Data Arangement: Y ------------------ (X) A C G U ------------------ 5' ==> 3' AX AY 3' <== 5' (A) . . . . (C) . . . . (G) . . . . (U) -0.7 -0.1 -0.7 -0.1 -------------------------------- STACKING ENERGIES : TERMINAL MISMATCHES AND BASE-PAIRS. Y Y Y Y ------------------ ------------------ ------------------ ------------------ A C G U A C G U A C G U A C G U ------------------ ------------------ ------------------ ------------------ 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' AX AX AX AX AY CY GY UY 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' . . . . . . . . . . . . -0.8 -1.0 -0.8 -1.0 . . . . . . . . . . . . -0.6 -0.7 -0.6 -0.7 . . . . . . . . . . . . -0.8 -1.0 -0.8 -1.0 . . . . . . . . . . . . -0.6 -0.8 -0.6 -0.8 Y Y Y Y ------------------ ------------------ ------------------ ------------------ A C G U A C G U A C G U A C G U ------------------ ------------------ ------------------ ------------------ 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' CX CX CX CX AY CY GY UY 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' . . . . . . . . -1.5 -1.5 -1.4 -1.5 . . . . . . . . . . . . -1.0 -1.1 -1.0 -0.8 . . . . . . . . . . . . -1.4 -1.5 -1.6 -1.5 . . . . . . . . . . . . -1.0 -1.4 -1.0 -1.2 . . . . Y Y Y Y ------------------ ------------------ ------------------ ------------------ A C G U A C G U A C G U A C G U ------------------ ------------------ ------------------ ------------------ 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' GX GX GX GX AY CY GY UY 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' . . . . -1.1 -1.5 -1.3 -1.5 . . . . -0.3 -1.0 -0.8 -1.0 . . . . -1.1 -0.7 -1.1 -0.5 . . . . -0.6 -0.7 -0.6 -0.7 . . . . -1.6 -1.5 -1.4 -1.5 . . . . -0.6 -1.0 -0.8 -1.0 . . . . -1.1 -1.0 -1.1 -0.7 . . . . -0.6 -0.8 -0.6 -0.6 Y Y Y Y ------------------ ------------------ ------------------ ------------------ A C G U A C G U A C G U A C G U ------------------ ------------------ ------------------ ------------------ 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' UX UX UX UX AY CY GY UY 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' -1.0 -0.8 -1.1 -0.8 . . . . -1.0 -0.8 -1.1 -0.8 . . . . -0.7 -0.6 -0.7 -0.5 . . . . -0.7 -0.6 -0.7 -0.5 . . . . -1.1 -0.8 -1.2 -0.8 . . . . -0.5 -0.8 -0.8 -0.8 . . . . -0.7 -0.6 -0.7 -0.5 . . . . -0.7 -0.6 -0.7 -0.5 . . . .