DNA cleavage by Cu(II)-desferal: identification of C1′-hydroxylation as the initial event for DNA damage

Joshi, Rajendra; Likhite, S.M.; Kumar, R. Krishna; Ganesh, Krishna N.

doi:10.1016/0304-4165(94)90008-6

Cited by 16 publications

(8 citation statements)

References 33 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The primary site of DNA cleavage is located at position 14 that resides within one of the putative stem structures of the 46-mer. The catalyst also promotes DNA cleavage within a region located apart from the main cleavage site (16), as might be expected for a deoxyribozyme that makes use of an oxidative cleavage mechanism (20). Details from the further characterization of class II deoxyribozyme function will be reported elsewhere (N.C., R. Baliga, D. M. Crothers, and R.R.B., unpublished data).…”

Section: Resultsmentioning

confidence: 95%

Cleaving DNA with DNA

Carmi

Balkhi

Breaker

1998

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

244

165

View full text Add to dashboard Cite

A DNA structure is described that can cleave single-stranded DNA oligonucleotides in the presence of ionic copper. This ''deoxyribozyme'' can self-cleave or can operate as a bimolecular complex that simultaneously makes use of duplex and triplex interactions to bind and cleave separate DNA substrates. Bimolecular deoxyribozyme-mediated strand scission proceeds with a k obs of 0.2 min ؊1 , whereas the corresponding uncatalyzed reaction could not be detected. The duplex and triplex recognition domains can be altered, making possible the targeted cleavage of single-stranded DNAs with different nucleotide sequences. Several small synthetic DNAs were made to function as simple ''restriction enzymes'' for the site-specific cleavage of single-stranded DNA.DNA in biological systems exists primarily in duplex form where it serves almost exclusively as a storage system for genetic information. Outside the confines of cells, DNA in its single-stranded form can be made to perform both molecular recognition and catalysis-biochemical operations that were until recently thought to be possible only with macromolecules made of protein or RNA. For example, a number of DNA ''aptamers'' (1) can be made that function as ligands for proteins or as highly specific receptors for small organic molecules (2-4). In addition, certain single-stranded DNAs act as artificial enzymes (4-6), catalyzing such chemical reactions as phosphoester transfer (7-12), phosphoester formation (13), porphyrin metalation (14), phosphoramidate cleavage (15), and DNA cleavage (16). Most likely, DNA can be made to perform a much broader repertoire of catalytic activities (6).These capabilities of DNA conceivably can be exploited to create a variety of structured DNAs that perform useful tasks, either in vitro or in vivo, involving molecular recognition and catalysis. Such functional DNAs offer several advantages, including ease of synthesis and chemical stability, that might make attractive properties for polymers that serve as artificial receptors or as biocatalysts for various applications. Characteristics such as thermostability and solvent͞solute preferences could be conferred upon deoxyribozymes by using both rational and combinatorial methods of molecular design. Catalytic DNAs may offer distinct advantages over natural protein enzymes for operation under nonbiological conditions.In a previous study (16), we reported the isolation of two distinct types of deoxyribozymes (classes I and II) that undergo oxidative self-cleavage in the presence of copper ions. By using in vitro selection (17), class II self-cleaving DNAs have been further optimized for catalytic function, and the most active structure obtained from this process has been engineered to act as a ''restriction endonuclease'' for single-stranded DNA substrates. MATERIALS AND METHODSOligonucleotides. Synthetic DNAs were prepared by automated chemical synthesis (Keck Biotechnology Resource Laboratory, Yale University) and were purified by denaturing (8 M urea) PAGE prior to use. Double-stran...

show abstract

Section: Resultsmentioning

confidence: 95%

Cleaving DNA with DNA

Carmi

Balkhi

Breaker

1998

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

244

165

View full text Add to dashboard Cite

show abstract

“…Since this transcription factor is implicated in Ulnar‐Mammary syndrome,26 the discovery of metal‐binding activity in this protein will help to understand the role of metals in regulating the transcription activity that will eventually provide information about the cause of this genetic disorder. There is at least one report in which a copper complex of desferal, a drug used for clinical treatment of a genetic disorder, has been shown to cleave DNA 62. Desferal is a siderophore of microbial origin that is used in the treatment of thalassemia.…”

Section: Discussionmentioning

confidence: 99%

ATCUN‐like metal‐binding motifs in proteins: Identification and characterization by crystal structure and sequence analysis

2004

View full text Add to dashboard Cite

The amino terminal Cu(II)- and Ni(II)-binding (ATCUN) motif is a small metal-binding site found in the N-terminus of many naturally occurring proteins. The ATCUN motif has been implicated in DNA cleavage and has been shown to have antitumor activity. In proteins, the ATCUN motif is formed from a histidine in the third position, its preceding residue and the free N-terminus. Four nitrogen atoms from these three residues act as metal ligands. Knowledge of metal-binding geometry helps in the design of metal-binding peptides and in understanding of the mechanisms of metal-mediated functions. Since the N-terminus region of ATCUN-containing proteins is highly disordered, no geometrical features can be derived from the protein structures. However, the crystal structure of a small metal-bound ATCUN peptide shows that the nitrogen ligands form a distorted square planar geometry. Distance constraints derived from this designed peptide were used to search 1949 polypeptide chains to find ATCUN-like motifs in any position along the polypeptide chain. Only approximately 1.9% and approximately 0.3% of histidines are involved in partial and full ATCUN-like geometric features, respectively. These two datasets were compared with the dataset of all histidines. None of the ATCUN-like motifs occur in the middle of an alpha-helix or a beta-strand. Further sequence analysis revealed total conservation of ATCUN histidines in four proteins including the transcription factor TBX3, implicated in Ulnar-Mammary Syndrome. Our analysis suggests that the ATCUN-like motif in TBX3 is a potential metal-binding site, although a structural role was not completely ruled out. Metal-binding activity in TBX3, if confirmed, will help us to understand the role of metals in transcriptional regulation and is likely to cast light on the causes of some serious genetic disorders. A conformational role is suggested for ATCUN-like motifs in other proteins.

show abstract

“…Class I self-cleaving deoxyribozymes require Cu 2+ and ascorbate to promote DNA cleavage, whereas class II DNAs require only the addition of Cu 2+ as a cofactor. Class II self-cleaning deoxyribozymes [50] appear to catalyze the cleavage at one particular internucleotide linkage by promoting the attack of a hydroxyl radical at the 4¢ carbon [51], thereby initiating a series of rearrangements [52] that lead to loss of a nucleotide base and chain cleavage ( fig. 3 a).…”

Section: Dna-cleaving Deoxyribozymesmentioning

confidence: 99%

Deoxyribozymes: new activities and new applications

Emilsson

Breaker

2002

Cellular and Molecular Life Sciences (CMLS)

142

View full text Add to dashboard Cite

DNA in its single-stranded form has the ability to fold into complex three-dimensional structures that serve as highly specific receptors or catalysts. Only protein enzymes and ribozymes are known to be responsible for biological catalysis, but deoxyribozymes with kinetic parameters that rival ribozymes can be created in the laboratory. Some of these engineered DNA catalysts are showing surprising potential as therapeutic agents, which makes them biologically relevant if not biologically derived. If DNA's natural role is strictly genomic, how significant is its innate catalytic prowess? New examples of engineered deoxyribozymes serve as empirical examples of the potential for catalysis by DNA. These results indicate that the true catalytic power of DNA is limited by discovery and not by chemistry.

show abstract

DNA cleavage by Cu(II)-desferal: identification of C1′-hydroxylation as the initial event for DNA damage

Cited by 16 publications

References 33 publications

Cleaving DNA with DNA

Cleaving DNA with DNA

ATCUN‐like metal‐binding motifs in proteins: Identification and characterization by crystal structure and sequence analysis

Deoxyribozymes: new activities and new applications

Contact Info

Product

Resources

About