Cleavage Of Double Helical DNA Research Articles

Sequence-selective recognition and cleavage of double-helical DNA.

Single sites within long double-helical DNA molecules can be recognized by a variety of mechanisms. Different strategies have been used to adapt sequence-specific recognition to sequence-specific cleavage of duplex DNA. Any nucleic acid can be converted into an artificial nuclease by the attachment of a cleaving reagent. Alternatively, a sequence-specific ligand can be used to protect a methylase recognition site from methylation. The protected site may then be cleaved selectively by a restriction endonuclease (the so-called 'Achilles heel' cleavage technique). Recent developments in this area have shown that it is possible to cleave chromosomal DNA at single sites within bacterial and eukaryotic genomes.

Cleavage of double helical DNA by Cu2+ ion in the presence of bisintercalator containing penta(ethylene glycol) connector chain

In designing new DNA recognizing and cleaving reagents, we introduce herein a bisacridine derivative (referred to as bisacridine) in which two acridine heterocycles are connected by a penta(ethylene glycol) bridging chain. This compound offers two possible functions: 1, stabilization of DNA bisacridine intercalator complex by metal ion. The penta(ethylene glycol) chain stabilizes metal ions binding to the phosphate site of DNA, where the penta(ethylene glycol) chain constitutes a part of a pseudomacrocyclic ligand for metal binding; and 2, enhancement of metal-assisted hydrolytic cleavage of DNA by means of a metal concentration effect by the pseudomacrocyclic ethereal chain. The binding isotherms of bisacridine with DNA in the presence of metal ions showed that the binding was mainly governed by the cation exchange reaction on the anionic DNA polymer chain, i.e., the exchange between metal ions and the cationic bisacridine. The bisacridine showed an increase DNA binding ability compared to quinacrine, the monoacridine counterpart, and caused an enhancement of DNA cleavage in the presence of Cu2+ ions. Additional experiments which included DNase 1 footprinting in the presence of bisacridine and the DNA cleavage by Cu2+/bisacridine using a 32P end-labelled DNA fragment, suggested that the Cu2(+)-assisted DNA cleavage sites in the presence of bisacridine were in reasonable overlap with the DNA binding sites of bisacridine.

ChemInform Abstract: Design and Chemical Synthesis of a Sequence‐Specific DNA‐Cleaving Protein.

We report the design and chemical synthesis of a sequence-specific DNA-cleaving protein consisting wholly of naturally occurring α-amino acids. The tripeptide, H-glyglyhis-OH (GGH), which is a consensus sequence for the copper-binding domain of serum albumin, was attached to the amino terminus of the DNA-binding domain of Hin recombinase (residues 139-190) to afford a new 55-residue protein, GGH(Hin 139-190) with two structural domains each with distinct functions, sequence-specific recognition, and cleavage of double helical DNA (Figure 1). The designed protein was synthesized by solid-phase techniques and shown, by footprinting, to be competent to bind at pM concentrations to four Hin sites, each 13 base pairs in length. In the presence of Cu(II), hydrogen peroxide, and sodium ascorbate, strong cleavage of DNA by GGH(Hin 139-190) occurs at one of the four sites by oxidative degradation of the deoxyribose backbone.

Double strand cleavage of genomic DNA at a single site by triple helix formation

The sequence-specific cleavage of double helical DNA by restriction endonucleases is essential for many techniques in molecular biology, including gene isolation, DNA sequencing, and recombinant DNA manipulations. With the advent of pulsed-field gel electrophoresis, the separation of large segments of DNA is now possible. However, the recognition sequences of naturally occurring restriction enzymes are in the range of 4-8 base pairs, and hence their sequence specificites may be inadequate for isolating genes from large chromosomes (10^8 base pairs in size) or mapping genomic DNA.

Sequence-specific cleavage of double helical DNA by triple helix formation.

Homopyrimidine oligodeoxyribonucleotides with EDTA-Fe attached at a single position bind the corresponding homopyrimidine-homopurine tracts within large double-stranded DNA by triple helix formation and cleave at that site. Oligonucleotides with EDTA.Fe at the 5' end cause a sequence specific double strand break. The location and asymmetry of the cleavage pattern reveal that the homopyrimidine-EDTA probes bind in the major groove parallel to the homopurine strand of Watson-Crick double helical DNA. The sequence-specific recognition of double helical DNA by homopyrimidine probes is sensitive to single base mismatches. Homopyrimidine probes equipped with DNA cleaving moieties could be useful tools for mapping chromosomes.

Antitumor antibiotics drug design. Part II. Synthesis of 4-ethylamido [5,(2′-thienyl)-2-thiophene] imidazole iron(II) complex, a new N 2S 2-metallocycle with a ‘built in’ intercalating moiety which causes DNA scissioning In Vitro

A new metal chelating moiety, 4-ethylamido [5,(2′- thienyl)-2-thiophene]imidazole iron(II) ( 1) was synthesized and showed antitumor activity in vitro. The bisthiophene moiety which sterically resembles the bithiazole units of bleomycin may allow us to probe further the mechanism of antitumor action by bleomycin. The cyclic voltammetry for the new compound 1 in DMSO showed a nearly reversible Fe 3+/Fe 2+ transition. The electron spin resonance spectrum consisted of a fairly broad band resonance centered at g = 2.00989, similar to that of a bleomycin-Fe 2+ complex. The new compound 1 causes cleavage of double helical DNA without the requirement of an extra intercalating group.

Synthesis of porphyrin(Fe)-intercalators which cause DNA scission

New Porphyrin(Fe)-intercalators were synthesized. We chose 2-aminodipyrido[1,2-a: 3′,2′-d]imidazones (Glu-P's), which were muta-carcinogens isolated from a pyrolysate of L-glutamic acid, as intercalator moieties. These porphyrin(Fe)-intercalators cause cleavage of double helical DNA.

Cleavage of double helical DNA by methidium-propyl-EDTA-iron(II)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCleavage of double helical DNA by methidium-propyl-EDTA-iron(II)Robert P. Hertzberg and Peter B. DervanCite this: J. Am. Chem. Soc. 1982, 104, 1, 313–315Publication Date (Print):January 1, 1982Publication History Published online1 May 2002Published inissue 1 January 1982https://doi.org/10.1021/ja00365a069RIGHTS & PERMISSIONSArticle Views772Altmetric-Citations352LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (384 KB) Get e-Alerts Get e-Alerts