6.13 Build DNA/RNA

By this tool, you can build a nucleic acid (DNA/RNA) from its primary structure in single or double strand form. To show the dialog window, you must select Edit Build DNA/RNA in the main menu.

In the big editing box, you can type the nucleotide sequence or copy & paste it from another application (the characters not corresponding to a nucleotideare automatically removed), using the single character codes. Alternatively, the input can be performed by the four buttons (one for each nucleotide) at the window bottom. In the Type box, you can specify the type of helix you want to build:

• Right handed A-DNA (Arnott)
• Right handed B-DNA (Arnott)
• Right handed B-DNA (Langridge)
• Left handed B-DNA (Sasisekharan)
• Right handed A-RNA (Arnott)
• Right handed A-PRIME RNA (Arnott)

In the Strand box, you can indicate if to build a single (5'  3' or 3'  5') or double (Both) strand, while checking Add hydrogens, the hydrogens are automatically added to the model.

The Build button starts the building of the DNA/RNA.

6.13.1 Copyright

The code implemented in VEGA ZZ is based on Fd_helix program, which is copyrighted by David A. Case. The References for the fiber-diffraction data are:

• Arnott S., Hukins D.W.L., Dover S.D., Fuller W., Hodgson, A.R. "Structures of synthetic polynucleotides in the A-RNA and A'-RNA conformations. X-ray diffraction analyses of the molecule conformations of polyadenylic acid, polyinosinic acid, polycytidylic acid", J. Mol. Biol.. Vol. 81-2, 107-122, 1973.
• Arnott S., Chandrasekaran R.,  Birdsall D.L., Leslie A.G.W., Ratliff R.L. "Left-handed DNA helices", Nature, Vol. 283, 743-745, 1980.
• Lakshimanarayanan A.V., Sasisekharan V. "Stereochemistry of nucleic acids and polynucleotides. II. Allowed conformations of the monomer unit for different ribose puckerings",  Biochim. Biophys. Acta, Vol. 204, 49-53, 1970.
• Fuller W., Wilkins M.H.F., Wilson H.R., Hamilton L.D., Arnott, S. "The molecular configuration of deoxyribonucleic acid: IV. X-ray diffraction study of the A form",  J. Mol. Biol., Vol. 12-1, 60-76, 1965.
• Arnott S., Campbell Smith P.J., Chandraseharan R. in "Handbook of Biochemistry and Molecular Biology", 3rd Edition. Nucleic Acids Volume II ,
  Fasman, G.P., ed. (Cleveland: CRC Press, 1976), 411-422.