1
|
Giassa IC, Rynes J, Fessl T, Foldynova-Trantirkova S, Trantirek L. Advances in the cellular structural biology of nucleic acids. FEBS Lett 2018; 592:1997-2011. [PMID: 29679394 DOI: 10.1002/1873-3468.13054] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 03/31/2018] [Accepted: 04/09/2018] [Indexed: 01/01/2023]
Abstract
Conventional biophysical and chemical biology approaches for delineating relationships between the structure and biological function of nucleic acids (NAs) abstract NAs from their native biological context. However, cumulative experimental observations have revealed that the structure, dynamics and interactions of NAs might be strongly influenced by a broad spectrum of specific and nonspecific physical-chemical environmental factors. This consideration has recently sparked interest in the development of novel tools for structural characterization of NAs in the native cellular context. Here, we review the individual methods currently being employed for structural characterization of NA structure in a native cellular environment with a focus on recent advances and developments in the emerging fields of in-cell NMR and electron paramagnetic resonance spectroscopy and in-cell single-molecule FRET of NAs.
Collapse
Affiliation(s)
- Ilektra-Chara Giassa
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Jan Rynes
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Tomas Fessl
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Silvie Foldynova-Trantirkova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Institute of Biophysics, Academy of Science of the Czech Republic, Brno, Czech Republic
| | - Lukas Trantirek
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| |
Collapse
|
2
|
Affiliation(s)
- Emil Paleček
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, 612
65 Brno, Czech Republic
| | - Martin Bartošík
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, 612
65 Brno, Czech Republic
| |
Collapse
|
3
|
Paleček E, Bartošík M, Ostatná V, Trefulka M. Electrocatalysis in proteins, nucleic acids and carbohydrates. CHEM REC 2012; 12:27-45. [DOI: 10.1002/tcr.201100029] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Indexed: 11/06/2022]
|
4
|
Bartošík M, Gajdoš V, Kostečka P, Fojta M, Paleček E, Volkov E, Oretskaya T, Hianik T. Detection of Abasic Sites in DNA by Electrochemical, Immunoelectrochemical and Acoustic Methods Using OsO4, 2,2′-bipyridine as a Probe for Unpaired Thymine Residues. ELECTROANAL 2009. [DOI: 10.1002/elan.200804380] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
5
|
|
6
|
Trefulka M, Ferreyra N, Ostatná V, Fojta M, Rivas G, Paleček E. Voltammetry of Osmium End-Labeled Oligodeoxynucleotides at Carbon, Mercury, and Gold Electrodes. ELECTROANAL 2007. [DOI: 10.1002/elan.200703849] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
7
|
Trefulka M, Ostatná V, Havran L, Fojta M, Paleček E. Covalent Labeling of Nucleosides with VIII- and VI-Valent Osmium Complexes. ELECTROANAL 2007. [DOI: 10.1002/elan.200703848] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
8
|
|
9
|
Bui CT, Rees K, Cotton RGH. Permanganate oxidation reactions of DNA: perspective in biological studies. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2004; 22:1835-55. [PMID: 14533885 DOI: 10.1081/ncn-120023276] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
KMnO4 has been well known as a powerful chemical probe for numerous applications in biological fields, particularly for those used in conformational studies of DNA. The KMnO4 assay provides essential information for understanding biochemical processes and detecting aberrant DNA, which is associated with many genetic diseases. Elegant examples are sequencing techniques, foot-printing assays for transcriptional studies, an interference method for hormone receptor binding assays as well as DNA conformational studies of Z-DNA, Z-Z junctions, hairpins, curvatures, short nucleotide base repeats, binding of intercalators and groove binders, etc. Recently, KMnO4 has been successfully applied to detect single base changes and mutations in DNA (chemical cleavage of mismatch method, CCM) as well as other types of base damage (8-oxoguanine and thymine dimers). This paper aims to review the usefulness and limitations of the permanganate oxidation reaction used in various biological studies of DNA.
Collapse
Affiliation(s)
- Chinh T Bui
- Genomic Disorders Research Centre, The University of Melbourne, St. Vincent Hospital, Fitzroy, Melbourne, Australia.
| | | | | |
Collapse
|
10
|
|
11
|
Bůzek J, Kuderová A, Pexa T, Stanková V, Lauerová L, Palecek E. Monoclonal antibody against DNA adducts with osmium structural probes. J Biomol Struct Dyn 1999; 17:41-50. [PMID: 10496420 DOI: 10.1080/07391102.1999.10508339] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Osmium tetroxide complexes with nitrogen ligands (Os,L) have been widely used as probes of the DNA structure. A monoclonal antibody OsBP7H8 against DNA adducts with Os,L was produced in mice. OsBP7H8 does not bind to proteins or total yeast RNA modified with Os,2,2'-bipyridine (bipy) nor to the unmodified nucleic acids and proteins. The antibody recognizes DNA modified with Os,bipy (DNA-Os,bipy) or with OsO4,1,10-phenanthroline (DNA-Os,phen) but it does not cross-react with oxidized DNA and with DNA adducts of osmium tetroxide complexes with other ligands (such as pyridine, TEMED and bathophenanthroline disulfonic acid). The affinity of OsBP7H8 to DNA-Os,phen is about five-fold higher as compared to DNA-Os,bipy. The antibody can be thus applied either for recognition of single-stranded and distorted regions in DNA (after DNA modification with Os,bipy) or for detection of both single-stranded and double-stranded DNAs (after DNA modification with Os,phen). A new simplified procedure for the dot-blot analysis is proposed, not requiring the purification of DNA-osmium adduct prior to its application to the membrane.
Collapse
Affiliation(s)
- J Bůzek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská
| | | | | | | | | | | |
Collapse
|
12
|
|
13
|
Teijeiro C, Nejedlý K, Palecek E. Cyclic voltammetry of submicrogram quantities of supercoiled, linear and denatured DNAs with DNA-modified mercury electrode. J Biomol Struct Dyn 1993; 11:313-31. [PMID: 8286059 DOI: 10.1080/07391102.1993.10508729] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We have previously shown that a DNA-modified electrode can be prepared by immersing the hanging mercury drop electrode (HMDE) in a small volume (about 5-10 microliters) of a DNA solution. Within a short period of time the DNA is irreversibly adsorbed at the electrode, resisting subsequent washing. The electrode is then transferred into a voltammetric cell filled with the background electrolyte (that does not contain any nucleic acid) in which the voltammetric measurements are performed. This procedure is called adsorptive transfer stripping voltammetry (AdTSV). In this paper AdTS cyclic voltammetry (CV) peaks of DNA were measured to report on the stability of the attachment of plasmid DNA molecules to the electrode surface. It was shown that the attachment of plasmid DNA to the electrode was, like the case of calf thymus DNA, sufficiently stable. If the DNA-modified electrode was immersed in a protein solution no significant exchange between the DNA and protein was observed. Submicrogram amounts of DNA were sufficient to attain full coverage of the electrode at relatively short waiting times and the detection limit of the denatured DNA was below 2 ng. The intensity of the AdTS CV signals of supercoiled, linearized and thermally denatured linear DNAs differed from one another. It was shown that alkaline denaturation of linear and supercoiled DNA in solution can be studied using AdTS CV technique. It was further shown that at neutral pH the linearized plasmid undergoes denaturation due to a prolonged contact with the electrode charged to potentials around -1.2 V. Such a surface denaturation has been previously observed with calf thymus DNA and synthetic double-stranded polynucleotides. Our results show that in contrast to linear DNA, supercoiled DNA was not significantly denatured as a result of its prolonged contact with the electrode charged to various potentials in the range between -0.1 to -1.5 V.
Collapse
Affiliation(s)
- C Teijeiro
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno
| | | | | |
Collapse
|
14
|
Palecek E, Robert-Nicoud M, Jovin TM. Local opening of the DNA double helix in eukaryotic cells detected by osmium probe and adduct-specific immunofluorescence. J Cell Sci 1993; 104 ( Pt 3):653-61. [PMID: 8314868 DOI: 10.1242/jcs.104.3.653] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The structure of DNA in mouse fibroblast 3T3 cells has been investigated with the single-strand-selective probe, the complex of osmium tetroxide and 2,2′-bipyridine (Os,bipy). DNA-Os,bipy adducts in the cells were detected by immunofluorescence using a highly specific, affinity-purified polyclonal antibody. Treatment of living cells with the chemical probe led to a distinct but nonuniform nuclear staining. We attribute the positive nuclear staining to the existence of single-stranded and distorted DNA regions in the living cell. Confocal laser scanning microscopy revealed dark areas corresponding to nucleoli and regions of condensed chromatin. These conclusions were supported by the results of experiments in which the chemical probe was applied to fixed cells treated with 45% acetic acid or with acidic buffers (pH 1.8-2.5). An inverse staining pattern was obtained, characterized by intense immunofluorescence of the condensed chromatin regions. Thus, the structural transitions and/or chemical alterations (e.g. depurination) induced by acid treatment increase the accessibility of normally unreactive DNA bases. We conclude that open DNA structures recognized by the chemical probe in the cells prior to their fixation are contained mainly in decondensed and transcriptionally active chromatin, but are virtually absent from nucleoli and condensed chromatin.
Collapse
Affiliation(s)
- E Palecek
- Institute of Biophysics, Czechoslovak Academy of Sciences, Brno, CSFR
| | | | | |
Collapse
|
15
|
Affiliation(s)
- E Palecek
- Institute of Biophysics, Czechoslovak Academy of Sciences, Brno
| |
Collapse
|