High and low twist at the GT & TG steps concomitant with disrupted stacking at the interruption sites.

<p>Helical twist angle variation at the overlapping GT and TG steps at the G_*GC interruption site (<b>A</b>) (<i>Sequence 4</i>) in the T_*AT triplex and in the G_*GC triplex (<i>Sequence 8</i>) with the T_*AT interruption (<b>C</b>). Note the loss of significant base stacking at the GT step of the interruption site (<b>B</b>) and (<b>D</b>) and partial stacking at the TC & CT steps of WC duplex.</p

Nature, degree of base triplet nonisostericity and their consequence.

<p>Nature, degree of base triplet nonisostericity and their consequence.</p

TFOs leading to an overwinding GT step triplex junction interface act as bending agent.

<p>Stereo view of parallel triplex with (<b>A</b>) a GT step junction interface (Sequence 10), (<b>B</b>) a TG step junction interface (Sequence 11) and (<b>C</b>) a triplex containing a GT and a TG step junction interface as well as interruptions (1 T_*AT & 1 G_*GC) (Sequence 15). Note a conspicuous bend in the triplex structure with GT step junction interface in the sequences 10 & 15 (<b>A</b> & <b>C</b>), while near uniform triplex structure prevails in the sequence 11 with a TG step junction interface (<b>B</b>). G_*GC and T_*AT triplets are coloured green and red respectively. Helical axis (blue stick) w.r.t WC duplex is shown. Phosphate atom of the third strand (TFO) is coloured yellow for reference.</p

Demonstration of unstable and stable nature of parallel and antiparallel triplex formed by alternating G_*GC & T_*AT triplets respectively.

<p><b>A</b> Frequency of incidence (red & gray filled part) and loss (void part) of canonical (<b>A</b>) Hoogsteen (<i>Sequence 1</i>) and (<b>B</b>) reverse Hoogsteen hydrogen bonds (<i>Sequence 2</i>) in the central 6 G_*GC and 7 T_*AT triplets of the 15-mer parallel and antiparallel triplex (terminal triplets not considered) over a simulation time of 250 and 100 ns respectively. Wide spread loss of Hoogsteen hydrogen bonds in the (<b>A</b>) parallel triplex (<i>Sequence 1</i>), and retention of reverse Hoogsteen hydrogen bonds in the (<b>B</b>) antiparallel triplex (<i>Sequence 2</i>) are apparent. Canonical Hoogsteen and reverse Hoogsteen hydrogen bonding schemes in the G_*GC & T_*AT base triplets in parallel & antiparallel orientations are shown on top for reference.</p

Transition from canonical to noncanonical Hoogsteen hydrogen bond schemes in the T_*AT (NC1 to NC4) and G_*GC (NC5 to NC8) triplets with reduced residual twists due to the effects of nonisostericity.

<p>Typical canonical Hoogsteen hydrogen bonding schemes in T_*AT (brown), G_*GC (green) triplets & their superposition are shown in A, C and B respectively. Noncanonical Hoogsteen hydrogen bonding schemes of T_*AT (D,E,F,G) & G_*GC (H,I,J,K) base triplets are shown along with their superposition with the canonical schemes to highlight reduction in the residual twist Δt° (right panel in <b>D to K</b>). Na⁺ ion (<b>E & J</b>) and oxygen atom of water molecule (<b>D-G, I & K</b>) are coloured in cyan and red respectively.</p

Demonstration of the retention of Canonical Hoogsteen hydrogen bonds at the G_*GC/T_*AT triplex junction interface.

<p>Frequency of incidence (red & gray colour part) and loss (void part) of Hoogsteen hydrogen bonds in the NIBTs at the GT step—<i>Sequence 10</i> (<b>A</b>) and at the TG step—<i>Sequence 11</i> (<b>B</b>) triplex junction interfaces. Hydrogen bonds retention is highlighted by the enclosed blue box.</p

Incidence of alternating G_*GC and T_*AT triplets in a parallel triplex disrupts base stacking.

<p>Stacking interaction at the GT and TG steps of the Hoogsteen strand in the various noncanonical Hoogsteen schemes seen for the <i>sequence</i> 1 during simulation: NC1 to NC4 for T_*AT and NC5 to NC7 for G_*GC triplets. Loss of stacking is indicated by dark arrows. C1’ atom of the sugar is shown as open circle.</p