Effects of Adenine Methylation on the Structure and Thermodynamic Stability of a DNA Minidumbbell
Abstract
:1. Introduction
2. Results
2.1. The 5′-TTTm1ATTTA-3′ MDB Containing a T·m1A Hoogsteen Base Pair
2.2. Conformational Exchange between Two MDB Structures in 5′-TTTm6ATTTA-3′
3. Discussion
4. Materials and Methods
4.1. DNA Samples
4.2. NMR Experiments
4.3. Resonance Assignments
4.4. Extraction of Experimental NMR Restraints
4.5. rMD–rEM Calculations
4.6. Analyses of Calculated Structures
4.7. UV Melting Experiments
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
m1A | N1-methyladenine |
m6A | N6-methyladenine |
MDB | minidumbbell |
Tm | melting temperature |
NMR | nuclear magnetic resonance |
NOESY | nuclear Overhauser effect spectroscopy |
HSQC | heteronuclear single-quantum correlation |
TOCSY | total correlation spectroscopy |
HMBC | heteronuclear multiple bond correlation |
rMD | restrained molecular dynamics |
rEM | restrained energy minimization |
UV | ultraviolet |
ROESY | rotating frame Overhauser effect spectroscopy |
DSS | 2,2-dimethyl-2-silapentane-5-sulfonate |
NaPi | sodium phosphate |
DQF-COSY | double-quantum-filtered correlation spectroscopy |
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MDB | Sequence | Tm (°C) | ∆H° (kcal·mol−1) | ∆S° (cal·K−1·mol−1) | ∆G°25 °C (kcal·mol−1) |
---|---|---|---|---|---|
m1A | 5′-TTTm1ATTTA-3′ | 23.2 ± 0.6 | −19 ± 2 | −64 ± 6 | 0.12 ± 0.04 |
TTTA b | 5′-TTTATTTA-3′ | 19.2 ± 0.9 | −22 ± 1 | −76 ± 4 | 0.43 ± 0.08 |
Restraint Satisfaction | |
---|---|
Number of distance restraint violation > 0.2 Å | 0 |
Number of angle restraint violation > 5° | 0 |
Deviation from ideal geometry | |
Bond distance (Å) | 0.0097 ± 0.0002 |
Angle (°) | 2.69 ± 0.08 |
Heavy atomic RMSD (Å) a | |
Average pairwise RMSD | 0.62 ± 0.09 |
RMSD from mean structure | 0.39 ± 0.07 |
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Wan, L.; Lam, S.L.; Lee, H.K.; Guo, P. Effects of Adenine Methylation on the Structure and Thermodynamic Stability of a DNA Minidumbbell. Int. J. Mol. Sci. 2021, 22, 3633. https://doi.org/10.3390/ijms22073633
Wan L, Lam SL, Lee HK, Guo P. Effects of Adenine Methylation on the Structure and Thermodynamic Stability of a DNA Minidumbbell. International Journal of Molecular Sciences. 2021; 22(7):3633. https://doi.org/10.3390/ijms22073633
Chicago/Turabian StyleWan, Liqi, Sik Lok Lam, Hung Kay Lee, and Pei Guo. 2021. "Effects of Adenine Methylation on the Structure and Thermodynamic Stability of a DNA Minidumbbell" International Journal of Molecular Sciences 22, no. 7: 3633. https://doi.org/10.3390/ijms22073633