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Quantum optical nanosensors for microRNA
Čopák, Jakub ; Cígler, Petr (advisor) ; Ménová, Petra (referee)
Several disease processes taking place in the cells are characterized by an increase of the concentration of nucleic acids, in particular micro RNAs (miRNAs). A detection system that could selectively detect the increased presence of the miRNAs directly in the living cells in real time with nanoresolution is therefore highly desired. Fluorescent nanodiamond particles are considered promising candidates thanks to their biocompatibility, small size, allowing them to penetrate the cell membrane, and stable fluorescent defects in the crystal lattice, namely nitrogen-vacancy (NV) centres. The NV centres are the most studied colour centres of nanodiamonds due to their unique room-temperature optical properties, allowing for highly sensitive detection of changes in the magnetic field (magnetic noise) with quantum sensing techniques. For instance, the length of the T1 relaxation time NV electronic spin is greatly influenced by the presence of paramagnetic species, which causes a shortening of the T1 relaxation time depending on the proximity to the NV centres. However, for selective quantum sensing with nanodiamonds, the use of molecular transducers is necessary to bind targeted molecules with high specificity and allow their detection via the change of the NV spin properties. In this work,...
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Preparation of modified oligonucleotides by nicking enzyme amplification reaction
Ménová, Petra ; Hocek, Michal
A method for the enzymatic synthesis of short (10-22 nt) base-modified oligonucleotides was developed, based on the nicking enzyme amplification reaction. The methodology, including product isolation and purification, was scaled up to nanomolar amounts. The modified oligonucleotides were successfully used as primers in primer extension and PCR, affording primer-modified oligonucleotides and DNA. Two simple and efficient methods for fluorescent labelling of the PCR products were also developed.
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Polymerase synthesis of base-modified DNA: New methods and new applications
Balintová, Jana ; Daďová, Jitka ; Kielkowski, Pavel ; Ménová, Petra ; Vaníková, Zuzana ; Riedl, Jan ; Raindlová, Veronika ; Fojta, Miroslav ; Hocek, Michal
Diverse base-modified oligonucleotides and double-stranded DNA molecules were prepared by polymerase incorporation of modified nucleoside triphosphates. The methods include primer extension, PCR, nicking enzyme amplification reaction and mixed incorporations. The modified nucleic acids were used in redox and fluorescence labelling and coding, as well as regulation of binding and cross-linking with proteins.
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