved TL specificity and conformational properties. Thus, RNAs may tune stability without altering the overall structure of these TL/TLRs. Furthermore, their stability correlated with natural frequency, suggesting thermodynamics as the dominant selection pressure. In contrast, other TL/TLRs displayed heterogenous conformational behavior and appear to not be under strong thermodynamic selection. Our results build toward a generalizable model of RNA-folding thermodynamics based on the properties of isolated motifs, and our characterized TL/TLR library can be used to engineer RNAs with predictable thermodynamic and conformational behavior.

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Conserved RNA motifs of EMCV IRES as potential building blocks to design RNA nanostructures

Chemical Communications ◽

10.1039/c2cc36034a ◽

2012 ◽

Vol 48 (94) ◽

pp. 11573 ◽

Cited By ~ 1

Author(s):

Kwong Kit Chan ◽

Vasudevan Ramesh

Keyword(s):

Building Blocks ◽

Rna Motifs

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Harnessing intrinsic fluorescence for typing of secondary structures of DNA

10.1101/2020.01.15.907501 ◽

2020 ◽

Cited By ~ 1

Author(s):

Michela Zuffo ◽

Aurélie Gandolfini ◽

Brahim Heddi ◽

Anton Granzhan

Keyword(s):

High Throughput ◽

Conformational Changes ◽

Emission Spectra ◽

Principal Component ◽

Secondary Structures ◽

Intrinsic Fluorescence ◽

Label Free ◽

Linear Discriminant ◽

Effective Manner

ABSTRACTDNA is polymorphic since, despite its ubiquitous presence as a double-stranded helix, it is able to fold into a plethora of other secondary structures both in vitro and in cells. Despite the considerable advances that have been made in understanding this structural diversity, its high-throughput investigation still faces severe limitations. This mainly stems from the lack of suitable label-free methods, combining a fast and cheap experimental workflow with high information content. Here, we explore the use of intrinsic fluorescence emitted by nucleic acids for this scope. After a preliminary assessment of the suitability of this phenomenon for tracking the conformational changes of DNA, we examined the intrinsic steady-state emission spectra of an 89-membered set of synthetic oligonucleotides with reported conformation (G-quadruplexes, i-motifs, single- and double stranded DNA) by means of multivariate analysis. Specifically, principal component analysis of emission spectra resulted in successful clustering of oligonucleotides into three corresponding conformational groups, albeit without discrimination between single- and double-stranded structures. Linear discriminant analysis of the same training set was exploited for the assessment of new sequences, allowing the evaluation of their G4-forming propensity. Our method does not require any labelling agent or dye, avoiding the related intrinsic bias, and can be utilized to screen novel sequences of interest in a high-throughput and cost-effective manner. In addition, we observed that left-handed (Z-) G4 structures were systematically more fluorescent than most other G4 structures, almost reaching the quantum yield of 5′-d[(G3T)3G3]-3′ (G3T), the most fluorescent G4 structure reported to date. This property is likely to arise from the similar base-stacking geometry in both types of structures.

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Origin and evolution of the large-scale structure of the universe

Canadian Journal of Physics ◽

10.1139/p90-117 ◽

1990 ◽

Vol 68 (9) ◽

pp. 799-807

Author(s):

Joseph Silk

Keyword(s):

Large Scale ◽

Background Radiation ◽

Building Blocks ◽

Large Scale Structure ◽

Big Bang ◽

Scale Structure ◽

Observational Cosmology ◽

Spontaneous Breaking ◽

Fluctuation Spectrum ◽

The Universe

Ever since the epoch of the spontaneous breaking of grand unification symmetry between the nuclear and electromagnetic interactions, the universe has expanded under the imprint of a spectrum of density fluctuations that is generally considered to have originated in this phase transition. I will discuss various possibilities for the form of the primordial fluctuation spectrum, spanning the range of adiabatic fluctuations, isocurvature fluctuations, and cosmic strings. Growth of the seed fluctuations by gravitational instability generates the formation of large-scale structures, from the scale of galaxies to that of clusters and superclusters of galaxies. There are three areas of confrontation with observational cosmology that will be reviewed. The large-scale distribution of the galaxies, including the apparent voids, sheets and filaments, and the coherent peculiar velocity field on scales of several tens of megaparsecs, probe the primordial fluctuation spectrum on scales that are only mildly nonlinear. Even larger scales are probed by study of the anisotropy of the cosmic microwave background radiation, which provides a direct glimpse of the primordial fluctuations that existed about 106 years or so after the initial big bang singularity. Galaxy formation is the process by which the building blocks of the universe have formed, involving a complex interaction between hydrodynamical and dynamical processes in a collapsing gas cloud. Both by detection of forming galaxies in the most remote regions of the universe and by study of the fundamental morphological characteristics of galaxies, which provide a fossilized memory of their past, can one relate the origin of galaxies to the same primordial fluctuation spectrum that gave rise' to the large-scale structure of the universe.

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Chiral 1,5-disubstituted 1,2,3-triazoles – versatile tools for foldamers and peptidomimetic applications

Organic & Biomolecular Chemistry ◽

10.1039/d0ob00168f ◽

2020 ◽

Vol 18 (10) ◽

pp. 1957-1967

Author(s):

Anna Said Stålsmeden ◽

Andrew J. Paterson ◽

Imola Cs. Szigyártó ◽

Linda Thunberg ◽

Johan R. Johansson ◽

...

Keyword(s):

Quantum Chemistry ◽

Building Blocks ◽

Conformational Properties

Eight chiral triazoles, for use as peptidomimetic building blocks, were prepared using the ruthenium-catalyzed click (RuAAC) reaction and their conformational properties evaluated by quantum chemistry.

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Microsecond and millisecond dynamics in the photosynthetic protein LHCSR1 observed by single-molecule correlation spectroscopy

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1821207116 ◽

2019 ◽

Vol 116 (23) ◽

pp. 11247-11252 ◽

Cited By ~ 10

Author(s):

Toru Kondo ◽

Jesse B. Gordon ◽

Alberta Pinnola ◽

Luca Dall’Osto ◽

Roberto Bassi ◽

...

Keyword(s):

Correlation Function ◽

Single Molecule ◽

Conformational Changes ◽

Protein Function ◽

Light Harvesting ◽

Building Blocks ◽

Complex Stress ◽

Correlation Spectroscopy ◽

Light Harvesting Complex ◽

Single Molecule Level

Biological systems are subjected to continuous environmental fluctuations, and therefore, flexibility in the structure and function of their protein building blocks is essential for survival. Protein dynamics are often local conformational changes, which allows multiple dynamical processes to occur simultaneously and rapidly in individual proteins. Experiments often average over these dynamics and their multiplicity, preventing identification of the molecular origin and impact on biological function. Green plants survive under high light by quenching excess energy, and Light-Harvesting Complex Stress Related 1 (LHCSR1) is the protein responsible for quenching in moss. Here, we expand an analysis of the correlation function of the fluorescence lifetime by improving the estimation of the lifetime states and by developing a multicomponent model correlation function, and we apply this analysis at the single-molecule level. Through these advances, we resolve previously hidden rapid dynamics, including multiple parallel processes. By applying this technique to LHCSR1, we identify and quantitate parallel dynamics on hundreds of microseconds and tens of milliseconds timescales, likely at two quenching sites within the protein. These sites are individually controlled in response to fluctuations in sunlight, which provides robust regulation of the light-harvesting machinery. Considering our results in combination with previous structural, spectroscopic, and computational data, we propose specific pigments that serve as the quenching sites. These findings, therefore, provide a mechanistic basis for quenching, illustrating the ability of this method to uncover protein function.

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Towards Building Blocks for Supramolecular Architectures Based on Azacryptates

Molecules ◽

10.3390/molecules25071733 ◽

2020 ◽

Vol 25 (7) ◽

pp. 1733 ◽

Cited By ~ 1

Author(s):

Ana Miljkovic ◽

Sonia La Cognata ◽

Greta Bergamaschi ◽

Mauro Freccero ◽

Antonio Poggi ◽

...

Keyword(s):

Conformational Changes ◽

Self Assembly ◽

Hydrophobic Interactions ◽

Building Blocks ◽

Water Mixture ◽

Molecular Systems ◽

Supramolecular Architectures ◽

Starting Point ◽

The Difference ◽

Supramolecular Devices

In this work, we report the synthesis of a new bis(tris(2-aminoethyl)amine) azacryptand L with triphenyl spacers. The binding properties of its dicopper complex for aromatic dicarboxylate anions (as TBA salts) were investigated, with the aim to obtain potential building blocks for supramolecular structures like rotaxanes and pseudo-rotaxanes. As expected, UV-Vis and emission studies of [Cu2L]4+ in water/acetonitrile mixture (pH = 7) showed a high affinity for biphenyl-4,4′-dicarboxylate (dfc2−), with a binding constant of 5.46 log units, due to the best match of the anion bite with the Cu(II)-Cu(II) distance in the cage’s cavity. Compared to other similar bistren cages, the difference of the affinity of [Cu2L]4+ for the tested anions was not so pronounced: conformational changes of L seem to promote a good interaction with both long (e.g., dfc2−) and short anions (e.g., terephthalate). The good affinity of [Cu2L]4+ for these dicarboxylates, together with hydrophobic interactions within the cage’s cavity, may promote the self-assembly of a stable 1:1 complex in water mixture. These results represent a good starting point for the application of these molecular systems as building units for the design of new supramolecular architectures based on non-covalent interactions, which could be of interest in all fields related to supramolecular devices.

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Actinide Complexation with Biomimetic Phosphorylated Molecules

MRS Proceedings ◽

10.1557/opl.2012.951 ◽

2012 ◽

Vol 1444 ◽

Cited By ~ 4

Author(s):

Samir Safi ◽

Marie Christine Charbonnel ◽

Gaelle Creff ◽

Aurélie Jeanson ◽

Sarah Mostapha ◽

...

Keyword(s):

Biological Systems ◽

Building Blocks ◽

Chemical Toxicity ◽

Tertiary Structures ◽

Post Translational Modifications ◽

Coordination Site ◽

Conformational Effects ◽

Phosphorylated Peptides ◽

Cation Coordination ◽

Biological Complexes

ABSTRACTMost data available on the interaction of actinides with biological systems are based on physiological or biokinetic measurements, with scarce information on the structure of the actinide coordination site. This proceeding article describes an approach for structural elucidation of actinide biological complexes. Indeed most of c.a. actinide circulation pathways are unknown, as they accumulate mostly in bones, kidney and liver. In case of accidental release of radionuclide in the environment, internal contamination under either acute or chronic conditions has the potential to induce both radiological and chemical toxicity through significant interaction with the metabolome or proteome followed by possible functional modifications. For instance, the metalloproteins present primary, secondary and tertiary structures, and also different post-translational modifications, all playing a crucial role in interacting with their partners, which can be altered by actinide bonding. When tightly bound, metal ions are critical to the function, structure, and stability of the proteins, by disabling specific interactions through significant local or global conformational modifications. In order to overcome the intricacy of actinide chemistry combined with that of metalloproteins, a simplified study toward better understanding the interaction of actinides and biological systems using simple biomolecules such as amino acids has therefore been considered. Focus is made on the cation coordination site itself, given that conformational effects are not taken into account in this approach. In a first step, we have selected simple phosphorylated building blocks that may be considered as chemical representatives of some ubiquitous target metalloproteins or some important phosphorylated peptides or proteins.

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Big Bang Nucleosynthesis in Visible and Hidden-Mirror Sectors

Advances in High Energy Physics ◽

10.1155/2014/702343 ◽

2014 ◽

Vol 2014 ◽

pp. 1-7

Author(s):

Paolo Ciarcelluti

Keyword(s):

Dark Matter ◽

Building Blocks ◽

Big Bang ◽

Dark Matter Candidate ◽

Big Bang Nucleosynthesis ◽

Enhanced Production ◽

The Standard Model ◽

The Big Bang ◽

The Universe ◽

Mirror Matter

One of the still viable candidates for the dark matter is the so-called mirror matter. Its cosmological and astrophysical implications were widely studied, pointing out the importance to go further with research. In particular, the Big Bang nucleosynthesis provides a strong test for every dark matter candidate, since it is well studied and involves relatively few free parameters. The necessity of accurate studies of primordial nucleosynthesis with mirror matter has then emerged. I present here the results of accurate numerical simulations of the primordial production of both ordinary nuclides and nuclides made of mirror baryons, in presence of a hidden mirror sector with unbroken parity symmetry and with gravitational interactions only. These elements are the building blocks of all the structures forming in the Universe; therefore, their chemical composition is a key ingredient for astrophysics with mirror dark matter. The production of ordinary nuclides shows differences from the standard model for a ratio of the temperatures between mirror and ordinary sectorsx=T′/T≳0.3, and they present an interesting decrease of the abundance ofLi7. For the mirror nuclides, instead, one observes an enhanced production ofHe4, which becomes the dominant element forx≲0.5, and much larger abundances of heavier elements.

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