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A new way to see RNA.

ABSTRACT: Unlike proteins, the RNA backbone has numerous degrees of freedom (eight, if one counts the sugar pucker), making RNA modeling, structure building and prediction a multidimensional problem of exceptionally high complexity. And yet RNA tertiary structures are not infinite in their structural morphology; rather, they are built from a limited set of discrete units. In order to reduce the dimensionality of the RNA backbone in a physically reasonable way, a shorthand notation was created that reduced the RNA backbone torsion angles to two (? and ?, analogous to ? and ? in proteins). When these torsion angles are calculated for nucleotides in a crystallographic database and plotted against one another, one obtains a plot analogous to a Ramachandran plot (the ?/? plot), with highly populated and unpopulated regions. Nucleotides that occupy proximal positions on the plot have identical structures and are found in the same units of tertiary structure. In this review, we describe the statistical validation of the ?/? formalism and the exploration of features within the ?/? plot. We also describe the application of the ?/? formalism in RNA motif discovery, structural comparison, RNA structure building and tertiary structure prediction. More than a tool, however, the ?/? formalism has provided new insights into RNA structure itself, revealing its fundamental components and the factors underlying RNA architectural form.

SUBMITTER: Keating KS

PROVIDER: S-EPMC4410278 | biostudies-literature | 2011 Nov

REPOSITORIES: biostudies-literature

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A new way to see RNA.

Keating Kevin S KS Humphris Elisabeth L EL Pyle Anna Marie AM

Quarterly reviews of biophysics 20110518 4

Unlike proteins, the RNA backbone has numerous degrees of freedom (eight, if one counts the sugar pucker), making RNA modeling, structure building and prediction a multidimensional problem of exceptionally high complexity. And yet RNA tertiary structures are not infinite in their structural morphology; rather, they are built from a limited set of discrete units. In order to reduce the dimensionality of the RNA backbone in a physically reasonable way, a shorthand notation was created that reduced ...[more]

PMID: 21729350

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Project description:The application of two-photon absorption (2PA) materials is a classical research field and has recently attracted increasing interest. It has generated a demand for new dyes with high 2PA cross-sections. In this short review, we briefly cover the structure-2PA property relationships of organic fluorophores, organic-inorganic nanohybrids and metal complexes explored by our group. (1) The two-photon absorption cross-section (?) of organic fluorophores increases with the extent of charge transfer, which is important to optimize the core, donor-acceptor pair, and conjugation-bridge to obtain a large ? value. Among the various cores, triphenylamine appears to be an efficient core. Lengthening of the conjugation with styryl groups in the D-?-D quadrupoles and D-?-A dipoles increased ? over a long wavelength range than when vinylene groups were used. Large values of ? were observed for extended conjugation length and moderate donor-acceptors in the near-IR wavelengths. The ? value of the three-arm octupole is larger than that of the individual arm, if the core has electron accepting groups that allow significant electronic coupling between the arms; (2) Optical functional organic/inorganic hybrid materials usually show high thermal stability and excellent optical activity; therefore the design of functional organic molecules to build functional organic-inorganic hybrids and optimize the 2PA properties are significant. Advances have been made in the design of organic-inorganic nanohybrid materials of different sizes and shapes for 2PA property, which provide useful examples to illustrate the new features of the 2PA response in comparison to the more thoroughly investigated donor-acceptor based organic compounds and inorganic components; (3) Metal complexes are of particular interest for the design of new materials with large 2PA ability. They offer a wide range of metals with different ligands, which can give rise to tunable electronic and 2PA properties. The metal ions, including transition metals and lanthanides, can serve as an important part of the structure to control the intramolecular charge-transfer process that drives the 2PA process. As templates, transition metal ions can assemble simple to more sophisticated ligands in a variety of multipolar arrangements resulting in interesting and tailorable electronic and optical properties, depending on the nature of the metal center and the energetics of the metal-ligand interactions, such as intraligand charge-transfer (ILCT) and metal-ligand charge-transfer (MLCT) processes. Lanthanide complexes are attractive for a number of reasons: (i) their visible emissions are quite long-lived; (ii) their absorption and emission can be tuned with the aid of appropriate photoactive ligands; (iii) the accessible energy-transfer path between the photo-active ligands and the lanthanide ion can facilitate efficient lanthanide-based 2PA properties. Thus, the above materials with excellent 2PA properties should be applied in two-photon applications, especially two-photon fluorescence microscopy (TPFM) and related emission-based applications. Furthermore, the progress of research into the use of those new 2PA materials with moderate 2PA cross section in the near-infrared region, good Materials 2017, 10, 223 2 of 37 biocompatibility, and enhanced two-photon excited fluorescence for two-photon bio-imaging is summarized. In addition, several possible future directions in this field are also discussed (146 references).

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A new way to see RNA.

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A new way to see RNA.

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