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

2014 ◽  
Vol 5 (1) ◽  
Author(s):  
Heidi S. Alvey ◽  
Federico L. Gottardo ◽  
Evgenia N. Nikolova ◽  
Hashim M. Al-Hashimi
Keyword(s):  
Duplex Dna ◽  
Base Pairs

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

Positive cooperativity of the specific binding between Hg2+ ion and T:T mismatched base pairs in duplex DNA

2012 ◽  
Vol 532 ◽  
pp. 28-35 ◽  
Author(s):  
Hidetaka Torigoe ◽  
Yukako Miyakawa ◽  
Akira Ono ◽  
Tetsuo Kozasa
Keyword(s):  
Specific Binding ◽  
Duplex Dna ◽  
Base Pairs ◽  
Positive Cooperativity

scholarly journals DNA polymerase β: effects of gapped DNA substrates on dNTP specificity, fidelity, processivity and conformational changes1

1998 ◽  
Vol 331 (1) ◽  
pp. 79-87 ◽  
Author(s):  
Jinwoo AHN ◽  
Vadim S. KRAYNOV ◽  
Xuejun ZHONG ◽  
Brian G. WERNEBURG ◽  
Ming-Daw TSAI
Keyword(s):  
Conformational Change ◽  
Dna Polymerase ◽  
Catalytic Efficiency ◽  
Duplex Dna ◽  
Gap Filling ◽  
Dna Polymerase Β ◽  
Base Pairs ◽  
Single Nucleotide ◽  
Dna Substrates ◽  
Gapped Dna

Pre-steady-state kinetic analysis was used to compare the catalytic properties of DNA polymerase β (Pol β) for single-base gap-filling and regular duplex DNA synthesis. The rate of polymerization (kpol) and the apparent equilibrium dissociation constant of dNTP (Kd) were determined with single-nucleotide gapped DNA substrates for all four possible correct base pairs and twelve possible incorrect base pairs, and the results were compared with those obtained previously with non-gapped primer/template duplex DNA substrates. For correct dNTP incorporation, the use of single-nucleotide gapped DNA led to significant decreases in the Kd of dNTP. Although kpol was little affected, the catalytic efficiency kpol/Kd increased significantly owing to the decreases in Kd. In contrast, for incorrect dNTP incorporation, the use of single-nucleotide gapped DNA substrates did not affect the Kd of dNTP appreciably but caused the kpol (and thus kpol/Kd) for incorrect dNTP incorporation to increase. As a consequence the fidelity of Pol β was not significantly affected by the use of single-nucleotide gapped DNA substrates. In addition we show that under processive polymerization conditions the processivity of Pol β increases in the gap-filling synthesis owing to a decreased rate of DNA dissociation. Finally, with a single-nucleotide gapped DNA substrate the rate-limiting conformational change step before chemistry was also observed. However, the preceding fast conformational change observed with duplex DNA substrates was not clearly detected. A possible cause is that in the complex with the gapped DNA, the 8 kDa N-terminal domain of Pol β already exists in a closed conformation. This interpretation was supported by tryptic digestion experiments.

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

2013 ◽  
Vol 135 (18) ◽  
pp. 6766-6769 ◽  
Author(s):  
Evgenia N. Nikolova ◽  
Garrett B. Goh ◽  
Charles L. Brooks ◽  
Hashim M. Al-Hashimi
Keyword(s):  
Duplex Dna ◽  
Protonation State ◽  
Base Pairs
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