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On the formation of the double helix between adenine single strands at acidic pH from synchrotron radiation circular dichroism experiments
Author(s) -
Holm Anne I. S.,
Munksgaard Nielsen Lisbeth,
Vrønning Hoffmann Søren,
Brøndsted Nielsen Steen
Publication year - 2012
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.22038
Subject(s) - chemistry , protonation , circular dichroism , crystallography , synchrotron radiation , guanine , spectral line , helix (gastropod) , duplex (building) , dna , nucleotide , ion , ecology , biochemistry , physics , snail , gene , organic chemistry , quantum mechanics , astronomy , biology
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. © 2012 Wiley Periodicals, Inc. Biopolymers 97:550–557, 2012.