TY  - JOUR
AU  - Đurišić, Ivana
AU  - Dražić, Miloš S.
AU  - Tomović, Aleksandar Ž.
AU  - Spasenović, Marko
AU  - Šlivančanin, Željko
AU  - Jovanović, Vladimir P.
AU  - Zikić, Radomir
PY  - 2020
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/3632
AB  - Fast, reliable, and inexpensive DNA sequencing is an important pursuit in healthcare, especially in personalized medicine with possible deep societal impacts. Despite significant progress in various nanopore-based sequencing configurations, challenges that remain in resolution and chromosome-size-long readout call for new approaches. Here we found strong rectification in the transversal current during single-stranded DNA translocation through a nanopore with side-embedded N-terminated carbon nanotube electrodes. Employing density functional theory and nonequilibrium Green’s function formalisms, we show that the rectifying ratio (response to square pulses of alternating bias) bears high nucleobase specificity. Rectification arises because of bias-dependent resistance asymmetry on the deoxyribonucleotide−electrode interfaces. The asymmetry induces molecular charging and highest occupied molecular orbital pinning to the electrochemical potential of one of the electrodes, assisted by an in-gap electric-field effect caused by dipoles at the terminated electrode ends. We propose the rectifying ratio, due to its order-of-magnitude-difference nucleobase selectivity and robustness to electrode-molecule orientation, as a promising readout quantifier for single-base resolution and chromosome-size-long single-read DNA sequencing. The proposed configurations are within experimental reach from the viewpoint of both nanofabrication and small current measurement.
PB  - American Chemical Society (ACS)
T2  - ACS Applied Nano Materials
T1  - DNA Sequencing with Single-Stranded DNA Rectification in a Nanogap Gated by N‑Terminated Carbon Nanotube Electrodes
VL  - 3
IS  - 3
SP  - 3034
EP  - 3043
DO  - 10.1021/acsanm.0c00385
ER  - 

@article{
author = "Đurišić, Ivana and Dražić, Miloš S. and Tomović, Aleksandar Ž. and Spasenović, Marko and Šlivančanin, Željko and Jovanović, Vladimir P. and Zikić, Radomir",
year = "2020",
abstract = "Fast, reliable, and inexpensive DNA sequencing is an important pursuit in healthcare, especially in personalized medicine with possible deep societal impacts. Despite significant progress in various nanopore-based sequencing configurations, challenges that remain in resolution and chromosome-size-long readout call for new approaches. Here we found strong rectification in the transversal current during single-stranded DNA translocation through a nanopore with side-embedded N-terminated carbon nanotube electrodes. Employing density functional theory and nonequilibrium Green’s function formalisms, we show that the rectifying ratio (response to square pulses of alternating bias) bears high nucleobase specificity. Rectification arises because of bias-dependent resistance asymmetry on the deoxyribonucleotide−electrode interfaces. The asymmetry induces molecular charging and highest occupied molecular orbital pinning to the electrochemical potential of one of the electrodes, assisted by an in-gap electric-field effect caused by dipoles at the terminated electrode ends. We propose the rectifying ratio, due to its order-of-magnitude-difference nucleobase selectivity and robustness to electrode-molecule orientation, as a promising readout quantifier for single-base resolution and chromosome-size-long single-read DNA sequencing. The proposed configurations are within experimental reach from the viewpoint of both nanofabrication and small current measurement.",
publisher = "American Chemical Society (ACS)",
journal = "ACS Applied Nano Materials",
title = "DNA Sequencing with Single-Stranded DNA Rectification in a Nanogap Gated by N‑Terminated Carbon Nanotube Electrodes",
volume = "3",
number = "3",
pages = "3034-3043",
doi = "10.1021/acsanm.0c00385"
}

Đurišić, I., Dražić, M. S., Tomović, A. Ž., Spasenović, M., Šlivančanin, Ž., Jovanović, V. P.,& Zikić, R.. (2020). DNA Sequencing with Single-Stranded DNA Rectification in a Nanogap Gated by N‑Terminated Carbon Nanotube Electrodes. in ACS Applied Nano Materials
American Chemical Society (ACS)., 3(3), 3034-3043.
https://doi.org/10.1021/acsanm.0c00385

Đurišić I, Dražić MS, Tomović AŽ, Spasenović M, Šlivančanin Ž, Jovanović VP, Zikić R. DNA Sequencing with Single-Stranded DNA Rectification in a Nanogap Gated by N‑Terminated Carbon Nanotube Electrodes. in ACS Applied Nano Materials. 2020;3(3):3034-3043.
doi:10.1021/acsanm.0c00385 .

Đurišić, Ivana, Dražić, Miloš S., Tomović, Aleksandar Ž., Spasenović, Marko, Šlivančanin, Željko, Jovanović, Vladimir P., Zikić, Radomir, "DNA Sequencing with Single-Stranded DNA Rectification in a Nanogap Gated by N‑Terminated Carbon Nanotube Electrodes" in ACS Applied Nano Materials, 3, no. 3 (2020):3034-3043,
https://doi.org/10.1021/acsanm.0c00385 . .

TY  - JOUR
AU  - Tomović, Aleksandar Ž.
AU  - Jovanović, Vladimir P.
AU  - Durisic, I
AU  - Cerovski, V Z
AU  - Nastasijevic, B
AU  - Veielovic, S R
AU  - Radulović, Katarina
AU  - Zikić, Radomir
PY  - 2015
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/1669
AB  - The photoluminescence (PL) quenching mechanism of UV light and air-exposed amorphous thin films of 4,4'-bis(2,2-diphenylvinyl)-1,1'-biphenyl (DPVBi), a well-known hole-transport material used in organic light-emitting diodes, is studied. Thin films of DPVBi are stable when exposed to UV light in vacuum but tend to degrade if oxygen is present simultaneously. This is evident from the changes in UV-vis absorption spectra of the latter, showing that degradation rate of DPVBi films is linearly proportional to both oxygen concentration and UV light intensity. Mass spectrometry study of such films revealed a number of different oxygen-containing molecules and fragments of DPVBi thus confirming apparent photo-oxidation process. Also, DFT study of molecular DPVBi with and without oxygen was carried out, the IR spectra calculated for the lowest energy molecules found and the results are compared with the experiment. The most sensitive to photo-oxidation is DPVBi photoluminescence, which decays exponentially with respect to the concentration of photo-oxidized DPVBi molecules (impurities). The PL quantum yield of DPVBi thin film drops to a half of its original value for 0.2% of the impurities present, at which point an average distance between DPVBi molecules (the donors) and photo-oxidized DPVBi species (acceptors) is an order of magnitude larger than the separation between two adjacent molecules. This implies a need for a long-range Forster energy transfer, which we rule out based on the lack of a donor-acceptor spectral overlap. The apparent discrepancy can be removed by postulating exciton self-diffusion in DPVBi thin films, for which there is supporting evidence in existing literature.
PB  - Elsevier
T2  - Journal of Luminescence
T1  - Fast photoluminescence quenching in thin films of 4,4 '-bis(2,2-diphenylvinyl)-1,1 '-biphenyl exposed to air
VL  - 167
SP  - 204
EP  - 210
DO  - 10.1016/j.jlumin.2015.06.036
ER  - 

@article{
author = "Tomović, Aleksandar Ž. and Jovanović, Vladimir P. and Durisic, I and Cerovski, V Z and Nastasijevic, B and Veielovic, S R and Radulović, Katarina and Zikić, Radomir",
year = "2015",
abstract = "The photoluminescence (PL) quenching mechanism of UV light and air-exposed amorphous thin films of 4,4'-bis(2,2-diphenylvinyl)-1,1'-biphenyl (DPVBi), a well-known hole-transport material used in organic light-emitting diodes, is studied. Thin films of DPVBi are stable when exposed to UV light in vacuum but tend to degrade if oxygen is present simultaneously. This is evident from the changes in UV-vis absorption spectra of the latter, showing that degradation rate of DPVBi films is linearly proportional to both oxygen concentration and UV light intensity. Mass spectrometry study of such films revealed a number of different oxygen-containing molecules and fragments of DPVBi thus confirming apparent photo-oxidation process. Also, DFT study of molecular DPVBi with and without oxygen was carried out, the IR spectra calculated for the lowest energy molecules found and the results are compared with the experiment. The most sensitive to photo-oxidation is DPVBi photoluminescence, which decays exponentially with respect to the concentration of photo-oxidized DPVBi molecules (impurities). The PL quantum yield of DPVBi thin film drops to a half of its original value for 0.2% of the impurities present, at which point an average distance between DPVBi molecules (the donors) and photo-oxidized DPVBi species (acceptors) is an order of magnitude larger than the separation between two adjacent molecules. This implies a need for a long-range Forster energy transfer, which we rule out based on the lack of a donor-acceptor spectral overlap. The apparent discrepancy can be removed by postulating exciton self-diffusion in DPVBi thin films, for which there is supporting evidence in existing literature.",
publisher = "Elsevier",
journal = "Journal of Luminescence",
title = "Fast photoluminescence quenching in thin films of 4,4 '-bis(2,2-diphenylvinyl)-1,1 '-biphenyl exposed to air",
volume = "167",
pages = "204-210",
doi = "10.1016/j.jlumin.2015.06.036"
}

Tomović, A. Ž., Jovanović, V. P., Durisic, I., Cerovski, V. Z., Nastasijevic, B., Veielovic, S. R., Radulović, K.,& Zikić, R.. (2015). Fast photoluminescence quenching in thin films of 4,4 '-bis(2,2-diphenylvinyl)-1,1 '-biphenyl exposed to air. in Journal of Luminescence
Elsevier., 167, 204-210.
https://doi.org/10.1016/j.jlumin.2015.06.036

Tomović AŽ, Jovanović VP, Durisic I, Cerovski VZ, Nastasijevic B, Veielovic SR, Radulović K, Zikić R. Fast photoluminescence quenching in thin films of 4,4 '-bis(2,2-diphenylvinyl)-1,1 '-biphenyl exposed to air. in Journal of Luminescence. 2015;167:204-210.
doi:10.1016/j.jlumin.2015.06.036 .

Tomović, Aleksandar Ž., Jovanović, Vladimir P., Durisic, I, Cerovski, V Z, Nastasijevic, B, Veielovic, S R, Radulović, Katarina, Zikić, Radomir, "Fast photoluminescence quenching in thin films of 4,4 '-bis(2,2-diphenylvinyl)-1,1 '-biphenyl exposed to air" in Journal of Luminescence, 167 (2015):204-210,
https://doi.org/10.1016/j.jlumin.2015.06.036 . .