scholarly journals Direct evidence for (G)O6···H2-N4(C)+ hydrogen bonding in transient G(syn)-C+ and G(syn)-m5C+ Hoogsteen base pairs in duplex DNA from cytosine amino nitrogen off-resonance R1ρ relaxation dispersion measurements

2019 ◽  
Vol 308 ◽  
pp. 106589 ◽  
Author(s):  
Atul Rangadurai ◽  
Johannes Kremser ◽  
Honglue Shi ◽  
Christoph Kreutz ◽  
Hashim M. Al-Hashimi
Keyword(s):  
Hydrogen Bonding ◽  
Direct Evidence ◽  
Amino Nitrogen ◽  
Relaxation Dispersion ◽  
Duplex Dna ◽  
Base Pairs

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

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.

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.

scholarly journals Transient Hoogsteen base pairs in canonical duplex DNA

Nature ◽  
2011 ◽  
Vol 470 (7335) ◽  
pp. 498-502 ◽  
Author(s):  
Evgenia N. Nikolova ◽  
Eunae Kim ◽  
Abigail A. Wise ◽  
Patrick J. O’Brien ◽  
Ioan Andricioaei ◽  
...  
Keyword(s):  
Duplex Dna ◽  
Base Pairs

scholarly journals A historical account of hoogsteen base-pairs in duplex DNA

Biopolymers ◽  
2013 ◽  
pp. n/a-n/a ◽  
Author(s):  
Evgenia N. Nikolova ◽  
Huiqing Zhou ◽  
Federico L. Gottardo ◽  
Heidi S. Alvey ◽  
Isaac J. Kimsey ◽  
...  
Keyword(s):  
Duplex Dna ◽  
Historical Account ◽  
Base Pairs

scholarly journals Direct Evidence for Hydrogen Bonding in Glycans: A Combined NMR and Molecular Dynamics Study

2013 ◽  
Vol 117 (17) ◽  
pp. 4860-4869 ◽  
Author(s):  
Marcos D. Battistel ◽  
Robert Pendrill ◽  
Göran Widmalm ◽  
Darón I. Freedberg
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Direct Evidence

Hydrogen Bonding Effects on the 15N and 1H Shielding Tensors in Nucleic Acid Base Pairs

2000 ◽  
Vol 145 (1) ◽  
pp. 142-146 ◽  
Author(s):  
Jiřı́ Czernek ◽  
Radovan Fiala ◽  
Vladimı́r Sklenář
Keyword(s):  
Hydrogen Bonding ◽  
Nucleic Acid ◽  
Acid Base ◽  
Base Pairs ◽  
Nucleic Acid Base ◽  
Shielding Tensors

scholarly journals Nanomechanics of negatively supercoiled diaminopurine-substituted DNA

2021 ◽  
Author(s):  
Domenico Salerno ◽  
Francesco Mantegazza ◽  
Valeria Cassina ◽  
Matteo Cristofalo ◽  
Qing Shao ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Single Molecule ◽  
Conformational Dynamics ◽  
Persistence Length ◽  
Base Stacking ◽  
Base Pairs ◽  
Left Handed ◽  
Negative Supercoiling ◽  
Mechanical Dynamics ◽  
Hydrogen Bonded

ABSTRACTSingle molecule experiments have demonstrated a progressive transition from a B- to an L-form helix as DNA is gently stretched and progressively unwound. Since the particular sequence of a DNA segment influences both base stacking and hydrogen bonding, the conformational dynamics of B-to-L transitions should be tunable. To test this idea, DNA with diaminopurine replacing adenine was synthesized to produce linear fragments with triply hydrogen-bonded A:T base pairs. Triple hydrogen bonding stiffened the DNA by 30% flexurally. In addition, DAP-substituted DNA formed plectonemes with larger gyres for both B- and L-form helices. Both unmodified and DAP-substituted DNA transitioned from a B- to an L-helix under physiological conditions of mild tension and unwinding. This transition avoids writhing by DNA stretched and unwound by enzymatic activity. The intramolecular nature and ease of this transition likely prevent cumbersome topological rearrangements in genomic DNA that would require topoisomerase activity to resolve. L-DNA displayed about tenfold lower persistence length indicating it is much more contractile and prone to sharp bends and kinks. However, left-handed DAP DNA was twice as stiff as unmodified L-DNA. Thus, significantly doubly and triply hydrogen bonded segments have very distinct mechanical dynamics at physiological levels of negative supercoiling and tension.

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