We are using Avogadro version 1.2.0 to build a single-stranded adenine-adenine Z-DNA dinucleotide with the Build extension.
Our preliminary understanding is that the Z-DNA generated by Avogadro has a right-handed conformation. However, Z-DNA is generally described as having a left-handed structure. So, we find it curious that Avogadro builds a right-handed DNA strand by default. Appended, you will find our simple criteria to determine if the Z-DNA from Avogadro is right-handed.
Does anybody know about the handedness of the Z-DNA generated by Avogadro?
P.S., Here is our criteria to determine right- and left-handed DNA:
It is pedagogical and useful to visualize the coordinate system using the traditional mnemonic of the right-hand rule. When viewing the single-stranded dinucleotide with the 3' base on the top and the 5$’$ base on the bottom, one may take one’s index finger as pointing along the in-plane vector of the 5’ nucleotide base as described above and the other three fingers as pointing along the in-plane vector of the 3’ nucleotide: considering one’s thumb points upward, the conformation is right-handed if the index finger rotates counter clock-wise to align the three other fingers.
Otherwise, the conformation is left-handed (\\varphi < 0). These definitions agree with the usual right- and left-handed conventions used to classify biological forms of single- and double-stranded DNA (A-, B-, and Z-DNA, specifically).