1
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Leone D, Hubálek M, Pohl R, Sýkorová V, Hocek M. 1,3-Diketone-Modified Nucleotides and DNA for Cross-Linking with Arginine-Containing Peptides and Proteins. Angew Chem Int Ed Engl 2021; 60:17383-17387. [PMID: 34107150 PMCID: PMC8362068 DOI: 10.1002/anie.202105126] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/27/2021] [Indexed: 12/28/2022]
Abstract
Linear or branched 1,3-diketone-linked thymidine 5'-O-mono- and triphosphate were synthesized through CuAAC click reaction of diketone-alkynes with 5-azidomethyl-dUMP or -dUTP. The triphosphates were good substrates for KOD XL DNA polymerase in primer extension synthesis of modified DNA. The nucleotide bearing linear 3,5-dioxohexyl group (HDO) efficiently reacted with arginine-containing peptides to form stable pyrimidine-linked conjugates, whereas the branched 2-acetyl-3-oxo-butyl (PDO) group was not reactive. Reaction with Lys or a terminal amino group formed enamine adducts that were prone to hydrolysis. This reactive HDO modification in DNA was used for bioconjugations and cross-linking with Arg-containing peptides or proteins (e.g. histones).
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Affiliation(s)
- Denise‐Liu' Leone
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
- Department of Organic ChemistryFaculty of ScienceCharles University in PragueHlavova 812843Prague 2Czech Republic
| | - Martin Hubálek
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
| | - Veronika Sýkorová
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
- Department of Organic ChemistryFaculty of ScienceCharles University in PragueHlavova 812843Prague 2Czech Republic
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2
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Leone D, Hubálek M, Pohl R, Sýkorová V, Hocek M. 1,3‐Diketone‐Modified Nucleotides and DNA for Cross‐Linking with Arginine‐Containing Peptides and Proteins. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202105126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Denise‐Liu' Leone
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic Chemistry Faculty of Science Charles University in Prague Hlavova 8 12843 Prague 2 Czech Republic
| | - Martin Hubálek
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Veronika Sýkorová
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic Chemistry Faculty of Science Charles University in Prague Hlavova 8 12843 Prague 2 Czech Republic
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3
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Güixens-Gallardo P, Hocek M. Acetophenyl-thienyl-aniline-Linked Nucleotide for Construction of Solvatochromic Fluorescence Light-Up DNA Probes Sensing Protein-DNA Interactions. Chemistry 2021; 27:7090-7093. [PMID: 33769635 DOI: 10.1002/chem.202100575] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Indexed: 12/20/2022]
Abstract
The synthesis of 2'-deoxycytidine and its 5'-O-triphosphate bearing solvatochromic acetophenyl-thienyl-aniline fluorophore was developed using the Sonogashira cross-coupling reaction as the key step. The triphosphate was used for polymerase synthesis of labelled DNA. The labelled nucleotide or DNA exerted weak red fluorescence when excited at 405 nm, but a significant colour change (to yellow or green) and light-up (up to 20 times) was observed when the DNA probes interacted with proteins or lipids.
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Affiliation(s)
- Pedro Güixens-Gallardo
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16000, Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 12843, Prague 2, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16000, Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 12843, Prague 2, Czech Republic
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4
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Ivancová I, Pohl R, Hubálek M, Hocek M. Squaramate-Modified Nucleotides and DNA for Specific Cross-Linking with Lysine-Containing Peptides and Proteins. Angew Chem Int Ed Engl 2019; 58:13345-13348. [PMID: 31328344 PMCID: PMC6771961 DOI: 10.1002/anie.201906737] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/12/2019] [Indexed: 01/31/2023]
Abstract
Squaramate-linked 2'-deoxycytidine 5'-O-triphosphate was synthesized and found to be good substrate for KOD XL DNA polymerase in primer extension or PCR synthesis of modified DNA. The resulting squaramate-linked DNA reacts with primary amines to form a stable diamide linkage. This reaction was used for bioconjugations of DNA with Cy5 and Lys-containing peptides. Squaramate-linked DNA formed covalent cross-links with histone proteins. This reactive nucleotide has potential for other bioconjugations of nucleic acids with amines, peptides or proteins without need of any external reagent.
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Affiliation(s)
- Ivana Ivancová
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
- Department of Organic ChemistryFaculty of ScienceCharles University in PragueHlavova 8CZ-12843Prague 2Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
| | - Martin Hubálek
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
- Department of Organic ChemistryFaculty of ScienceCharles University in PragueHlavova 8CZ-12843Prague 2Czech Republic
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5
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Ivancová I, Pohl R, Hubálek M, Hocek M. Squaramate‐Modified Nucleotides and DNA for Specific Cross‐Linking with Lysine‐Containing Peptides and Proteins. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201906737] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Ivana Ivancová
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic ChemistryFaculty of ScienceCharles University in Prague Hlavova 8 CZ-12843 Prague 2 Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Martin Hubálek
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic ChemistryFaculty of ScienceCharles University in Prague Hlavova 8 CZ-12843 Prague 2 Czech Republic
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6
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Dual redox labeling of DNA as a tool for electrochemical detection of p53 protein-DNA interactions. Anal Chim Acta 2019; 1050:123-131. [DOI: 10.1016/j.aca.2018.10.053] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 10/04/2018] [Accepted: 10/23/2018] [Indexed: 12/18/2022]
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7
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Olszewska A, Pohl R, Hocek M. Trifluoroacetophenone-Linked Nucleotides and DNA for Studying of DNA-Protein Interactions by 19F NMR Spectroscopy. J Org Chem 2018; 82:11431-11439. [PMID: 28991457 DOI: 10.1021/acs.joc.7b01920] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A series of 7-[4-(trifluoroacetyl)phenyl]-7-deazaadenine and -7-deazaguanine as well as 5-substituted uracil and cytosine 2'-deoxyribonucleosides and mono- and triphosphates were synthesized through aqueous Suzuki-Miyaura crosscoupling of halogenated nucleosides or nucleotides with 4-(trifluoroacetyl)phenylboronic acid. The modified nucleoside triphosphates were good substrates for DNA polymerases applicable in primer extension or PCR synthesis of modified oligonucleotides or DNA. Attempted cross-linking with a serine-containing protein did not proceed, however the trifluoroacetophenone group was a sensitive probe for the study of DNA-protein interactions by 19F NMR.
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Affiliation(s)
- Agata Olszewska
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo namesti 2, 160 00 Prague 6, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo namesti 2, 160 00 Prague 6, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo namesti 2, 160 00 Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague , Hlavova 8, 12843 Prague 2, Czech Republic
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8
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Tichy V, Sebest P, Orsag P, Havran L, Pivonkova H, Fojta M. Protein p53 Binding to Cisplatin-modified DNA Targets Evaluated by Modification-specific Electrochemical Immunoprecipitation Assay. ELECTROANAL 2016. [DOI: 10.1002/elan.201600480] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Vlastimil Tichy
- Institute of Biophysics; Academy of Sciences of the Czech Republic, v.v.i.,; Kralovopolska 135 61265 Brno Czech Republic
| | - Peter Sebest
- Institute of Biophysics; Academy of Sciences of the Czech Republic, v.v.i.,; Kralovopolska 135 61265 Brno Czech Republic
| | - Petr Orsag
- Institute of Biophysics; Academy of Sciences of the Czech Republic, v.v.i.,; Kralovopolska 135 61265 Brno Czech Republic
- CEITEC-Central European Institute of Technology; Masaryk University; Kamenice 5 62500 Brno Czech Republic
| | - Ludek Havran
- Institute of Biophysics; Academy of Sciences of the Czech Republic, v.v.i.,; Kralovopolska 135 61265 Brno Czech Republic
| | - Hana Pivonkova
- Institute of Biophysics; Academy of Sciences of the Czech Republic, v.v.i.,; Kralovopolska 135 61265 Brno Czech Republic
| | - Miroslav Fojta
- Institute of Biophysics; Academy of Sciences of the Czech Republic, v.v.i.,; Kralovopolska 135 61265 Brno Czech Republic
- CEITEC-Central European Institute of Technology; Masaryk University; Kamenice 5 62500 Brno Czech Republic
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9
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Dziuba D, Pospíšil P, Matyašovský J, Brynda J, Nachtigallová D, Rulíšek L, Pohl R, Hof M, Hocek M. Solvatochromic fluorene-linked nucleoside and DNA as color-changing fluorescent probes for sensing interactions. Chem Sci 2016; 7:5775-5785. [PMID: 30034716 PMCID: PMC6021979 DOI: 10.1039/c6sc02548j] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 06/20/2016] [Indexed: 12/16/2022] Open
Abstract
A nucleoside bearing a solvatochromic push-pull fluorene fluorophore (dCFL ) was designed and synthesized by the Sonogashira coupling of alkyne-linked fluorene 8 with 5-iodo-2'-deoxycytidine. The fluorene building block 8 and labeled nucleoside dCFL exerted bright fluorescence with significant solvatochromic effect providing emission maxima ranging from 421 to 544 nm and high quantum yields even in highly polar solvents, including water. The solvatochromism of 8 was studied by DFT and ADC(2) calculations to show that, depending on the polarity of the solvent, emission either from the planar or the twisted conformation of the excited state can occur. The nucleoside was converted to its triphosphate variant dCFLTP which was found to be a good substrate for DNA polymerases suitable for the enzymatic synthesis of oligonucleotide or DNA probes by primer extension or PCR. The fluorene-linked DNA can be used as fluorescent probes for DNA-protein (p53) or DNA-lipid interactions, exerting significant color changes visible even to the naked eye. They also appear to be suitable for time-dependent fluorescence shift studies on DNA, yielding information on DNA hydration and dynamics.
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Affiliation(s)
- Dmytro Dziuba
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Gilead & IOCB Research Center , Flemingovo nam. 2 , CZ-16610 Prague 6 , Czech Republic .
| | - Petr Pospíšil
- J. H eyrovský Institute of Physical Chemistry , Czech Academy of Sciences , Dolejskova 3 , CZ-182 23 Prague , Czech Republic
| | - Ján Matyašovský
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Gilead & IOCB Research Center , Flemingovo nam. 2 , CZ-16610 Prague 6 , Czech Republic .
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Gilead & IOCB Research Center , Flemingovo nam. 2 , CZ-16610 Prague 6 , Czech Republic .
| | - Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Gilead & IOCB Research Center , Flemingovo nam. 2 , CZ-16610 Prague 6 , Czech Republic .
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Gilead & IOCB Research Center , Flemingovo nam. 2 , CZ-16610 Prague 6 , Czech Republic .
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Gilead & IOCB Research Center , Flemingovo nam. 2 , CZ-16610 Prague 6 , Czech Republic .
| | - Martin Hof
- J. H eyrovský Institute of Physical Chemistry , Czech Academy of Sciences , Dolejskova 3 , CZ-182 23 Prague , Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Gilead & IOCB Research Center , Flemingovo nam. 2 , CZ-16610 Prague 6 , Czech Republic .
- Department of Organic Chemistry , Faculty of Science , Charles University in Prague , Hlavova 8 , CZ-12843 Prague 2 , Czech Republic
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10
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Olszewska A, Pohl R, Brázdová M, Fojta M, Hocek M. Chloroacetamide-Linked Nucleotides and DNA for Cross-Linking with Peptides and Proteins. Bioconjug Chem 2016; 27:2089-94. [PMID: 27479485 DOI: 10.1021/acs.bioconjchem.6b00342] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Nucleotides, 2'-deoxyribonucleoside triphosphates (dNTPs), and DNA probes bearing reactive chloroacetamido group linked to nucleobase (cytosine or 7-deazadaenine) through a propargyl tether were prepared and tested in cross-linking with cysteine- or histidine-containing peptides and proteins. The chloroacetamide-modifed dNTPs proved to be good substrates for DNA polymerases in the enzymatic synthesis of modified DNA probes. Modified nucleotides and DNA reacted efficiently with cysteine and cysteine-containing peptides, whereas the reaction with histidine was sluggish and low yielding. The modified DNA efficiently cross-linked with p53 protein through alkylation of cysteine and showed potential for cross-linking with histidine (in C277H mutant of p53).
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Affiliation(s)
- Agata Olszewska
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Gilead Sciences & IOCB Research Center , Flemingovo namesti 2, 166 10 Prague 6, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Gilead Sciences & IOCB Research Center , Flemingovo namesti 2, 166 10 Prague 6, Czech Republic
| | - Marie Brázdová
- Institute of Biophysics, Czech Academy of Sciences , Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Miroslav Fojta
- Institute of Biophysics, Czech Academy of Sciences , Kralovopolska 135, 612 65 Brno, Czech Republic.,Central European Institute of Technology, Masaryk University , Kamenice 753/5, CZ-625 00 Brno, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Gilead Sciences & IOCB Research Center , Flemingovo namesti 2, 166 10 Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague , Hlavova 8, 12843 Prague 2, Czech Republic
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11
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Dziuba D, Jurkiewicz P, Cebecauer M, Hof M, Hocek M. A Rotational BODIPY Nucleotide: An Environment-Sensitive Fluorescence-Lifetime Probe for DNA Interactions and Applications in Live-Cell Microscopy. Angew Chem Int Ed Engl 2015; 55:174-8. [PMID: 26768820 DOI: 10.1002/anie.201507922] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 10/20/2015] [Indexed: 12/16/2022]
Abstract
Fluorescent probes for detecting the physical properties of cellular structures have become valuable tools in life sciences. The fluorescence lifetime of molecular rotors can be used to report on variations in local molecular packing or viscosity. We used a nucleoside linked to a meso-substituted BODIPY fluorescent molecular rotor (dC(bdp)) to sense changes in DNA microenvironment both in vitro and in living cells. DNA incorporating dC(bdp) can respond to interactions with DNA-binding proteins and lipids by changes in the fluorescence lifetimes in the range 0.5-2.2 ns. We can directly visualize changes in the local environment of exogenous DNA during transfection of living cells. Relatively long fluorescence lifetimes and extensive contrast for detecting changes in the microenvironment together with good photostability and versatility for DNA synthesis make this probe suitable for analysis of DNA-associated processes, cellular structures, and also DNA-based nanomaterials.
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Affiliation(s)
- Dmytro Dziuba
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences & IOCB Research Center, Flemingovo nam. 2, 16610 Prague 6 (Czech Republic) http://www.uochb.cas.cz/hocekgroup
| | - Piotr Jurkiewicz
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Dolejskova 3, 18223 Prague 8 (Czech Republic) http://www.hof-fluorescence-group.weebly.com/
| | - Marek Cebecauer
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Dolejskova 3, 18223 Prague 8 (Czech Republic) http://www.hof-fluorescence-group.weebly.com/
| | - Martin Hof
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Dolejskova 3, 18223 Prague 8 (Czech Republic) http://www.hof-fluorescence-group.weebly.com/.
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences & IOCB Research Center, Flemingovo nam. 2, 16610 Prague 6 (Czech Republic) http://www.uochb.cas.cz/hocekgroup. .,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 12843 Prague 2 (Czech Republic).
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12
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Dziuba D, Jurkiewicz P, Cebecauer M, Hof M, Hocek M. A Rotational BODIPY Nucleotide: An Environment-Sensitive Fluorescence-Lifetime Probe for DNA Interactions and Applications in Live-Cell Microscopy. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507922] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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13
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Dadová J, Vrábel M, Adámik M, Brázdová M, Pohl R, Fojta M, Hocek M. Azidopropylvinylsulfonamide as a New Bifunctional Click Reagent for Bioorthogonal Conjugations: Application for DNA–Protein Cross‐Linking. Chemistry 2015; 21:16091-102. [DOI: 10.1002/chem.201502209] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Indexed: 01/03/2023]
Affiliation(s)
- Jitka Dadová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences & IOCB Research Center, Flemingovo nám. 2, 16610 Prague 6 (Czech Republic)
| | - Milan Vrábel
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences & IOCB Research Center, Flemingovo nám. 2, 16610 Prague 6 (Czech Republic)
| | - Matej Adámik
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 61265 Brno (Czech Republic)
| | - Marie Brázdová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 61265 Brno (Czech Republic)
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences & IOCB Research Center, Flemingovo nám. 2, 16610 Prague 6 (Czech Republic)
| | - Miroslav Fojta
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 61265 Brno (Czech Republic)
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno (Czech Republic)
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences & IOCB Research Center, Flemingovo nám. 2, 16610 Prague 6 (Czech Republic)
- Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 12843 Prague 2 (Czech Republic)
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14
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Bowater RP, Cobb AM, Pivonkova H, Havran L, Fojta M. Biophysical and electrochemical studies of protein–nucleic acid interactions. MONATSHEFTE FUR CHEMIE 2015. [DOI: 10.1007/s00706-014-1405-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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15
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Šebest P, Brázdová M, Fojta M, Pivoňková H. Differential salt-induced dissociation of the p53 protein complexes with circular and linear plasmid DNA substrates suggest involvement of a sliding mechanism. Int J Mol Sci 2015; 16:3163-77. [PMID: 25647416 PMCID: PMC4346886 DOI: 10.3390/ijms16023163] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 01/26/2015] [Indexed: 01/30/2023] Open
Abstract
A study of the effects of salt conditions on the association and dissociation of wild type p53 with different ~3 kbp long plasmid DNA substrates (supercoiled, relaxed circular and linear, containing or lacking a specific p53 binding site, p53CON) using immunoprecipitation at magnetic beads is presented. Salt concentrations above 200 mM strongly affected association of the p53 protein to any plasmid DNA substrate. Strikingly different behavior was observed when dissociation of pre-formed p53-DNA complexes in increased salt concentrations was studied. While contribution from the p53CON to the stability of the p53-DNA complexes was detected between 100 and 170 mM KCl, p53 complexes with circular DNAs (but not linear) exhibited considerable resistance towards salt treatment for KCl concentrations as high as 2 M provided that the p53 basic C-terminal DNA binding site (CTDBS) was available for DNA binding. On the contrary, when the CTDBS was blocked by antibody used for immunoprecipitation, all p53-DNA complexes were completely dissociated from the p53 protein in KCl concentrations ≥200 mM under the same conditions. These observations suggest: (a) different ways for association and dissociation of the p53-DNA complexes in the presence of the CTDBS; and (b) a critical role for a sliding mechanism, mediated by the C-terminal domain, in the dissociation process.
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Affiliation(s)
- Peter Šebest
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, Brno CZ-612 65, Czech Republic.
| | - Marie Brázdová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, Brno CZ-612 65, Czech Republic.
| | - Miroslav Fojta
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, Brno CZ-612 65, Czech Republic.
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, Brno CZ-625 00, Czech Republic.
| | - Hana Pivoňková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, Brno CZ-612 65, Czech Republic.
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16
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Balintová J, Špaček J, Pohl R, Brázdová M, Havran L, Fojta M, Hocek M. Azidophenyl as a click-transformable redox label of DNA suitable for electrochemical detection of DNA-protein interactions. Chem Sci 2014; 6:575-587. [PMID: 28970873 PMCID: PMC5618110 DOI: 10.1039/c4sc01906g] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 09/09/2014] [Indexed: 12/17/2022] Open
Abstract
A new azido-based DNA redox label which can be transformed into nitrophenyltriazole by a CuAAC click reaction was developed. It was used for the mapping of DNA–protein interactions with electrochemical detection.
New redox labelling of DNA by an azido group which can be chemically transformed to nitrophenyltriazole or silenced to phenyltriazole was developed and applied to the electrochemical detection of DNA–protein interactions. 5-(4-Azidophenyl)-2′-deoxycytidine and 7-(4-azidophenyl)-7-deaza-2′-deoxyadenosine nucleosides were prepared by aqueous-phase Suzuki cross-coupling and converted to nucleoside triphosphates (dNTPs) which served as substrates for incorporation into DNA by DNA polymerase. The azidophenyl-modified nucleotides and azidophenyl-modified DNA gave a strong signal in voltammetric studies, at –0.9 V, due to reduction of the azido function. The Cu-catalyzed click reaction of azidophenyl-modified nucleosides or azidophenyl-modified DNA with 4-nitrophenylacetylene gave nitrophenyl-substituted triazoles, exerting a reduction peak at –0.4 V under voltammetry, whereas the click reaction with phenylacetylene gave electrochemically silent phenyltriazoles. The transformation of the azidophenyl label to nitrophenyltriazole was used for electrochemical detection of DNA–protein interactions (p53 protein) since only those azidophenyl groups in the parts of the DNA not shielded by the bound p53 protein were transformed to nitrophenyltriazoles, whereas those covered by the protein were not.
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Affiliation(s)
- Jana Balintová
- Institute of Organic Chemistry and Biochemistry , Academy of Sciences of the Czech Republic , Gilead & IOCB Research Center , Flemingovo nam. 2 , CZ-16610 Prague 6 , Czech Republic .
| | - Jan Špaček
- Institute of Biophysics , v.v.i. Academy of Sciences of the Czech Republic , Kralovopolska 135 , 61265 Brno , Czech Republic .
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry , Academy of Sciences of the Czech Republic , Gilead & IOCB Research Center , Flemingovo nam. 2 , CZ-16610 Prague 6 , Czech Republic .
| | - Marie Brázdová
- Institute of Biophysics , v.v.i. Academy of Sciences of the Czech Republic , Kralovopolska 135 , 61265 Brno , Czech Republic .
| | - Luděk Havran
- Institute of Biophysics , v.v.i. Academy of Sciences of the Czech Republic , Kralovopolska 135 , 61265 Brno , Czech Republic . .,Central European Institute of Technology , Masaryk University , Kamenice 753/5 , CZ-625 00 Brno , Czech Republic
| | - Miroslav Fojta
- Institute of Biophysics , v.v.i. Academy of Sciences of the Czech Republic , Kralovopolska 135 , 61265 Brno , Czech Republic . .,Central European Institute of Technology , Masaryk University , Kamenice 753/5 , CZ-625 00 Brno , Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry , Academy of Sciences of the Czech Republic , Gilead & IOCB Research Center , Flemingovo nam. 2 , CZ-16610 Prague 6 , Czech Republic . .,Department of Organic Chemistry , Faculty of Science , Charles University in Prague , Hlavova 8 , CZ-12843 Prague 2 , Czech Republic
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Němcová K, Sebest P, Havran L, Orság P, Fojta M, Pivoňková H. Electrochemical detection of DNA binding by tumor suppressor p53 protein using osmium-labeled oligonucleotide probes and catalytic hydrogen evolution at the mercury electrode. Anal Bioanal Chem 2014; 406:5843-52. [PMID: 25056872 DOI: 10.1007/s00216-014-7996-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Revised: 06/22/2014] [Accepted: 06/24/2014] [Indexed: 11/28/2022]
Abstract
In this paper, we present an electrochemical DNA-protein interaction assay based on a combination of protein-specific immunoprecipitation at magnetic beads (MBIP) with application of oligonucleotide (ON) probes labeled with an electroactive oxoosmium complex (Os,bipy). We show that double-stranded ONs bearing a dT20 tail labeled with Os,bipy are specifically recognized by the tumor suppressor p53 protein according to the presence or absence of a specific binding site (p53CON) in the double-stranded segment. We demonstrate the applicability of the Os,bipy-labeled probes in titration as well as competition MBIP assays to evaluate p53 relative affinity to various sequence-specific or structurally distinct unlabeled DNA substrates upon modulation of the p53-DNA binding by monoclonal antibodies used for the immunoprecipitation. To detect the p53-bound osmium-labeled probes, we took advantage of a catalytic peak yielded by Os,bipy-modified DNA at the mercury-based electrodes, allowing facile determination of subnanogram quantities of the labeled oligonucleotides. Versatility of the electrochemical MBIP technique and its general applicability in studies of any DNA-binding protein is discussed.
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Affiliation(s)
- Kateřina Němcová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65, Brno, Czech Republic
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18
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Dadová J, Orság P, Pohl R, Brázdová M, Fojta M, Hocek M. Vinylsulfonamide and Acrylamide Modification of DNA for Cross-linking with Proteins. Angew Chem Int Ed Engl 2013; 52:10515-8. [DOI: 10.1002/anie.201303577] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 06/24/2013] [Indexed: 12/15/2022]
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19
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Dadová J, Orság P, Pohl R, Brázdová M, Fojta M, Hocek M. Vinylsulfonamide and Acrylamide Modification of DNA for Cross-linking with Proteins. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201303577] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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20
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Preferential binding of hot spot mutant p53 proteins to supercoiled DNA in vitro and in cells. PLoS One 2013; 8:e59567. [PMID: 23555710 PMCID: PMC3608670 DOI: 10.1371/journal.pone.0059567] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 02/19/2013] [Indexed: 11/21/2022] Open
Abstract
Hot spot mutant p53 (mutp53) proteins exert oncogenic gain-of-function activities. Binding of mutp53 to DNA is assumed to be involved in mutp53-mediated repression or activation of several mutp53 target genes. To investigate the importance of DNA topology on mutp53-DNA recognition in vitro and in cells, we analyzed the interaction of seven hot spot mutp53 proteins with topologically different DNA substrates (supercoiled, linear and relaxed) containing and/or lacking mutp53 binding sites (mutp53BS) using a variety of electrophoresis and immunoprecipitation based techniques. All seven hot spot mutp53 proteins (R175H, G245S, R248W, R249S, R273C, R273H and R282W) were found to have retained the ability of wild-type p53 to preferentially bind circular DNA at native negative superhelix density, while linear or relaxed circular DNA was a poor substrate. The preference of mutp53 proteins for supercoiled DNA (supercoil-selective binding) was further substantiated by competition experiments with linear DNA or relaxed DNA in vitro and ex vivo. Using chromatin immunoprecipitation, the preferential binding of mutp53 to a sc mutp53BS was detected also in cells. Furthermore, we have shown by luciferase reporter assay that the DNA topology influences p53 regulation of BAX and MSP/MST1 promoters. Possible modes of mutp53 binding to topologically constrained DNA substrates and their biological consequences are discussed.
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21
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Riedl J, Ménová P, Pohl R, Orság P, Fojta M, Hocek M. GFP-like fluorophores as DNA labels for studying DNA-protein interactions. J Org Chem 2012; 77:8287-93. [PMID: 22935023 DOI: 10.1021/jo301684b] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
GFP-like 3,5-difluoro-4-hydroxybenzylideneimidazolinone (FBI) and 3,5-bis(methoxy)-4-hydroxy-benzylideneimidazolinone (MBI) labels were attached to dCTP through a propargyl linker, and the resulting labeled nucleotides (dC(MBI)TP and dC(FBI)TP) were used for a facile enzymatic synthesis of oligonucleotide or DNA probes by polymerase-catalyzed primer extension. The MBI/FBI-labeled DNA probes exerted low fluorescence that was increased 2-3.2 times upon binding of a protein. The concept was demonstrated on sequence-specific binding of p53 to dsDNA and on nonspecific binding of single strand binding protein to an oligonucleotide. The FBI label was also used for a time-resolved experiment monitoring a single-nucleotide incorporation followed by primer extension by Vent(exo-) polymerase.
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Affiliation(s)
- Jan Riedl
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
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22
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Riedl J, Pohl R, Ernsting NP, Orság P, Fojta M, Hocek M. Labelling of nucleosides and oligonucleotides by solvatochromic 4-aminophthalimide fluorophore for studying DNA–protein interactions. Chem Sci 2012. [DOI: 10.1039/c2sc20404e] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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23
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Miriyala S, Holley AK, St Clair DK. Mitochondrial superoxide dismutase--signals of distinction. Anticancer Agents Med Chem 2011; 11:181-90. [PMID: 21355846 DOI: 10.2174/187152011795255920] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Accepted: 02/17/2011] [Indexed: 11/22/2022]
Abstract
Mitochondrial superoxide dismutase (MnSOD) neutralizes the highly reactive superoxide radical (O(2)(˙-)), the first member in a plethora of mitochondrial reactive oxygen species (ROS). Over the past decades, research has extended the prevailing view of mitochondrion well beyond the generation of cellular energy to include its importance in cell survival and cell death. In the normal state of a cell, endogenous antioxidant enzyme systems maintain the level of reactive oxygen species generated by the mitochondrial respiratory chain. Mammalian mitochondria are important to the production of reactive oxygen species, which underlie oxidative damage in many pathological conditions and contribute to retrograde redox signaling from the organelle to the cytosol and nucleus. Mitochondria are further implicated in various metabolic and aging-related diseases that are now postulated to be caused by misregulation of physiological systems rather than pure accumulation of oxidative damage. Thus, the signaling mechanisms within mitochondria, and between the organelle and its environment, have gained interest as potential drug targets. Here, we discuss redox events in mitochondria that lead to retrograde signaling, the role of redox events in disease, and their potential to serve as therapeutic targets.
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Affiliation(s)
- Sumitra Miriyala
- Graduate Center for Toxicology, University of Kentucky, Lexington, KY 40536, USA
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24
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Holley AK, Dhar SK, St Clair DK. Manganese superoxide dismutase vs. p53: regulation of mitochondrial ROS. Mitochondrion 2010; 10:649-61. [PMID: 20601193 DOI: 10.1016/j.mito.2010.06.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2009] [Revised: 06/18/2010] [Accepted: 06/22/2010] [Indexed: 01/10/2023]
Abstract
Coordination of mitochondrial and nuclear activities is vital for cellular homeostasis, and many signaling molecules and transcription factors are regulated by mitochondria-derived reactive oxygen species (ROS) to carry out this interorganellar communication. The tumor suppressor p53 regulates myriad cellular functions through transcription-dependent and -independent mechanisms at both the nucleus and mitochondria. p53 affect mitochondrial ROS production, in part, by regulating the expression of the mitochondrial antioxidant enzyme manganese superoxide dismutase (MnSOD). Recent evidence suggests mitochondrial regulation of p53 activity through mechanisms that affect ROS production, and a breakdown of communication amongst mitochondria, p53, and the nucleus can have broad implications in disease development.
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Affiliation(s)
- Aaron K Holley
- Graduate Center for Toxicology, University of Kentucky, Lexington, KY 40536, United States
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25
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Němcová K, Havran L, Šebest P, Brázdová M, Pivoňková H, Fojta M. A label-free electrochemical test for DNA-binding activities of tumor suppressor protein p53 using immunoprecipitation at magnetic beads. Anal Chim Acta 2010; 668:166-70. [DOI: 10.1016/j.aca.2010.04.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2010] [Revised: 04/02/2010] [Accepted: 04/07/2010] [Indexed: 01/27/2023]
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26
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Selective binding of tumor suppressor p53 protein to topologically constrained DNA: Modulation by intercalative drugs. Biochem Biophys Res Commun 2010; 393:894-9. [DOI: 10.1016/j.bbrc.2010.02.120] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2010] [Accepted: 02/18/2010] [Indexed: 11/17/2022]
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27
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Jagelská EB, Pivonková H, Fojta M, Brázda V. The potential of the cruciform structure formation as an important factor influencing p53 sequence-specific binding to natural DNA targets. Biochem Biophys Res Commun 2010; 391:1409-14. [PMID: 20026061 DOI: 10.1016/j.bbrc.2009.12.076] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Accepted: 12/11/2009] [Indexed: 11/29/2022]
Abstract
p53 is one of the most important tumor suppressors which responds to DNA damage by binding to DNA and regulating the transcription of genes involved in cell cycle arrest, apoptosis, or senescence. As it was shown previously, p53 binding to DNA is strongly influenced by DNA topology. DNA supercoiling is fundamentally important for a wide range of biological processes including DNA transcription, replication, recombination, control of gene expression and genome organization. In this study, we investigated the cruciform structures formation of various inverted repeats in p53-responsive sequences from p21, RGC, mdm2 and GADD45 promoters under negative superhelical stress, and analyzed the effects of these DNA topology changes on p53-DNA binding. We demonstrated using three different methods (gel retardation analyses, ELISA and magnetic immunoprecipitation assay) that the p53 protein binds preferentially to negatively supercoiled plasmid DNAs with p53-responsive sequence presented as a cruciform structure. Not only the appearance of the cruciform structures within naked supercoiled DNA, but also the potential of the binding sites for adopting the non-B structures can contribute to a more favorable p53-DNA complex.
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Affiliation(s)
- Eva B Jagelská
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
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28
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Abstract
p53 has been referred to as the 'guardian of the genome' because of its role in protecting the cell from DNA damage. p53 performs its duties by regulating cell-cycle progression and DNA repair and, in cases of irreparable DNA damage, by executing programmed cell death. Mitochondria are an important target of transcription-dependent and -independent actions of p53 to carry out the apoptotic function. However, increasing evidence suggests that p53 activity is regulated by mitochondria. Cellular insults that alter mitochondrial function can have important consequences on p53 activity. In light of these new findings, the following review focuses on p53/mitochondria connections, in particular how reactive oxygen species generated at mitochondria regulate p53 activity. A better understanding of the mechanisms by which mitochondria regulate p53 may have an impact on our understanding of the development and progression of many diseases, especially cancer.
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Affiliation(s)
- Aaron K Holley
- Graduate Center for Toxicology, University of Kentucky, Lexington, KY 40536, USA
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29
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Millau JF, Bastien N, Drouin R. P53 transcriptional activities: a general overview and some thoughts. Mutat Res 2008; 681:118-133. [PMID: 18639648 DOI: 10.1016/j.mrrev.2008.06.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2007] [Revised: 05/05/2008] [Accepted: 06/19/2008] [Indexed: 12/20/2022]
Abstract
P53 is a master transcriptional regulator controlling several main cellular pathways. Its role is to adapt gene expression programs in order to maintain cellular homeostasis and genome integrity in response to stresses. P53 is found mutated in about half of human cancers and most mutations are clustered within the DNA-binding domain of the protein resulting in altered p53 transcriptional activity. This illustrates the importance of the gene regulations achieved by p53. The aim of this review is to provide a global overview of the current understanding of p53 transcriptional activities and to discuss some ongoing questions and unresolved points about p53 transcriptional activity.
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Affiliation(s)
- Jean-François Millau
- Service of Genetics, Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, 3001, 12th Avenue North, Sherbrooke J1H 5N4, QC, Canada
| | - Nathalie Bastien
- Service of Genetics, Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, 3001, 12th Avenue North, Sherbrooke J1H 5N4, QC, Canada
| | - Régen Drouin
- Service of Genetics, Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, 3001, 12th Avenue North, Sherbrooke J1H 5N4, QC, Canada.
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30
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Enzyme-Linked Electrochemical Detection of PCR-Amplified Nucleotide Sequences Using Disposable Screen-Printed Sensors. Applications in Gene Expression Monitoring. SENSORS 2008; 8:193-210. [PMID: 27879703 PMCID: PMC3681127 DOI: 10.3390/s8010193] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2007] [Accepted: 01/07/2008] [Indexed: 11/17/2022]
Abstract
Electrochemical enzyme-linked techniques for sequence-specific DNA sensing are presented. These techniques are based on attachment of streptavidin-alkaline phosphatase conjugate to biotin tags tethered to DNA immobilized at the surface of disposable screen-printed carbon electrodes (SPCE), followed by production and electrochemical determination of an electroactive indicator, 1-naphthol. Via hybridization of SPCE surface-confined target DNAs with end-biotinylated probes, highly specific discrimination between complementary and non-complementary nucleotide sequences was achieved. The enzyme-linked DNA hybridization assay has been successfully applied in analysis of PCR-amplified real genomic DNA sequences, as well as in monitoring of plant tissue-specific gene expression. In addition, we present an alternative approach involving sequence-specific incorporation of biotin-labeled nucleotides into DNA by primer extension. Introduction of multiple biotin tags per probe primer resulted in considerable enhancement of the signal intensity and improvement of the specificity of detection.
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31
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Laptenko O, Prives C. Transcriptional regulation by p53: one protein, many possibilities. Cell Death Differ 2007; 13:951-61. [PMID: 16575405 DOI: 10.1038/sj.cdd.4401916] [Citation(s) in RCA: 371] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The p53 tumor suppressor protein is a DNA sequence-specific transcriptional regulator that, in response to various forms of cellular stress, controls the expression of numerous genes involved in cellular outcomes including among others, cell cycle arrest and cell death. Two key features of the p53 protein are required for its transcriptional activities: its ability to recognize and bind specific DNA sequences and to recruit both general and specialized transcriptional co-regulators. In fact, multiple interactions with co-activators and co-repressors as well as with the components of the general transcriptional machinery allow p53 to either promote or inhibit transcription of different target genes. This review focuses on some of the salient features of the interactions of p53 with DNA and with factors that regulate transcription. We discuss as well the complexities of the functional domains of p53 with respect to these interactions.
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Affiliation(s)
- O Laptenko
- Department of Biological Sciences, Columbia University, 530 120th Street, New York, NY 10027, USA
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32
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Sasaki T, Gan EC, Wakeham A, Kornbluth S, Mak TW, Okada H. HLA-B-associated transcript 3 (Bat3)/Scythe is essential for p300-mediated acetylation of p53. Genes Dev 2007; 21:848-61. [PMID: 17403783 PMCID: PMC1838535 DOI: 10.1101/gad.1534107] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In response to DNA damage, p53 undergoes post-translational modifications (including acetylation) that are critical for its transcriptional activity. However, the mechanism by which p53 acetylation is regulated is still unclear. Here, we describe an essential role for HLA-B-associated transcript 3 (Bat3)/Scythe in controlling the acetylation of p53 required for DNA damage responses. Depletion of Bat3 from human and mouse cells markedly impairs p53-mediated transactivation of its target genes Puma and p21. Although DNA damage-induced phosphorylation, stabilization, and nuclear accumulation of p53 are not significantly affected by Bat3 depletion, p53 acetylation is almost completely abolished. Bat3 forms a complex with p300, and an increased amount of Bat3 enhances the recruitment of p53 to p300 and facilitates subsequent p53 acetylation. In contrast, Bat3-depleted cells show reduced p53-p300 complex formation and decreased p53 acetylation. Furthermore, consistent with our in vitro findings, thymocytes from Bat3-deficient mice exhibit reduced induction of puma and p21, and are resistant to DNA damage-induced apoptosis in vivo. Our data indicate that Bat3 is a novel and essential regulator of p53-mediated responses to genotoxic stress, and that Bat3 controls DNA damage-induced acetylation of p53.
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Affiliation(s)
- Toru Sasaki
- The Campbell Family Institute for Breast Cancer Research (CFIBCR), Ontario Cancer Institute (OCI), University Health Network, Toronto, Ontario M5G 2C1, Canada
| | - Eugene C. Gan
- Department of Pharmacology and Cancer Biology, C370 LSRC, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Andrew Wakeham
- The Campbell Family Institute for Breast Cancer Research (CFIBCR), Ontario Cancer Institute (OCI), University Health Network, Toronto, Ontario M5G 2C1, Canada
| | - Sally Kornbluth
- Department of Pharmacology and Cancer Biology, C370 LSRC, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Tak W. Mak
- The Campbell Family Institute for Breast Cancer Research (CFIBCR), Ontario Cancer Institute (OCI), University Health Network, Toronto, Ontario M5G 2C1, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 2C1, Canada
- Department of Immunology, University of Toronto, Toronto, Ontario M5G 2C1, Canada
| | - Hitoshi Okada
- The Campbell Family Institute for Breast Cancer Research (CFIBCR), Ontario Cancer Institute (OCI), University Health Network, Toronto, Ontario M5G 2C1, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 2C1, Canada
- Corresponding author.E-MAIL ; FAX (416) 204 2277
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Pivonková H, Pecinka P, Cesková P, Fojta M. DNA modification with cisplatin affects sequence-specific DNA binding of p53 and p73 proteins in a target site-dependent manner. FEBS J 2006; 273:4693-706. [PMID: 16981908 DOI: 10.1111/j.1742-4658.2006.05472.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Proteins p53 and p73 act as transcription factors in cell cycle control, regulation of cell development and/or in apoptotic pathways. Both proteins bind to response elements (p53 DNA-binding sites), typically consisting of two copies of a motif RRRCWWGYYY. It has been demonstrated previously that DNA modification with the antitumor drug cisplatin inhibits p53 binding to a synthetic p53 DNA-binding site. Here we demonstrate that the effects of global DNA modification with cisplatin on binding of the p53 or p73 proteins to various p53 DNA-binding sites differed significantly, depending on the nucleotide sequence of the given target site. The relative sensitivities of protein-DNA binding to cisplatin DNA treatment correlated with the occurrence of sequence motifs forming stable bifunctional adducts with the drug (namely, GG and AG doublets) within the target sites. Binding of both proteins to mutated p53 DNA-binding sites from which these motifs had been eliminated was only negligibly affected by cisplatin treatment, suggesting that formation of the cisplatin adducts within the target sites was primarily responsible for inhibition of the p53 or p73 sequence-specific DNA binding. Distinct effects of cisplatin DNA modification on the recognition of different response elements by the p53 family proteins may have impacts on regulation pathways in cisplatin-treated cells.
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Affiliation(s)
- Hana Pivonková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
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34
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Brázda V, Jagelská EB, Fojta M, Palecek E. Searching for target sequences by p53 protein is influenced by DNA length. Biochem Biophys Res Commun 2006; 341:470-7. [PMID: 16426567 DOI: 10.1016/j.bbrc.2005.12.202] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2005] [Accepted: 12/28/2005] [Indexed: 11/16/2022]
Abstract
One of the most important functions of the tumor suppressor p53 protein is its sequence-specific binding to DNA. Using a competition assay on agarose gels we found that the p53 consensus sequences in longer DNA fragments are better targets than the same sequences in shorter DNAs. Semi-quantitative evaluation of the competition experiments showed a correlation between the relative p53-DNA binding and the DNA lengths. Our results are consistent with a model of the p53-DNA interactions involving one-dimensional migration of the p53 protein along the DNA for distances of about 1000 bp while searching for its target sites. Positioning of the p53 target in the DNA fragment did not substantially affect the apparent p53-DNA binding, suggesting that p53 can slide along the DNA in a bi-directional manner. In contrast to full-length p53, the isolated core domain did not show any significant correlation between sequence-specific DNA binding and fragment length.
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Affiliation(s)
- Václav Brázda
- Institute of Biophysics, Academy of Sciences of the Czech Republic, 612 65 Brno, Czech Republic.
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35
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Pivonková H, Brázdová M, Kaspárková J, Brabec V, Fojta M. Recognition of cisplatin-damaged DNA by p53 protein: Critical role of the p53 C-terminal domain. Biochem Biophys Res Commun 2006; 339:477-84. [PMID: 16300733 DOI: 10.1016/j.bbrc.2005.11.038] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2005] [Accepted: 11/03/2005] [Indexed: 11/21/2022]
Abstract
It was shown previously that the p53 protein can recognize DNA modified with antitumor agent cisplatin (cisPt-DNA). Here, we studied p53 binding to the cisPt-DNA using p53 deletion mutants and via modulation of the p53-DNA binding by changes of the protein redox state. Isolated p53 C-terminal domain (CTD) bound to the cisPt-DNA with a significantly higher affinity than to the unmodified DNA. On the other hand, p53 constructs involving the core domain but lacking the C-terminal DNA binding site (CTDBS) exhibited only small binding preference for the cisPt-DNA. Oxidation of cysteine residues within the CD of posttranslationally unmodified full length p53 did not affect its ability to recognize cisPt-DNA. Blocking of the p53 CTDBS by a monoclonal antibody Bp53-10.1 resulted in abolishment of the isolated CTD binding to the cisPt-DNA. Our results demonstrate a crucial role of the basic region of the p53 CTD (aa 363-382) in the cisPt-DNA recognition.
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Affiliation(s)
- Hana Pivonková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
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