4.7 Article

Entropy-driven conformational transition of flexible Z-DNA to a novel non-B helix by double-methylated guanosine

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Multidisciplinary Sciences

ADAR1 masks the cancer immunotherapeutic promise of ZBP1-driven necroptosis

Ting Zhang et al.

Summary: ADAR1 is a determinant of resistance to ICB therapy by repressing immunogenic dsRNA and Z-RNA. CBL0137 is a small molecule that activates ZBP1, reverses ICB unresponsiveness, and induced necroptosis.

NATURE (2022)

Article Biochemistry & Molecular Biology

Selective and stable base pairing by alkynylated nucleosides featuring a spatially-separated recognition interface

Hidenori Okamura et al.

Summary: Unnatural base pairs (UBPs) with selective pairing properties have been widely used in nucleic acid-based technologies. In this study, we demonstrate a new design concept for achieving exclusive base pairing through the spatial separation of recognition units. By introducing alkynylated purines and pyridazines with pseudo-nucleobases, we successfully achieved stable and exclusive pairing properties in the DNA major groove. This study highlights the potential of separating the recognition interface as a strategy for developing new types of UBPs.

NUCLEIC ACIDS RESEARCH (2022)

Article Biochemistry & Molecular Biology

Parallel reaction pathways accelerate folding of a guanine quadruplex

Robert W. Harkness et al.

Summary: G-quadruplexes are nucleic acid structures that can influence biological processes such as gene transcription and DNA replication. Multiple folded conformations of a G4 sequence can coexist, potentially leading to accelerated folding rates via specific mechanisms. This study demonstrates that the presence of multiple pathways can significantly accelerate the folding of G4s, potentially by more than an order of magnitude.

NUCLEIC ACIDS RESEARCH (2021)

Article Multidisciplinary Sciences

Recognition of non-CpG repeats in Alu and ribosomal RNAs by the Z-RNA binding domain of ADAR1 induces A-Z junctions

Parker J. Nichols et al.

Summary: The study demonstrates the binding of Z alpha protein to various RNA sequences and adoption of Z-RNA conformation, specifically with non-CpG sequences. This work contributes to proposing a model of how Z alpha could influence the RNA binding specificity of ADAR1.

NATURE COMMUNICATIONS (2021)

Article Biochemistry & Molecular Biology

Systematic Approach to Find the Global Minimum of Relaxation Dispersion Data for Protein-Induced B-Z Transition of DNA

Kwang-Im Oh et al.

Summary: A new global search algorithm was developed to determine the dynamics and mechanism of protein binding, revealing that the α-helical segment plays a key role in the three-state conformational changes of the hZα(ADAR1)-DNA complex, providing information on the global minimum of the conformational transition process.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

Article Chemistry, Multidisciplinary

Unraveling the Kinetics of Spare-Tire DNA G-Quadruplex Folding

J. Tassilo Gruen et al.

Summary: This study unravels the folding dynamics of a G4 sequence containing five G-tracts from cMYC, a major oncogene, and dissects the individual kinetics and thermodynamics of the spare-tire mechanism of cMYC-G4.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2021)

Review Biochemistry & Molecular Biology

Non-Canonical Helical Structure of Nucleic Acids Containing Base-Modified Nucleotides

Thananjeyan Balasubramaniyam et al.

Summary: This review article summarizes the synthesis methods of chemically modified nucleotides, focusing on the methylation, bromination, and arylation of purines and pyrimidines at specific positions. It also introduces the non-canonical structures of nucleic acids containing these modifications.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

Article Cell Biology

ADAR1 interaction with Z-RNA promotes editing of endogenous double-stranded RNA and prevents MDA5-dependent immune activation

Richard de Reuver et al.

Summary: Disruption of the interaction between ADAR1 and Z-RNA leads to reduced A-to-I editing of dsRNA structures, triggering an MDA5/MAVS-mediated type I interferon response and causing the development of lethal autoinflammation.

CELL REPORTS (2021)

Review Chemistry, Multidisciplinary

Recent progress in non-native nucleic acid modifications

Luke K. McKenzie et al.

Summary: Natural RNA and DNA are used by Nature to store and process genetic information, but modified oligonucleotides at the nucleobase, sugar, and/or phosphate backbone level are widely used in medicine and technology to overcome limitations. This review provides an overview of non-native modifications and challenges in the design, synthesis, application, and outlook of novel modified oligonucleotides.

CHEMICAL SOCIETY REVIEWS (2021)

Article Biochemistry & Molecular Biology

Influenza Virus Z-RNAs Induce ZBP1-Mediated Necroptosis

Ting Zhang et al.

Article Multidisciplinary Sciences

Z-nucleic-acid sensing triggers ZBP1-dependent necroptosis and inflammation

Huipeng Jiao et al.

NATURE (2020)

Article Biochemistry & Molecular Biology

Dual conformational recognition by Z-DNA binding protein is important for the B-Z transition process

Chaehee Park et al.

NUCLEIC ACIDS RESEARCH (2020)

Article Chemistry, Medicinal

Thermodynamics of DNA Minor Groove Binders

Hasan Y. Alniss

JOURNAL OF MEDICINAL CHEMISTRY (2019)

Review Genetics & Heredity

Non-duplex G-Quadruplex Structures Emerge as Mediators of Epigenetic Modifications

Ananda Kishore Mukherjee et al.

TRENDS IN GENETICS (2019)

Article Biochemistry & Molecular Biology

Study of conformational transitions of i-motif DNA using time-resolved fluorescence and multivariate analysis methods

Sanae Benabou et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biochemistry & Molecular Biology

Polymorphic G:G mismatches act as hotspots for inducing right-handed Z DNA by DNA intercalation

Roshan Satange et al.

NUCLEIC ACIDS RESEARCH (2019)

Review Chemistry, Multidisciplinary

Chemical Regulation of DNA i-Motifs for Nanobiotechnology and Therapeutics

Manish Debnath et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2019)

Article Biochemistry & Molecular Biology

Stability and properties of Z-DNA containing artificial nucleobase 2′-O-methyl-8-methyl guanosine

Thananjeyan Balasubramaniyam et al.

BIOORGANIC & MEDICINAL CHEMISTRY (2019)

Review Chemistry, Organic

C8-Guanine modifications: effect on Z-DNA formation and its role in cancer

V. Vongsutilers et al.

ORGANIC & BIOMOLECULAR CHEMISTRY (2018)

Article Biochemistry & Molecular Biology

2 '-O-Methyl-8-methylguanosine as a Z-Form RNA Stabilizer for Structural and Functional Study of Z-RNA

Thananjeyan Balasubramaniyam et al.

MOLECULES (2018)

Article Biochemistry & Molecular Biology

Synthesis and incorporation of 13C-labeled DNA building blocks to probe structural dynamics of DNA by NMR

Felix Nussbaumer et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Multidisciplinary Sciences

RIPK1 counteracts ZBP1-mediated necroptosis to inhibit inflammation

Juan Lin et al.

NATURE (2016)

Article Biochemistry & Molecular Biology

Studying Z-DNA and B- to Z-DNA transitions using a cytosine analogue FRET-pair

Blaise Dumat et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Chemistry, Multidisciplinary

C-Linked 8-aryl guanine nucleobase adducts: biological outcomes and utility as fluorescent probes

Richard A. Manderville et al.

CHEMICAL SCIENCE (2016)

Article Biochemical Research Methods

NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy

Woonghee Lee et al.

BIOINFORMATICS (2015)

Article Chemistry, Medicinal

Single C8-Arylguanine Modifications Render Oligonucleotides in the Z-DNA Conformation under Physiological Conditions

Brian C. Train et al.

CHEMICAL RESEARCH IN TOXICOLOGY (2014)

Article Multidisciplinary Sciences

Widespread transient Hoogsteen base pairs in canonical duplex DNA with variable energetics

Heidi S. Alvey et al.

NATURE COMMUNICATIONS (2014)

Article Chemistry, Multidisciplinary

The G-Triplex DNA

Vittorio Limongelli et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2013)

Review Chemistry, Multidisciplinary

Molecular Engineering of Guanine-Rich Sequences: Z-DNA, DNA Triplexes, and G-Quadruplexes

Osman Doluca et al.

CHEMICAL REVIEWS (2013)

Article Biochemistry & Molecular Biology

Structural basis for Z-DNA binding and stabilization by the zebrafish Z-DNA dependent protein kinase PKZ

Matteo de Rosa et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Biochemistry & Molecular Biology

Incorporation of CC Steps into Z-DNA: Interplay between B-Z Junction and Z-DNA Helical Formation

Jameson R. Bothe et al.

BIOCHEMISTRY (2012)

Article Chemistry, Medicinal

Fluorescent C-Linked C8-Aryl-guanine Probe for Distinguishing syn from anti Structures in Duplex DNA

Richard A. Manderville et al.

CHEMICAL RESEARCH IN TOXICOLOGY (2012)

Article Biochemistry & Molecular Biology

Effects of 8-methylguanine on structure, stability and kinetics of formation of tetramolecular quadruplexes

Phong Lan Thao Tran et al.

BIOCHIMIE (2011)

Article Biochemistry & Molecular Biology

High regularity of Z-DNA revealed by ultra high-resolution crystal structure at 0.55 A†

Krzysztof Brzezinski et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Chemistry, Multidisciplinary

Solution structure of a DNA double helix with consecutive metal-mediated base pairs

Silke Johannsen et al.

NATURE CHEMISTRY (2010)

Article Chemistry, Organic

A non-empirical chromophoric interpretation of CD spectra of DNA G-quadruplex structures

Stefano Masiero et al.

ORGANIC & BIOMOLECULAR CHEMISTRY (2010)

Review Biochemistry & Molecular Biology

The triple helix: 50 years later, the outcome

Maria Duca et al.

NUCLEIC ACIDS RESEARCH (2008)

Review Chemistry, Physical

Using Xplor-NIH for NMR molecular structure determination

CD Schwieters et al.

PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY (2006)

Article Chemistry, Multidisciplinary

Direct observation of enhanced translocation of a homeodomain between DNA cognate sites by NMR exchange spectroscopy

J Iwahara et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)

Article Chemistry, Multidisciplinary

(P)-helicene displays chiral selection in binding to Z-DNA

Y Xu et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2004)

Article Chemistry, Multidisciplinary

8-methylguanosine: A powerful Z-DNA stabilizer

Y Xu et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2003)

Article Biochemical Research Methods

The Xplor-NIH NMR molecular structure determination package

CD Schwieters et al.

JOURNAL OF MAGNETIC RESONANCE (2003)

Article Multidisciplinary Sciences

A crystallographic map of the transition from B-DNA to A-DNA

JM Vargason et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2001)