Model of intramolecular DNA triplexes and common triplets.

<p>In genomic DNA in vivo or in supercoiled plasmid DNA in vitro, homopurine–homopyrimidine tracts with mirror-repeat symmetry, i.e., AGGAA…AAGGA-TCCTT…TTCCT (top) may form four types of triplex structures: two in which half (either the 5′ or 3′ half; only the 3′ case is shown) of the single-stranded purine-rich strand folds back, engaging in reverse Hoogsteen interactions with the purine-rich strand of the remaining duplex in an antiparallel orientation (R•R–Y type triplex, left); and two in which half (either the 5′ or 3′ half; only the 3′ case is shown) of the single-stranded pyrimidine-rich strand folds back, engaging in Hoogsteen interactions with the purine-rich strand of the remaining duplex in a parallel orientation (or Y•R–Y type triplex, right). The most common triplets, both in intramolecular and intermolecular (triplex-forming oligonucleotide [TFO]-derived) triplexes, include A•A–T, G•G–C, and T•A–T for R•R–Y type triplexes (bottom left), and C⁺•G–C and T•A–T for Y•R–Y type triplexes (bottom right). C⁺ indicates a protonated cytosine.</p

RNA triplexes perform critical functions in biological systems.

<p>(A) Schematic of the two catalytic steps of splicing. In the first step (branching), the 2′-hydroxyl of an intronic adenosine (branch point) attacks the phosphodiester bond at the 5′-exon-intron boundary, releasing the 5′-exon with a free 3′-hydroxyl and a lariat structure comprising the 5′-intronic phosphate group linked to the 2′-hydroxyl of the attacking adenosine. In the second step (exon ligation), the 3′-hydroxyl of the free 5′-exon attacks the 3′-intron-exon boundary, thereby releasing the intron lariat and the fused 5′-to-3′-exons. (B) Illustration of the triplex formed by U2-U6 RNAs of yeast spliceosome. Bases from U6 (blue) and U2 (orange) create a triplex structure that coordinates two magnesium ions (red) required for both steps of catalysis on pre-mRNAs (gray). The first catalytic reaction is shown, i.e., attack of the 2′-OH of an intronic adenosine on the 5′-exon-intron junction phosphate group. (C) Outline of the TR component of telomerase (medaka), displaying the core pseudoknot region comprising two loops (L1 and L2) and two stems (S1 and S2), template (red), and two triplexes (orange), one at the pseudoknot and the other at the CR4/5 domain (blue shading). (D) Close-up of the CR4/5 domain showing base-pair interactions in the absence (left) and in the presence (right) of the TR-binding domain (TRBD). TRBD binding reorganizes critical bases (red) at the junction between P5, P6, and P6.1 and form a mini-triplex, causing P6.1 to rotate by approximately 180° (blue shading).</p

Model of DNA triplex-induced mutagenesis and genomic diversity.

<p>DNA repair proteins (shown as scissors) recognize and process DNA triplex structures in replication-independent (left) and replication-related (right) pathways, and may contribute to genomic instability and, perhaps, genomic diversity.</p

Noncoding RNAs achieve gene regulation through triplex interactions.

<p>(A) Illustration of the organization on the mouse genome of the <i>Fendrr</i> and <i>Foxf1</i> genes. The <i>Foxf1</i> gene comprises two coding exons (large rectangles) separated by a short intron (small rectangle), and 5′ and 3′ untranslated exons (medium rectangles). Different splice variants have been identified for the <i>Fendrr</i> gene, which include lncRNA transcripts (medium rectangles) that contain a sequence involved in triplex interactions with <i>Foxf1</i> and other genes (red). The two genes are transcribed in the opposite orientation (arrows) from a shared promoter. (B) Diagram showing the scaffolding role of <i>Fendrr</i> lncRNA, achieving gene regulation by anchoring to target genes (<i>Foxf1</i>) through triplex interactions with cognate duplex sequences (red lines), and delivering chromatin modifiers (PRC2) to key histone tail residues (red circle). (C) Illustration of rDNA gene silencing by noncoding RNAs binding to T₀ through triplex interactions at one end and to the nucleolar remodeling complex (NorC) silencing complex at the opposite end, and by cytosine methylation catalyzed by DNA cytosine-5-methyltransferase 3b (DNMT3b).</p

Vertical ionization potentials (VIPs) of guanine-centered DGN sequences.

<p>VIPs for the centrally (italicized) guanine computed at the M06-2X/6-31G(<i>d</i>) level of theory;</p>a<p>VIP of free unalkylated guanine;</p>b<p>from reference <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003816#pgen.1003816-Zaytseva1" target="_blank">[57]</a>.</p

Germline mutations are affected by transcription.

<p><i>Panel A</i>, HGMD dataset; <i>y-axis</i>, as in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003816#pgen-1003816-g001" target="_blank">Figure 1C</a>; <i>x-axis</i>, ratio of mutated NGNN sequences in protein coding genes containing the P2-guanine base on the non-transcribed (<i>NT</i>) <i>vs</i>. transcribed (<i>T</i>) strand; <i>solid circles</i>, HGMD dataset (<i>r</i>² 0.32, P(α)_0.05 0.991, P<0.001); <i>open circles</i>, 1000 Genomes Project dataset. <i>Panel B</i>, inherited splicing mutations dataset; <i>top</i>, cartoon of exon-intron boundaries showing the conserved GT and AG bases at the donor (<i>ds</i>) and acceptor (<i>as</i>) splice sites; <i>bottom</i>, graph of splicing mutations; <i>y-axis</i>, number of SBSs; <i>x-axis</i>, position of SBSs relative to +/−20 nt of splice junctions; <i>Panel C</i>, model for sequence-dependent SBSs in cancer and human inherited disease. In the first step, an electron is lost from within a tetranucleotide sequence, leaving a hole. In the second step, the hole migrates to and from various competing sites, including nearby bases and chromatin-associated amino acids (not shown), eventually being trapped by a guanine base. The resulting guanine radical cation either causes DNA-protein crosslinking or undergoes subsequent chemical modifications. If the modified base is not corrected by DNA repair, it may give rise to a mutation (X-Y base-pair) as a result of error-prone DNA polymerase synthesis during DNA replication (dashed arrow).</p

SBSs and VIPs.

<p><i>Panel A</i>, whisker plot of the fractions of SBSs at G•C bp for the EWS and GWS datasets computed using AgilentV2 and Duke35 mappability counts, respectively; <i>red line</i>, mean; <i>black line</i>, median; <i>green lines</i>, average GC-contents in the mappable AgilentV2 (EWS) and Duke35 (GWS) sets. <i>Panel B</i>, NGRA sequences are enriched in SBSs in melanoma. <i>y-axis</i>, for each 4-member sequence combination with matching P1–P3 bases, the fraction of mutations at P4-A was divided by the average fraction of mutations at P4-(C/T/G); <i>x-axis</i>, P3 base composition; <i>R</i>, purine; <i>Y</i>, pyrimidine; mean ± SD; P-value from two-tailed <i>t</i>-test. <i>Panel C</i>, the <i>ln</i> of normalized fractions of mutated DGNN (D = A/G/T) sequences, <i>F_i</i>, for the seven cancer datasets with −logP ≥3 for DGRN>DGYN (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003816#pgen-1003816-t001" target="_blank">Table 1</a>) were combined and plotted as a function of the average absolute free energy of base stacking, ΔG(ν), for each of the 48 DGNN sequences. <i>Panel D</i>, three-dimensional model of the (5′-GGG-3′)•(5′-CCC-3′) trinucleotide showing the LUBMO (lowest unoccupied beta molecular orbital) of the ionized sequence. <i>Panel E</i>, plot of the normalized fractions (<i>log f_i</i>×10³) of mutated DGN sequences (Duke35 counts) for the Lung_nsc cancer dataset <i>vs.</i> VIPs; <i>outer circle</i>, 5′D base; <i>inner circle</i>, 3′N base; <i>blue</i>, adenine; <i>green</i>, guanine; <i>red</i>, thymine; <i>yellow</i>, cytosine. <i>Panel F</i>, agglomerative hierarchical clustering of 14 cancer genome datasets obtained from linear correlations with <i>ln</i> VIP values, as obtained from T_hg19 counts; <i>colored boxes</i>, elements found to be clustered at the 90% confidence interval.</p