Artificial transcriptional terminators
The goal is to create a series of transcriptional terminators with varying efficiencies. The majority of transcriptional terminators have a G+C rich stem of 7(+/-1)bp and a loop of 4(+/-1) nucleodtides followed by a poly(U) tail. Two common loops are UUCG and GAAA, both of which are known to increase RNA hairpin stability. The sequence GCGGG(G) is a common sequence found on the 3' arm of the stem. 
Effects of stem loop sequence on terminator efficiency
Bulges and mismatches in the stem, as well low G+C content of the stem will lower TE more than reducing the length of or elimination of the poly(U) tail . The sequences downstream of the poly(U) tail and between the stop codon and the start of the stem loop structure also affect the TE of a terminator, particularly T7Te or T3Te.
Several sources  [Chamberlin 79] measured the termination efficiency(TE) of T7Te at around 90%. However, efficiency for the biobricks part BBa_B0012 , also T7Te, is around 30%. T7Te has a very short poly(U) tail and requires the further downstream sequence for efficiecent termination , and this further downstream sequence is lacking in BBa_B0012. If the sequence for BBa_B0012 is lengthened to include this downstream segment, then the TE of part should be improved.
Predicting terminator efficiency
d = nt*18.16+Y*96.59-116.87
The score d will give a rough estimate of how efficient a terminator is.
- has 6 base stem with 3' sequence of GCGGGG
- 4 base loop, either UUCG or GAAA
- tail containing >8 uridines
- for a biobrick part, flanking regions will be biobrick site
The score d is calculated as mentioned above. The energy of hairpin formation, delG, is caluclated using UNAFold.
- Terminator 1:
delG=-12.6 d=59.31 %T>90
delG reverse=-10.2 d=44.82 %T>90
stem loop: ccccgcttcggcggggttttttttt
primer 1: gaattcgcggcgcttctagatcgcgtgaaaaaaaaaccccgcttcggc
primer 2: gcttcggcggggtttttttttcgcgagtactagtagcggcggctgcag
- Terminator 2:
delG=-12.6 d=35.78 %T>90
delG reverse=-10.2 d=21.28 %T=75
stem loop: ccccgcttcggcggggtttttt
primer 1: gaattcgcggcgcttctagatcgcgtggggaaaaaaccccgcttcggc
primer 2: gcttcggcggggttttttgggcgcgagtactagtagcggcggctgcag
- Terminator 3:
delG=-12.6 d=26.12 %T=80
delG reverse=-10.2 d=11.64 %T=40
stem loop: ccccgcttcggcggggttttt
primer 1: gaattcgcggcgcttctagatcgcgtgggggaaaaaccccgcttcggc
primer 2: gcttcggcggggtttttggggcgcgagtactagtagcggcggctgcag
- Terminator 4:
delG=-12.6 d=15.40 %T=55
delG reverse=-10.2 d=0.91 %T=<20
stem loop: ccccgcttcggcggggtttt
primer 1: gaattcgcggcgcttctagatcgcgtggggggaaaaccccgcttcggc
primer 2: gcttcggcggggttttgggggcgcgagtactagtagcggcggctgcag
- Terminator 5:
delG=-12.6 d=3.49 %T=25
delG reverse=-10.2 d=-11 %T<10
stem loop: ccccgcttcggcggggttt
primer 1: gaattcgcggcgcttctagatcgcgtgggggggaaaccccgcttcggc
primer 2: gcttcggcggggtttggggggcgcgagtactagtagcggcggctgcag
- Terminator 6:
delG=-16.2 d=54.38 %T>90
delG reverse=-18.9 d=66.22 %T>90
stem loop: ccccgccccugacagggcggggttttttttt
primer 1: gaattcgcggcgcttctagatcgcgtgaaaaaaaaaccccgccccugacagg
primer 2: cccugacagggcggggtttttttttcgcgagtactagtagcggcggctgcag
- Terminator 7:
delG=-16.2 d=30.84 %T=80
delG reverse=-18.9 d=42.69 %T>90
stem loop: ccccgccccugacagggcggggtttttt
primer 1: gaattcgcggcgcttctagatcgcgtggggaaaaaaccccgccccugacagg
primer 2: cccugacagggcggggttttttgggcgcgagtactagtagcggcggctgcag
- Terminator 8:
delG=-16.2 d=21.19 %T=70
delG reverse=-18.9 d=33.03 %T=80
stem loop: ccccgccccugacagggcggggttttt
primer 1: gaattcgcggcgcttctagatcgcgtgggggaaaaaccccgccccugacagg
primer 2: cccugacagggcggggtttttggggcgcgagtactagtagcggcggctgcag
- Terminator 9:
delG=-16.2 d=10.46 %T=40
delG reverse=-18.9 d=22.31 %T=75
stem loop: ccccgccccugacagggcggggtttt
primer 1: gaattcgcggcgcttctagatcgcgtggggggaaaaccccgccccugacagg
primer 2: cccugacagggcggggttttgggggcgcgagtactagtagcggcggctgcag
- Terminator 10:
delG=-16.2 d=-1.45 %T<10
delG reverse=-18.9 d=10.40 %T=40
stem loop: ccccgccccugacagggcggggttt
primer 1: gaattcgcggcgcttctagatcgcgtgggggggaaaccccgccccugacagg
primer 2: cccugacagggcggggtttggggggcgcgagtactagtagcggcggctgcag
- Terminator 11: this is not supposed to work. if it does, then something is wrong
delG=-3.3 d=-52.65 %T=0
delG reverse=-0.5 d=-69.56 %T=0
stem loop: ttttatgaaaataaaattt
primer 1: gaattcgcggcgcttctagatcgcgtgggggggaaattttatgaaaat
primer 2: atgaaaataaaatttggggggcgcgagtactagtagcggcggctgcag
- d'Aubenton Carafa Y, Brody E, and Thermes C. . pmid:1702475.
- Abe H and Aiba H. . pmid:9150882.
- Reynolds R and Chamberlin MJ. . pmid:1372366.
- Brendel V, Hamm GH, and Trifonov EN. . pmid:3078109.
- Cheng SW, Lynch EC, Leason KR, Court DL, Shapiro BA, and Friedman DI. . pmid:1835546.
- Christie GE, Farnham PJ, and Platt T. . pmid:7027254.
- Ermolaeva MD, Khalak HG, White O, Smith HO, and Salzberg SL. . pmid:10926490.
- Lesnik EA, Sampath R, Levene HB, Henderson TJ, McNeil JA, and Ecker DJ. . pmid:11522828.
- Lynn SP, Kasper LM, and Gardner JF. . pmid:2961747.
- Petrillo M, Silvestro G, Di Nocera PP, Boccia A, and Paolella G. . pmid:16820051.
- Reynolds R, Bermúdez-Cruz RM, and Chamberlin MJ. . pmid:1372365.
- Unniraman S, Prakash R, and Nagaraja V. . pmid:11809879.
- Uptain SM and Chamberlin MJ. . pmid:9391063.
- von Hippel PH and Yager TD. . pmid:1536005.
- Wilson KS and von Hippel PH. . pmid:7966320.
- Wilson KS and von Hippel PH. . pmid:7568019.
- Yager TD and von Hippel PH. . pmid:1703438.
- Gusarov I and Nudler E. . pmid:10230402.
- de Hoon MJ, Makita Y, Nakai K, and Miyano S. . pmid:16110342.