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Stasińska AR, Putaj P, Chmielewski MK. Disulfide bridge as a linker in nucleic acids' bioconjugation. Part II: A summary of practical applications. Bioorg Chem 2019; 95:103518. [PMID: 31911308 DOI: 10.1016/j.bioorg.2019.103518] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 12/11/2019] [Accepted: 12/16/2019] [Indexed: 12/15/2022]
Abstract
Disulfide conjugation invariably remains a key tool in research on nucleic acids. This versatile and cost-effective method plays a crucial role in structural studies of DNA and RNA as well as their interactions with other macromolecules in a variety of biological systems. In this article we review applications of disulfide-bridged conjugates of oligonucleotides with other (bio)molecules such as peptides, proteins etc. and present key findings obtained with their help.
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Affiliation(s)
- Anna R Stasińska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, ul. Noskowskiego 12/14, 61-704 Poznań, Poland; FutureSynthesis sp. z o.o. ul. Rubież 46H, 61-612 Poznań, Poland
| | - Piotr Putaj
- FutureSynthesis sp. z o.o. ul. Rubież 46H, 61-612 Poznań, Poland
| | - Marcin K Chmielewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, ul. Noskowskiego 12/14, 61-704 Poznań, Poland; FutureSynthesis sp. z o.o. ul. Rubież 46H, 61-612 Poznań, Poland.
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2
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Abstract
This protocol presents a simple and general means of modifying nucleic acids with disulfide cross-links. These cross-links serve as powerful tools to probe the structure, dynamics, thermodynamics, folding, and function of DNA and RNA, much in the way that cystine cross-links have been used to study proteins. The chemistry described has been used to synthesize disulfide-cross-linked hairpins and duplexes, higher-order structures such as triplexes, non-ground-state conformations, and tRNAs. since the cross-links form quantitatively by mild air oxidation and do not purturb either secondary or tertiary structure, this modification should prove quite useful for the study of nucleic acids.
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Affiliation(s)
- Gary D Glick
- University of Michigan, Ann Arbor, Michigan, USA
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Tona R, Haner R. Crosslinking of diene-modified DNA with bis-maleimides. MOLECULAR BIOSYSTEMS 2005; 1:93-8. [PMID: 16880969 DOI: 10.1039/b418502a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The chemical crosslinking of modified nucleic acids via the Diels-Alder reaction is reported. For this purpose, 1,3-butadiene derived building blocks were incorporated into complementary oligodeoxynucleotides. Treatment of the obtained duplex with difunctional dienophiles results in the clean crosslinking of the two strands. Non-crosslinked adducts arising from a single Diels-Alder reaction of a maleimide to only one strand were not observed, indicating that the first reaction is the rate determining step of the overall process. Based on their thermal denaturation profiles, the crosslinked hybrids behave like two separate, hairpin-like structures, rather than like a single, continuous duplex.
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Affiliation(s)
- Rolf Tona
- Department of Chemistry, University of Bern, CH-3012 Bern, Switzerland
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Beltz H, Azoulay J, Bernacchi S, Clamme JP, Ficheux D, Roques B, Darlix JL, Mély Y. Impact of the terminal bulges of HIV-1 cTAR DNA on its stability and the destabilizing activity of the nucleocapsid protein NCp7. J Mol Biol 2003; 328:95-108. [PMID: 12684000 DOI: 10.1016/s0022-2836(03)00244-4] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Reverse transcription of HIV-1 genomic RNA to double-stranded DNA by reverse transcriptase (RT) is a critical step in HIV-1 replication. This process relies on two viral proteins, the RT enzyme and nucleocapsid protein NCp7 that has well documented nucleic acid chaperone properties. At the beginning of the linear DNA synthesis, the newly made minus-strand strong-stop DNA ((-)ssDNA) is transferred to the 3'end of the genomic RNA by means of an hybridization reaction between transactivation response element (TAR) RNA and cTAR DNA sequences. Since both TAR sequences exhibit stable hairpin structures, NCp7 needs to destabilize the TAR structures in order to chaperone their hybridization. To further characterize the relationships between TAR stability and NC-mediated destabilization, the role of the A(49) and G(52) bulged residues in cTAR DNA stability was investigated. The stability of cTAR and mutants where one or the two terminal bulges were replaced by base-pairs as well as the NCp7-mediated destabilization of these cTAR sequences were examined. Thermodynamic data indicate that the two bulges cooperatively destabilize cTAR by reducing the stacking interactions between the bases. This causes a free energy change of about 6.4 kcal/mol and seems to be critical for NC activity. Time-resolved fluorescence data of doubly labelled cTAR derivatives suggest that NC-mediated melting of cTAR ends propagates up to the 10C.A(44) mismatch or T(40) bulge. Fluorescence correlation spectroscopy using two-photon excitation was also used to monitor cTAR ends fraying by NC. Results show that NC causes a very significant increase of cTAR ends fraying, probably limited to the terminal base-pair in the case of cTAR mutants. Since the TAR RNA and cTAR DNA bulges or mismatches appear well conserved among all HIV-1 strains, the present data support the notion of a co-evolutionary relationship between TAR and NC activity.
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Affiliation(s)
- Hervé Beltz
- Laboratoire de Pharmacologie et Physico-Chimie des Interactions Cellulaires et Moléculaires, UMR 7034 CNRS, Faculté de Pharmacie, Université Louis Pasteur, Strasbourg 1, 74, Route du Rhin, 67401 Illkirch Cedex, France
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Bernacchi S, Stoylov S, Piémont E, Ficheux D, Roques BP, Darlix JL, Mély Y. HIV-1 nucleocapsid protein activates transient melting of least stable parts of the secondary structure of TAR and its complementary sequence. J Mol Biol 2002; 317:385-99. [PMID: 11922672 DOI: 10.1006/jmbi.2002.5429] [Citation(s) in RCA: 119] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The nucleocapsid protein NCp7 of HIV-1 possesses a nucleic acid chaperone activity that is critical in minus and plus strand transfer during reverse transcription. The minus strand transfer notably relies on the ability of NCp7 to destabilize the stable stem with five contiguous, double-stranded segments of both the TAR sequence at the 3' end of the viral genome and the complementary sequence, cTAR, in minus strong-stop DNA. In order to examine the nature and the extent of NCp7 destabilizing activity, we investigated, by absorbance and fluorescence spectroscopy, the interaction of TAR and cTAR with a (12-55)NCp7 peptide containing the zinc-finger motifs but lacking the ability to aggregate the oligonucleotides. The absorbance changes in the UV band of cTAR show that seven to eight base-pairs, on average, are melted per oligonucleotide at a ratio of one peptide to 7.5 nucleotides. In contrast, the melting of TAR does not exceed an average of one base-pair per oligonucleotide. This may be linked to the greater stability of TAR, since a strong correlation between NCp7 destabilizing effect and oligonucleotide stability was observed. The effect of (12-55)NCp7 on the stem terminus was investigated by using a cTAR molecule doubly labeled at the 3' and 5' ends by a donor/acceptor couple. In the absence of the peptide, about 80 % of the oligonucleotides are in a dark non-fluorescent state, having a close proximity of the two dyes. The remaining 20 % are distributed between three fluorescent species, having either the terminal segment, the two terminal segments or all segments of the stem melted. This is in line with a fraying mechanism wherein the stem terminus fluctuates rapidly between open and closed states. Addition of (12-55)NCp7 shifts the equilibrium toward the open species, suggesting that NC enhances fraying of the stem terminus. Taken together, our data suggest that NCp7 activates the transient opening of base-pairs in the least stable parts of the stem. Also, this activity of NCp7 was found to be dependent on the zinc-finger motifs, since no melting was observed with a fingerless NCp7 peptide.
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MESH Headings
- Base Pairing
- Base Sequence
- Capsid/chemistry
- Capsid/metabolism
- Capsid Proteins
- Crystallography, X-Ray
- Gene Products, gag/chemistry
- Gene Products, gag/metabolism
- HIV Long Terminal Repeat/genetics
- HIV-1/genetics
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/metabolism
- Sequence Alignment
- Spectrometry, Fluorescence
- Spectrophotometry, Ultraviolet
- Structure-Activity Relationship
- Viral Proteins
- Zinc Fingers
- gag Gene Products, Human Immunodeficiency Virus
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Affiliation(s)
- Serena Bernacchi
- Laboratoire de Pharmacologie et Physico-Chimie des Interactions Cellulaires et Moléculaires, UMR 7034 CNRS, Faculté de Pharmacie, Université Louis Pasteur, 74, Route du Rhin, Strasbourg 1, 67401, France
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Abstract
In this review I discuss straightforward and general methods to modify nucleic acid structure with disulfide cross-links. A motivating factor in developing this chemistry was the notion that disulfide bonds would be excellent tools to probe the structure, dynamics, thermodynamics, folding, and function of DNA and RNA, much in the way that cystine cross-links have been used to study proteins. The chemistry described has been used to synthesize disulfide cross-linked hairpins and duplexes, higher order structures like triplexes, nonground-state conformations, and tRNAs. Since the cross-links form quantitatively by mild air oxidation and do not perturb either secondary or tertiary structure, this modification should prove quite useful for the study of nucleic acids.
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Affiliation(s)
- G D Glick
- Department of Chemistry, University of Michigan, Ann Arbor 48109, USA.
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Abstract
Nucleic acid-derived drugs exhibit both chemical and physical instability. This mini-review focuses on the prevalent hydrolytic and oxidative pathways of chemical degradation as they are affected by various endogenous (primary structure, chemical modifications in bases, sugars and phosphate residues) and exogenous (pH, buffer concentration, metal cation presence, oxygen presence) factors.
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Affiliation(s)
- D Pogocki
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS 66047, USA
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Chemical ligation and recombination of DNA fragments through formation (exchange) of disulfide bonds located in the sugar-phosphate backbone. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2000. [DOI: 10.1007/bf02759167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Plessow R, Brockhinke A, Eimer W, Kohse-Höinghaus K. Intrinsic Time- and Wavelength-Resolved Fluorescence of Oligonucleotides: A Systematic Investigation Using a Novel Picosecond Laser Approach. J Phys Chem B 2000. [DOI: 10.1021/jp994132u] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Regina Plessow
- Physikalische Chemie I, Fakultät für Chemie, Universität Bielefeld, Universitätsstr. 25, D-33615 Bielefeld, Germany
| | - Andreas Brockhinke
- Physikalische Chemie I, Fakultät für Chemie, Universität Bielefeld, Universitätsstr. 25, D-33615 Bielefeld, Germany
| | - Wolfgang Eimer
- Physikalische Chemie I, Fakultät für Chemie, Universität Bielefeld, Universitätsstr. 25, D-33615 Bielefeld, Germany
| | - Katharina Kohse-Höinghaus
- Physikalische Chemie I, Fakultät für Chemie, Universität Bielefeld, Universitätsstr. 25, D-33615 Bielefeld, Germany
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Coleman RS, McCary JL, Perez RJ. Thionucleoside disulfides as covalent constraints of DNA conformation. Tetrahedron 1999. [DOI: 10.1016/s0040-4020(99)00704-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Maglott EJ, Glick GD. Probing structural elements in RNA using engineered disulfide cross-links. Nucleic Acids Res 1998; 26:1301-8. [PMID: 9469841 PMCID: PMC147396 DOI: 10.1093/nar/26.5.1301] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Three analogs of unmodified yeast tRNAPhe, each possessing a single disulfide cross-link, have been designed and synthesized. One cross-link is between G1 and C72 in the amino acid acceptor stem, a second cross-link is in the central D region of yeast tRNAPhe between C11 and C25 and the third cross-link bridges U16 and C60 at the D loop/T loop interface. Air oxidation to form the cross-links is quantitative and analysis of the cross-linked products by native and denaturing PAGE, RNase T1 mapping, Pb(II) cleavage, UV cross-linking and thermal denaturation demonstrates that the disulfide bridges do not alter folding of the modified tRNAs relative to the parent sequence. The finding that cross-link formation between thiol-derivatized residues correlates with the position of these groups in the crystal structure of native yeast tRNAPhe and that the modifications do not significantly perturb native structure suggests that this methodology should be applicable to the study of RNA structure, conformational dynamics and folding pathways.
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MESH Headings
- Base Sequence
- Cross-Linking Reagents
- Disulfides/chemistry
- Hot Temperature
- Magnetic Resonance Spectroscopy
- Models, Molecular
- Molecular Sequence Data
- Molecular Structure
- Nucleic Acid Conformation
- Nucleic Acid Denaturation
- RNA, Fungal/chemical synthesis
- RNA, Fungal/chemistry
- RNA, Fungal/genetics
- RNA, Transfer, Phe/chemical synthesis
- RNA, Transfer, Phe/chemistry
- RNA, Transfer, Phe/genetics
- Saccharomyces cerevisiae/genetics
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Affiliation(s)
- E J Maglott
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
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