If we allow a DNA solution to dry, it will become a solid film. What are the techniques that we can employ to obtain information on what forms (A-, B-, or Z-) the DNA assume? Besides x-ray diffraction, are there any quicker method? Are there ways to determine the extent of base-stacking and base pairing?
You can use the vibrational spectroscopy methods (IR spectroscopy or Raman spectroscopy). At frequency range from 600 cm-1 to 1500 cm-1 DNA modes exist. Different forms of the double helix (A-, B-, or Z-DNA) have different mode frequencies and intensities that is usually used to identify the form of the double helix.It is also possible to use the low-frequency modes of the DNA helix (10 cm-1 -- 200 cm-1) characterizing the vibrations of atomic groups as whole.
Literature:
1. Duguid J., Bloomfield V. Benevides A.,J., Thomas G.J.Jr. Raman spectroscopy of DNA-metal complexes. I. Interactions and conformational effects of the divalent cations: Mg, Ca, Ba, Mn, Co, Ni, Cu, // Biophys. J. –1993. – Vol. 65. – P. 1916 – 1928.
2. Duguid J., Bloomfield V.A., Benevides J., Thomas G.J.Jr. Raman spectroscopy of DNA-metal complexes. II. The thermal denaturation of DNA in the presence of Sr2+, Ba2+, Mg2+, Ca2+, Mn2+, Co2+, Ni2+, Cd2+ // Biophys. J. – 1995. – Vol. 69. – P. 2623 – 2641.
3. Semenov M.A., Bol’bukh T.V., Kashpur V.A., Maleyev V.Ya., Mrevlishvili G.M. Hydration and stability of the B-form of LiDNA // Biofizika. – 1994. – Vol. 39, № 1. – P. 50 – 57.
4. Guzman M.R., Liquier J., Taillandier E., Hydration and conformational transitions in DNA, RNA, and mixed DNA-RNA triplexes studied by gravimetry and FTRI spectroscopy // J. Biomolec. Struct. Dyn. – 2005. – Vol. 23, № 3. – P. 1 – 9.
5. Lamba Om P., Wang A.H.-J., Thomas G.J.Jr, Low-frequency dynamics of crystals, of B-, A-, Z-DNA, and Fibers of C-DNA // Biopolymers. –1989. – Vol. 28. – P. 667 – 678.
Dear Dr. Kan Fu,
It is also important to remember that in dry state the DNA may be in the A- form of the double helix or in even in the disordered state. B-DNA conformation of the double helix forms under high humidity (more than 90% r.h.) of the semple. The formation of DNA Z-form usually occurs under the high concentration of counterions (Na+ and Mg2+) and GC base pair sequence.
1. Lindsay S.M., Lee S.A., Powell J.W., Weidlich T., Demarco C., Lewen G.D., Tao N.J., Rupprecht A., The origin of the A to B transition in DNA fibers and films // Biopolymers. – 1988. – Vol. 27. – P. 1015 –1043.
Dear Prof. Andrey Luchnik,
Certainly, the double helix can adopt A-form and even Z-form in the processes of DNA biological functioning, but I meant the conditions of the sample where DNA macromolecule is free of proteins and other possible action factors, existing in the living cell. This is the result of many experimental studies.
For example: Малеев В.Я., Семенов М.А., Гасан А.И., Кашпур В.А. Физические свойства системы ДНК-вода // Биофизика. – 1993. – Vol. 38, № 5. – P. 768 - 790.
- Badges
- Science method
- Similar topics
- Methodology
- Crystallography
- X-ray Diffraction