DNA oligonucleotides with A, T, G or C opposite an abasic site: structure and dynamics

Chen, Jingyang; Dupradeau, François‐Yves; Case, David A.; Turner, Christopher J.; Stubbe, JoAnne

doi:10.1093/nar/gkm622

Cited by 63 publications

(66 citation statements)

References 42 publications

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“…Influence of DNA Sequence on Insertion Specificity Opposite an AP Site-It has long been recognized that the conformations and dynamics of an AP site, in the context of duplex DNA, are dependent on the nucleotide opposite this site and the surrounding DNA sequence (54,55). When pyrimidines are positioned opposite an AP site, the local structure is more perturbed than when purines are opposite this lesion.…”

Section: Discussionmentioning

confidence: 99%

DNA Polymerase β Substrate Specificity

Beard

Shock

Batra

et al. 2009

Journal of Biological Chemistry

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Apurinic/apyrimidinic (AP) sites are continuously generated in genomic DNA. Left unrepaired, AP sites represent noninstructional premutagenic lesions that are impediments to DNA synthesis. When DNA polymerases encounter an AP site, they generally insert dAMP. This preferential insertion is referred to as the A-rule. Crystallographic structures of DNA polymerase (pol) ␤, a family X polymerase, with active site mismatched nascent base pairs indicate that the templating (i.e. coding) base is repositioned outside of the template binding pocket thereby diminishing interactions with the incorrect incoming nucleotide. This effectively produces an abasic site because the template pocket is devoid of an instructional base. However, the template pocket is not empty; an arginine residue (Arg-283) occupies the space vacated by the templating nucleotide. In this study, we analyze the kinetics of pol ␤ insertion opposite an AP site and show that the preferential incorporation of dAMP is lost with the R283A mutant. The crystallographic structures of pol ␤ bound to gapped DNA with an AP site analog (tertrahydrofuran) in the gap (binary complex) and with an incoming nonhydrolyzable dATP analog (ternary complex) were solved. These structures reveal that binding of the dATP analog induces a closed polymerase conformation, an unstable primer terminus, and an upstream shift of the templating residue even in the absence of a template base. Thus, dATP insertion opposite an abasic site and dATP misinsertions have common features.DNA polymerases are responsible for template-directed DNA synthesis during genomic replication and repair. Genomic DNA is continuously assaulted with endogenous and environmental stresses that result in steady-state levels of 50,000 -200,000 apurinic/apyrimidinic (AP) 2 sites per eukaryotic cell (1). AP sites are generated through spontaneous or enzymatic hydrolysis of the N-glycosyl bond between the deoxyribose and base. The rate of spontaneous depurination has been estimated to be ϳ10,000/cell/day (2, 3). In addition, AP sites are produced as intermediates during the base excision repair of oxidized and alkylated bases. Left unrepaired, AP sites represent noninstructional premutagenic lesions that can block DNA synthesis. When DNA polymerases confront an AP site, they generally insert dAMP. This preferential insertion has become known as the A-rule (4).The sugar of a natural AP site is in equilibrium between three species as follows: the ␣-and ␤-hemiacetals and the open chain aldehyde. The predominant form in solution is the closed hemiacetal with the ring-opened form representing less than 1% of the total AP sites at equilibrium (5). Tetrahydrofuran (THF) (Fig. 1A) is a useful and accepted AP site analog to study the repair of AP sites or the influence of such lesions on polymerase function. Additionally, crystallographic structures of DNA polymerases from various families bound to THF-containing DNA are available (6 -10).DNA polymerase (Pol) ␤ contributes two enzymatic activities during the repair of simple...

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Section: Discussionmentioning

confidence: 99%

DNA Polymerase β Substrate Specificity

Beard

Shock

Batra

et al. 2009

Journal of Biological Chemistry

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“…103,[105][106][107][108] More recent structures were determined for oligonucleotides containing a hemiacetal abasic site (both a and b) opposite all four canonical bases. 109,110 In all cases the orphaned base was in an intrahelical conformation. The helical location of the abasic residue is determined by the orphaned base: purine-intrahelical and pyrimidine-extrahelical.…”

Section: Abasic Site Recognitionmentioning

confidence: 96%

“…The extrahelical conformation is a result of transient hydrogen bonds being formed between the orphaned pyrimidine base and a purine base on the 3 0 side of the abasic site. 110 Despite these variations, the site is recognized and repaired by the same enzyme. APE1 can process abasic sites regardless of sequence, moreover APE1 recognizes and binds to most, if not all of the abasic analogs studied, including those where the sugar is replaced with propyl chains.…”

Section: Abasic Site Recognitionmentioning

confidence: 99%

Recognition of Damaged DNA: Structure and Dynamic Markers

Germann

Johnson

Spring

2010

Medicinal Research Reviews

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DNA damage, a consequence of external factors and inherent metabolic processes, is omnipresent. Nature has devised multiple strategies to safeguard the genetic information and developed intricate repair mechanisms and pathways to reverse an array of different DNA lesions, including mismatches. Failure of the DNA repair systems may result in mutation, premature ageing, and cancer. In this review, we focus on structural and dynamic aspects of detection of lesions in base excision and mismatch repair. A thorough understanding of repair, pathways, and regulation is necessary to develop strategies for targeting DNA-related pathologies.

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“…9 Given that the DNA is weakened at these abasic sites, the chain undergoes cleavage by b-elimination within a few days. 8,10 Because these processes are acid and base catalyzed, respectively 11 the methods to enhance the stability of DNA in aqueous pharmaceutical formulations usually rely in controlling the solution pH. 12 Additionally, most methods used for maintaining plasmid integrity in solution involve controlling the temperature (DNA samples are stored at À808C, À208C or in liquid nitrogen) or the characteristics of the storage medium, like ionic strength, the presence of metal ions, metal chelators, antioxidants/scavengers or cationic agents (e.g., lipids, polymers), etc.…”

Section: Introductionmentioning

confidence: 99%