Sequence-specific chemical modification of double-stranded DNA with alkylating oligodeoxyribonucleotide derivatives

Vlassov, V. V.; Gaidamakov, Sergei; Зарытова, В. Ф.; Knorre, D.G.; Левина, А. С.; Никонова, А. А.; Podust, Larisa M.; Fedorova, Olga S.

doi:10.1016/0378-1119(88)90158-8

Cited by 44 publications

(8 citation statements)

References 13 publications

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“…Several chemically reactive agents have been appended to TFOs and shown to cross-link within a pyrimidine motif triplex. These include 2-chloroethylamine (22), aziridine (23), N-bromoacetyl (24), binuclear platinum (25) and transplatin (26) reagents.…”

Section: Introductionmentioning

confidence: 99%

Factors influencing the extent and selectivity of alkylation within triplexes by reactive G/A motif oligonucleotides

Lampe

Kutyavin

Rhinehart

et al. 1997

Nucleic Acids Research

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G/A motif triplex-forming oligonucleotides (TFOs) complementary to a 21 base pair homopurine/homopyrimidine run were conjugated at one or both ends to chlorambucil. These TFOs were incubated with several synthetic duplexes containing the targeted homopurine run flanked by different sequences. The extent of mono and interstrand cross-linking was compared with the level of binding at equilibrium. Covalent modification took place within a triple-stranded complex and usually occurred at guanine residues in the flanking double-stranded DNA. The efficiency of alkylation was dependent upon the sequence of the flanking duplex, the solution conditions, and the rate of triplex formation relative to the rate of chlorambucil reaction. Self-association of the TFOs as parallel duplexes was demonstrated and this did not interfere with triple strand formation. With an optimal target, cross-linking of the triplex was very efficient when incubation was carried in a physiological buffer supplemented with the triplex selective intercalator coralyne.

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Section: Introductionmentioning

confidence: 99%

Factors influencing the extent and selectivity of alkylation within triplexes by reactive G/A motif oligonucleotides

Lampe

Kutyavin

Rhinehart

et al. 1997

Nucleic Acids Research

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“…Adducts of oligonucleotides covalently linked to a cleaving agent have been delivered to complementary sequences within duplex DNAs by both Watson-Crick base-pairing (D-loop formation) (2,10) and Hoogsteen base-pairing interactions (triple-helix formation) (4,5,8,9). Although there appears to be no sequence limitation to D-loop formation, its use is currently limited to supercoiled substrates.…”

mentioning

confidence: 99%

Site-specific cleavage of duplex DNA by a semisynthetic nuclease via triple-helix formation.

Pei

Corey

Schultz

1990

Proc. Natl. Acad. Sci. U.S.A.

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A Lys-84 --Cys mutant staphylococcal nu-clease was selectively linked to the 5' and/or 3' terminus of a thiol-containing polypyrimidine oligonucleotide via a disulfide bond. The oligonucleotide-staphylococcal nuclease adduct is capable of binding to a homopurine-homopyrimidine region of Watson-Crick duplex DNA by the formation of a triple-helical structure. Upon the addition of Ca2+, the nuclease cleaves DNA at sites adjacent to the homopurine tract. Specific doublestrand cleavage occurred predominantly at A+T-rich sites to the 5' side of the homopurine tract for both the 5'-derivatized and the 5',3'-diderivatized nucleases; the 3'-derivatized nuclease gave no cleavage. The cleavage pattern is asymmetric and consists of multiple cleavage sites shifted to the 5' side on each strand, centered at the terminal base pair of the binding site. Microgram amounts of plasmid pDP20 DNA (4433 base pairs) containing a homopurine-homopyrimidine tract were selectively cleaved by a semisynthetic nuclease with greater than 75% efficiency at room temperature within 1 hr. Cleavage reaction conditions were optimized with respect to pH, temperature, reaction times, and reaction components. Semisynthetic nucleases of this type should provide a powerful tool in chromosomal DNA manipulations.Restriction endonucleases are important tools for molecular cloning, genetic mapping, and other manipulations of nucleic acids. However, the recognition site sizes (4-8 bases) and sequence specificities of the naturally occurring enzymes limit their usefulness for many applications. The development of artificial or semisynthetic nucleases capable of highly specific DNA cleavage at any desired sequence would greatly facilitate DNA manipulations, especially physical chromosomal mapping (1). Strategies for generating nucleases of this type include the coupling ofoligonucleotides or DNA-binding proteins to either naturally occurring nucleases (2, 3), or oxidative or photoactive DNA cleaving moieties (4-9).Adducts of oligonucleotides covalently linked to a cleaving agent have been delivered to complementary sequences within duplex DNAs by both Watson-Crick base-pairing (D-loop formation) (2, 10) and Hoogsteen base-pairing interactions (triple-helix formation) (4,5,8,9). Although there appears to be no sequence limitation to D-loop formation, its use is currently limited to supercoiled substrates. Triple-helix formation, on the other hand, is limited largely to homopurine-homopyrimidine sequences, but it does not require supercoiled substrates (11). Previous examples of the triplehelix-directed cleavage of DNA have required a large excess of oligonucleotide-linked cleaving agents, resulting in oxidative cleavage of DNA with efficiencies generally below 25% (4,5,8,9). We report here the coupling of staphylococcal nuclease, an enzyme that efficiently but relatively nonspecifically hydrolyzes both single-stranded and doublestranded DNAs (12-14), to a homopyrimidine oligonucleotide. The resulting semisynthetic nuclease can bind to DNA via triple-heli...

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“…Alkylating agents such as the N-bromoacetyl group (POVSIC and DERVAN 1990;Povsic et al 1992;GRAND and DERVAN 1996), ethan-5-methycytidine (SHAW et al 1991b), or aromatic chloroethylamine (FEDOROVA et al 1988VLASSOV et al 1988) have been incorporated in TFOs so as to cause sequence specific alkylation of the underlying duplex. The alkylation at N7 of guanine, which is most susceptible for reaction by such a nucleophile, has been targeted in this strategy.…”

Section: A Introductionmentioning

confidence: 99%

Antisense Research and Application

1998

Handbook of Experimental Pharmacology

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Sequence-specific chemical modification of double-stranded DNA with alkylating oligodeoxyribonucleotide derivatives

Cited by 44 publications

References 13 publications

Factors influencing the extent and selectivity of alkylation within triplexes by reactive G/A motif oligonucleotides

Factors influencing the extent and selectivity of alkylation within triplexes by reactive G/A motif oligonucleotides

Site-specific cleavage of duplex DNA by a semisynthetic nuclease via triple-helix formation.

Antisense Research and Application

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