Influence of abasic and anucleosidic sites on the stability, conformation, and melting behavior of a DNA duplex: correlations of thermodynamic and structural data.

Vesnaver, Gorazd; Chang, Chien-Neng; Eisenberg, Moshe; Grollman, Arthur P.; Breslauer, Kenneth J.

doi:10.1073/pnas.86.10.3614

Cited by 120 publications

(100 citation statements)

References 21 publications

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“…Because this is clearly not the case, formation of apurinic sites may serve some functional role. Thus, apurinic sites also slightly destabilize DNA duplexes (24) and increase local DNA flexibility (25), which may, for example, facilitate formation of open DNA-protein complexes and͞or play a role in DNA packaging in viruses, in nucleosome formation or positioning, or in facilitating genetic recombination.…”

Section: Discussionmentioning

confidence: 99%

Self-catalyzed site-specific depurination of guanine residues within gene sequences

Amosova

Coulter

Fresco

2006

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

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A self-catalyzed, site-specific guanine-depurination activity has been found to occur in short gene sequences with a potential to form a stem-loop structure. The critical features of that catalytic intermediate are a 5 -G-T-G-G-3 loop and an adjacent 5 -T⅐A-3 base pair of a short duplex stem stable enough to fix the loop structure required for depurination of its 5 -G residue. That residue is uniquely depurinated with a rate some 5 orders of magnitude faster than that of random ''spontaneous'' depurination. In contrast, all other purine residues in the sequence depurinate at the spontaneous background rate. The reaction requires no divalent cations or other cofactors and occurs under essentially physiological conditions. Such stem-loops can form in duplex DNA under superhelical stress, and their critical sequence features have been found at numerous sites in the human genome. Self-catalyzed stem-loop-mediated depurination leading to flexible apurinic sites may therefore serve some important biological role, e.g., in nucleosome positioning, genetic recombination, or chromosome superfolding.DNA self-catalysis ͉ guanine depurination ͉ stem-loop structure D epurination in DNA has been recognized as a spontaneous form of intracellular DNA damage that affects both G and A residues in an essentially random way (1). In mammalian cells, such damage has been estimated to occur with a k obs of 3 ϫ 10 Ϫ9 min Ϫ1 (2). A complex and elaborate cellular DNA repair machinery has evolved to repair apurinic sites (3, 4). It has long been known that some G residues are more prone to depurination than others (5, 6), and such depurination hot spots have been associated with elevated mutation rates (6, 7). Notwithstanding these insights, notions to account for DNA depurination that go beyond recognition that hydrolysis of the purine-deoxyribose glycosyl bond is acid-catalyzed have not been forthcoming.In the course of studies using a 29-residue single-stranded coding strand fragment encompassing the mutation site of the sickle cell ␤-globin gene (8-10), we found that this 29-nt oligomer as well as its shortened 18-nt segment self-catalyze site-specific depurination of a singular G residue adjacent to the mutation site. In this report, we identify the precise location of the depurination site, the reaction mechanism and its immediate products, the structure of the catalytic intermediate, and some of the sequence requirements and their tolerance for variation within the intermediate. We also note the wide distribution of such putative self-depurinating sequences in the human genome. Results Specific Backbone Cleavage Is the Result of Site-Specific Depurination.It is as a consequence of slow spontaneous backbone cleavage at apurinic sites that the self-catalyzed site-specific depurination we report here was discovered. At the outset, it was observed that this cleavage occurs whether or not 10 Ϫ3 M EDTA is present, indicating that divalent cations are not required for the cleavage. Incubation of the highly purified and homogeneous 29-nt ol...

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Section: Discussionmentioning

confidence: 99%

Self-catalyzed site-specific depurination of guanine residues within gene sequences

Amosova

Coulter

Fresco

2006

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

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“…The aldehyde residue of abasic sites can generate an interstrand crosslink by reacting with the exocyclic amino group of a guanine base (34 ). Furthermore, abasic sites in DNA strongly destabilize the double helix (35 ), leading to local denaturation of the DNA. Because the rate of DNA damage in single-stranded DNA is higher than in double-stranded DNA, the DNA denaturation, induced by formaldehyde, may promote further DNA damage.…”

Section: Abasic Sitesmentioning

confidence: 99%

Sequence Artifacts in DNA from Formalin-Fixed Tissues: Causes and Strategies for Minimization

2015

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BACKGROUND: Precision medicine is dependent on identifying actionable mutations in tumors. Accurate detection of mutations is often problematic in formalinfixed paraffin-embedded (FFPE) tissues. DNA extracted from formalin-fixed tissues is fragmented and also contains DNA lesions that are the sources of sequence artifacts. Sequence artifacts can be difficult to distinguish from true mutations, especially in the context of tumor heterogeneity, and are an increasing interpretive problem in this era of massively parallel sequencing. Understanding of the sources of sequence artifacts in FFPE tissues and implementation of preventative strategies are critical to improve the accurate detection of actionable mutations.CONTENT: This mini-review focuses on DNA template lesions in FFPE tissues as the source of sequence artifacts in molecular analysis. In particular, fragmentation, base modification (including uracil and thymine deriving from cytosine deamination), and abasic sites are discussed as indirect or direct sources of sequence artifacts. We discuss strategies that can be implemented to minimize sequence artifacts and to distinguish true mutations from sequence artifacts. These strategies are applicable for the detection of actionable mutations in both single amplicon and massively parallel amplicon sequencing approaches.

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“…studies indicate that apurinic sites, apyrimidinic sites, and base mismatches all destabilize the double helix (45)(46)(47). Therefore, to further explore the structural basis for enhancement of enzyme-mediated DNA cleavage by spontaneous lesions, their effects on the stability of a topoisomerase II cleavage site were examined.…”

Section: Cleavage Enhancement Is Not Due To Destabilization Of the Domentioning

confidence: 99%

Spontaneous DNA Damage Stimulates Topoisomerase II-mediated DNA Cleavage

Kingma¹,

Osheroff

1997

Journal of Biological Chemistry

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Apurinic sites are position-specific poisons of topoisomerase II and stimulate DNA scission ϳ10 -18-fold when they are located within the 4-base overhang generated by enzyme-mediated cleavage (Kingma, P. S., and Osheroff, N. (1997) J. Biol. Chem. 272, 1148 -1155). To determine whether other major forms of spontaneous DNA damage also act as topoisomerase II poisons, the effects of position-specific apyrimidinic sites and deaminated cytosines (i.e. uracil:guanine mismatches) on the type II enzyme were determined. Both of these lesions stimulated topoisomerase II-mediated DNA scission with the same positional specificity as apurinic sites but were less efficacious. Moreover, apurinic sites dominated the effects of apyrimidinic sites in substrates that contained multiple lesions. The differential ability of spontaneous lesions to enhance DNA cleavage did not correlate with either a decreased stability of the double helix or the size of the gap formed by base loss. Rather, it appears to be due (at least in part) to increased rates of religation for substrates containing apyrimidinic sites or deaminated cytosines. These results suggest that several forms of spontaneous DNA damage are capable of acting as endogenous poisons of topoisomerase II.The integrity of the genetic material is constantly challenged by events that generate damage in DNA (1-3). An important source of this damage originates from spontaneous alterations within the double helix such as the loss of bases (i.e. generation of apurinic or apyrimidinic sites) and the deamination of cytosine residues (i.e. conversion of cytosine to uracil) (1, 3).Of all spontaneous DNA lesions, apurinic sites are the most commonly formed (1, 3). It is estimated that ϳ10,000 apurinic sites are created per mammalian cell on a daily basis (4). Although rates of spontaneous pyrimidine hydrolysis and cytosine deamination in duplex DNA are ϳ20-and 70-fold lower than that of purine loss (3), respectively, these lesions are frequently induced by exogenous mutagens such as UV irradiation, oxidation, and DNA-reactive chemicals (1, 3, 5-7).In addition to the reported mutagenic properties of apurinic/ apyrimidinic sites and deaminated cytosines (1, 3, 5-7), the induction of spontaneous damage in DNA by heat-acid treatment also enhances the formation of topoisomerase II-cleaved DNA complexes ϳ6-fold in vitro (8). These cleavage complexes are normally short-lived intermediates in the catalytic cycle of the enzyme and are tolerated by the cell (9 -12). However, conditions that shift the cleavage/religation equilibrium of the enzyme toward the cleaved state "poison" topoisomerase II and trigger numerous mutagenic events, such as insertions, deletions, illegitimate recombination, and potentially, cancer-related chromosomal translocations (13-19). When topoisomerase II-mediated DNA breaks are present in sufficient numbers, they initiate a programmed series of events that ultimately culminates in cell death (20 -23).The potentially lethal nature of topoisomerase II has been exploited by seve...

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Influence of abasic and anucleosidic sites on the stability, conformation, and melting behavior of a DNA duplex: correlations of thermodynamic and structural data.

Cited by 120 publications

References 21 publications

Self-catalyzed site-specific depurination of guanine residues within gene sequences

Self-catalyzed site-specific depurination of guanine residues within gene sequences

Sequence Artifacts in DNA from Formalin-Fixed Tissues: Causes and Strategies for Minimization

Spontaneous DNA Damage Stimulates Topoisomerase II-mediated DNA Cleavage

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