Table 1.

Summary of the most broadly applied secondary structure probing methods. Different techniques may fit best for different applications.

Technique	Type	Pro	Contra	Reagent
PARS [10]	enzymatic	digests paired/unpaired bases; suited for riboswitches; transcriptome	poly(A) selected; over-digestion of RNA; in vitro	ssRNase S1 dsRNase V1
Fraq-Seq [13]	enzymatic	P1 is thermal stable; transcriptome	control needed; for smaller RNA molecules; poly(A) selection; in vitro	ssRNAase P1
DMS-Seq [14,16]	chemical	in vitro/in vivo; DMS cell permeable; transcriptome in vivo	poly(A) selection; needs control sample; RBPs influence; in vivo	DMS
SHAPE [18]	chemical	single nucleotide resolution; multiple RNA profiling	in vitro; needs control sample	IM7, NMIA, NAI-N3, FAI
IcSHAPE [22]	chemical	in vivo; single nucleotide resolution; transcriptome	influenced by RBP binding	IM7, NMIA, NAI-N3, FAI