I-motif and quadruplex-based device that can control a protein release or bind and release small molecule to influence biological processes

Xu, Yan; Hirao, Yuuka; Nishimura, Yoshifumi; Sugiyama, Hiroshi

doi:10.1016/j.bmc.2006.11.021

Cited by 23 publications

(16 citation statements)

References 22 publications

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“…This yields quenched donor and increased acceptor fluorescence, being the efficiency dependent on distance and dynamics of the structure. Fluorophores such as FAM or TAMRA may be used with this purpose 41 . Finally, it has been shown that DNA sequences functionalized with pyrene moieties at both 5' and 3' ends show fluorescent properties that allow the study of the thermal stability of i-motif structures 23,42 .…”

Section: Instrumental Approaches To Study the I-motif Structuresmentioning

confidence: 99%

Fundamental aspects of the nucleic acid i-motif structures

et al. 2014

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Section: Instrumental Approaches To Study the I-motif Structuresmentioning

confidence: 99%

Fundamental aspects of the nucleic acid i-motif structures

et al. 2014

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“…Furthermore, small molecule-G-quadruplex recognition is currently being explored for creating nanomolecular devices10 and developing nucleic acid based catalysis 11. Most G-quadruplex ligands reported so far comprise a planar, aromatic core designed to stack on the terminal tetrads of a G-quadruplex 12.…”

Section: Introductionmentioning

confidence: 99%

Diarylethynyl Amides That Recognize the Parallel Conformation of Genomic Promoter DNA G-Quadruplexes

et al. 2008

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We report bis-phenylethynyl amide derivatives as a potent G-quadruplex binding small molecule scaffold. The amide derivatives were efficiently prepared in 3 steps by employing Sonogashira coupling, ester hydrolysis and a chemoselective amide coupling. Ligand-quadruplex recognition has been evaluated using a fluorescence resonance energy transfer (FRET) melting assay, surface plasmon resonance (SPR), circular dichroism (CD) and 1 H nuclear magnetic resonance (NMR) spectroscopy. While most of the G-quadruplex ligands reported so far comprise a planar, aromatic core designed to stack on the terminal tetrads of a G-quadruplex, these compounds are neither polycyclic, nor macrocyclic and have free rotation around the triple bond enabling conformational flexibility. Such molecules show very good binding affinity, excellent quadruplex:duplex selectivity and also promising discrimination between intramolecular promoter quadruplexes. Our results indicate that the recognition of the c-kit2 quadruplex by these ligands is achieved through groove binding, which favors the formation of a parallel conformation.

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“…[3][4][5][6][7] In addition, the polymorphic nature has made the quadruplex an excellent candidate for the construction of a variety of novel nanomechanical devices with many potential applications in drug delivery, miniaturized biosensors, nanorobotics and dynamic nanomaterials etc. [8][9][10][11][12][13][14] Although these quadruplexbased DNA structures/devices hold great promise in nanotechnology and nanomedicine, how to create and expand addressable materials with increasing patterns of complexity, molecular diversity and further functions still remains a big challenge in this field.…”

Section: Introductionmentioning

confidence: 99%

Logic gates and pH sensing devices based on a supramolecular telomere DNA/conjugated polymer system

Wang

et al. 2010

Mol. BioSyst.

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A conceptually new class of telomere DNA/conjugated polymer system has been constructed to enable sensing of pH changes and create robust logic gates capable of multiplex logic operations. It combines the advantages of quadruplex-duplex conversion and efficient energy transfer from the polymer to the DNA binding molecule. The system is simple in design, fast in operation, and allows the detection of pH changes with high accuracy and sensitivity. In addition, the approach could be adopted for the investigation of other biomolecular conformational changes upon binding to their targets. More importantly, the present logic operations showed advantages over other nucleic acid-based logic gates: (1) The system does not require any CP modification or oligonucleotide labeling, which offers the advantages of simplicity and cost efficiency. (2) The reversibility of the switch makes the logic gates feasible to realize system reset. (3) The system could be implemented to perform multiple logic functions by using distinct input signals.

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I-motif and quadruplex-based device that can control a protein release or bind and release small molecule to influence biological processes

Cited by 23 publications

References 22 publications

Fundamental aspects of the nucleic acid i-motif structures

Fundamental aspects of the nucleic acid i-motif structures

Diarylethynyl Amides That Recognize the Parallel Conformation of Genomic Promoter DNA G-Quadruplexes

Logic gates and pH sensing devices based on a supramolecular telomere DNA/conjugated polymer system

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