I'm interested in bacterial single cell transcriptomics. However, current single cell RNA-seq methodology are unsuited to bacterial transcriptomics as they generally involve the use of poly-dT capture probes to trap transcripts.

I've been looking for ways to adapt microfluidic, bead-based single cell technology like Drop-Seq to bacterial transcription.

Since there is some consensus between the shine delgarno sequences within bacterial transcriptomes, would it be possible to use this 6 nt sequence in place of a poly-dT capture tag?

My concern is that, being only 6 nt, the SD sequence would be too non-specific and would hybridise mid-transcript, preventing subsequent reverse transcription from common priming sites upstream of the SD capture tag.