TY  - CONF
AU  - Sarić, Ana
AU  - Rajić, Jovana
AU  - Tolić, Anja
AU  - Đorđević, Marija
AU  - Grdović, Nevena
AU  - Uskoković, Aleksandra
AU  - Dinić, Svetlana
AU  - Arambašić Jovanović, Jelena
AU  - Mihailović, Mirjana
AU  - Vidaković, Melita
AU  - Dučić, Tanja
PY  - 2023
UR  - http://radar.ibiss.bg.ac.rs/handle/123456789/6304
AB  - Introduction: DNA methylation is a major regulator of transcriptional activity and alongside other epigenetic modifications it introduces specific level of chromatin complexity. Fourier transform infrared (FTIR) spectroscopy is a rapid, non-destructive, and label-free technique for identifying subtle changes in all bio-macromolecules, and it has been used as a method of choice for studying DNA conformation. The present study was designed to explore the use of synchrotron-based FTIR spectroscopy to monitor the subtle changes on molecular level regarding the DNA methylation status of cytosine in the whole genome.
Methods: For FTIR-based DNA methylation analysis in situ, DNA-HALO samples were prepared using slightly modified methodology for nuclear HALO preparations where DNA-HALOs are liberated of any protein residues but preserve higher order chromatin structure.
Results: Using FTIR spectroscopy we analysed and compared methylation profiles of isolated genomic DNA and DNA-HALO samples. DNA-HALO structure shows more distinct peaks in fingerprint region of spectra. DNA-HALO structure is more accurate for detecting bonds in unmemthylated cytosine as specific infrared peaks are defined as vibrations of bonds in unmethylated cytosine at 1151 cm-1 and 1357 cm-1. The ratio of integrated area under the peak 1151 cm-1 over integrated area under the peak that represents PO2-backbone vibrations can be used to assess level of unmethylated cytosine and thus methylation rate in the DNA-HALO samples.
Conclusion: This study demonstrates potential of FTIR spectroscopy to detect DNA methylation in DNA-HALO samples more precisely compared to classical DNA extraction procedure that yield unstructured whole genomic DNA.
PB  - Belgrade: Institute of Molecular Genetics and Genetic Engineering, University of Belgrade
C3  - Abstract Book: CoMBoS2 - the Second Congress of Molecular Biologists of Serbia; 2023 Oct 6-8; Belgrade, Serbia
T1  - Methylation profile analysis of Of DNA-HALO structure by synchrotron-based FTIR spectroscopy
SP  - 68
EP  - 68
UR  - https://hdl.handle.net/21.15107/rcub_ibiss_6304
ER  - 

@conference{
author = "Sarić, Ana and Rajić, Jovana and Tolić, Anja and Đorđević, Marija and Grdović, Nevena and Uskoković, Aleksandra and Dinić, Svetlana and Arambašić Jovanović, Jelena and Mihailović, Mirjana and Vidaković, Melita and Dučić, Tanja",
year = "2023",
abstract = "Introduction: DNA methylation is a major regulator of transcriptional activity and alongside other epigenetic modifications it introduces specific level of chromatin complexity. Fourier transform infrared (FTIR) spectroscopy is a rapid, non-destructive, and label-free technique for identifying subtle changes in all bio-macromolecules, and it has been used as a method of choice for studying DNA conformation. The present study was designed to explore the use of synchrotron-based FTIR spectroscopy to monitor the subtle changes on molecular level regarding the DNA methylation status of cytosine in the whole genome.
Methods: For FTIR-based DNA methylation analysis in situ, DNA-HALO samples were prepared using slightly modified methodology for nuclear HALO preparations where DNA-HALOs are liberated of any protein residues but preserve higher order chromatin structure.
Results: Using FTIR spectroscopy we analysed and compared methylation profiles of isolated genomic DNA and DNA-HALO samples. DNA-HALO structure shows more distinct peaks in fingerprint region of spectra. DNA-HALO structure is more accurate for detecting bonds in unmemthylated cytosine as specific infrared peaks are defined as vibrations of bonds in unmethylated cytosine at 1151 cm-1 and 1357 cm-1. The ratio of integrated area under the peak 1151 cm-1 over integrated area under the peak that represents PO2-backbone vibrations can be used to assess level of unmethylated cytosine and thus methylation rate in the DNA-HALO samples.
Conclusion: This study demonstrates potential of FTIR spectroscopy to detect DNA methylation in DNA-HALO samples more precisely compared to classical DNA extraction procedure that yield unstructured whole genomic DNA.",
publisher = "Belgrade: Institute of Molecular Genetics and Genetic Engineering, University of Belgrade",
journal = "Abstract Book: CoMBoS2 - the Second Congress of Molecular Biologists of Serbia; 2023 Oct 6-8; Belgrade, Serbia",
title = "Methylation profile analysis of Of DNA-HALO structure by synchrotron-based FTIR spectroscopy",
pages = "68-68",
url = "https://hdl.handle.net/21.15107/rcub_ibiss_6304"
}

Sarić, A., Rajić, J., Tolić, A., Đorđević, M., Grdović, N., Uskoković, A., Dinić, S., Arambašić Jovanović, J., Mihailović, M., Vidaković, M.,& Dučić, T.. (2023). Methylation profile analysis of Of DNA-HALO structure by synchrotron-based FTIR spectroscopy. in Abstract Book: CoMBoS2 - the Second Congress of Molecular Biologists of Serbia; 2023 Oct 6-8; Belgrade, Serbia
Belgrade: Institute of Molecular Genetics and Genetic Engineering, University of Belgrade., 68-68.
https://hdl.handle.net/21.15107/rcub_ibiss_6304

Sarić A, Rajić J, Tolić A, Đorđević M, Grdović N, Uskoković A, Dinić S, Arambašić Jovanović J, Mihailović M, Vidaković M, Dučić T. Methylation profile analysis of Of DNA-HALO structure by synchrotron-based FTIR spectroscopy. in Abstract Book: CoMBoS2 - the Second Congress of Molecular Biologists of Serbia; 2023 Oct 6-8; Belgrade, Serbia. 2023;:68-68.
https://hdl.handle.net/21.15107/rcub_ibiss_6304 .

Sarić, Ana, Rajić, Jovana, Tolić, Anja, Đorđević, Marija, Grdović, Nevena, Uskoković, Aleksandra, Dinić, Svetlana, Arambašić Jovanović, Jelena, Mihailović, Mirjana, Vidaković, Melita, Dučić, Tanja, "Methylation profile analysis of Of DNA-HALO structure by synchrotron-based FTIR spectroscopy" in Abstract Book: CoMBoS2 - the Second Congress of Molecular Biologists of Serbia; 2023 Oct 6-8; Belgrade, Serbia (2023):68-68,
https://hdl.handle.net/21.15107/rcub_ibiss_6304 .

TY  - JOUR
AU  - Sarić, Ana
AU  - Rajić, Jovana
AU  - Tolić, Anja
AU  - Dučić, Tanja
AU  - Vidaković, Melita
PY  - 2023
UR  - http://radar.ibiss.bg.ac.rs/handle/123456789/5948
AB  - Fourier transform infrared (FTIR) spectroscopy is a rapid, non-destructive and label-free technique for identifying subtle changes in all bio-macromolecules, and has been used as a method of choice for studying DNA conformation, secondary DNA structure transition and DNA damage. In addition, the specific level of chromatin complexity is introduced via epigenetic modifications forcing the technological upgrade in the analysis of such an intricacy. As the most studied epigenetic mechanism, DNA methylation is a major regulator of transcriptional activity, involved in the suppression of a broad spectrum of genes and its deregulation is involved in all non-communicable diseases. The present study was designed to explore the use of synchrotron-based FTIR analysis to monitor the subtle changes in molecule bases regarding the DNA methylation status of cytosine in the whole genome. In order to reveal the conformation-related best sample for FTIR-based DNA methylation analysis in situ, we used methodology for nuclear HALO preparations and slightly modified it to isolated DNA in HALO formations. Nuclear DNA-HALOs represent samples with preserved higher-order chromatin structure liberated of any protein residues that are closer to native DNA conformation than genomic DNA (gDNA) isolated by the standard batch procedure. Using FTIR spectroscopy we analyzed the DNA methylation profile of isolated gDNA and compared it with the DNA-HALOs. This study demonstrated the potential of FTIR microspectroscopy to detect DNA methylation marks in analyzed DNA-HALO specimens more precisely in comparison with classical DNA extraction procedures that yield unstructured whole genomic DNA. In addition, we used different cell types to assess their global DNA methylation profile, as well as defined specific infrared peaks that can be used for screening DNA methylation.
PB  - Elsevier
T2  - Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy
T1  - Synchrotron-based FTIR microspectroscopy reveals DNA methylation profile in DNA-HALO structure
IS  - 123090
VL  - 302
DO  - 10.1016/j.saa.2023.123090
ER  - 

@article{
author = "Sarić, Ana and Rajić, Jovana and Tolić, Anja and Dučić, Tanja and Vidaković, Melita",
year = "2023",
abstract = "Fourier transform infrared (FTIR) spectroscopy is a rapid, non-destructive and label-free technique for identifying subtle changes in all bio-macromolecules, and has been used as a method of choice for studying DNA conformation, secondary DNA structure transition and DNA damage. In addition, the specific level of chromatin complexity is introduced via epigenetic modifications forcing the technological upgrade in the analysis of such an intricacy. As the most studied epigenetic mechanism, DNA methylation is a major regulator of transcriptional activity, involved in the suppression of a broad spectrum of genes and its deregulation is involved in all non-communicable diseases. The present study was designed to explore the use of synchrotron-based FTIR analysis to monitor the subtle changes in molecule bases regarding the DNA methylation status of cytosine in the whole genome. In order to reveal the conformation-related best sample for FTIR-based DNA methylation analysis in situ, we used methodology for nuclear HALO preparations and slightly modified it to isolated DNA in HALO formations. Nuclear DNA-HALOs represent samples with preserved higher-order chromatin structure liberated of any protein residues that are closer to native DNA conformation than genomic DNA (gDNA) isolated by the standard batch procedure. Using FTIR spectroscopy we analyzed the DNA methylation profile of isolated gDNA and compared it with the DNA-HALOs. This study demonstrated the potential of FTIR microspectroscopy to detect DNA methylation marks in analyzed DNA-HALO specimens more precisely in comparison with classical DNA extraction procedures that yield unstructured whole genomic DNA. In addition, we used different cell types to assess their global DNA methylation profile, as well as defined specific infrared peaks that can be used for screening DNA methylation.",
publisher = "Elsevier",
journal = "Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy",
title = "Synchrotron-based FTIR microspectroscopy reveals DNA methylation profile in DNA-HALO structure",
number = "123090",
volume = "302",
doi = "10.1016/j.saa.2023.123090"
}

Sarić, A., Rajić, J., Tolić, A., Dučić, T.,& Vidaković, M.. (2023). Synchrotron-based FTIR microspectroscopy reveals DNA methylation profile in DNA-HALO structure. in Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy
Elsevier., 302(123090).
https://doi.org/10.1016/j.saa.2023.123090

Sarić A, Rajić J, Tolić A, Dučić T, Vidaković M. Synchrotron-based FTIR microspectroscopy reveals DNA methylation profile in DNA-HALO structure. in Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy. 2023;302(123090).
doi:10.1016/j.saa.2023.123090 .

Sarić, Ana, Rajić, Jovana, Tolić, Anja, Dučić, Tanja, Vidaković, Melita, "Synchrotron-based FTIR microspectroscopy reveals DNA methylation profile in DNA-HALO structure" in Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 302, no. 123090 (2023),
https://doi.org/10.1016/j.saa.2023.123090 . .

TY  - JOUR
AU  - Sarić, Ana
AU  - Rajić, Jovana
AU  - Tolić, Anja
AU  - Dučić, Tanja
AU  - Vidaković, Melita
PY  - 2023
UR  - http://radar.ibiss.bg.ac.rs/handle/123456789/5947
AB  - Fourier transform infrared (FTIR) spectroscopy is a rapid, non-destructive and label-free technique for identifying subtle changes in all bio-macromolecules, and has been used as a method of choice for studying DNA conformation, secondary DNA structure transition and DNA damage. In addition, the specific level of chromatin complexity is introduced via epigenetic modifications forcing the technological upgrade in the analysis of such an intricacy. As the most studied epigenetic mechanism, DNA methylation is a major regulator of transcriptional activity, involved in the suppression of a broad spectrum of genes and its deregulation is involved in all non-communicable diseases. The present study was designed to explore the use of synchrotron-based FTIR analysis to monitor the subtle changes in molecule bases regarding the DNA methylation status of cytosine in the whole genome. In order to reveal the conformation-related best sample for FTIR-based DNA methylation analysis in situ, we used methodology for nuclear HALO preparations and slightly modified it to isolated DNA in HALO formations. Nuclear DNA-HALOs represent samples with preserved higher-order chromatin structure liberated of any protein residues that are closer to native DNA conformation than genomic DNA (gDNA) isolated by the standard batch procedure. Using FTIR spectroscopy we analyzed the DNA methylation profile of isolated gDNA and compared it with the DNA-HALOs. This study demonstrated the potential of FTIR microspectroscopy to detect DNA methylation marks in analyzed DNA-HALO specimens more precisely in comparison with classical DNA extraction procedures that yield unstructured whole genomic DNA. In addition, we used different cell types to assess their global DNA methylation profile, as well as defined specific infrared peaks that can be used for screening DNA methylation.
PB  - Elsevier
T2  - Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy
T1  - Synchrotron-based FTIR microspectroscopy reveals DNA methylation profile in DNA-HALO structure
IS  - 123090
VL  - 302
DO  - 10.1016/j.saa.2023.123090
ER  - 

@article{
author = "Sarić, Ana and Rajić, Jovana and Tolić, Anja and Dučić, Tanja and Vidaković, Melita",
year = "2023",
abstract = "Fourier transform infrared (FTIR) spectroscopy is a rapid, non-destructive and label-free technique for identifying subtle changes in all bio-macromolecules, and has been used as a method of choice for studying DNA conformation, secondary DNA structure transition and DNA damage. In addition, the specific level of chromatin complexity is introduced via epigenetic modifications forcing the technological upgrade in the analysis of such an intricacy. As the most studied epigenetic mechanism, DNA methylation is a major regulator of transcriptional activity, involved in the suppression of a broad spectrum of genes and its deregulation is involved in all non-communicable diseases. The present study was designed to explore the use of synchrotron-based FTIR analysis to monitor the subtle changes in molecule bases regarding the DNA methylation status of cytosine in the whole genome. In order to reveal the conformation-related best sample for FTIR-based DNA methylation analysis in situ, we used methodology for nuclear HALO preparations and slightly modified it to isolated DNA in HALO formations. Nuclear DNA-HALOs represent samples with preserved higher-order chromatin structure liberated of any protein residues that are closer to native DNA conformation than genomic DNA (gDNA) isolated by the standard batch procedure. Using FTIR spectroscopy we analyzed the DNA methylation profile of isolated gDNA and compared it with the DNA-HALOs. This study demonstrated the potential of FTIR microspectroscopy to detect DNA methylation marks in analyzed DNA-HALO specimens more precisely in comparison with classical DNA extraction procedures that yield unstructured whole genomic DNA. In addition, we used different cell types to assess their global DNA methylation profile, as well as defined specific infrared peaks that can be used for screening DNA methylation.",
publisher = "Elsevier",
journal = "Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy",
title = "Synchrotron-based FTIR microspectroscopy reveals DNA methylation profile in DNA-HALO structure",
number = "123090",
volume = "302",
doi = "10.1016/j.saa.2023.123090"
}

Sarić, A., Rajić, J., Tolić, A., Dučić, T.,& Vidaković, M.. (2023). Synchrotron-based FTIR microspectroscopy reveals DNA methylation profile in DNA-HALO structure. in Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy
Elsevier., 302(123090).
https://doi.org/10.1016/j.saa.2023.123090

Sarić A, Rajić J, Tolić A, Dučić T, Vidaković M. Synchrotron-based FTIR microspectroscopy reveals DNA methylation profile in DNA-HALO structure. in Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy. 2023;302(123090).
doi:10.1016/j.saa.2023.123090 .

Sarić, Ana, Rajić, Jovana, Tolić, Anja, Dučić, Tanja, Vidaković, Melita, "Synchrotron-based FTIR microspectroscopy reveals DNA methylation profile in DNA-HALO structure" in Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 302, no. 123090 (2023),
https://doi.org/10.1016/j.saa.2023.123090 . .

TY  - DATA
AU  - Sarić, Ana
AU  - Rajić, Jovana
AU  - Tolić, Anja
AU  - Dučić, Tanja
AU  - Vidaković, Melita
PY  - 2023
UR  - http://radar.ibiss.bg.ac.rs/handle/123456789/5960
AB  - Supplementary Figure 1:
Curve fitting of FTIR spectra for analyzing differences in DNA regions.
PB  - Elsevier
T2  - Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy
T1  - Supplementary material for the article: Synchrotron-based FTIR microspectroscopy reveals DNA methylation profile in DNA-HALO structure
IS  - 123090
VL  - 302
UR  - https://hdl.handle.net/21.15107/rcub_ibiss_5960
ER  - 

@misc{
author = "Sarić, Ana and Rajić, Jovana and Tolić, Anja and Dučić, Tanja and Vidaković, Melita",
year = "2023",
abstract = "Supplementary Figure 1:
Curve fitting of FTIR spectra for analyzing differences in DNA regions.",
publisher = "Elsevier",
journal = "Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy",
title = "Supplementary material for the article: Synchrotron-based FTIR microspectroscopy reveals DNA methylation profile in DNA-HALO structure",
number = "123090",
volume = "302",
url = "https://hdl.handle.net/21.15107/rcub_ibiss_5960"
}

Sarić, A., Rajić, J., Tolić, A., Dučić, T.,& Vidaković, M.. (2023). Supplementary material for the article: Synchrotron-based FTIR microspectroscopy reveals DNA methylation profile in DNA-HALO structure. in Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy
Elsevier., 302(123090).
https://hdl.handle.net/21.15107/rcub_ibiss_5960

Sarić A, Rajić J, Tolić A, Dučić T, Vidaković M. Supplementary material for the article: Synchrotron-based FTIR microspectroscopy reveals DNA methylation profile in DNA-HALO structure. in Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy. 2023;302(123090).
https://hdl.handle.net/21.15107/rcub_ibiss_5960 .

Sarić, Ana, Rajić, Jovana, Tolić, Anja, Dučić, Tanja, Vidaković, Melita, "Supplementary material for the article: Synchrotron-based FTIR microspectroscopy reveals DNA methylation profile in DNA-HALO structure" in Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 302, no. 123090 (2023),
https://hdl.handle.net/21.15107/rcub_ibiss_5960 .