title: On the formation of the double helix between adenine single strands at acidic pH from synchrotron radiation circular dichroism experiments.
abstract: Here, we present synchrotron radiation circular dichroism spectra for a series of DNA adenine strands, (dA)(n) , n = 2-10, 15, at acidic pH. Reference spectra of a protonated single strand, (dAH(+) )(n) , and a protonated double helix, (dAH(+) )(n) :(dAH(+) )(n) , are provided in the wavelength region from 175 to 330 nm. The largest spectral difference between single and double strands is in the vacuum ultraviolet, where a band changes sign. This new spectral feature that characterizes double helix formation may be useful for analytical purposes but also for shedding light on the underlying complexation mechanism. Furthermore, we find that a minimum of eight or nine bases in a strand is needed for two (dAH(+) )(n) strands to form a duplex. This is a relatively high number as compared with guanine quadruplex and cytosine i-motif formation, which is likely linked to the significant Coulomb repulsion between the all-protonated bases. Finally, spectra recorded as a function of time after sample preparation indicates that the equilibrium is slowly reached, in certain cases taking an hour or more.
authors.affiliation: Institute for Storage Ring Facilities, Department of Physics and Astronomy, Aarhus University, DK-8000 Aarhus C, Denmark. aish@phys.au.dk
authors.forename: Anne I S
authors.initials: AI
authors.lastname: Holm
authors.forename: Lisbeth
authors.initials: L
authors.lastname: Munksgaard Nielsen
authors.forename: Søren
authors.initials: S
authors.lastname: Vrønning Hoffmann
authors.forename: Steen
authors.initials: S
authors.lastname: Brøndsted Nielsen
mesh_terms: D000143:Acids / Q000737:chemistry*; D000225:Adenine / Q000737:chemistry*; D002942:Circular Dichroism / Q000379:methods*; D006863:Hydrogen-Ion Concentration; D017356:Synchrotrons; D013696:Temperature
chemical_list: D000143:Acids; D000225:Adenine