4.8 Article

Probing Watson-Crick and Hoogsteen base pairing in duplex DNA using dynamic nuclear polarization solid-state NMR spectroscopy

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 Chemistry, Multidisciplinary

Histone H4 Tails in Nucleosomes: a Fuzzy Interaction with DNA

Sevastyan O. Rabdano et al.

Summary: The positively charged N-terminal histone tails interact with nucleosomal DNA, influencing their susceptibility to modifications and recognition by chromatin-binding proteins. The NMR data reveals that H4 tails are dynamically disordered in nucleosomes, showing a reduced conformational flexibility compared to free peptides. The findings suggest a fuzzy interaction between histone H4 tails and nucleosomal DNA, characterized by variable salt bridges and hydrogen bonds.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2021)

Article Biochemistry & Molecular Biology

Revealing A-T and G-C Hoogsteen base pairs in stressed protein-bound duplex DNA

Honglue Shi et al.

Summary: This study identified a type of base pairs called 'Hoogsteen' in DNA, which may have a broad role in stressed regions of the genome, calling for a community-wide effort to identify these base pairs in current and future crystal structures of DNA and its complexes.

NUCLEIC ACIDS RESEARCH (2021)

Article Chemistry, Physical

Conformational Dynamics of Histone H3 Tails in Chromatin

Mohamad Zandian et al.

Summary: In this study, high-resolution NMR measurements were used to investigate the dynamics and interactions of H3 tails in nucleosome arrays with different lengths of linker DNA. The H3 tail dynamics in nucleosome arrays were found to be significantly attenuated compared to nucleosomes with or without linker DNA, but were not modulated by the specific linker DNA length investigated.

JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2021)

Article Biochemistry & Molecular Biology

Hoogsteen base pairs increase the susceptibility of double-stranded DNA to cytotoxic damage

Yu Xu et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2020)

Article Biochemistry & Molecular Biology

DNP NMR of biomolecular assemblies

Kristaps Jaudzems et al.

JOURNAL OF STRUCTURAL BIOLOGY (2019)

Article Chemistry, Multidisciplinary

Dynamic Nuclear Polarization-Enhanced Biomolecular NMR Spectroscopy at High Magnetic Field with Fast Magic-Angle Spinning

Kristaps Jaudzems et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2018)

Article Chemistry, Multidisciplinary

Structure and Dynamics in the Nucleosome Revealed by Solid-State NMR

Xiangyan Shi et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2018)

Article Chemistry, Multidisciplinary

Site-Specific Studies of Nucleosome Interactions by Solid-State NMR Spectroscopy

ShengQi Xiang et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2018)

Article Multidisciplinary Sciences

Modulation of Hoogsteen dynamics on DNA recognition

Yu Xu et al.

NATURE COMMUNICATIONS (2018)

Article Biochemistry & Molecular Biology

Protein-nucleotide contacts in motor proteins detected by DNP-enhanced solid-state NMR

Thomas Wiegand et al.

JOURNAL OF BIOMOLECULAR NMR (2017)

Review Biophysics

Structural biology of supramolecular assemblies by magic-angle spinning NMR spectroscopy

Caitlin M. Quinn et al.

QUARTERLY REVIEWS OF BIOPHYSICS (2017)

Article Multidisciplinary Sciences

DNA binding drives the association of BRG1/hBRM bromodomains with nucleosomes

Emma A. Morrison et al.

NATURE COMMUNICATIONS (2017)

Article Biochemical Research Methods

Mismodeled purines: implicit alternates and hidden Hoogsteens

Bradley J. Hintze et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2017)

Article Biochemistry & Molecular Biology

m1A and m1G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs

Huiqing Zhou et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2016)

Article Biochemistry & Molecular Biology

m1A and m1G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs

Huiqing Zhou et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2016)

Article Biochemistry & Molecular Biology

AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules

Jason Swails et al.

JOURNAL OF BIOMOLECULAR NMR (2015)

Article Biochemistry & Molecular Biology

Dynamic nuclear polarization of nucleic acid with endogenously bound manganese

Patricia Wenk et al.

JOURNAL OF BIOMOLECULAR NMR (2015)

Article Biochemistry & Molecular Biology

New insights into Hoogsteen base pairs in DNA duplexes from a structure-based survey

Huiqing Zhou et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Multidisciplinary Sciences

RNA structure determination by solid-state NMR spectroscopy

Alexander Marchanka et al.

NATURE COMMUNICATIONS (2015)

Article Chemistry, Physical

15N chemical shift referencing in solid state NMR

Philippe Bertani et al.

SOLID STATE NUCLEAR MAGNETIC RESONANCE (2014)

Article Multidisciplinary Sciences

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

Heidi S. Alvey et al.

NATURE COMMUNICATIONS (2014)

Review Chemistry, Multidisciplinary

Structural Investigations of Molecular Machines by Solid-State NMR

Antoine Loquet et al.

ACCOUNTS OF CHEMICAL RESEARCH (2013)

Article Chemistry, Multidisciplinary

ProteinRNA Interfaces Probed by 1H-Detected MAS Solid-State NMR Spectroscopy

Sam Asami et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2013)

Article Chemistry, Multidisciplinary

Highly Efficient, Water-Soluble Polarizing Agents for Dynamic Nuclear Polarization at High Frequency

Claire Sauvee et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2013)

Article Chemistry, Multidisciplinary

Characterizing the Protonation State of Cytosine in Transient G•C Hoogsteen Base Pairs in Duplex DNA

Evgenia N. Nikolova et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2013)

Article Chemistry, Multidisciplinary

Histone H3 and H4 N-Terminal Tails in Nucleosome Arrays at Cellular Concentrations Probed by Magic Angle Spinning NMR Spectroscopy

Min Gao et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2013)

Article Biochemistry & Molecular Biology

Computational mapping reveals dramatic effect of Hoogsteen breathing on duplex DNA reactivity with formaldehyde

Tanggis Bohnuud et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Chemistry, Multidisciplinary

Chemical Shifts for the Unusual DNA Structure in Pf1 Bacteriophage from Dynamic-Nuclear-Polarization-Enhanced Solid-State NMR Spectroscopy

Ivan V. Sergeyev et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2011)

Article Multidisciplinary Sciences

Transient Hoogsteen base pairs in canonical duplex DNA

Evgenia N. Nikolova et al.

NATURE (2011)

Article Chemistry, Multidisciplinary

High-Resolution Studies of Uniformly C-13,N-15-Labeled RNA by Solid-State NMR Spectroscopy

Alexey V. Cherepanov et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2010)

Article Biochemistry & Molecular Biology

Crystal Structures of Nucleosome Core Particles Containing the '601' Strong Positioning Sequence

Dileep Vasudevan et al.

JOURNAL OF MOLECULAR BIOLOGY (2010)

Article Chemistry, Multidisciplinary

13C/15N-19F Intermolecular REDOR NMR Study of the Interaction of TAR RNA with Tat Peptides

Wei Huang et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2010)

Article Biochemistry & Molecular Biology

Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs

Malka Kitayner et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2010)

Review Physics, Atomic, Molecular & Chemical

High-field dynamic nuclear polarization for solid and solution biological NMR

A. B. Barnes et al.

APPLIED MAGNETIC RESONANCE (2008)

Article Biochemistry & Molecular Biology

Characterisation of hydrogen bonding networks in RNAs via magic angle spinning solid state NMR spectroscopy

K Riedel et al.

JOURNAL OF BIOMOLECULAR NMR (2005)

Article Biochemical Research Methods

Structures of complexes between echinomycin and duplex DNA

JA Cuesta-Seijo et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2005)

Article Multidisciplinary Sciences

Replication by human DNA polymerase-ι occurs by Hoogsteen base-pairing

DT Nair et al.

NATURE (2004)

Article Multidisciplinary Sciences

Replication of a cis-syn thymine dimer at atomic resolution

H Ling et al.

NATURE (2003)

Article Biochemical Research Methods

Chemical shift referencing in MAS solid state NMR

CR Morcombe et al.

JOURNAL OF MAGNETIC RESONANCE (2003)

Article Chemistry, Multidisciplinary

3D TEDOR NMR experiments for the simultaneous measurement of multiple carbon-nitrogen distances in uniformly 13C, 15N-labeled solids

CP Jaroniec et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2002)

Article Biochemistry & Molecular Biology

Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 Å resolution

CA Davey et al.

JOURNAL OF MOLECULAR BIOLOGY (2002)

Article Biochemistry & Molecular Biology

The Protein Data Bank

HM Berman et al.

NUCLEIC ACIDS RESEARCH (2000)

Article Biochemical Research Methods

An improved broadband decoupling sequence for liquid crystals and solids

BM Fung et al.

JOURNAL OF MAGNETIC RESONANCE (2000)