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. Author manuscript; available in PMC: 2014 Jan 15.
Published in final edited form as: Biochemistry. 2013 Jan 3;52(2):365–377. doi: 10.1021/bi301510v

Table 2.

Kd measurements of methylphosphonate analogs for the class I and class II c-di-GMP binding riboswitches determined by the competition gel-shift assay.

Class I Class II
Analog Kd (nM) Fold
Changea 		ΔΔGbind
(kcal/mol)a 		Kd (nM) Fold
Changea 		ΔΔGbind
(kcal/mol)a
c-di-dGMPb 2600 ± 88 − − 11 ± 1.2 − −
c-di-GMPb 1.4 ± 0.1 [1900]c −4.4 2.2 ± 0.2 [5] −0.9
c-di-dGP(Me)-I > 100,000 >38 >2.2 1000 ± 93 91 2.7
c-di-dGP(Me)-II 540 ± 57 [5] −0.9 2.4 ± 0.3 [5] −0.9
c-(RPRP)-di-Gps 150 ± 33 [17] −1.7 3.6 ± 0.6 [3] −0.7
c-(RPSP)-di-Gpsb 750 ± 63 [3] −0.7 4.0 ± 0.8 [3] −0.6
a

Calculated relative to the parental dinucleotide c-di-dGMP.

b

Binding data for these compounds was previously reported34.

c

Brackets indicate fold increase in binding.