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1.
N Biotechnol ; 33(3): 311-30, 2016 May 25.
Artículo en Inglés | MEDLINE | ID: mdl-26514324

RESUMEN

The REvolutionary Approaches and Devices for Nucleic Acid analysis (READNA) project received funding from the European Commission for 41/2 years. The objectives of the project revolved around technological developments in nucleic acid analysis. The project partners have discovered, created and developed a huge body of insights into nucleic acid analysis, ranging from improvements and implementation of current technologies to the most promising sequencing technologies that constitute a 3(rd) and 4(th) generation of sequencing methods with nanopores and in situ sequencing, respectively.


Asunto(s)
Biotecnología/métodos , ADN/análisis , ADN/genética , Animales , Química Clic , Exoma/genética , Humanos , Espectrometría de Masas , Análisis de Secuencia de ADN
2.
PLoS One ; 10(4): e0121905, 2015.
Artículo en Inglés | MEDLINE | ID: mdl-25875920

RESUMEN

Optical mapping by direct visualization of individual DNA molecules, stretched in nanochannels with sequence-specific fluorescent labeling, represents a promising tool for disease diagnostics and genomics. An important challenge for this technique is thermal motion of the DNA as it undergoes imaging; this blurs fluorescent patterns along the DNA and results in information loss. Correcting for this effect (a process referred to as kymograph alignment) is a common preprocessing step in nanochannel-based optical mapping workflows, and we present here a highly efficient algorithm to accomplish this via pattern recognition. We compare our method with the one previous approach, and we find that our method is orders of magnitude faster while producing data of similar quality. We demonstrate proof of principle of our approach on experimental data consisting of melt mapped bacteriophage DNA.


Asunto(s)
Algoritmos , ADN/análisis , Quimografía/métodos , Imagen Óptica/métodos , Análisis de Secuencia de ADN/métodos , Bacteriófagos/genética , Mapeo Cromosómico/métodos , ADN Viral/análisis , Genómica/economía , Genómica/métodos , Quimografía/economía , Movimiento (Física) , Imagen Óptica/economía , Análisis de Secuencia de ADN/economía , Programas Informáticos , Factores de Tiempo
3.
Anal Biochem ; 443(2): 261-8, 2013 Dec 15.
Artículo en Inglés | MEDLINE | ID: mdl-23994563

RESUMEN

Low throughput is an inherent problem associated with most single-molecule biophysical techniques. We have developed a versatile tool for high-throughput analysis of DNA and DNA-binding molecules by combining microfluidic and dense DNA arrays. We use an easy-to-process microfluidic flow channel system in which dense DNA arrays are prepared for simultaneous imaging of large amounts of DNA molecules with single-molecule resolution. The Y-shaped microfluidic design, where the two inlet channels can be controlled separately and precisely, enables the creation of a concentration gradient across the microfluidic channel as well as rapid and repeated addition and removal of substances from the measurement region. A DNA array stained with the fluorescent DNA-binding dye YOYO-1 in a gradient manner illustrates the method and serves as a proof of concept. We have applied the method to studies of the repair protein Rad51 and could directly probe the concentration-dependent DNA-binding behavior of human Rad51 (HsRad51). In the low-concentration regime used (100 nM HsRad51 and below), we detected binding to double-stranded DNA (dsDNA) without positive cooperativity.


Asunto(s)
Benzoxazoles/análisis , ADN/metabolismo , Colorantes Fluorescentes/análisis , Técnicas Analíticas Microfluídicas/instrumentación , Compuestos de Quinolinio/análisis , Recombinasa Rad51/metabolismo , Benzoxazoles/metabolismo , Diseño de Equipo , Colorantes Fluorescentes/metabolismo , Humanos , Microscopía Fluorescente , Análisis de Secuencia por Matrices de Oligonucleótidos/instrumentación , Compuestos de Quinolinio/metabolismo
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