Significance Damage to DNA bases due oxidative stress is thought be deleterious, leading stalled replication forks and mutations. Similarly, folding of strands into G-quadruplexes slows the progression polymerases, requiring specialized helicases for unfolding before transcription. In case damage in a G-quadruplex–forming sequence promoter, we show that presence lesion 8-oxoguanine (OG) leads an ∼300% increase gene expression. This concept was demonstrated by chemical synthesis segment...

The breadth and importance of RNA modifications are growing rapidly as modified ribonucleotides can impact the sequence, structure, function, stability, fate RNAs their interactions with other molecules. Therefore, knowing cellular at single-base resolution could provide important information regarding cell status fate. A current major limitation is lack methods that allow reproducible profiling multiple simultaneously, transcriptome-wide resolution. Here we developed RBS-Seq, a modification...

Oxidative damage to the genome can yield base 8-oxo-7,8-dihydroguanine (OG). In vitro studies suggested OG would preferentially form in 5′-GG-3′ sequence contexts after exposure reactive oxygen species. Herein, locations were studied by development of "OG-Seq" sites via next-generation sequencing at ∼0.15-kb resolution. The results this study found ∼10 000 regions enrichment WT mouse embryonic fibroblasts and ∼18 when repair glycosylase Ogg1 was knocked out. Gene promoters UTRs harbor more...

Telomere shortening occurs during oxidative and inflammatory stress with guanine (G) as the major site of damage. In this work, a comprehensive profile sites oxidation structures products observed from G-quadruplex duplex human telomere sequence was studied in folds (hybrid (K+), basket (Na+), propeller (K+ + 50% CH3CN)) resulting 5′-(TAGGGT)4T-3′ an appropriate containing one repeat. Oxidations four oxidant systems consisting riboflavin photosensitization, carbonate radical generation,...

G-quadruplex is a four-stranded G-rich DNA structure that highly susceptible to oxidation. Despite the important roles G-quadruplexes play in telomere biology and gene transcription, neither impact of guanine lesions on stability quadruplexes nor their repair are well understood. Here, we show oxidized 8-oxo-7,8-dihydroguanine (8-oxoG), guanidinohydantoin (Gh) spiroiminodihydantoin (Sp) reduce thermostability alter folding telomeric location-dependent manner. Also, NEIL1 NEIL3 glycosylases...

Uncontrolled inflammation or oxidative stress generates electron-deficient species that oxidize the genome increasing its instability in cancer. The G-quadruplex (G4) sequences regulating c-MYC, KRAS, VEGF, BCL-2, HIF-1α, and RET oncogenes, as examples, are targets for oxidation at loop 5'-core guanines (G) showcased this study by CO3•- of VEGF G4. Products observed include 8-oxo-7,8-dihydroguanine (OG), spiroiminodihydantoin (Sp), 5-guanidinohydantoin (Gh). Our previous studies found OG Gh,...

Zika virus has emerged as a global concern because neither vaccine nor antiviral compounds targeting it exist. A structure for the positive-sense RNA genome not been established, leading us to look potential G-quadruplex sequences (PQS) in genome. The analysis identified >60 PQSs To minimize PQS population, conserved Flaviviridae family were found by sequence alignment, identifying seven prM, E, NS1, NS3, and NS5 genes. Next, alignment of 78 strain genomes unique near end 3'-UTR. Structural...

Living in an oxygen atmosphere demands ability to thrive the presence of reactive species (ROS). Aerobic organisms have successfully found solutions oxidative threats imposed by ROS evolving elaborate detoxification system, upregulating during inflammation, and utilizing as messenger molecules. In this Perspective, recent studies are discussed that demonstrate signaling molecules for gene regulation combining two emergent properties guanine (G) heterocycle DNA, namely, oxidation sensitivity...

Strands of DNA with four or more contiguous runs 2'-deoxycytidine (dC) nucleotides have the potential to adopt i-motif folds, generally under mildly acidic conditions. Analysis dC homo-oligonucleotide strands ranging in length from 10 30 by five different pH-dependent methods identified a pattern strand vs stability. Beginning dC11, which does not fold, transition pH (pHT) increased chain addition up nucleotides, after stability dramatically decreased, and trend repeated this cycle dC27. The...

Interplay between DNA repair of the oxidatively modified base 8-oxo-7,8-dihydroguanine (OG) and transcriptional activation has been documented in mammalian genes. Previously, we synthesized OG into VEGF potential G-quadruplex sequence (PQS) coding strand a luciferase promoter to identify that excision (BER) unmasked (G4) fold for gene activation. In present work, was site-specifically reporter plasmid follow time-dependent expression cells when PQS context located vs template strands...

Direct RNA sequencing for the epitranscriptomic modification pseudouridine (Ψ), an isomer of uridine (U), was conducted with a protein nanopore sensor using helicase brake to slowly feed into sensor. Synthetic RNAs 100% Ψ or U in 20 different known human sequence contexts identified differences during base-calling, ionic current, and dwell time sensor; however, signals were found have dependency on context that would result biases when unknown samples. A solution challenge identification...

The bacterium Escherichia coli possesses 16S and 23S rRNA strands that have 36 chemical modification sites with 17 different structures. Nanopore direct RNA sequencing using a protein nanopore sensor helicase brake, which is also sensor, was applied to the rRNAs. current levels, base calling profile, dwell times for modifications relative unmodified synthetic controls found signatures nearly all modifications. Signatures clustered were determined by selective of writer knockout E. RNAs...

The ability to detect DNA damage within the context of surrounding sequence is an important goal in medical diagnosis and therapies, but there are no satisfactory methods available a damaged base while providing information. One most common lesions 8-oxo-7,8-dihydroguanine, which occurs during oxidation guanine. In work presented here, we demonstrate detection single oxidative site using ion channel nanopore employing α-hemolysin. Hydantoin produced from further as well spirocyclic adducts...

DNA abasic (AP) sites are one of the most frequent lesions in genome and have a high mutagenic potential if unrepaired. After selective attachment 2-aminomethyl-18-crown-6 (18c6), individual AP detected during electrophoretic translocation through bacterial protein ion channel α-hemolysin (α-HL) embedded lipid bilayer. Interactions between 18c6 Na + produce characteristic pulse-like current amplitude signatures that allow identification single molecules homopolymeric or heteropolymeric...

The human telomere repeat sequence 5′-TTAGGG-3′ is a hot spot for oxidation at guanine, yielding 8-oxo-7,8-dihydroguanine (OG), biomarker of oxidative stress. Telomere shortening resulting from will ultimately induce cellular senescence. In this study, α-hemolysin (α-HL) nanopore technology was applied to detect and quantify OG in the telomeric DNA sequence. This adopts basket G-quadruplex NaCl electrolyte used analysis that enters α-HL channel, slowly unfolds, translocates. fold containing...

Base excision repair is the major pathway for removal of oxidative DNA base damage. This initiated by glycosylases, which recognize and excise damaged bases from DNA. In this work, we have purified glycosylase domain (GD) human NEIL3. The substrate specificity has been characterized elucidated catalytic mechanisms. GD NEIL3 excised hydantoin lesions spiroiminodihydantoin (Sp) guanidinohydantoin (Gh) in single-stranded (ss) double-stranded (ds) efficiently. also removed...

Neural stem/progenitor cell proliferation and differentiation are required to replace damaged neurons regain brain function after hypoxic-ischemic events. DNA base lesions accumulating during stress removed by glycosylases in the base-excision repair pathway prevent cytotoxicity mutagenesis. Expression of glycosylase endonuclease VIII-like 3 (Neil3) is confined regenerative subregions embryonic perinatal brains. Here we show profound neuropathology Neil3-knockout mice characterized a reduced...

Abstract Damage to the genome is implicated in progression of cancer and stress-induced diseases. DNA lesions exist low levels, cannot be amplified by standard PCR because they are frequently strong blocks polymerases. Here, we describe a method for amplification lesion-containing which site identity could marked, copied sequenced. Critical this installation either dNaM or d5SICS nucleotides at lesion after processing via base excision repair process. These marker constitute an unnatural...

Reactive oxygen species attack both base and sugar moieties in DNA with a preference among the bases for reaction at guanine. In present study, 2′-deoxyguanosine (dG) was oxidized by copper-mediated Fenton reductants ascorbate or N-acetyl-cysteine, yielding oxidation on sugar. The primary lesions observed these studies include 2′-deoxyribonucleosides of 8-oxo-7,8-dihydroguanosine (dOG), spiroiminodihydantoin (dSp), guanidinohydantoin (dGh), oxazolone (dZ),...

The unzipping kinetics for lesion-containing DNA duplexes was studied in an α-hemolysin (α-HL) nanopore. lesion of focus the guanine two-electron oxidation product, 8-oxo-7,8-dihydroguanine (OG), and its further products, hydantoins guanidinohydantoin (Gh) spiroiminodihydantoin (Sp). voltage-driven individual duplex molecules with symmetrical overhangs carried out by pulling one strand through α-HL channel using electrical field. Entry from 3' or 5' end produced distinct current blockages,...

Human telomeric DNA consists of tandem repeats the sequence 5'-TTAGGG-3' that can fold into various G-quadruplexes, including hybrid, basket, and propeller folds. In this report, we demonstrate use α-hemolysin ion channel to analyze these subtle topological changes at a nanometer scale by providing structure-dependent electrical signatures through DNA-protein interactions. Whereas dimensions hybrid basket folds allowed them enter protein vestibule, exceeds size latch region, producing only...