¹³C transverse relaxation rates (<i>R₁ρ</i>) versus applied spin lock field strength (in Hertz) at 500 MHz for aromatic and anomeric carbons of mini-cTAR DNA. (A) G4 C8; (B) A3 C1′; (C) A21 C8; (D) G16 C1′.

<p>¹³C transverse relaxation rates (<i>R₁ρ</i>) versus applied spin lock field strength (in Hertz) at 500 MHz for aromatic and anomeric carbons of mini-cTAR DNA. (A) G4 C8; (B) A3 C1′; (C) A21 C8; (D) G16 C1′.</p

Relaxation times for aromatic C6/C8 spins of mini-cTAR DNA at 500 MHz.

<p>Top to bottom: ¹³C <i>T₁</i>, ¹³C <i>T₁ρ</i> and hetNOEs. Errors represent uncertainties in the fit of the primary relaxation data to mono-exponential decays. No data are associated to residues corresponding to a broad or overlapped cross peak. The color codes used for the residues are the following: blue (lower stem), orange (internal loop), black (upper stem) and magenta (apical loop).</p

Gel retardation assays of NC(11–55):mini-cTAR DNA complexes formed <i>in vitro</i>.

<p>(A) Mini-cTAR ³²P-DNAs were incubated in presence of NC(11–55) and analyzed by electrophoresis on a 14% polyacrylamide gel as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038905#s2" target="_blank">Materials and Methods</a>. Lanes 1, controls mini-cTAR dimerization induced by NC(11–55) at a protein to nucleotide molar ratio of 1∶1 (NC(11–55) was removed by phenol/chloroform before gel electrophoresis); lanes 2, heat-denatured mini-cTAR DNAs; lanes 3, controls without protein; lanes 4–7, protein to nucleotide molar ratios were 1∶8, 1∶4, 1∶2 and 1∶1. Monomeric and dimeric forms of free mini-cTAR DNAs are indicated by fm and fd, respectively. CI and CII indicate the NC(11–55):mini-cTAR complexes. (B) Fraction of bound mini-cTAR as a function of the protein:oligonucleotide (expressed in nt) ratio. Each data point represents the mean of three experiments. Symbols: filled circles, mini-cTAR; filled triangles, mini-cTARCT; open triangles, mini-cTARIN2; open circles, mini-cTARIN2CT.</p

Imino region of 1D spectra (pH 6.5, in H₂O, 10°C, 60 ms) showing the difference between mini-cTARGC (A) and mini-cTAR (B).

<p>The new resonances observable in the mutant and corresponding to the imino protons of the lower stem are indicated by asteriks.</p

Average Relaxation times <i>T₁</i>, <i>T₁ρ</i> and NOE ratios for base and sugar resonances for each domain of mini-cTAR DNA.

<p>Average Relaxation times <i>T₁</i>, <i>T₁ρ</i> and NOE ratios for base and sugar resonances for each domain of mini-cTAR DNA.</p

Internal motion parameters for mini-cTAR DNA. Due to overlapped cross-peaks and a broad peak, no models were fitted for C11, C22 sugars residues and for G14 base, respectively.

<p>Other residues without values correspond to residues that do not fit any model well.</p

Exchange contribution to transverse relaxation versus sequence for aromatic C8 and C6 carbons (A) of mini-cTAR DNA determined from <i>T₁ρ</i> power dependence experiments.

<p>(B) Secondary structure for the mini-cTAR sequence showing the possible transient base-pairs for G4–C22, A5–G20 and C11–G14. The color codes used for the residues are the following: blue (lower stem), orange (internal loop), black (upper stem) and magenta (apical loop).</p

S² as extracted from model-free analysis <i>versus</i> sequence at 500 MHz.

<p>(<b>A</b>) <b>C6/C8 spins;</b> (<b>B</b>) <b>C1′ spin.</b> Residues for which no results are shown correspond to overlapped cross-peaks or data that could not be fit well with any model-free model. The color codes used for the residues are the following: blue (lower stem), orange (internal loop), black (upper stem) and magenta (apical loop).</p

DNA oligonucleotides and peptides used in the study (A) Secondary structures for the mini-cTAR sequences.

<p>The single base mutations are boxed. (B) Sequences of NC and NC(11–55).</p