An Excimer Clamp for Measuring Damaged-Base Excision by the DNA Repair Enzyme NTH1

Direct measurement of DNA repair enzyme activities is important both for the basic study of cellular repair pathways as well as for potential new translational applications in their associated diseases. NTH1, a major glycosylase targeting oxidized pyrimidines, prevents mutations arising from this damage, and the regulation of NTH1 activity is important in resisting oxidative stress and in suppressing tumor formation. Herein, we describe a novel molecular strategy for the direct detection of damaged DNA base excision activity by a ratiometric fluorescence change. This strategy utilizes glycosylase-induced excimer formation of pyrenes, and modified DNA probes, incorporating two pyrene deoxynucleotides and a damaged base, enable the direct, real-time detection of NTH1 activity in vitro and in cellular lysates. The probe design was also applied in screening for potential NTH1 inhibitors, leading to the identification of a new small-molecule inhibitor with sub-micromolar potency.     

Structural Basis for Bulky‐Adduct DNA‐Lesion Recognition by the Nucleotide Excision Repair Protein Rad14

Heterocyclic aromatic amines react with purine bases and result in bulky DNA adducts that cause mutations. Such structurally diverse lesions are substrates for the nucleotide excision repair (NER). It is thought that the NER machinery recognises and verifies distorted DNA conformations, also involving the xeroderma pigmentosum group A and C proteins (XPA, XPC) that act as a scaffold between the DNA substrate and several other NER proteins. Here we present the synthesis of DNA molecules containing the polycyclic, aromatic amine C8‐guanine lesions acetylaminophenyl, acetylaminonaphthyl, acetylaminoanthryl, and acetylaminopyrenyl, as well as their crystal structures in complex with the yeast XPA homologue Rad14. This work further substantiates the indirect lesion‐detection mechanism employed by the NER system that recognises destabilised and deformable DNA structures.     

Ribose‐Protonated DNA Base Excision Repair: A Combined Theoretical and Experimental Study

Living organisms protect the genome against external influences by recognizing and repairing damaged DNA. A common source of gene mutation is the oxidized guanine, which undergoes base excision repair through cleavage of the glycosidic bond between the ribose and the nucleobase of the lesion. We unravel the repair mechanism utilized by bacterial glycosylase, MutM, using quantum‐chemical calculations involving more than 1000 atoms of the catalytic site. In contrast to the base‐protonated pathway currently favored in the literature, we show that the initial protonation of the lesion’s ribose paves the way for an almost barrier‐free glycosidic cleavage. The combination of theoretical and experimental data provides further insight into the selectivity and discrimination of MutM’s binding site toward various substrates.     

浅谈2015年诺贝尔化学奖:DNA的损伤修复

DNA是生物体发挥功能的遗传基础,随时都承受着来自体内或体外环境的各种压力。这些压力可以使DNA的化学结构发生变化,即产生"DNA损伤";如果这些损伤不能被及时修复,会对生命体产生严重的后果。为了应对这样的挑战,细胞存在一系列的DNA损伤修复机制;这些机制的存在使得基因组在很长的时间内得以稳定维持。2015年度诺贝尔化学奖授予了托马斯·林达尔、保罗·莫德里奇以及阿齐兹·桑贾尔,以表彰他们在DNA损伤修复研究领域的杰出贡献。本文简述了DNA损伤修复机制研究的发展历程及其与人类健康密不可分的联系。     

Fluorescence Probes for ALKBH2 Allow the Measurement of DNA Alkylation Repair and Drug Resistance Responses

The DNA repair enzyme ALKBH2 is implicated in both tumorigenesis as well as resistance to chemotherapy in certain cancers. It is currently under study as a potential diagnostic marker and has been proposed as a therapeutic target. To date, however, there exist no direct methods for measuring the repair activity of ALKBH2 in vitro or in biological samples. Herein, we report a highly specific, fluorogenic probe design based on an oligonucleotide scaffold that reports directly on ALKBH2 activity both in vitro and in cell lysates. Importantly, the probe enables the monitoring of cellular regulation of ALKBH2 activity in response to treatment with the chemotherapy drug temozolomide through a simple fluorescence assay, which has only previously been observed through indirect means such as qPCR and western blots. Furthermore, the probe provides a viable high‐throughput assay for drug discovery.     

O6‐Alkylguanine DNA Alkyltransferase Repair Activity Towards Intrastrand Cross‐Linked DNA is Influenced by the Internucleotide Linkage

Oligonucleotides containing an alkylene intrastrand cross‐link (IaCL) between the O⁶‐atoms of two consecutive 2′‐deoxyguanosines (dG) were prepared by solid‐phase synthesis. UV thermal denaturation studies of duplexes containing butylene and heptylene IaCL revealed a 20 °C reduction in stability compared to the unmodified duplexes. Circular dichroism profiles of these IaCL DNA duplexes exhibited signatures consistent with B‐form DNA. Human O⁶‐alkylguanine DNA alkyltransferase (hAGT) was capable of repairing both IaCL containing duplexes with slightly greater efficiency towards the heptylene analog. Interestingly, repair efficiencies of hAGT towards these IaCL were lower compared to O⁶‐alkylene linked IaCL lacking the 5′‐3′‐phosphodiester linkage between the connected 2′‐deoxyguanosine residues. These results demonstrate that the proficiency of hAGT activity towards IaCL at the O⁶‐atom of dG is influenced by the backbone phosphodiester linkage between the cross‐linked residues.     

DNA Triplexes‐Guided Assembly of G‐Quadruplexes for Constructing Label‐free Fluorescent Logic Gates

Assembly of G‐quadruplexes guided by DNA triplexes in a controlled manner is achieved for the first time. The folding of triplex sequences in acidic conditions brings two separated guanine‐rich sequences together and subsequently a G‐quadruplex structure is formed in the presence of K⁺. Based on this novel platform, label‐free fluorescent logic gates, such as AND, INHIBIT, and NOR, are constructed with ions as input and the fluorescence of a G‐quadruplex‐specific fluorescent probe NMM as output.     

Fluorescent Nucleobase Analogues with Extended Pi Surfaces Stabilize DNA Duplexes Containing O6‐Alkylguanine Adducts

Chemical alkylation of DNA produces potentially toxic and mutagenic damage such as O⁶‐alkylguanine (O⁶‐alkylG) adducts. Non‐natural nucleoside analogues that pair with DNA adducts provide a potential basis for studying damaged DNA. Herein, we evaluated the base pairing properties of elongated nucleoside analogues containing napthalene‐derived tricyclic nucleobases as DNA adduct‐pairing nucleoside analogues in DNA hybridization probes. DNA duplex melting studies revealed that the elongated nucleoside analogs formed more stable base pairs opposite O⁶‐alkylG than G and were better able to distinguish between G, O⁶‐alkylG, and an abasic site than any previously described nucleoside analogue. DNA duplexes containing an elongated base analogue exhibited different fluorescence intensities when paired opposite O⁶‐alkylG vs. G or abasic sites. Their selectivity for stabilizing alkylated DNA make the elongated hydrophobic base analogues improved candidates for incorporating into DNA hybridization probes targeting O⁶‐alkylG.     

Imino‐ and Azasugar Protonation Inside Human Acid β‐Glucosidase,the Enzyme that is Defective in Gaucher Disease

Gaucher disease is caused by mutations in human acid β‐glucosidase or glucocerebrosidase (GCase), the enzyme responsible for hydrolysis of glucosyl ceramide in the lysosomes. Imino‐ and azasugars such as 1‐deoxynojirimycin and isofagomine are strong inhibitors of the enzyme and are of interest in pharmacological chaperone therapy of the disease. Despite several crystal structures of the enzyme with the imino‐ and azasugars bound in the active site having been resolved, the actual acid–base chemistry of the binding is not known. In this study we show, using photoinduced electron transfer (PET), that 1‐deoxynojirimycin and isofagomine derivatives are protonated by human acid β‐glucosidase when bound, even if they are completely unprotonated outside the enzyme. While isofagomine derivative protonation to some degree was foreshadowed by earlier crystal structures, 1‐deoxynojirimycin derivatives were not believed to act as basic amines in the enzyme.     

A Rotational BODIPY Nucleotide: An Environment‐Sensitive Fluorescence‐Lifetime Probe for DNA Interactions and Applications in Live‐Cell Microscopy

Fluorescent probes for detecting the physical properties of cellular structures have become valuable tools in life sciences. The fluorescence lifetime of molecular rotors can be used to report on variations in local molecular packing or viscosity. We used a nucleoside linked to a meso‐substituted BODIPY fluorescent molecular rotor ( dC^bdp ) to sense changes in DNA microenvironment both in vitro and in living cells. DNA incorporating dC^bdp can respond to interactions with DNA‐binding proteins and lipids by changes in the fluorescence lifetimes in the range 0.5–2.2 ns. We can directly visualize changes in the local environment of exogenous DNA during transfection of living cells. Relatively long fluorescence lifetimes and extensive contrast for detecting changes in the microenvironment together with good photostability and versatility for DNA synthesis make this probe suitable for analysis of DNA‐associated processes, cellular structures, and also DNA‐based nanomaterials.     

Fluorescence Quenching‐based Assay for Measuring Golgi endo‐α‐Mannosidase

Golgi endo‐α‐mannosidase (G‐EM) catalyzes an alternative deglucosylation process for N‐glycans and plays important roles in the post‐endoplasmic reticulum (ER) quality control pathway. To understand the post‐ER quality control mechanism, we synthesized a tetrasaccharide probe for the detection of the hydrolytic activity of G‐EM based on a fluorescence quenching assay. The probe was labeled with an N‐methylanthraniloyl group as a reporter dye at the non‐reducing end and a 2,4‐dinitrophenyl group as a quencher at the reducing end. This probe is hydrolyzed to disaccharide derivatives by G‐EM, resulting in increased fluorescence intensity. Thus, the fluorescence signal is directly proportional to the amount of disaccharide derivative present, allowing the G‐EM activity to be evaluated easily and quantitatively.