Reverse transcriptase mapping

Reverse transcriptase j Synthesizes DNA from RNA template. Synthesis of cDNA from mRNA RNA (S end) mapping studies. 

Fig. 2. Expression map of human tissue kallikreins in a variety of tissues, as determined by reverse transcriptase polymerase chain reaction. The relative semiquantitative expression levels for each gene are indicated.

Five of the 11 sets of inhibitors described in Section 6.4 were used again in the second scenario, namely the thrombin, gelatinase A, HIV protease, HIV reverse transcriptase, and COX2 data sets. A set of 29 p38 MAP kinase inhibitors was assembled from PDB crystal structures and Ref. [100]. A set of 40 estrogen receptor ligands was taken from the Protherics web site [101]. These two data sets were converted to Sybyl mol2 format and protonation states were adjusted as described above. 

F., et al., Lymph node micrometastasis and lymphatic mapping determined by reverse transcriptase-polymerase chain reaction in pNO gastric carcinoma. Surgery 131, 630-635 (2002). 

The site of initiation of transcription of the R. rubrum atp 2 operon was determined by two independent methods, mapping with SI nuclease and primer extension analysis. The result of the SI mapping experiment using probes no 1 and 2 (Table 1) indicated a 5 -end around nucleotide 620 (see Ref. 4 for nucleotide numbers in sequence). Primer extension analysis were then performed with probes 3 and 4 (Table 1). They extend from nucleotides 880 and 829 respectively to the SacII restriction enzyme site at 640. They were annealed with R. rubrum RNA, and after extension with reverse transcriptase gave products extended by 21 nucleotides upstream from the SacII site. This corresponds to a 5 -end for the Rs . rubrum atp 2 operon mRNA at nucleotide 620, thus supporting the result obtained by SI nuclease mapping. The DNA sequence upstream of this site contain -10 and -35 regions similar to those of E. coli promoters (Fig. 2). 

After mapping, tJie candidate cleavage sites that represented possible internal priming by reverse transcriptase are discarded using a strategy similar to that described in [3], You can use the following script to remove internal priming candidates see Note 4) ... 

Allawi HT, Dong F, Ip HS, Neri BP, Lyamichev VI (2001) Mapping of RNA accessible sites by extension of random oligonucleotide libraries with reverse transcriptase. RNA 7 314—327... 

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