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. Author manuscript; available in PMC: 2008 Jul 15.
Published in final edited form as: Biochemistry. 2006 Jan 17;45(2):604–616. doi: 10.1021/bi0517178

FIGURE 2.

FIGURE 2

Duplexes used in these studies. DNA duplexes are denoted D-I through D-V. An RNA version of D-I is denoted R(D-I). The component strands of each duplex are labeled S1 and S2. Invariant terminal regions of the DNA duplexes and R(D-I) are indicated by gray boxes. Purines are indicated by boldfaced nucleotides. As one moves from D-I to D-V in the series of DNA duplexes, purines decrease in number and/or contiguity within the variable region of S1 in each duplex, a design feature intended to systematically reduce stacking propensity within those strands. These variations in purine content were made such that the total GC content of all duplexes remained constant, as did the overall stability; all duplexes exhibit experimental TMs within a few degrees of one another