Various G-quadruplex structures of the human telomere sequence studied by circular dichroism and Raman spectroscopies
Abstract
In this work, we combine conventional CD measurements with Raman spectroscopy (RS) to probe solution structures adopted by the 22-mer DNA sequence of AG3(TTAG3)3 (wild type, referred to as wt hereinafter) derived from the human telomere repeat region as well as its abasic modification, in which adenine in one loop at the position 19 (ap19) or three loop adenines at the positions 7, 13 and 19 (ap7,13,19) were removed. As shown by us, CD spectra unambiguously differentiate between quadruplex structures adopted by wt, ap19 and ap7,13,19 in the presence of different stabilizing cations (Na+ or K+), at different ionic strengths and temperatures.
Here we aim to provide additional and complementary information to the earlier CD studies by means of RS. As demonstrated by several researchers over the last five decades, conventional non-resonant RS is highly sensitive to DNA structure and its conformational transitions induced by various physicochemical parameters.
We have already shown that RS can be used to monitor transition from antiparallel to parallel G-quadruplex folding induced by increasing oligonucleotide concentration. In the present study, Raman spectra of wt, ap19 and ap7,13,19 quadruplexes stabilized by Na+ and K+ cations at rather high oligonucleotide concentrations (~ 1 mM) have been compared with those measured in the absence of stabilizing cations.
The greatest difference was observed between the Raman spectra of ap7,13,19 and those of the other two sequences, wt and ap19, reflecting the fact that ap7,13,19 forms a predominantly parallel quadruplex, whereas wt and ap19 seem to adopt mixture of parallel/antiparallel alignment. Specific Raman markers also reflect further increase in the extent of parallel folding of ap7,13,19 with increasing temperature (max. at ~50°C), as well as thermal denaturation of all three quadruplex structures above this temperature.