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Fig. 3 | BMC Plant Biology

Fig. 3

From: Novel alleles of the VERNALIZATION1 genes in wheat are associated with modulation of DNA curvature and flexibility in the promoter region

Fig. 3

Mutations within the promoter of VRN-B1 indicate tree sequence variants. a Identification of the VRN-B1 variants during PCR with primer pair Pr1/Pr2. Separation of PCR fragments under conditions of low conformational dynamics of DNA molecules contribute to the clear discrimination of the alternative promoter variants. 1 – non-optimized PAA electrophoresis at room temperature without cooling, in 10 % gel, mono/bis-acrylamide ratio 29:1, under 5 V/cm; 2 – the same amplicons resolved in PAGE optimized for low temperature conditions; 3 – support for the contribution of localized DNA bends as determined by the 7 bp deletion within the A-tract rich segment in anomalously migrating PCR fragments of VRN-B1.s, the 7 bp deletion distinguishes VRN-B1.s from VRN-B1.m, observed splitting of VRN-B1.m on two variants. b Comparison of DNA sequences encompassing the center of PCR fragments detecting VRN-B1 variants (GenBank: KR782252 (VRN-B1.s), KT361212 (VRN-B1.m.2), KR782253 (VRN-B1.f from T. turgidum), KR782254 (VRN-B1.f from T. polonicum)). Region showed includes three deletions in VRN-B1.s, two located within the A-tract rich segment and T-tract cause local bends and lead to increased curvature of the DNA molecule. Positions are indicated relative to the start of the VRN-B1.f PCR fragment. c Superposition of predicted DNA paths of PCR fragments of the VRN-B1 promoter variants. Sites of local DNA bends caused by the 7 and 2 bp deletions within the A-tract rich segment and T-tract are indicated

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