Purine stacks, cross-strand

Cross-strand purine stacks The cross-strand (rather than same-strand) stacking formed by the six-member ring of an A or G in one strand stacks on the six-manber of an A or G in the other (either A s stack on A s or G s stack on G s). The consensns sequence for cross-strand A-stack motifs is 5 (G/C)(G/A)A 3 (C/G)A(U/A). The initial (G C) pair is Watson-Crick type. The next pair is usually side-by-side (A G) or (A A via AN — N3 A) and the following pair can be either reversed Hoogsteen (A U vis UN3— Ny, UO2— N6A) or side-by-side AA. Additional nonhelical sequence must follow before an internal loop containing a cross-strand A-stack can be terminated and A-helix resumes. 

The detailed nuclear Overhauser effect (NOE) analysis of contacts between Pl and its flanking thymidine residues involving imino and methyl protons attested to a stacked-in conformation for this base, with a regular right-handed helical conformation [69]. Cross-strand NOE patterns between protons on adjacent triplexes suggested no structural distortions with an altered width for the groove formed by purines and pyrimidines in the third strand. The Pl base was found to be readily accommodated in an otherwise all-pyrimidine third... 

The small number of the observed internucleotide NOEs between C72 and A73 suggests a weak stacking. However, there are cross peaks of the C2 proton of A73 with both, the aromatic C8H and the I -ribose proton of G1 of the opposite strand. The former cross peaks indicate an overlap of the purine base plane of A73 with that of Gl, which corroborates the before-mentioned interlocking effect of the purine base in position 73 and provides a structural explanation for the stabilizing effect of 3 -dangling purine nucleotides. At the same time, the C8 proton of A73 is moved away from the aromatic protons of C72 making the lack of the aromatic-aromatic cross peaks conceivable. Some NOE contacts have been... 

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