We derive an equation that can accurately predict codon elongation rates based on the abundances of free tRNA in the cell, and can be used to assist transcript design.
To overcome possible complications from 5′UTR secondary structures — due to the presence of multiple λCl binding sites within the same mRNA transcript — design IV, which comprised synthetic hybrid promoters of pBAD-Cl2B and pRHAB-Cl2B expressing RFPasv in two discrete expression cassettes, was also developed.
Gene ontology (GO) and Reactome pathway information from homologous genes was transferred to barnacle contigs using a transcript designed in-house.
The whole-transcript design yields the potential for examining expression of individual exons and consequently, as already demonstrated in the well-studied Exon Array, the profiling of isoform variation.
Actually it is not a 3′ versus whole-transcript design issue, but a far more complex issue that involves varying RNA amplification and/or probe hybridization efficiencies, different sets of alternatively spliced transcripts in measurement, and different infrastructures of microarrays (spot size, spot distance, background composition, etc).
Trans-splicing strategies for mRNA repair involve engineered transcripts designed to anneal target mRNAs in order to interfere with their natural splicing, giving rise to mRNA chimeras where endogenous mutated exons have been replaced by exogenous replacement sequences.
The employed arrays were Agilent 60-mer 4×44 K custom microarrays, containing 31,918 C. gigas transcripts, designed by Dheilly et al. [ 45].
Saccharification of Medicago sativa expressing antisense transcripts designed to silence lignin biosynthesis genes showed an inverse relationship between lignin content and sugar yield, revealing that lignin is indeed a significant obstacle to obtaining high yields of cell wall sugars [ 7].
To test if elimination of antisense transcription prevents early termination of the sense transcript, we designed two recombinant constructs with the At5g67300/At5g67310 gene pair linked to both the sense and antisense promoter, or only to the sense promoter, respectively.
qPCR assays were designed to measure the level of spliced and unspliced transcript, by designing primer pairs and probes specific to the IFIH1 pre-mRNA and mRNA at the appropriate splicing junction.
Primers suitable for amplification for each transcript were designed using an online tool from Invitrogen, OligoPerfect™ Designer (http://tools.invitrogen.com/content.cfm?pageid=9716).
