Tuneable DNA-based asymmetric catalysis using a G-quadruplex supramolecular assembly

2010 ◽  
Vol 46 (24) ◽  
pp. 4309 ◽  
Author(s):  
Stephen Roe ◽  
Dougal J. Ritson ◽  
Tom Garner ◽  
Mark Searle ◽  
John E. Moses
Keyword(s):  
Asymmetric Catalysis ◽  
Supramolecular Assembly ◽  
G Quadruplex

Targeting of parallel c-myc G-quadruplex by dimeric cyanine dye supramolecular assembly: dependence on the linker length

The Analyst ◽  
2015 ◽  
Vol 140 (5) ◽  
pp. 1637-1646 ◽  
Author(s):  
Lijia Yu ◽  
Qianfan Yang ◽  
Junfeng Xiang ◽  
Hongxia Sun ◽  
Lixia Wang ◽  
...  
Keyword(s):  
Supramolecular Assembly ◽  
Cyanine Dyes ◽  
Cyanine Dye ◽  
Linker Length ◽  
G Quadruplex

The recognizing ability of parallel c-myc G-quadruplex by dimeric cyanine dyes depends on their linker length.

scholarly journals Disassembly of Dimeric Cyanine Dye Supramolecular Assembly by Tetramolecular G-quadruplex Dependence on Linker Length and Layers of G-quartet

Molecules ◽  
2019 ◽  
Vol 24 (10) ◽  
pp. 2015 ◽  
Author(s):  
Lijia Yu ◽  
Yansong Zhang ◽  
Chunguang Ding ◽  
Xiaodong Shi
Keyword(s):  
Supramolecular Assembly ◽  
Cyanine Dyes ◽  
Binding Mode ◽  
Cyanine Dye ◽  
Linker Length ◽  
Disassembly Process ◽  
1H Nmr Titration ◽  
Repeat Units ◽  
G Quadruplex ◽  
Photochemical Properties

Cyanine dyes have been widely applied in various biological systems owing to their specific photochemical properties. Assembly and disassembly process of cyanine dyes were constructed and regulated by special biomolecules. In this paper, dimeric cyanine dyes with different repeat units (oligo-oxyethylene) in linker (TC-Pn) (n = 3–6) were found to form H-aggregates or mixture aggregates in PBS. These aggregates could be disassembled into dimer and/or monomer by (TGnT) tetramolecular G-quadruplexes (n = 3–6, 8), which were affected by the linker length of dimeric cyanine dyes and layers of G-quartets. The 1H-NMR titration results suggest that the binding mode of dimeric cyanine dye with TGnT might be on both ends—stacking like a clip. This binding mode could clearly explain that matching structures between dimeric cyanine dyes and TGnT quadruplexes could regulate the disassembly properties of aggregates. These results could provide clues for the development of highly specific G-quadruplex probes.

A regular thymine tetrad and a peculiar supramolecular assembly in the first crystal structure of an all-LNA G-quadruplex

2014 ◽  
Vol 70 (2) ◽  
pp. 362-370 ◽  
Author(s):  
Irene Russo Krauss ◽  
Gary Nigel Parkinson ◽  
Antonello Merlino ◽  
Carlo Andrea Mattia ◽  
Antonio Randazzo ◽  
...  
Keyword(s):  
Self Assembly ◽  
Supramolecular Assembly ◽  
Building Blocks ◽  
Crystallographic Analysis ◽  
Order Structure ◽  
Promising Tool ◽  
G Quadruplex ◽  
Nuclease Resistance ◽  
Diagnostic Applications ◽  
Structural Descriptions

Locked nucleic acids (LNAs) are formed by bicyclic ribonucleotides where the O2′ and C4′ atoms are linked through a methylene bridge and the sugar is blocked in a 3′-endoconformation. They represent a promising tool for therapeutic and diagnostic applications and are characterized by higher thermal stability and nuclease resistance with respect to their natural counterparts. However, structural descriptions of LNA-containing quadruplexes are rather limited, since few NMR models have been reported in the literature. Here, the first crystallographically derived model of an all-LNA-substituted quadruplex-forming sequence 5′-TGGGT-3′ is presented refined at 1.7 Å resolution. This high-resolution crystallographic analysis reveals a regular parallel G-quadruplex arrangement terminating in a well defined thymine tetrad at the 3′-end. The detailed picture of the hydration pattern reveals LNA-specific features in the solvent distribution. Interestingly, two closely packed quadruplexes are present in the asymmetric unit. They face one another with their 3′-ends giving rise to a compact higher-order structure. This new assembly suggests a possible way in which sequential quadruplexes can be disposed in the crowded cell environment. Furthermore, as the formation of ordered structures by molecular self-assembly is an effective strategy to obtain nanostructures, this study could open the way to the design of a new class of LNA-based building blocks for nanotechnology.

The 3-Dimensional Molecular Structure of the Actin Filament Revisited

1985 ◽  
Vol 43 ◽  
pp. 480-481
Author(s):  
U. Aebi ◽  
R. Millonig ◽  
H. Salvo
Keyword(s):  
Actin Filament ◽  
Supramolecular Assembly ◽  
Specimen Preparation ◽  
X Ray Diffraction ◽  
Single Filament ◽  
X Ray ◽  
3 Dimensional ◽  
Filament Diameter ◽  
Preparation Conditions ◽  
Apparent Diameter

To date, most 3-D reconstructions of undecorated actin filaments have been obtained from actin filament paracrystal data (for refs, see 1,2). However, due to the fact that (a) the paracrystals may be several filament layers thick, and (b) adjacent filaments may sustantially interdigitate, these reconstructions may be subject to significant artifacts. None of these reconstructions has permitted unambiguous tracing or orientation of the actin subunits within the filament. Furthermore, measured values for the maximal filament diameter both determined by EM and by X-ray diffraction analysis, vary between 6 and 10 nm. Obviously, the apparent diameter of the actin filament revealed in the EM will critically depend on specimen preparation, since it is a rather flexible supramolecular assembly which can easily be bent or distorted. To resolve some of these ambiguities, we have explored specimen preparation conditions which may preserve single filaments sufficiently straight and helically ordered to be suitable for single filament 3-D reconstructions, possibly revealing molecular detail.

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