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Help:Terminators/Glossary
From partsregistry.org
![Design of a rho-independent transcriptional terminator [1].](/Image:IntrinsicTranscrptionalTerminator.jpg)
Stem loop
A self-complementary or palindromic sequence of DNA usually 4-18 base pairs in length and rich in G-C base pairs that forms a "hairpin" structure. The hairpin causes the E. coli RNA polymerase to pause transcription.
Poly(T) tract
A stretch of T nucleotides on the sense DNA strand just downstream of the stem loop. Transcription of the corresponding A nucleotides results in an RNA:DNA duplex that is quite weak, because A-U base pairs only have 2 hydrogen bonds versus 3 for G-C base pairs.
Loop
3-10 nucleotides in the middle of the self-complementary or palindromic sequence that do not base pair but enable the terminator to fold back on itself into the hairpin structure.
Terminator efficiency
In the Registry, termination efficiency is usually defined as the number of terminated transcripts divided by the total number of transcripts (terminated transcripts + read-through transcripts). However, some papers instead define termination efficiency as number of read-through transcripts divided by the total number of transcripts (terminated transcripts + read-through transcripts) [2], so be careful when interpreting termination efficiencies from papers.
References
- Lesnik EA, Sampath R, Levene HB, Henderson TJ, McNeil JA, and Ecker DJ. Prediction of rho-independent transcriptional terminators in Escherichia coli. Nucleic Acids Res 2001 Sep 1; 29(17) 3583-94. pmid:11522828.
- McDowell JC, Roberts JW, Jin DJ, and Gross C. Determination of intrinsic transcription termination efficiency by RNA polymerase elongation rate. Science 1994 Nov 4; 266(5186) 822-5. pmid:7526463.
