New and Notable
Novel NMR Techniques to Study Structural and Dynamical Properties of DNA Quadruplexes Richard Sheardy1,* 1
Texas Woman’s University, Denton, Texas
Since the right-handed double helical conformation was first described by Watson and Crick (1), we have realized that DNA is highly polymorphic as evidenced by left-handed DNA (2), parallel-stranded DNA (3), DNA quadruplexes (4), and DNA i-motifs (5), to name a few. The conformation a particular segment of DNA assumes, as well as its thermodynamic stability and ligand binding properties, depend highly upon its sequence context and also on environmental conditions (e.g., temperature, cations present, pH, and so on). Researchers have taken advantage of DNA’s polymorphism and have constructed DNA-based objects and devices (6). Conformational properties (conformation, stability, ligand binding) are primarily governed by hydrogen bonding and base stacking interactions. These interactions also play a role in the flexibility and dynamical motion of the particular DNA conformation. Probing the dynamical motion of a particular conformation can provide clues to the nature of the fundamental forces that influence DNA structure and stability. The article titled ‘‘Rotation of Guanine Amino Groups in G-Quadruplexes: A Probe for Local Structure
Submitted June 7, 2017, and accepted for publication June 12, 2017. *Correspondence: [email protected] Editor: Nadrian Seeman.
and Ligand Binding’’ (7) presents an economical NMR method to study the rotations of the G amino groups involved in the hydrogen bonding of the G tetrads found in DNA quadruplexes. NMR techniques have been used previously to study the dynamical motions of double-stranded DNA by measuring imino exchange rates (8). The challenge with this study was to pinpoint a particular amino group and enhance its signal with resolution from baseline. The authors addressed this issue by modifying the amino group with one methyl group—leading to restriction of rotation and subsequent sharpening of the NMR signal for the remaining proton. Rotational rates for the amino groups were then estimated from NMR line shape analysis. The first study focused on the parallel stranded quadruplex formed from the association of four individual single-stranded oligomers of sequence (50 -TTAGGGGT-30 ). This quadruplex possesses four G-tetrads stacked on top of each other. Their results indicated that the amino groups of the second and third layers in the middle of the stack had slower rotational rates than those of the layers on the ends of the stack. Subsequent studies also revealed that amino rotational rates were influenced by the local conformation of the quadruplex, ligand binding to the quadruplex, and formation of additional hydrogen bonds between the amino
group and neighboring H-bond accepting groups. Although the correlation between amino group rotation and basepair opening (so-called ‘‘breathing motions’’) has been established for DNA duplexes via NMR approaches (8), it is a little more difficult to correlate the rotational rates measured here with breathing motions within the G tetrad because these dynamics are not well understood. However, the observed slower rates for the interior tetrad amino groups compared to the end-stacking tetrads makes perfect sense because end fraying is certainly happening, as confirmed by the much higher rotational rates for the end-stacked tetrads at elevated temperatures. The authors presented several examples of the utility of this technique. Even within the quadruplex family of conformations, there is a great diversity of structures that vary by molecularity, loop orientation, and strand orientation. This technique has the potential to reveal unique structural and dynamical information about each of these. In addition, this approach could also discriminate between intercalation and end stacking of planar aromatic DNA binding molecules. Further, this method could also be applied to DNA triplexes where one of the strands is G-rich. The structural and dynamical information learned from these types of studies can be fundamental in the design of new DNA binding agents and DNA oligomers as building blocks
http://dx.doi.org/10.1016/j.bpj.2017.06.060 Ó 2017 Biophysical Society.
Biophysical Journal 113, 757–758, August 22, 2017 757
Sheardy
for DNA-based nanostructures and devices. REFERENCES
3. Il’ychova, I. A., Lysov YuP, ., V. A. Florentiev. 1990. Parallel double helices of DNA. conformational analysis of regular helices with the second order symmetry axis. J. Biomol. Struct. Dyn. 7:879–897.
1. Watson, J. D., and F. H. C. Crick. 1953. Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature. 171:737–738.
4. Antonacci, C., J. B. Chaires, and R. D. Sheardy. 2007. Biophysical characterization of the human telomeric (TTAGGG)4 repeat in a potassium solution. Biochemistry. 46:4654–4660.
2. Wang, A. H., G. J. Quigley, ., A. Rich. 1979. Molecular structure of a left-handed double helical DNA fragment at atomic resolution. Nature. 282:680–686.
5. Mergny, J. -L., L. Lacroix, ., C. Helene. 1995. Intramolecular folding of pyrimidine oligodeoxynucleotides into an i-DNA motif. J. Am. Chem. Soc. 117:8887–8898.
758 Biophysical Journal 113, 757–758, August 22, 2017
6. Yudong, H., M. Kristiansen, ., N. C. Seeman. 2017. A device that operates within a self-assembled 3D DNA crystal. Nat. Chem. http://dx.doi.org/10.1038/nchem.2745. 7. Adrian, M., F. R. Winnerdy, ., A. T. Phan. 2017. Rotation of guanine amino groups in G-quadruplexes: a probe for local structure and ligand binding. Biophys. J. 113:775–784. 8. Gueron, M., M. Kochoyan, and J. L. Leroy. 1987. A single mode of DNA base-pair opening drives imino proton exchange. Nature. 328:89–92.
Novel NMR Techniques to Study Structural and Dynamical Properties of DNA Quadruplexes Richard Sheardy1,* 1
Texas Woman’s University, Denton, Texas
Since the right-handed double helical conformation was first described by Watson and Crick (1), we have realized that DNA is highly polymorphic as evidenced by left-handed DNA (2), parallel-stranded DNA (3), DNA quadruplexes (4), and DNA i-motifs (5), to name a few. The conformation a particular segment of DNA assumes, as well as its thermodynamic stability and ligand binding properties, depend highly upon its sequence context and also on environmental conditions (e.g., temperature, cations present, pH, and so on). Researchers have taken advantage of DNA’s polymorphism and have constructed DNA-based objects and devices (6). Conformational properties (conformation, stability, ligand binding) are primarily governed by hydrogen bonding and base stacking interactions. These interactions also play a role in the flexibility and dynamical motion of the particular DNA conformation. Probing the dynamical motion of a particular conformation can provide clues to the nature of the fundamental forces that influence DNA structure and stability. The article titled ‘‘Rotation of Guanine Amino Groups in G-Quadruplexes: A Probe for Local Structure
Submitted June 7, 2017, and accepted for publication June 12, 2017. *Correspondence: [email protected] Editor: Nadrian Seeman.
and Ligand Binding’’ (7) presents an economical NMR method to study the rotations of the G amino groups involved in the hydrogen bonding of the G tetrads found in DNA quadruplexes. NMR techniques have been used previously to study the dynamical motions of double-stranded DNA by measuring imino exchange rates (8). The challenge with this study was to pinpoint a particular amino group and enhance its signal with resolution from baseline. The authors addressed this issue by modifying the amino group with one methyl group—leading to restriction of rotation and subsequent sharpening of the NMR signal for the remaining proton. Rotational rates for the amino groups were then estimated from NMR line shape analysis. The first study focused on the parallel stranded quadruplex formed from the association of four individual single-stranded oligomers of sequence (50 -TTAGGGGT-30 ). This quadruplex possesses four G-tetrads stacked on top of each other. Their results indicated that the amino groups of the second and third layers in the middle of the stack had slower rotational rates than those of the layers on the ends of the stack. Subsequent studies also revealed that amino rotational rates were influenced by the local conformation of the quadruplex, ligand binding to the quadruplex, and formation of additional hydrogen bonds between the amino
group and neighboring H-bond accepting groups. Although the correlation between amino group rotation and basepair opening (so-called ‘‘breathing motions’’) has been established for DNA duplexes via NMR approaches (8), it is a little more difficult to correlate the rotational rates measured here with breathing motions within the G tetrad because these dynamics are not well understood. However, the observed slower rates for the interior tetrad amino groups compared to the end-stacking tetrads makes perfect sense because end fraying is certainly happening, as confirmed by the much higher rotational rates for the end-stacked tetrads at elevated temperatures. The authors presented several examples of the utility of this technique. Even within the quadruplex family of conformations, there is a great diversity of structures that vary by molecularity, loop orientation, and strand orientation. This technique has the potential to reveal unique structural and dynamical information about each of these. In addition, this approach could also discriminate between intercalation and end stacking of planar aromatic DNA binding molecules. Further, this method could also be applied to DNA triplexes where one of the strands is G-rich. The structural and dynamical information learned from these types of studies can be fundamental in the design of new DNA binding agents and DNA oligomers as building blocks
http://dx.doi.org/10.1016/j.bpj.2017.06.060 Ó 2017 Biophysical Society.
Biophysical Journal 113, 757–758, August 22, 2017 757
Sheardy
for DNA-based nanostructures and devices. REFERENCES
3. Il’ychova, I. A., Lysov YuP, ., V. A. Florentiev. 1990. Parallel double helices of DNA. conformational analysis of regular helices with the second order symmetry axis. J. Biomol. Struct. Dyn. 7:879–897.
1. Watson, J. D., and F. H. C. Crick. 1953. Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature. 171:737–738.
4. Antonacci, C., J. B. Chaires, and R. D. Sheardy. 2007. Biophysical characterization of the human telomeric (TTAGGG)4 repeat in a potassium solution. Biochemistry. 46:4654–4660.
2. Wang, A. H., G. J. Quigley, ., A. Rich. 1979. Molecular structure of a left-handed double helical DNA fragment at atomic resolution. Nature. 282:680–686.
5. Mergny, J. -L., L. Lacroix, ., C. Helene. 1995. Intramolecular folding of pyrimidine oligodeoxynucleotides into an i-DNA motif. J. Am. Chem. Soc. 117:8887–8898.
758 Biophysical Journal 113, 757–758, August 22, 2017
6. Yudong, H., M. Kristiansen, ., N. C. Seeman. 2017. A device that operates within a self-assembled 3D DNA crystal. Nat. Chem. http://dx.doi.org/10.1038/nchem.2745. 7. Adrian, M., F. R. Winnerdy, ., A. T. Phan. 2017. Rotation of guanine amino groups in G-quadruplexes: a probe for local structure and ligand binding. Biophys. J. 113:775–784. 8. Gueron, M., M. Kochoyan, and J. L. Leroy. 1987. A single mode of DNA base-pair opening drives imino proton exchange. Nature. 328:89–92.
