Assuming that the oligonucleotide is comprised of nucleotides with deoxyribose (D isomer), then how would the bonds concerning the sugar’s noncyclic form, or representation other than the Haworth projection, be depicted?
Would the base still be attached to carbon 1? If so, what happens to the carbonyl group?
Normally, when I see the 5’ to 3’ phosphodiester linkage, the phosphate group on 5’ (cyclic sugar) comes first, and, then, it is followed by the sugar. The second phosphate group follows on 3’. For the straight chain sugar, how are the phosphate groups organized in relation to one another? For 4’ to 5’, would the phosphate groups be on the same side (be in the same positions where their respective OH groups were)?
Thank you for any response.