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.

Probing electronic coupling between adenine bases in RNA strands from synchrotron radiation circular dichroism experiments

“…We have in previous works used a synchrotron radiation (SR) source to obtain CD spectra of DNA strands not only in the ultraviolet (UV) region but also in the vacuum ultraviolet (VUV, o200 nm) where the photon fluxes delivered by the source are high in contrast to conventional CD instruments. [14][15][16][17] In the case of DNA strands of adenine we found that the initially reached state after UV excitation is delocalised over just two bases while its spatial extent is increased to about eight bases in the VUV. 14 Here we now turn to RNA strands of adenine where the geometrical orientation of the bases is different from that found in the corresponding DNA strands due to the extra OH group at the 2 0 -position of the furanose ring.…”

“…The simplest case is no electronic coupling between bases which implies that the signal is proportional to n. Examples include DNA single strands of all-protonated bases (cytosine or adenine). 15,16 If two neighbour bases interact, the signal instead follows c (n À 1) where the coefficient is determined by the rotational strength of the exciton state. This behaviour is seen for DNA single strands of thymine and cytosine.…”

Parallel Polyadenine Duplex Formation at Low pH Facilitates DNA Conjugation onto Gold Nanoparticles

“…Parallel poly-A duplexes have been studied in terms of biophysical properties, , structure, ,,, and analytical applications. ,− Most previous work used pure adenine homopolymers. In our system, however, poly-A DNA is only a fraction of the whole sequence.…”

“…Characterizing the A-Motif DNA by CD Spectroscopy. Parallel poly-A duplexes have been studied in terms of biophysical properties, 36,37 structure, 32,33,38,39 and analytical applications. 35,40−42 Most previous work used pure adenine homopolymers.…”

Synchrotron-radiation vacuum-ultraviolet circular dichroism spectroscopy in structural biology: an overview

“…and Holm, A. I. et al . systematically investigated the contributions of the base composition and sequence to the VUVCD spectra of various types of DNA down to 175 nm [21,143,144,150]. They clarified the spectral characteristics of strands of polynucleotides composed of four bases as a function of strand length.…”