Thermodynamic and structural contributions of the 6-thioguanosine residue to helical properties of RNA

Gładysz, Michał; Andrałojć, Witold; Czapik, Tomasz; Gdaniec, Zofia; Kierzek, Ryszard

doi:10.1038/s41598-019-40715-2

Cited by 7 publications

(4 citation statements)

References 47 publications

(51 reference statements)

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“…These modifications resulted in significantly decreased melting temperatures of double helical oligonucleotides (Supporting Information, Figure S2; for 6sG see also ref. ). Furthermore, when we crystallized a short palindromic RNA duplex containing the A′ modification and solved its crystal structure at 1.0 Å resolution (Supporting Information, Figure S3 and Table S1), we found that the Watson–Crick mode for A′ pairing with U and the double helical geometry were retained (Figure B and Supporting Information, Figure S3), as encountered in the native duplex …”

Section: Resultsmentioning

confidence: 97%

Thioguanosine Conversion Enables mRNA‐Lifetime Evaluation by RNA Sequencing Using Double Metabolic Labeling (TUC‐seq DUAL)

Gasser¹,

Delazer

Neuner³

et al. 2020

Angewandte Chemie

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Temporal information about cellular RNAp opulations is essential to understand the functional roles of RNA. We have developed the hydrazine/NH 4 Cl/OsO 4 -based conversion of 6-thioguanosine (6sG) into A',w here A' constitutes a6hydrazino purine derivative.A' retains the Watson-Crickbasepair mode and is efficiently decoded as adenosine in primer extension assays and in RNAs equencing.B ecause 6sG is applicable to metabolic labeling of freshly synthesized RNA and because the conversion chemistry is fully compatible with the conversion of the frequently used metabolic label 4thiouridine (4sU) into C, the combination of both modified nucleosides in dual-labeling setups enables high accuracy measurements of RNAdecay. This approach, termed TUC-seq DUAL, uses the two modified nucleosides in subsequent pulses and their simultaneous detection, enabling mRNA-lifetime evaluation with unprecedented precision.

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Section: Resultsmentioning

confidence: 97%

Thioguanosine Conversion Enables mRNA‐Lifetime Evaluation by RNA Sequencing Using Double Metabolic Labeling (TUC‐seq DUAL)

Gasser¹,

Delazer

Neuner³

et al. 2020

Angewandte Chemie

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“…Menadione, also named VK3, is a redox cycling agent that has an antitumor effect against prostate, hepatic, lung, and breast cancer[ 32 , 33 ]. A previous study indicated that 6-thioguanosine, which inhibits PTHrP transcription, was used in the treatment of leukemia[ 34 ]. Phenoxybenzamine, a nonselective first-generation α1- and α2-AR antagonist, has been administered to treat lower urinary tract symptoms[ 35 ].…”

Section: Discussionmentioning

confidence: 99%

Development and validation of an epithelial–mesenchymal transition-related gene signature for predicting prognosis

Zhou¹,

Du²,

Fu³

et al. 2022

WJCC

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BACKGROUND Currently, there are many therapeutic methods for lung adenocarcinoma (LUAD), but the 5-year survival rate is still only 15% at later stages. Epithelial– mesenchymal transition (EMT) has been shown to be closely associated with local dissemination and subsequent metastasis of solid tumors. However, the role of EMT in the occurrence and development of LUAD remains unclear. AIM To further elucidate the value of EMT-related genes in LUAD prognosis. METHODS Univariate, least absolute shrinkage and selection operator, and multivariate Cox regression analyses were applied to establish and validate a new EMT-related gene signature for predicting LUAD prognosis. The risk model was evaluated by Kaplan–Meier survival analysis, principal component analysis, and functional enrichment analysis and was used for nomogram construction. The potential structures of drugs to which LUAD is sensitive were discussed with respect to EMT-related genes in this model. RESULTS Thirty-three differentially expressed genes related to EMT were found to be highly associated with overall survival (OS) by using univariate Cox regression analysis (log2FC ≥ 1, false discovery rate < 0.001). A prognostic signature of 7 EMT-associated genes was developed to divide patients into two risk groups by high or low risk scores. Kaplan–Meier survival analysis showed that the OS of patients in the high-risk group was significantly poorer than that of patients in the low-risk group ( P < 0.05). Multivariate Cox regression analysis showed that the risk score was an independent risk factor for OS (HR > 1, P < 0.05). The results of receiver operator characteristic curve analysis suggested that the 7-gene signature had a perfect ability to predict prognosis (all area under the curves > 0.5). CONCLUSION The EMT-associated gene signature classifier could be used as a feasible indicator for predicting OS.

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“…Similarly, TUC-seq has been upgraded to TUC-seq DUAL method [ 119 ], which first uses NH

Cl and OsO

to oxidize 6SG to 6-sulfoguanosine (6soG), and then converts 6soG to 6-hydrazino-2-aminopurine ( 28 ) in a buffered hydrazine solution. The thermodynamic stability of ( 28 )-U pair is comparable to that of the natural A-U pair in short RNA oligonucleotides, but neither the pair of U-6SG nor U-6soG is stable [ 120 ]. In addition, the primer extension experiment using Superscript III reverse transcriptase revealed that 6SG and ( 28 ) had a moderate blocking effect on RT and were recognized as G and A, respectively, but 6soG had a high blocking rate and was recognized as G. The cellular 6SG/4SU dual labeling experiments demonstrated the feasibility of TUC-seq DUAL.…”

Section: Chemical Sequencing Methods For Detecting Artificial Nucleos...mentioning

confidence: 99%

Determining RNA Natural Modifications and Nucleoside Analog-Labeled Sites by a Chemical/Enzyme-Induced Base Mutation Principle

Bao

Liu

2023

Molecules

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The natural chemical modifications of messenger RNA (mRNA) in living organisms have shown essential roles in both physiology and pathology. The mapping of mRNA modifications is critical for interpreting their biological functions. In another dimension, the synthesized nucleoside analogs can enable chemical labeling of cellular mRNA through a metabolic pathway, which facilitates the study of RNA dynamics in a pulse-chase manner. In this regard, the sequencing tools for mapping both natural modifications and nucleoside tags on mRNA at single base resolution are highly necessary. In this work, we review the progress of chemical sequencing technology for determining both a variety of naturally occurring base modifications mainly on mRNA and a few on transfer RNA and metabolically incorporated artificial base analogs on mRNA, and further discuss the problems and prospects in the field.

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Thermodynamic and structural contributions of the 6-thioguanosine residue to helical properties of RNA

Cited by 7 publications

References 47 publications

Thioguanosine Conversion Enables mRNA‐Lifetime Evaluation by RNA Sequencing Using Double Metabolic Labeling (TUC‐seq DUAL)

Thioguanosine Conversion Enables mRNA‐Lifetime Evaluation by RNA Sequencing Using Double Metabolic Labeling (TUC‐seq DUAL)

Development and validation of an epithelial–mesenchymal transition-related gene signature for predicting prognosis

Determining RNA Natural Modifications and Nucleoside Analog-Labeled Sites by a Chemical/Enzyme-Induced Base Mutation Principle

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