C-DNA

Not to be confused with complementary DNA, also known as cDNA.

C-DNA, also known as C-form DNA, is one of many possible double helical conformations of DNA. DNA can be induced to take this form in particular conditions such as relatively low humidity and the presence of certain ions, such as Li⁺ or Mg²⁺, but C-form DNA is not very stable and does not occur naturally in living organisms. In 1961, it was found by Marvin, when he tried to repeat for the Li salt the higher water content pattern of the Na salt. What Marvin found is the semicrystalline C-DNA. "Semicrystalline" describes a diffraction pattern for which crystalline reflexions are seen at low resolution but continuous transform at higher resolution.

structure

The C-DNA is a non-integral helix of slightly variable dimensions, with mean values of 3.32Å for the unit rise and 38.60° for the unit twist, giving about 9 1/3 rather that 10 unites per turn. There are some different models for C-DNA proposed over years. In 2000, van Dam and Levitt found that both C-DNA and B-DNA consist of two distinct nucleotide conformations, B-I and B-II. The ratio of B-II conformation in C-DNA is more than 40%, but in B-DNA the ratio is only about 10%. Figure in that paper shows the ideal modal of these two conformations published by them.

Counterions such as primary amides under basic conditions have been used in experiments to show the relationship between B and C forms of DNA. The overall shape and orientation of DNA is heavily dependent on its primary sequence as well as hydrogen bonding between its base pairs, which stabilizes and maintains the double helix conformation. C-DNA was shown to hold its conformation in the absence of water and was able to form upon dehydration.[1] Some amides under basic conditions and low humidity were shown to hold the C-form conformation, but smoothly transitioned to B-form DNA as the humidity was increased.This may suggest a strong correlation between C-form and B-form DNA, which was also seen using lithium salt at low humidity.

comparison geometies of the most common DNA form

Geometry attributes

	A-form	B-form	C-form	Z-form
Helix sense	right-handed	right-handed	right-handed	left-handed
Repeating unit	1 bp	1bp	1bp	2bp
Rotation/bp	32.7°	34.3°	38.6°	60°/2
Mean bp/turn	11	10	9.33	12
Rise/bp along axis	2.6Å	3.4Å	3.3Å	3.6-3.8 Å

Also See

• B-DNA
• A-DNA
• Z-DNA
• Mechanical properties of DNA
• DNA

References

• [1,2] Marvin, D. A. (2017-08-01). "Fibre diffraction studies of biological macromolecules". Progress in Biophysics and Molecular Biology. 127: 43–87. doi:10.1016/j.pbiomolbio.2017.04.005. ISSN 0079-6107.
• [3] van Dam, M H Levitt (2000). "BII nucleotides in the B and C forms of natural-sequence polymeric DNA: A new model for the C form of DNA". Journal of Molecular Biology. 304 (4): 541–61. doi:10.1006/jmbi.2000.4194. PMID 11099379.
• [4] Portugal, J.; Subirana, J.A. (September 1985). "Counterions which favour the C form of DNA". The EMBO Journal. 4 (9): 2403–2408. doi:10.1002/j.1460-2075.1985.tb03946.x. ISSN 0261-4189. PMC 554517.
• [5] Marvin, D.A.; Spencer, M.; Wilkins, M.H.F.; Hamilton, L.D. (October 1961). "The molecular configuration of deoxyribonucleic acid III. X-ray diffraction study of the C form of the lithium salt". Journal of Molecular Biology. 3 (5): 547–IN14. doi:10.1016/s0022-2836(61)80021-1. ISSN 0022-2836.
• [6]Portugal, Franklin H. (1977). A century of DNA : a history of the discovery of the structure and function of the genetic substance. MIT Press. ISBN 978-0-262-16067-4. OCLC 2964854.
• [7]Ghosh, Bansal, Anirban, Manju (2003). "A glossary of DNA structures from A to Z". Acta Crystallographica Section D. 59 (4): 620–6. doi:10.1107/S0907444903003251. PMID 12657780.
• [8]Zimmerman, S. B. (1982). "The Three-Dimensional Structure of DNA". Annual Review of Biochemistry. 51: 395–427. doi:10.1146/annurev.bi.51.070182.002143. PMID 7051961.