CD spectra of telomeric oligonucleotides mutated in the loop.

<p>A) Each oligonucleotide contained one single base mutated to C in each loop; B) each oligonucleotide contained the three nucleotides mutated to C in one loop; C) A bases in the loops were moved from the third to the second and first positions or mutated to T.</p

Frequency of the occurrence of the hydrogen bonds.

<p>Frequency of the occurrence of the hydrogen bonds (HBs), monitored over 2 ns, every 10 ps, in the guanine core in the presence of C3 and A1T3 mutated G-quadruplex sequences. </p

Thermal difference spectra (TDS) and TDS factor plots of three representative oligonucleotides.

<p>A) TDS of C1, C2 and C3 sequences; B) TDS factors of C1, C2 and C3 sequences. TDS and TDS factors of all oligonucleotides are available in Figure S8 in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0084113#pone.0084113.s004" target="_blank">File S4</a>.</p

RMSd conformation of C3 and A1T3 mutated G-quadruplex sequences.

<p>Lowest (A) and highest (B) RMSd conformation of C3 and A1T3 mutated G-quadruplex sequences during 2 ns MD simulations with respect to the starting structure (2HY9). The DNA is shown in purple (C3) and aquamarine (A1T3) wireframe rendering and its strand as orange cartoon. The K⁺ coordinating ions are represented as blue spheres. The RMSd value of each conformation is reported and expressed in Å. </p

CD spectra of telomeric oligonucleotides mutated in the loop.

<p>In each oligonucleotide one single base was mutated. </p

Model structures of conformations reported for the human telomeric sequence.

<p>Guanosines in dark grey are <i>syn</i>, and those in light gray are <i>anti</i>.</p

Clerocidin protection assay of the wt, C1, C2 and C3 telomeric oligonucleotides.

<p>Sequences were heat denatured, folded in the presence or absence of K⁺ and treated with CL followed by hot piperidine (CL lanes) or just treated with piperidine (C lanes). M indicates the marker lane obtained with the Maxam and Gilbert protocol. Base sequences are shown aside each gel image. Symbols * and ~ indicate protected G and C bases, respectively.</p

CD-monitored thermal denaturing assays of wt, C1, C2 and C3 telomeric oligonucleotides.

<p>A-D) CD spectra of each indicated oligonucleotide measured at increasing temperatures (20°C-95°). Arrows indicate curve trend at increasing temperatures. E) Molar ellipticities, measured at wavelength of maximum intensity, were plotted against temperature.</p