scholarly journals Probing Transient Hoogsteen Hydrogen Bonds in Canonical Duplex DNA Using NMR Relaxation Dispersion and Single-Atom Substitution

2012 ◽  
Vol 134 (8) ◽  
pp. 3667-3670 ◽  
Author(s):  
Evgenia N. Nikolova ◽  
Federico L. Gottardo ◽  
Hashim M. Al-Hashimi
Keyword(s):  
Hydrogen Bonds ◽  
Nmr Relaxation ◽  
Relaxation Dispersion ◽  
Single Atom ◽  
Duplex Dna ◽  
Hoogsteen Hydrogen Bonds

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

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.

Identification of a Collapsed Intermediate with Non-native Long-range Interactions on the Folding Pathway of a Pair of Fyn SH3 Domain Mutants by NMR Relaxation Dispersion Spectroscopy

2006 ◽  
Vol 363 (5) ◽  
pp. 958-976 ◽  
Author(s):  
Philipp Neudecker ◽  
Arash Zarrine-Afsar ◽  
Wing-Yiu Choy ◽  
D. Ranjith Muhandiram ◽  
Alan R. Davidson ◽  
...  
Keyword(s):  
Long Range ◽  
Nmr Relaxation ◽  
Sh3 Domain ◽  
Relaxation Dispersion ◽  
Folding Pathway ◽  
Long Range Interactions

scholarly journals Analysis of Artifacts Caused by Pulse Imperfections in CPMG Pulse Trains in NMR Relaxation Dispersion Experiments

2018 ◽  
Vol 4 (3) ◽  
pp. 33 ◽  
Author(s):  
Tsuyoshi Konuma ◽  
Aritaka Nagadoi ◽  
Jun-ichi Kurita ◽  
Takahisa Ikegami
Keyword(s):  
Dipolar Coupling ◽  
Residual Dipolar Coupling ◽  
Nmr Relaxation ◽  
Relaxation Dispersion ◽  
Conformational Exchange ◽  
Resonance Effects ◽  
Pulse Trains ◽  
At Resonance ◽  
Selective Inversion ◽  
Resonance Relaxation

Nuclear magnetic resonance relaxation dispersion (rd) experiments provide kinetics and thermodynamics information of molecules undergoing conformational exchange. Rd experiments often use a Carr-Purcell-Meiboom-Gill (CPMG) pulse train equally separated by a spin-state selective inversion element (U-element). Even with measurement parameters carefully set, however, parts of 1H–15N correlations sometimes exhibit large artifacts that may hamper the subsequent analyses. We analyzed such artifacts with a combination of NMR measurements and simulation. We found that particularly the lowest CPMG frequency (νcpmg) can also introduce large artifacts into amide 1H–15N and aromatic 1H–13C correlations whose 15N/13C resonances are very close to the carrier frequencies. The simulation showed that the off-resonance effects and miscalibration of the CPMG π pulses generate artifact maxima at resonance offsets of even and odd multiples of νcpmg, respectively. We demonstrate that a method once introduced into the rd experiments for molecules having residual dipolar coupling significantly reduces artifacts. In the method the 15N/13C π pulse phase in the U-element is chosen between x and y. We show that the correctly adjusted sequence is tolerant to miscalibration of the CPMG π pulse power as large as ±10% for most amide 15N and aromatic 13C resonances of proteins.

scholarly journals Accelerating 2D NMR relaxation dispersion experiments using iterated maps

2019 ◽  
Vol 73 (10-11) ◽  
pp. 561-576 ◽  
Author(s):  
Jared Rovny ◽  
Robert L. Blum ◽  
J. Patrick Loria ◽  
Sean E. Barrett
Keyword(s):  
Nmr Relaxation ◽  
2D Nmr ◽  
Relaxation Dispersion ◽  
Iterated Maps

scholarly journals Dynamic ensemble of HIV-1 RRE stem IIB reveals non-native conformations that disrupt the Rev-binding site

2019 ◽  
Vol 47 (13) ◽  
pp. 7105-7117 ◽  
Author(s):  
Chia-Chieh Chu ◽  
Raphael Plangger ◽  
Christoph Kreutz ◽  
Hashim M Al-Hashimi
Keyword(s):  
Binding Site ◽  
Nuclear Export ◽  
Dynamic Equilibrium ◽  
Nmr Relaxation ◽  
Conformational Flexibility ◽  
Relaxation Dispersion ◽  
Conformational States ◽  
Rev Response Element ◽  
Local Secondary Structure ◽  
Hiv 1

AbstractThe HIV-1 Rev response element (RRE) RNA element mediates the nuclear export of intron containing viral RNAs by forming an oligomeric complex with the viral protein Rev. Stem IIB and nearby stem II three-way junction nucleate oligomerization through cooperative binding of two Rev molecules. Conformational flexibility at this RRE region has been shown to be important for Rev binding. However, the nature of the flexibility has remained elusive. Here, using NMR relaxation dispersion, including a new strategy for directly observing transient conformational states in large RNAs, we find that stem IIB alone or when part of the larger RREII three-way junction robustly exists in dynamic equilibrium with non-native excited state (ES) conformations that have a combined population of ∼20%. The ESs disrupt the Rev-binding site by changing local secondary structure, and their stabilization via point substitution mutations decreases the binding affinity to the Rev arginine-rich motif (ARM) by 15- to 80-fold. The ensemble clarifies the conformational flexibility observed in stem IIB, reveals long-range conformational coupling between stem IIB and the three-way junction that may play roles in cooperative Rev binding, and also identifies non-native RRE conformational states as new targets for the development of anti-HIV therapeutics.

Adenine ribbon stabilized by Watson–Crick and Hoogsteen hydrogen Bonds: WFT and DFT study

2010 ◽  
Vol 12 (12) ◽  
pp. 2888 ◽  
Author(s):  
Wiktor Zierkiewicz ◽  
Danuta Michalska ◽  
Pavel Hobza
Keyword(s):  
Hydrogen Bonds ◽  
Dft Study ◽  
Hoogsteen Hydrogen Bonds

High-field liquid state NMR hyperpolarization: a combined DNP/NMRD approach

2014 ◽  
Vol 16 (35) ◽  
pp. 18781-18787 ◽  
Author(s):  
Petr Neugebauer ◽  
Jan G. Krummenacker ◽  
Vasyl P. Denysenkov ◽  
Christina Helmling ◽  
Claudio Luchinat ◽  
...  
Keyword(s):  
Magnetic Field ◽  
High Magnetic Field ◽  
Dynamic Nuclear Polarization ◽  
Liquid State ◽  
High Field ◽  
Nuclear Polarization ◽  
Nmr Relaxation ◽  
Relaxation Dispersion ◽  
Liquid Solutions ◽  
High Fields

Dynamic nuclear polarization and NMR relaxation dispersion measurements have been performed on liquid solutions of TEMPOL radicals in solvents with different viscosities at a high magnetic field of 9.2 T. The results indicate that fast dynamics significantly contribute to DNP enhancements at high fields.

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