Last modified on 18 April 2012.

Table 2. Base-Pair Stack Statistics

Base pair 1 Base pair 2 Decomp base-pair SE Decomp stacking SE Decomp. base pair + stack SE BP-ST SE Exp BP-ST energy Difference of decomp. BP-ST SE and exp BP-ST energy
CG CG -3.1814 -0.2416 -3.01 -2.43 -2.40 0.61
GC CG -3.2819 -0.2444 -3.12 -3.40 -3.30 -0.18
GC GC -3.3824 -0.0578 -3.03 -2.70 -3.40 -0.37
GU CG -1.7603 -0.1206 -1.47 -2.32 -2.10 -0.63
GU GC -1.8608 -0.1169 -1.57 -2.35 -2.50 -0.93
GU GU -0.3392 -0.1761 -0.11 0.14 1.30 1.41
UG CG -1.7240 -0.2009 -1.52 -1.76 -1.40 0.12
UG GC -1.8245 -0.2202 -1.64 -1.93 -1.50 0.14
UG GU -0.3029 -0.0461 0.06 -0.83 -0.50 -0.56
UG UG -0.2667 -0.1602 -0.02 -1.22 0.30 0.32
AU CG -2.6577 0.1496 -2.10 -3.19 -2.10 0.00
AU GC -2.7583 -0.0203 -2.37 -3.09 -2.20 0.17
AU GU -1.2367 0.1435 -0.68 -2.03 -1.40 -0.72
AU UG -1.2004 0.2242 -0.57 -1.33 -0.60 -0.03
AU AU -2.1341 0.4631 -1.26 -1.65 -1.10 0.16
UA CG -2.8042 0.0226 -2.37 -3.19 -2.10 0.27
UA GC -2.9048 -0.0084 -2.50 -2.91 -2.40 0.10
UA GU -1.3832 0.1658 -0.81 -1.62 -1.30 -0.49
UA UG -1.3469 0.1261 -0.81 -1.07 -1.00 -0.19
UA AU -2.2806 0.4795 -1.39 -2.53 -0.90 0.49
UA UA -2.4271 0.4124 -1.61 -2.04 -1.30 0.31

For each base-pair stack, the decomposed base-pair SE, decomposed stacking SE, base-pair stack energy computed from the decomposition model (Eq. (6)), base-pair stack SE, experimental base-pair stack energy (kcal/mol), and the difference between the sum of decomposed base-pair and stack SEs and experimental base-pair stack energy derived from experiment are presented. SE are in units of kcal/mol and are derived from statistics using all sequences.