Oligo box F

Directions for using this storage box template

Box: Oligo box F
1) Plac4	2) Plac1	3) Pry1	4) Pry2	5) Pwht1	6) Sp1	7) Spep1	8 T7-hsp70
9) HSP 70 GAGA-A	10) HSP 70 GAGA-A	11) HSP 70 GAGA-B	12) HSP 70 GAGA-B	13) GAGA 5'	14) GAGA 3'	15) PL-1	16) PL-1
17) 1346 lacO 5'	18) 1347 lacO 3'	19) Seq. primer Oligo111	20) Rev. seq.primer Oligo113	21) CBP20_5'	22) CBP20_3'	23) CBP80_5'	24) CBP80_3'
25) CBP80_N3'	26) CBP80_m1	27) CBP80_m2	28) CBP80_m3	29) GAGA F	30) GAGA R	31) Zinc F	32) Zinc R
33) rp49-A	34)rp49-B	35)hsp70/+286	36) CTD1_5’	37) CTD1_3’	38) CTD2_3’	39) CTD3_3’	40) CTD4_5’
41) HSF AD.1	42) HSF AD.2	43)	44)	45)	46)	47)	48)
49)	50)	51)	52)	53)	54)	55)	56)
57)	58)	59)	60)	61)	62)	63)	64)

Description of contents:

Row 1 (return to top)
1)	Plac4: ACT GTG CGT TAG GTC CTG TTC ATT GTT
2)	Plac1: CAC CCA AGG CTC TGC TCC CAC AAT
3)	Pry1: CCT TAG CAT GTC CGT GGG GTT TGA AT
4)	Pry2: CTT GCC GAC GGG ACC ACC TTA TGT TAT T
5)	Pwht1: GTA ACG CTA ATC ACT CCG AAC AGG TCA CA
6)	Sp1: ACA CAA CCT TTC CTC TCA ACA A
7)	Spep1: GAC ACT CAG AAT ACT ATT C
8)	T7-hsp70: gga att cta ata cga ctc act ata ggg att caa ttc aaa caa gc. Benjamin's primer used to make T7-hsp70. see p. 47 of his thesis.

Row 2 (return to top)
9)	HSP 70 GAGA-A: (synthesis file 03071003): TCGATTCGAGGCGCGCTCTC This was going to be used by P.Emanuel to introduce the GAGA sequence upstream of the -50 hsp70 and eliminate the HSE.
10)	HSP 70 GAGA-A: (synthesis file 03071003): TCGATTCGAGGCGCGCTCTC This was going to be used by P.Emanuel to introduce the GAGA sequence upstream of the -50 hsp70 and eliminate the HSE.
11)	HSP 70 GAGA-B: (synthesis file 03071203): TCGAGAGAGCGCGCCTCGAA This was going to be used by P.Emanuel to introduce the GAGA sequence upstream of the -50 hsp70 and eliminate the HSE.
12)	HSP 70 GAGA-B: (synthesis file 03071203): TCGAGAGAGCGCGCCTCGAA This was going to be used by P.Emanuel to introduce the GAGA sequence upstream of the -50 hsp70 and eliminate the HSE.
13)	GAGA 5': ggc cgc gag aga gca aag gcc tct cgt tca ttg ctc tct cgt tct aga aac aga gag ctt agc tct ctc. Benjamin used this to insert a GAGA element downstream from the hsp70 start site. see thesis p. 34
14)	GAGA 3': ggc cga gag agc taa gct ctc tgt ttc tag aac gag aga gca atg aac gag agg cct ttg ctc tct cgc. Benjamin used this to insert a GAGA element downstream from the hsp70 start site. see thesis p. 34
15)	PL-1: tgg gct gca ggt cga cc. Used by Benjamin to do permanganate footprinting on hsp70 XBS plasmids. see thesis p. 32
16)	PL-1: tgg gct gca ggt cga cc. Used by Benjamin to do permanganate footprinting on hsp70 XBS plasmids. see thesis p. 32

Row 3 (return to top)
17)	1346, lacO 5': need to search notes for sequence, used to insert a lac operator downstream from hsp70 txn start
18)	1347 lacO 3': need to search notes for sequence, used to insert a lac operator downstream from hsp70 txn start
19)	Seq. primer, Oligo111: GACGTTGTAAAACGACGGCCAGT Hybridizes adjacent to the EcoR1 site in pUC13 and extends towards the polylinker. From Wash U. (also see oligo box A)
20)	Rev. seq.primer Oligo113: AACAGCTATGACCATGATTACG Hybridizes adjacent to the HindIII site in pUC13 and extends towards the polylinker. From Wash U. (also see oligo box A)
21)	CBP20_5': GCT ATG CTA GCA TGT TCG CAT CTG TG
22)	CBP20_3': CCG AAG AAT TCC TAG CGA TTG TCC GT
23)	CBP80_5': GCT ATG CTA GCA TGA GTC GCA GGA GG
24)	CBP80_3': CCG AAG AAT TCT TAG GCA CGC AGG GC

Row 4 (return to top)
25)	CBP80_N3': CCG AAG AAT TCA CCG CAA CTT GCG TAT
26)	CBP80_m1: GCC TGT GGG CGC AGA TAC GCA
27)	CBP80_m2: TGC CGT CGG ACA TCT CCT CGC
28)	CBP80_m3: TTG AAG GAT ATA CCG AAT AGC
29)	GAGA F: AGC TGG TAC CTA TGT CGC TGC CAA TGA A, for making GAF-rtM2 fusion
30)	GAGA R: TAA TGC GGC CGC CTA CTG CGG CTG CGG, for making GAF-rtM2 fusion
31)	Zinc F: TTC GTC AAT CCG CCG ACC TGC GGC GCC ATC, for making GAF-rtM2 fusion and mutating Zn finger
32)	Zinc R: GCG CCG CAG GTC GGC GGA TTG ACG AAT GAC, for making GAF-rtM2 fusion and mutating Zn finger

Row 5 (return to top)
33)	rp49-A: TAC AGG CCC AAG ATC GTG AA, this oligo along with the next one are designed to monitor splicing of RP49 by RT-PCR. Note that a no RT control is needed to insure that the signal is due to RNA and not DNA.
34)	rp49-B: ACG TTG TGC ACC AGG AAC TT
35)	hsp70/+286: TGG GTG TCT ACC AGC ATG GCA AGG, Chwen-huey is using this to amplify an hsp70 fragment from Weber's plasmid called hsp70/87C. Use this primer with the Forward sequencing primer.
36)	CTD1_5’: GCG CGG ATC CTC TCC CTC TTA TTC GCC A, Zhiqiang is using this along with subsequent oligos to produce a collection of GST-CTD fusions.
37)	CTD1_3’: CCG AGA ATT CTC AGT CTT CGC TCT CCT C
38)	CTD2_3’: CCG AGA ATT CGT AGT TGG ACG AGC TGG G
39)	CTD3_3’: CCG AGA ATT CCG GCG ACG CTG AAT AGT T
40)	CTD4_5’: GCG CGG ATC CCA ATA TTC TCC AGC CTC G

Row 6 (return to top)
41)	HSF AD.1: GGC CGA AAA AGA AGA GAA, HSF AD.1 and HSF AD.2 were prepared so we can construct an rtM2-mini HSF.
42)	HSF AD.2: TAA TGC GGC CGC TAG TCC GTG TCC AAA ATG TC
43)
44)
45)
46)
47)
48)

Row 7 (return to top)
49)
50)
51)
52)
53)
54)
55)
56)

Row 8 (return to top)
57)
58)
59)
60)
61)
62)
63)
64)

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