Abstract
Under different conditions, the DNA double helix can take different geometric forms. Of the large number of its conformations, in addition to the “canonical” B form, the A, C, and Z forms are widely known, and the D, Hoogsteen, and X forms are less known. DNA locally takes the A, C, and Z forms in the cell, in complexes with proteins. We compare different methods for detecting non-canonical DNA conformations: X-ray, IR, and Raman spectroscopy, linear and circular dichroism in both the infrared and ultraviolet regions, as well as NMR (measurement of chemical shifts and their anisotropy, scalar and residual dipolar couplings and inter-proton distances from NOESY (nuclear Overhauser effect spectroscopy) data). We discuss the difficulties in applying these methods, the problems of theoretical interpretation of the experimental results, and the prospects for reliable identification of non-canonical DNA conformations.
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Abbreviations
- 2D:
-
Two-dimensional
- 3D:
-
Three-dimensional
- A (a), T (t), G (g), C (c) in DNA sequences:
-
Adenine, thymine, guanine, cytosine
- a.s.:
-
Additional salt
- AFH:
-
Anti-ferromagnetic Heisenberg
- AFI:
-
Anti-ferromagnetic Ising
- AFP:
-
Anti-ferromagnetic Potts
- asym:
-
Antisymmetric
- C:
-
Carbon
- Ca:
-
Calcium
- Cd:
-
Cadmium
- CD:
-
Circular dichroism
- chem.shift:
-
Chemical shift
- Cl:
-
Chloride
- Co:
-
Cobalt
- Cr:
-
Chromium
- cryo-EM:
-
Cryogenic electron microscopy
- Cs:
-
Cesium
- CSA:
-
Chemical shift anisotropy
- DFT:
-
Density functional theory
- DNA:
-
Deoxyribonucleic acid
- ECD:
-
Electronic circular dichroism
- eNOE:
-
Exact nuclear Overhauser effect
- F:
-
FluorideFM - ferromagnetic
- Freq.:
-
Frequency
- GAFF:
-
General AMBER force field
- H:
-
Hydrogen
- IR:
-
Infrared
- K:
-
Potassium
- KDNA:
-
Deoxyribonucleic acid potassium salt
- LD:
-
Linear dichroism
- LD\(^r\) :
-
Reduced linear dichroism
- LiDNA:
-
Deoxyribonucleic acid lithium salt
- MD:
-
Molecular dynamics
- Mg:
-
Magnesium
- MG:
-
Major groove width
- mG:
-
Minor groove width
- MM:
-
Molecular mechanics
- Mn:
-
Manganese
- N:
-
Nitrogen
- Na:
-
Sodium
- NaDNA:
-
Deoxyribonucleic acid sodium salt
- Ni:
-
Nickel
- NMR:
-
Nuclear magnetic resonance
- NOE:
-
Nuclear Overhauser effect
- NOESY:
-
Nuclear Overhauser effect spectroscopy
- O:
-
Oxygen
- O-P-O:
-
group of DNA atoms O3’-P-O5’
- P:
-
Phosphorus
- PDB:
-
Protein data bank
- pH:
-
Pondus Hydrogenii
- PSI, \(\psi \) :
-
Polymer and Salt Induced
- r.h.:
-
Relative humidity
- Rb:
-
Rubidium
- RDC:
-
Residual dipolar coupling
- RNA:
-
Ribonucleic acid
- ROA:
-
Raman optical activity
- sym:
-
Symmetric
- T[MYAMP:
-
F] Taylor & Francis
- Tb:
-
Terbium
- TD-DFT:
-
Time-dependent density functional theory
- Tl:
-
Thallium
- U:
-
Purine
- UV:
-
Ultraviolet
- VCD:
-
Vibrational circular dichroism
- VMD:
-
Visual molecular dynamics
- Y:
-
Pyrimidine
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This work was supported by the Program of Fundamental Researches of the Russian Academy of Sciences (project FFZE-2022-0009, registration number 122040500069-7).
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The review conception and design belong to EAZ. Literature search and analysis were performed by both authors. IAS carried out the PDB data analysis. The first draft of the manuscript was written by EAZ; IAS commented on all the versions of the manuscript, and he also read and approved the final version.
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Zubova, E.A., Strelnikov, I.A. Experimental detection of conformational transitions between forms of DNA: problems and prospects. Biophys Rev 15, 1053–1078 (2023). https://doi.org/10.1007/s12551-023-01143-9
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DOI: https://doi.org/10.1007/s12551-023-01143-9