Synapsable quadruplex-mediated fibers

Méndez, Miguel; Szalai, Veronika A.

doi:10.1186/1556-276x-8-210

Cited by 14 publications

(24 citation statements)

References 48 publications

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“…[14] However, the construction of nanostructures based on non-canonical pairing is gaining importance and nanodevices based on motifs such as quadruplexes or triplexes have been described. [3] Both motifs (duplexes and quadruplexes) may be combined and the synapsis between duplexes and quadruplex structures have been shown at the molecular level [15,16] and have already been applied as a tool for the construction of nanomaterials [17,18] . In order to expand the applications of this hybrid duplexquadruplex structure, a deep understanding of their properties and folding process is required.…”

Section: Introductionmentioning

confidence: 99%

Orienting Tetramolecular G‐Quadruplex Formation: The Quest for the Elusive RNA Antiparallel Quadruplex

Mendoza

Porrini

Salgado

et al. 2015

Chemistry A European J

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DNA and RNA G-quadruplexes (G4) are unusual nucleic acid structures involved in a number of key biological processes. RNA G-quadruplexes are less studied although recent evidence demonstrates that they are biologically relevant. Compared to DNA quadruplexes, RNA G4 are generally more stable and less polymorphic. Duplexes and quadruplexes may be combined to obtain pure tetrameric species. Here, we investigated whether classical antiparallel duplexes can drive the formation of antiparallel tetramolecular quadruplexes. This concept was first successfully applied to DNA G4. In contrast, RNA G4 were found to be much more unwilling to adopt the forced antiparallel orientation, highlighting that the reason RNA adopts a different structure must not be sought in the loops but in the G-stem structure itself. RNA antiparallel G4 formation is likely to be restricted to a very small set of peculiar sequences, in which other structural features overcome the formidable intrinsic barrier preventing its formation.

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Section: Introductionmentioning

confidence: 99%

Orienting Tetramolecular G‐Quadruplex Formation: The Quest for the Elusive RNA Antiparallel Quadruplex

Mendoza

Porrini

Salgado

et al. 2015

Chemistry A European J

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“…Bajo otras condiciones también hemos observado la formación de nanofibras [13]. Considerando que las unidades fundamentales solo tienen 39 nucleótidos, el tamaño de estas fibras indica el ensam- ble de varias decenas de unidades como constituyentes de estas nanofibras.…”

Section: Resultados Y Discusiónunclassified

“…Comparando los resultados que hemos reportado previamente [13], y las condiciones aquí descritas observamos que efectivamente un cambio en condiciones experimentales afecta profundamente la morfología (tamaño, distribución, longitud) de las nanofibras. Finalmente, considerando la potencial importancia de estructuras de autoensamblaje de ADN en nanotecnología [2,18], los resultados reportados en el presente trabajo muestran una vía sencilla para combinar dos tipos muy distintos de estructuras en base a ADN (con sus propias características y propiedades como biomateriales) en una misma nanoestructura.…”

Section: Resultados Y Discusiónunclassified

“…Se utilizó cloruro de tetrametil amonio (ClTMA), persulfato de amonio, mercaptoetanol, MgCl 2 , KCl, tris (hidrometil) aminometano (TRIS), ácido bórico de grado bioquímico o equivalente. Los experimentos de gel electroforesis y microscopía de fuerza atómica se realizaron como fue previamente reportado por nosotros [13]. Las soluciones amortiguadoras que se utilizaron se reportan en la Tabla 1.…”

Section: Materiales Y Métodosunclassified

“…La electroforésis se realizó de acuerdo a procedimientos estándar [13]. En el caso de las muestras a analizar con ADN de doble cadena (Ej.…”

Section: Gel Electroforesis No Desnaturalizanteunclassified

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Nanoestructuras inusuales de ácidos nucleicos basados en ADN G-cuádruple

Méndez

2015

Av. Cienc. Ing. (Quito)

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IntroducciónLa Nanotecnología está rápidamente cambiando el paradigma de los sistemas de fabricación de una estrategia "top -down" a una estrategia "bottom-up" [1]. Estos procesos que siguen la estrategia "bottom-up" explotan el "autoensamblaje" del material involucrado. Uno de tales materiales con la habilidad de auto ensamblarse es el ADN [2,3] Unusual Nucleic acid nanostructures based on G-quadruplex DNA AbstractA nano-assembly based on non-canonical DNA structures is reported. For the nanofabrication of a DNA-based structure the self-assembly of guanine quadruplex (Hoogsteen base pairing) and doublestranded DNA (Watson-Crick base pairing) was exploited. In general, an important number of nanostructures have being build exploiting the base pairing capability of canonical double stranded DNA. There are alternative approaches for construction using other DNA elements such as G-quadruplex, Imotifs, or triplexes. As a proof of principle, we have previously reported the use of duplex DNA (short synthetic DNA oligonucleotides) with sections of miss paired sites able to mediate formation of tetramolecular sections (G-quadruplex DNA prove) in order to ensemble the components into high molecular weight structures. Gel electrophoresis as well as atomic force microscopy show the formation of nanofibers. Gel electrophoresis as well as circular dichroism gave evidence of the presence of G-quadruplex sections. From AFM we estimated that the structures lengths expand from 250 to 2,000 nm with heights from 0.45 to 4.0 nm. Here we present another example of such nanofibers. We suggest that similar methodologies can be used to build more complex nano-structures that will exploit the properties of different DNA nano-oddities into functional applications.Keywords. Unusual nucleic acid assembly, nanofibers, G-quadruplexes, nano-oddity. ResumenSe reporta la preparación de un nano-ensamble basado en estructuras de ADN no canónico. Para la nanofabricación de una estructura basada en ADN el auto ensamblaje de ADN G-cuádruple (apareamiento de bases tipo hoogsteen) y ADN de doble cadena (apareamiento de bases tipo Watson-Crick) fueron utilizados. En general, un número importante de nanoestructuras se han construido explotando la capacidad de apareamiento de bases del ADN canónico de doble cadena. Hay formas alternativas para construcción utilizando otros elementos de ADN tales como G-cuadruple, motivos I, o ADN de triple cadena. Como prueba de prinicipio, previamente hemos reportado el uso de ADN de doble cadena (oligonucleótidos de ADN sintéticos cortos) con secciones de sitios no apareados capaz de mediar la formación de secciones tetramoleculares (pruebas G-cuádruple) con la finalidad de ensamblar los componentes en estructuras de alto peso molecular. Gel electroforesis como también microscopia de fuerza atómica muestran la formación de nanofibras. La electroforesis de Gel como el dicroismo circular dan evidencia de la presencia de secciones G-cuádruple. De las imágenes de microscopía de fuerza atómica se estimó que el largo de las...

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Structural Implications of Homopyrimidine Base Pairs in the Parallel‐Stranded d(YGA) Motif

Tripathi

Paukstelis

2016

ChemBioChem

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DNA can adopt many other structures beyond the canonical B-form double helix. These alternative DNA structures have become increasingly significant as new biological roles are found for them. Additionally, there has been a growing interest in using non-canonical base pairs to provide structural diversity for designing DNA architectures for nanotechnology applications. We recently described the crystal structure of d(ACTCGGATGAT), which forms a tetraplex through parallel-stranded homo-base pairs and nucleobase intercalation. The homoduplex region contains a d(YGA⋅YGA) motif observed in crystal and solution structures. Here, we examine the structural implications of the homopyrimidine base pair within this motif. We determined crystal structures of two variants that differ from the original structure in the homopyrimidine base pairs and number of d(YGA) motifs. Our results show that the intercalation-locked tetraplex motif is predictable in these different sequence contexts and that substituting C⋅C base pairs for T⋅T base pairs introduces asymmetry to the homoduplex. These results have important implications for utilizing d(YGA) motifs in DNA crystal design and could provide a basis for understanding how local structures could be associated with repeat expansions.

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Synapsable quadruplex-mediated fibers

Cited by 14 publications

References 48 publications

Orienting Tetramolecular G‐Quadruplex Formation: The Quest for the Elusive RNA Antiparallel Quadruplex

Orienting Tetramolecular G‐Quadruplex Formation: The Quest for the Elusive RNA Antiparallel Quadruplex

Nanoestructuras inusuales de ácidos nucleicos basados en ADN G-cuádruple

Structural Implications of Homopyrimidine Base Pairs in the Parallel‐Stranded d(YGA) Motif

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