Probing conformational transitions towards mutagenic Watson–Crick-like G·T mismatches using off-resonance sugar carbon R1ρ relaxation dispersion

Abstract NMR off-resonance R1ρ relaxation dispersion measurements on base carbon and nitrogen nuclei have revealed that wobble G·T/U mismatches in DNA and RNA duplexes exist in dynamic equilibrium with short-lived, low-abundance, and mutagenic Watson–Crick-like conformations. As Watson–Crick-like G·T mismatches have base pairing geometries similar to Watson–Crick base pairs, we hypothesized that they would mimic Watson–Crick base pairs with respect to the sugar-backbone conformation as well. Using off-resonance R1ρ measurements targeting the sugar C3′ and C4′ nuclei, a structure survey, and molecular dynamics simulations, we show that wobble G·T mismatches adopt sugar-backbone conformations that deviate from the canonical Watson–Crick conformation and that transitions toward tautomeric and anionic Watson–Crick-like G·T mismatches restore the canonical Watson–Crick sugar-backbone. These measurements also reveal kinetic isotope effects for tautomerization in D2O versus H2O, which provide experimental evidence in support of a transition state involving proton transfer. The results provide additional evidence in support of mutagenic Watson–Crick-like G·T mismatches, help rule out alternative inverted wobble conformations in the case of anionic G·T−, and also establish sugar carbons as new non-exchangeable probes of this exchange process.

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The structural plasticity of nucleic acid duplexes revealed by WAXS and MD

Science Advances ◽

10.1126/sciadv.abf6106 ◽

2021 ◽

Vol 7 (17) ◽

pp. eabf6106

Author(s):

Weiwei He ◽

Yen-Lin Chen ◽

Lois Pollack ◽

Serdal Kirmizialtin

Keyword(s):

Structural Diversity ◽

Conformational Ensemble ◽

Structural Variations ◽

Dna And Rna ◽

X Ray Scattering ◽

Double Stranded Dna ◽

Binding Partners ◽

Rna Duplexes ◽

Dynamics Simulations ◽

Integrate Solution

Double-stranded DNA (dsDNA) and RNA (dsRNA) helices display an unusual structural diversity. Some structural variations are linked to sequence and may serve as signaling units for protein-binding partners. Therefore, elucidating the mechanisms and factors that modulate these variations is of fundamental importance. While the structural diversity of dsDNA has been extensively studied, similar studies have not been performed for dsRNA. Because of the increasing awareness of RNA’s diverse biological roles, such studies are timely and increasingly important. We integrate solution x-ray scattering at wide angles (WAXS) with all-atom molecular dynamics simulations to explore the conformational ensemble of duplex topologies for different sequences and salt conditions. These tightly coordinated studies identify robust correlations between features in the WAXS profiles and duplex geometry and enable atomic-level insights into the structural diversity of DNA and RNA duplexes. Notably, dsRNA displays a marked sensitivity to the valence and identity of its associated cations.

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Rapid assessment of Watson–Crick to Hoogsteen exchange in unlabeled DNA duplexes using high-power SELOPE imino <sup>1</sup>H CEST

Magnetic Resonance ◽

10.5194/mr-2-715-2021 ◽

2021 ◽

Vol 2 (2) ◽

pp. 715-731

Author(s):

Bei Liu ◽

Atul Rangadurai ◽

Honglue Shi ◽

Hashim M. Al-Hashimi

Keyword(s):

High Power ◽

Dna Sequences ◽

Dynamic Equilibrium ◽

Chemical Exchange ◽

Rapid Assessment ◽

Relaxation Dispersion ◽

Duplex Dna ◽

Dna Duplexes ◽

Base Pairs ◽

1H Cest

Abstract. In duplex DNA, Watson–Crick A–T and G–C base pairs (bp's) exist in dynamic equilibrium with an alternative Hoogsteen conformation, which is low in abundance and short-lived. Measuring how the Hoogsteen dynamics varies across different DNA sequences, structural contexts and physiological conditions is key for identifying potential Hoogsteen hot spots and for understanding the potential roles of Hoogsteen base pairs in DNA recognition and repair. However, such studies are hampered by the need to prepare 13C or 15N isotopically enriched DNA samples for NMR relaxation dispersion (RD) experiments. Here, using SELective Optimized Proton Experiments (SELOPE) 1H CEST experiments employing high-power radiofrequency fields (B1 > 250 Hz) targeting imino protons, we demonstrate accurate and robust characterization of Watson–Crick to Hoogsteen exchange, without the need for isotopic enrichment of the DNA. For 13 residues in three DNA duplexes under different temperature and pH conditions, the exchange parameters deduced from high-power imino 1H CEST were in very good agreement with counterparts measured using off-resonance 13C / 15N spin relaxation in the rotating frame (R1ρ). It is shown that 1H–1H NOE effects which typically introduce artifacts in 1H-based measurements of chemical exchange can be effectively suppressed by selective excitation, provided that the relaxation delay is short (≤ 100 ms). The 1H CEST experiment can be performed with ∼ 10× higher throughput and ∼ 100× lower cost relative to 13C / 15N R1ρ and enabled Hoogsteen chemical exchange measurements undetectable by R1ρ. The results reveal an increased propensity to form Hoogsteen bp's near terminal ends and a diminished propensity within A-tract motifs. The 1H CEST experiment provides a basis for rapidly screening Hoogsteen breathing in duplex DNA, enabling identification of unusual motifs for more in-depth characterization.

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Symmetry in Nucleic-Acid Double Helices

Symmetry ◽

10.3390/sym12050737 ◽

2020 ◽

Vol 12 (5) ◽

pp. 737

Author(s):

Udo Heinemann ◽

Yvette Roske

Keyword(s):

Nucleic Acid ◽

Base Pair ◽

Rna Structure ◽

Test Tube ◽

Base Pairs ◽

Dna And Rna ◽

Left Handed ◽

Double Helices ◽

Rna Duplexes ◽

The Right

In nature and in the test tube, nucleic acids occur in many different forms. Apart from single-stranded, coiled molecules, DNA and RNA prefer to form helical arrangements, in which the bases are stacked to shield their hydrophobic surfaces and expose their polar edges. Focusing on double helices, we describe the crucial role played by symmetry in shaping DNA and RNA structure. The base pairs in nucleic-acid double helices display rotational pseudo-symmetry. In the Watson–Crick base pairs found in naturally occurring DNA and RNA duplexes, the symmetry axis lies in the base-pair plane, giving rise to two different helical grooves. In contrast, anti-Watson–Crick base pairs have a dyad axis perpendicular to the base-pair plane and identical grooves. In combination with the base-pair symmetry, the syn/anti conformation of paired nucleotides determines the parallel or antiparallel strand orientation of double helices. DNA and RNA duplexes in nature are exclusively antiparallel. Watson–Crick base-paired DNA or RNA helices display either right-handed or left-handed helical (pseudo-) symmetry. Genomic DNA is usually in the right-handed B-form, and RNA double helices adopt the right-handed A-conformation. Finally, there is a higher level of helical symmetry in superhelical DNA in which B-form double strands are intertwined in a right- or left-handed sense.

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Rapid measurement of Watson-Crick to Hoogsteen exchange in unlabeled DNA duplexes using high-power SELOPE imino <sup>1</sup>H CEST

10.5194/mr-2021-58 ◽

2021 ◽

Author(s):

Bei Liu ◽

Atul Rangadurai ◽

Honglue Shi ◽

Hashim Al-Hashimi

Keyword(s):

High Power ◽

Dna Sequences ◽

Dynamic Equilibrium ◽

Chemical Exchange ◽

Nmr Relaxation ◽

Relaxation Dispersion ◽

Duplex Dna ◽

Dna Duplexes ◽

Base Pairs ◽

1H Cest

Abstract. In duplex DNA, Watson-Crick A-T and G-C base pairs (bps) exist in dynamic equilibrium with an alternative Hoogsteen conformation, which is low in abundance and short-lived. Measuring how the Hoogsteen dynamics varies across different DNA sequences, structural contexts and physiological conditions is key for understanding the role of these non-canonical bps in DNA recognition and repair. However, such studies are hampered by the need to prepare 13C or 15N isotopically enriched DNA samples for NMR relaxation dispersion (RD) experiments. Here, using SELective Optimized Proton Experiments (SELOPE) 1H CEST experiments employing high-power radiofrequency fields (B1 > 250 Hz) targeting imino protons, we demonstrate accurate and robust characterization of Waston-Crick to Hoogsteen exchange, without the need for isotopic enrichment of the DNA. For 13 residues in three DNA duplexes under different temperature and pH conditions, the exchange parameters deduced from high-power imino 1H CEST were in very good agreement with counterparts measured using off-resonance 13C/15N spin relaxation in the rotating frame (R1ρ). It is shown that 1H-1H NOE effects which typically introduce artifacts in 1H based measurements of chemical exchange can be effectively suppressed by selective excitation, provided that the relaxation delay is short (≤ 100 ms). The 1H CEST experiment can be performed with ~10X higher throughput and ~100X lower cost relative to 13C/15N R1ρ, and enabled Hoogsteen chemical exchange measurements undetectable by R1ρ. The results reveal an increased propensity to form Hoogsteen bps near terminal ends and a diminished propensity within A-tract motifs. The 1H CEST experiment opens the door to more comprehensively characterizing Hoogsteen breathing in duplex DNA.

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Local structure and distortions of mixed methane-carbon dioxide hydrates

Communications Chemistry ◽

10.1038/s42004-020-00441-7 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Bernadette R. Cladek ◽

S. Michelle Everett ◽

Marshall T. McDonnell ◽

Matthew G. Tucker ◽

David J. Keffer ◽

...

Keyword(s):

Carbon Dioxide ◽

Exchange Process ◽

Carbon Dioxide Sequestration ◽

Distribution Functions ◽

Atomic Scale ◽

Mixed Gas ◽

Pure Compounds ◽

Dynamics Simulations ◽

Pair Distribution Functions ◽

Methane Carbon

AbstractA vast source of methane is found in gas hydrate deposits, which form naturally dispersed throughout ocean sediments and arctic permafrost. Methane may be obtained from hydrates by exchange with hydrocarbon byproduct carbon dioxide. It is imperative for the development of safe methane extraction and carbon dioxide sequestration to understand how methane and carbon dioxide co-occupy the same hydrate structure. Pair distribution functions (PDFs) provide atomic-scale structural insight into intermolecular interactions in methane and carbon dioxide hydrates. We present experimental neutron PDFs of methane, carbon dioxide and mixed methane-carbon dioxide hydrates at 10 K analyzed with complementing classical molecular dynamics simulations and Reverse Monte Carlo fitting. Mixed hydrate, which forms during the exchange process, is more locally disordered than methane or carbon dioxide hydrates. The behavior of mixed gas species cannot be interpolated from properties of pure compounds, and PDF measurements provide important understanding of how the guest composition impacts overall order in the hydrate structure.

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Targeting the ALS/FTD-associated A-DNA kink with anthracene-based metal complex causes DNA backbone straightening and groove contraction

Nucleic Acids Research ◽

10.1093/nar/gkab227 ◽

2021 ◽

Author(s):

Cyong-Ru Jhan ◽

Roshan Satange ◽

Shun-Ching Wang ◽

Jing-Yi Zeng ◽

Yih-Chern Horng ◽

...

Keyword(s):

Hot Spot ◽

Hydration Shell ◽

Repeat Motif ◽

Dna Duplex ◽

Base Pairs ◽

Dna And Rna ◽

Detailed Structural Analysis ◽

Small Molecule Compound ◽

Dna Backbone ◽

Locomotor Deficits

Abstract The use of a small molecule compound to reduce toxic repeat RNA transcripts or their translated aberrant proteins to target repeat-expanded RNA/DNA with a G4C2 motif is a promising strategy to treat C9orf72-linked disorders. In this study, the crystal structures of DNA and RNA–DNA hybrid duplexes with the -GGGCCG- region as a G4C2 repeat motif were solved. Unusual groove widening and sharper bending of the G4C2 DNA duplex A-DNA conformation with B-form characteristics inside was observed. The G4C2 RNA–DNA hybrid duplex adopts a more typical rigid A form structure. Detailed structural analysis revealed that the G4C2 repeat motif of the DNA duplex exhibits a hydration shell and greater flexibility and serves as a ‘hot-spot’ for binding of the anthracene-based nickel complex, NiII(Chro)2 (Chro = Chromomycin A3). In addition to the original GGCC recognition site, NiII(Chro)2 has extended specificity and binds the flanked G:C base pairs of the GGCC core, resulting in minor groove contraction and straightening of the DNA backbone. We have also shown that Chro-metal complexes inhibit neuronal toxicity and suppresses locomotor deficits in a Drosophila model of C9orf72-associated ALS. The approach represents a new direction for drug discovery against ALS and FTD diseases by targeting G4C2 repeat motif DNA.

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Comparison of Cis- and Oxaliplatin-induced Destabilization of 15-mer DNA- and RNA Duplexes by Binding to Centrally Located GG- and GNG Sequences

Zeitschrift für anorganische und allgemeine Chemie ◽

10.1002/zaac.201300060 ◽

2013 ◽

Vol 639 (8-9) ◽

pp. 1655-1660 ◽

Cited By ~ 5

Author(s):

Christopher Polonyi ◽

Ingrid Albertsson ◽

Mariana S. Damian ◽

Sofi K. C. Elmroth

Keyword(s):

Dna And Rna ◽

Rna Duplexes

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On the dynamics of some small structural motifs in rRNA upon ligand binding

Journal of the Serbian Chemical Society ◽

10.2298/jsc0801041r ◽

2008 ◽

Vol 73 (1) ◽

pp. 41-53

Author(s):

Aleksandra Rakic ◽

Petar Mitrasinovic

Keyword(s):

Molecular Dynamics ◽

Conformational Changes ◽

Binding Sites ◽

De Novo ◽

Reference Structure ◽

Base Pairs ◽

Rna Sequences ◽

Conformational Model ◽

Thermodynamic Variables ◽

Dynamics Simulations

The present study characterizes using molecular dynamics simulations the behavior of the GAA (1186-1188) hairpin triloops with their closing c-g base pairs in large ribonucleoligand complexes (PDB IDs: 1njn, 1nwy, 1jzx). The relative energies of the motifs in the complexes with respect to that in the reference structure (unbound form of rRNA; PDB ID: 1njp) display the trends that agree with those of the conformational parameters reported in a previous study1 utilizing the de novo pseudotorsional (?,?) approach. The RNA regions around the actual RNA-ligand contacts, which experience the most substantial conformational changes upon formation of the complexes were identified. The thermodynamic parameters, based on a two-state conformational model of RNA sequences containing 15, 21 and 27 nucleotides in the immediate vicinity of the particular binding sites, were evaluated. From a more structural standpoint, the strain of a triloop, being far from the specific contacts and interacting primarily with other parts of the ribosome, was established as a structural feature which conforms to the trend of the average values of the thermodynamic variables corresponding to the three motifs defined by the 15-, 21- and 27-nucleotide sequences. From a more functional standpoint, RNA-ligand recognition is suggested to be presumably dictated by the types of ligands in the complexes.

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