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Spectroscopic data for the G-quadruplex DNA to duplex DNA reaction.

ABSTRACT: This article describes additional data related to a research article entitled "Kinetics of Quadruplex to Duplex Conversion" (Mendoza et al. 2015 [1]). We followed the opening reaction of a series of intramolecular G-quadruplex structures by the addition of their corresponding complementary strand. Fluorolabeled complementary strands allowed to monitor the reaction in real-time. An adapted kinetic model was then applied in order to obtain the kinetic parameters of this reaction. We present a series of kinetic traces providing raw data of the G4 opening reaction and the fitting model applied in every case. In addition CD spectra and UV melting data is also provided to confirm the stability of all the DNA structures considered (G-quadruplex and duplex DNA).

SUBMITTER: Mendoza O

PROVIDER: S-EPMC4660241 | biostudies-literature | 2015 Dec

REPOSITORIES: biostudies-literature

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Spectroscopic data for the G-quadruplex DNA to duplex DNA reaction.

Mendoza Oscar O Elezgaray Juan J Mergny Jean-Louis JL

Data in brief 20151105

This article describes additional data related to a research article entitled "Kinetics of Quadruplex to Duplex Conversion" (Mendoza et al. 2015 [1]). We followed the opening reaction of a series of intramolecular G-quadruplex structures by the addition of their corresponding complementary strand. Fluorolabeled complementary strands allowed to monitor the reaction in real-time. An adapted kinetic model was then applied in order to obtain the kinetic parameters of this reaction. We present a seri ...[more]

PMID: 26693518

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Project description:Telomere shortening occurs during oxidative and inflammatory stress with guanine (G) as the major site of damage. In this work, a comprehensive profile of the sites of oxidation and structures of products observed from G-quadruplex and duplex structures of the human telomere sequence was studied in the G-quadruplex folds (hybrid (K(+)), basket (Na(+)), and propeller (K(+) + 50% CH3CN)) resulting from the sequence 5'-(TAGGGT)4T-3' and in an appropriate duplex containing one telomere repeat. Oxidations with four oxidant systems consisting of riboflavin photosensitization, carbonate radical generation, singlet oxygen, and the copper Fenton-like reaction were analyzed under conditions of low product conversion to determine relative reactivity. The one-electron oxidants damaged the 5'-G in G-quadruplexes leading to spiroiminodihydantoin (Sp) and 2,2,4-triamino-2H-oxazol-5-one (Z) as major products as well as 8-oxo-7,8-dihydroguanine (OG) and 5-guanidinohydantoin (Gh) in low relative yields, while oxidation in the duplex context produced damage at the 5'- and middle-Gs of GGG sequences and resulted in Gh being the major product. Addition of the reductant N-acetylcysteine (NAC) to the reaction did not alter the riboflavin-mediated damage sites but decreased Z by 2-fold and increased OG by 5-fold, while not altering the hydantoin ratio. However, NAC completely quenched the CO3(•-) reactions. Singlet oxygen oxidations of the G-quadruplex showed reactivity at all Gs on the exterior faces of G-quartets and furnished the product Sp, while no oxidation was observed in the duplex context under these conditions, and addition of NAC had no effect. Because a long telomere sequence would have higher-order structures of G-quadruplexes, studies were also conducted with 5'-(TAGGGT)8-T-3', and it provided oxidation profiles similar to those of the single G-quadruplex. Lastly, Cu(II)/H2O2-mediated oxidations were found to be indiscriminate in the damage patterns, and 5-carboxamido-5-formamido-2-iminohydantoin (2Ih) was found to be a major duplex product, while nearly equal yields of 2Ih and Sp were observed in G-quadruplex contexts. These findings indicate that the nature of the secondary structure of folded DNA greatly alters both the reactivity of G toward oxidative stress as well as the product outcome and suggest that recognition of damage in telomeric sequences by repair enzymes may be profoundly different from that of B-form duplex DNA.

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Spectroscopic data for the G-quadruplex DNA to duplex DNA reaction.

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Spectroscopic data for the G-quadruplex DNA to duplex DNA reaction.

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