Table 1

Stability of mRNA secondary structures

Protocol

Mean ΔG

P

Mean Z(ΔG)

Mean %pairs

Real (mouse)

-737.98 ± 55.52

60.96 ± 0.28

Modification

Swap G4C4

-734.10 ± 55.08

0.0169

62.11 ± 0.33

Randomization

Sh.4-fold

-725.76 ± 54.71

9e-15

-1.41 ± 0.14

60.77 ± 0.23

Sh.codon

-728.49 ± 55.01

6e-10

-1.04 ± 0.14

60.61 ± 0.23

Re-sub.K

-733.28 ± 55.15

4e-05

-0.64 ± 0.15

61.06 ± 0.24

Re-sub.N3

-734.14 ± 55.20

4e-04

-0.51 ± 0.14

61.09 ± 0.24

Means ± SEM are shown, N = 70. P-values for modifications were determined by paired t-tests (μ = Real < Modification) on ΔG. P-values for randomizations were by one-sample t-tests (expected mean (μ) = 0) on Z(ΔG). %Pairs is the proportion of the coding sequence involved in base-pairing interactions. Artificial sequences generated by the first five protocols encode the same protein as the mouse sequence. A brief description of each protocol follows (see Results for details). 'Sh.4-fold': nucleotides at all 4-fold degenerate sites are shuffled. 'Sh.codon': for each amino acid, the synonymous codons are permuted. 'Re-sub.K': synonymous substitutions are reverted back to the rat-mouse common ancestor (rat-mouse common ancestor) state, followed by reallocation of the same number of synonymous point mutations. 'Re-sub.N3': like the previous protocol, except that the nucleotide replacement is also selected at random from the nucleotide distribution at third sites observed in the mouse sequence. 'Swap G4C4': all guanine bases at 4-fold sites are replaced by cytosine, and vice versa.

Chamary and Hurst Genome Biology 2005 6:R75   doi:10.1186/gb-2005-6-9-r75