Table 1, Intermolecular triplexes and transcription - Madame Curie Bioscience Database

Table 1Intermolecular triplexes and transcription

Target^a	Multiplex^b	Triplex Proof^c	Transcription Assay^d	Maxium Effect^e	Controls^f	Ref.
human c-myc P1 promoter,linear plasmid	27mer GAT PO TFO,“parallel”	EMSA, DNase I FP	in vitro, HeLa NE, c-myc P2 runoff	-95% @ 160 nM TFO	complement ODN	35
human IL2Rα promoter, SRE, chromosome	28mer PO TFO, 3'- amine parallel	REPA	in vivo, PBMC cells , northern, media TFO	-55% @ 15 μM TFO	31mer GT ODN/c-myc or β-actin mRNA	36
human c-myc P1 promoter, chromosome	27mer GAT PO TFO, Pu3	EMSA, chromatin DNase I hyper sensitivity	in vivo, HeLa cells, northern, media TFO	-90% @ 125 μM TFO	complement ODN/β-actin mRNA	37
syn., + 180 G-free cassette Ad2 MLP, linear plasmid	15mer MT PO TFO, 3'-C^*, Py3	DMS FP	in vitro, Jurkat NE, G-free, pre. 3plx	-90% @ 10 μM TFO, covalent	MT TFO noncovalent, scrambled ODN covalent	38
syn., 1-5 copies, Sp1 site, Ad E4 core promoter, supercoiled plasmid	21mer T^5meC PO TFO, Py3	n.s.(prior work)	in vitro, Drosophila K_c cell NE, primer ext., pre. 3plx	-90% @ 205 μM TFO, pre. 3plx, basal transcription (-Sp1)	scrambled ODN/ftz promoter (co-transcribed)	39
E. coli bla gene, +22, DNA fragment	13mer T^5meC PO TFO, 5'- psoralen, Py3	DNase I FP /DNase I FP	in vitro, E. coli RNA pol holoenzyme, runoff, pre.3plx	-80% @ 50 μM TFO, covalent	unmod. TFO, nonspecific pso-16-mer (-20% each)/tetR gene	40
human IL-2Rα , enhancer, NF-κ B site, plasmid	15mer T^5meC PO TFO, 3'- acridine, Py3	EMSA, / REPA, DNase I FP	in vivo, HSB2 Not cells, CAT assay, pre. 3plx	-90% @ 10 μM TFO	HIV LTR CAT	41
HIV-1 promoter, Sp1 and +1 sites, plasmid	31 & 38mer GT PO TFO, 3'-amine, parallel	EMSA, CD	in vitro, HeLa NE, smear; in vivo, U937/ HIV-1 cells, media TFO	-80% (in vitro) & -90% (in vivo)@ 10 μM TFO	scrambled ODN	42
syn., f 10 promoter, +1, linear plasmid	21mer T^5meC PO TFO Py3; 22mer GT GU PO TFOs, Pu3	DNase I & MPE FP	in vitro, T7 pol., runoff	-92% @ 1 μM T^5meC; - 99% @ 1 mM GT TFO	scrambled ODN / wt f 10 promoter (co-transcribed)	43
humanIL-2Rα , enhancer, NF-κB site, plasmid	15mer T^5meC PO TFO, 3'- acridine, Py3	DNase I FP	in vitro, C8166 NE, primer extension, pre. 3plx; in vivo, HSB2 cells, CAT assay, pre. 3plx	-80% @ 1 μM TFO covalent (in vitro) -80% @ 0.2 μM TFO, covalent (in vivo)	mutant 3plx site / HIV LTR	44
syn., f 10 promoter, +1, linear plasmid	21mer T^5meC PO TFO, Py3; 22mer GT GU PO TFOs, Pu3	n.s. (prior work)	in vitro, T7 pol., runoff, pre. 3plx	-90% @ 1 μM T^5meC, GT, GU TFO	wt f 10 promoter (co-transcribed)	45
human IL-2Rα , enhancer, NF-κB site, plasmid	15mer T^5meC PO TFO, 3'- acridine, Py3	DNase I FP	in vivo, HSB2 cells, CAT assay, pre. 3plx?	-90% @ 5 μM TFO	unmod. TFO, mutant mod. ODN / mutant 3plx site	46
syn., PRE site, Lov core promoter, plasmid	38mer GT PO TFO,3'- cholesterol, Pu3	EMSA, DNase I FP	in vitro, HeLa NE, G-free, pre. 3plx; in vivo, CV-1 cells, CAT assay, media TFO	-105% @ 200 nM TFO (in vitro); @ 20 μM TFO, (in vivo)	(in vitro) mut. ODN (-50% @ 200 nM) / mut. promoter, Ad2 MLP (in vivo) (co-transcribed); mut. ODN (-15% @ 20 μM) / SV2CAT	47
human 6-16 promoter, IRE, plasmid syn. +63 or +103, linear plasmid	21mer AGT PO TFO, Pu3	EMSA, DNase I & Cu-phen. FP	in vivo, HeLa cells, CAT, co-transfect	-99% @ 1.8 μM TFO, (-50% for controls)	GA ODN / SV40 or minimal TK promoter	48
syn. +63 or +103, linear plasmid	53mer GT PO TFO, 3' -amino, Pu3	EMSA	in vitro, T3 or T7 RNA pol., truncated transcript, pre. 3plx	-80% @ 0.2 μM TFO, (-30% @ 4 μM reverse ODN)	reverse ODN	49
syn., +204, plasmid	15mer T^5meC PO TFO, 5'-psoralen, Py3	PCR / PCR	in vivo, HeLa or XP2Y0(SV) cells, β -gal assay, pre. 3plx	-75% @ 1.8 μM TFO (24h HeLa), -85% (72h XP)	mut. ODN	50
human H-ras promoter, -8, linear plasmid	21mer GC PO TFO, Pu3	EMSA, DNase I FP	in vitro, HeLa NE, runoff, pre. 3plx	-50% @ 15 μM TFO	reverse ODN / CMV promoter	51
syn., +46,linear plasmid	11mer CT PO PS TFO, Py3	T_m, CD	in vitro, T7 RNA pol., runoff, pre. 3plx	-95% @ 5 μM PO TFO	11mer CT ODN, -TFO	52
IgH 3' a enhancer, Pax5 site, plasmid & chromosomal	41mer GT PO TFO, 3'- amine, Pu3	EMSA / in vivo DMS FP	in vivo, CH12.LX.A2 cells, luciferase, northern, (co)transfect TFO	+160% @ 25 μg TFO	mut. ODN/ mut. enhancer	53
human c-myc, P2 promoter, MAZ & E2F sites, linear plasmid human ALDH2 downstream promoter, chromosome	21mer GT PO, PS, & PO/PS TFO, Pu3	EMSA, DNase I FP	in vitro, HeLa NE, runoff, pre. 3plx	-80% @ 20 μM TFO	reverse ODN / CMV promoter	54
human ALDH₂ downstream promoter, chromosome	21mer GT PO, PS, & PO/PS TFO, Pu3	EMSA	in vivo, HepG2 cells, RT-PCR, transfect TFO	-90% @ 600 nM PS TFO	albumin mRNA	55
rat α 1(I) collagen promoter, -138, fragment or plasmid	30mer GA PO TFO, parallel	EMSA	in vitro, RCF NE, runoff, pre. 3plx; vitro); in vivo, RCF cells, CAT, post transfect TFO	-95% @ 250 μM TFO, (in vitro);-60% @ 1 μM TFO (in vivo)	20mer AGCT ODN / mut. & CMV IE promoter	56
human HER2 core promoter, chromosome	28mer GAC PO TFO, Pu3	EMSA, FTIR	in vivo, MCF7 cells, ELISA, northern, transfect TFO	-28% protein, -49% mRNA @ 0.22 μM TFO, 6 h post transfect.	mut., complement, scrambled / EGFR protein, GAPDH mRNA	57
HIV1 nef gene, linear plasmid	11mer TGC PN TFO, Py3	REPA, T_m	in vitro, HeLa NE, truncated transcript, pre. 3plx	-60% @ 2 μM TFO	PO & other modif. TFOs	58
human GM-CSF promoter, NF-κ B site, plasmid & chromosome	15mer GT PO TFO, Pu3	EMSA, DNase I FP	in vivo, Jurkat cells, luciferase, RNase protect, ELISA, media TFO	-70% @ 2.4 μM TFO	random GT ODN / IL3 promoter, mRNA	59
HIV1 nef gene, linear plasmid	15mer TG^5meC PO TFO, 5'-acridine, Py3, stabilized with BePI	T_m	in vitro, HeLa NE or SP6 or T7 RNA pol., truncated transcript, pre. 3plx	-77% @ 10 μM TFO (pol II), -60% @ 10 μM TFO + 25 μM BEPI (SP6)	unsub. TFO & random ODN	60
HIV1 nef gene, linear plasmid	16mer TC or T^5meC PN TFO, Py3	n.s.	in vitro, HeLa NE or SP6 RNA pol., truncated transcript, pre. 3plx	-77% @ 1 μM TC TFO (pol II), -60% @ 10 mM T^5meC TFO (SP6)	titration	61
human TNF gene, 3^rd intron, chromosome	27mer GT PO TFO, 3'- cholesterol, Pu3	EMSA	in vivo, THP-1 cells, TNF bioassay, RT -PCR, media TFO	-75% @ 0.6 μM TFO	other GT ODNs / IL-β mRNA	62
syn., +400, plasmid	19mer GT PO TFO, 5'- psoralen, Pu3	REPA, PCR/ REPA, PCR	in vivo, HeLa cells, luciferase, pre. 3plx	-79% @ 0.6 μM TFO, covalent	-pre. 3plx & -crosslink / β -gal	63
murine c-Ki-ras promoter, -290, plasmid	20mer GA PO TFO, Pu3	EMSA, T_m, CD	in vivo, NIH 3T3 cells, CAT, pre. 3plx	-90% @ 1 μg TFO (-40% @ 1 μg non- specific ODN)	non-specific ODN	64
human IGF-I gene, 1^st exon, chromosome	RNA cont. 23 nt. GA sequence, Pu3?	n.s. for RNA	in vivo, C6 cells, stable clones, northern, in situ TFO	-95%	complement RNA	65
rat α 1(I) collagen promoter, -141, plasmid	18mer GA PS TFO, Pu3	EMSA, DNase I FP	in vivo, 2TK cells, CAT, pre. 3plx	-80% @ 50 μg TFO	18mer ACGT ODN	66
rat IGF-IR gene, 3' (+4504), chromosome	RNA cont. 24 nt. GA sequence, Pu3?	n.s.	in vivo, C6(t1) cells, stable clones, northern, in situ TFO	-75%?, (similar inhibition IGF-I mRNA)	complement RNA / β -actin	67
syn., +185, linear plasmid	15mer TG^5meC PO TFO, Py3	n.s.	in vitro, HeLa NE, runoff	-90% @ 10 μM TFO, crosslink	-UV	68
human, c-myc, P1 promoter PuF site & P2 promoter MAZ site, plasmid	26 & 23mer GAT PS TFOs, Pu3	EMSA	in vivo, HeLa cells, luciferase, Do pre. 3plx	90% @ 100 μM, both TFOs	reverse ODNs	69
human cyclin D1 promoter, Sp1, chromosome	18mer GT PS TFO, Pu3	EMSA, DNase I FP	in vivo, HeLa cells, luciferase, transfect TFO	-60% @ 10 μM TFO	reverse ODN/ CMV luc	70
human α 1(I) collagen promoter, -140, fragment or plasmid	30mer GAT PO TFO, Pu3	EMSA	in vitro, HeLa NE, runoff, pre. 3plx; in vivo, CK-Y cells, GFP, pre. 3plx	-75% @ 200 ng TFO, (in vitro); -55% @ 30 nM TFO (in vivo)	mut. & control? ODN / CMV IE promoter	71
human HER2,+205, linear plasmid	23mer ^PPGAT PO TFO, 5'-pam, Pu3	EMSA	in vitro, HeLa NE, truncated transcript, pre. 3plx	-80% @ 1 μM TFO	titration, diff. TFOs	72
syn., -40, minimal c-fos promoter, plasmid	20mer GA PO TFO, 5' -or 3' -peptide, Pu3	EMSA, co-migrate	in vivo, NIH 3T3 cells, luciferase, pre. 3plx	+250% @ 1:1 TFO:plasmid (+10% @ 2:1)	titration, unmod. TFO	73
human c-src promoter, Sp1 & SPY sites, plasmid	11mer GA PO TFO, Pu3	n.s.	in vivo, 10T1/2 cells, CAT, pre. 3plx	-70% @ 500:1 TFO:plasmid	GA & ACGT ODNs	74
CAT gene, +578, plasmid	19mer GAT PD TFO, Pu3	n.s.	in vivo, Xenopus oocyte, CAT, northern, pre. 3plx	-90% @ 180 μM TFO	+/- TFO / Cyclin B1 mRNA	75
syn., +113, plasmid & chromosome	15mer TG5^meC PN TFO, 5'-acridine or psoralen, Py3	EMSA / REPA	in vivo, P4 cells or nuclei, luciferase, northern, co-transfect TFO or steptolysin permeabilize	-70% @ 0.5 μM TFO (5' acridine, cell, plasmid); -50% @ 0.5 μM TFO (5' psoralen, nuclei, chromosome	mut. & reverse ODN / mut. site	76
human c-myc, P2 promoter, MAZ site, chromosome	23mer GT PO TFO, 3'-amine, Pu3	EMSA, DNase I FP	in vivo, CEM cells, northern, RT-PCR, Not media TFO	-63% @ 20 μM TFO	GA & scrambled ODNs / GAPDH mRNA	77
human rhodopsin gene, 1^st or 2^nd intron, plasmid	18 or 28mer GA(T or C) PO TFO, 5'-psoralen & 3'-amine, Pu3	n.s. (prior)	in vivo, HT1080 cells, IFM, pre. 3plx	-90% @ 1 μM, both TFOs	-TFO, -UV	78
human bcl-2 3' UTR, + 1946, plasmid	18mer GAT PO(PS ends) TFO, 3'- amine, Pu3	EMSA, co-migrate	in vivo, Tet-On HeLa, western, pre. 3plx	-90% @ 12.5:1 TFO:plasmid	random, scrambled ODN/ actin protein	79
murine Ki-ras promoter, plasmid	20mer, PO/PS GA TFO, Pu3	EMSA, DMS & DNase I FP	in vivo, 293 cells, CAT, co-transfect TFO	-75% @ 5 μM TFO	-TFO	80
syn., HIV-1PPT, +113, plasmid	15mer TG^5meC PN TFO, Py3	n.s. / REPA	in vivo, P4 cells, single-cell luciferase, microinject TFO	-85% @ 32 μM TFO	reverse ODN, Renilla luciferase	81
human IgE promoter, STAT6 & Pu.1/NF-κ B sites, plasmid	21mer TC AE TFO, Py3	EMSA	in vivo, DG75 cells, luciferase, pre. 3plx	-80% @ 200:1 TFO: plasmid, (-20% mut. AE ODN)	random PO ODN, mut. AE ODN	82
human ICAM-1 gene, 3^rd intron, chromosome	16mer GT PO TFO, 3'- or 5'-psoralen, Py3	EMSA / capture- PCR	in vivo, A431 cells, FACS, northern, transfect TFO	-60% @ 3 μM TFO (northern), +/- UV?	scrambled ODN, HLA-DR expression/ GAPDH mRNA	83
human bcr promoter, +1, chromosome	13mer GA PO TFO, 3'-PEG, Pu3	EMSA, DMS FP	in vivo, K562 cells, RT-PCR, media TFO	-35% @ 15 μM TFO, (random ODN, -15%)	G-rich PEG'd random ODN /abl mRNA	84
syn., 5 sites upstream core Ad E4 promoter, linear plasmid	22mer, GT PO TFO, 3' -peptide, Pu3	co-migrate	in vitro, HeLa NE, runoff, pre. 3plx; in vivo, HeLa cells, CAT, co-transfect TFO	+1000% @ 2.5 nM TFO in vitro (+100% @ 50 nM?); +3000% @ 50 nM TFO in vivo	GAL4 E4 promoter	85
human Ets2 promoter, Sp1, plasmid & chromosome	25mer GT PO TFO, Pu3	EMSA	in vivo, DU145 cells, luciferase, RT-PCR, northern, co-transfect TFO	-80% @ 250 nM TFO (plasmid), -62% @ 400 nM TFO (chromosome)	scrambled ODN, c-src reporters	86
human HER2, core promoter, plasmid	25mer ^PPGAT PO TFO, 5'- /3'-pam, Pu3	EMSA, alkylation/ Southern	in vivo, HeLa cells, luciferase, pre. 3plx	70% @ 2 mM TFO (5' & 3' pam)	different modified TFOs	87

: ^a Target information is indicated as gene name, site, and whether located on an extrachromosomal DNA (e.g., plasmid) or on a chromosome. Syn., synthetic target. Ad, adenovirus. MLP, major late promoter.
: ^b Triplex information is indicated as length, base composition (in order of abundance), backbone composition, modifications (indicated by 5'- or 3'-), auxiliary compounds (“stabilized with...”), and triplex motif. Bases include N⁶-methyl-8-oxo-adenine (M), 5-methylcytidine (^5meC), and pyrazolopyrimidine guanine (^ppG). Backbone compositions include phosphodiester (PO), phosphorothioate (PS), N3'-P5' phosphoramidate (PN), 2'-aminoethoxyribose (AE), and N,N-diethylethylenediamine phosphoramidate (PD). Modifications include N⁴,N⁴-ethano-2'-deoxycytidine (C^*), phenylacetate mustard (pam), polyethylene glycol (PEG). Motifs include purine (Pu3), pyrimidine (Py3), and parallel. Additional abbreviations include triplex-forming oligonucleotide (TFO), containing (cont.), nucleotide (nt.).
: ^c Assays used to demonstrate triplex formation include electrophoretic mobility shift assays (EMSA), footprinting (FP) with enzymes like DNase I or with chemicals including dimethyl sulfate (DMS), copper-1,10 phenanthroline (Cu-phen.), and methidiumpropyl-EDTA-iron (MPE), circular dichroism (CD), melting temperature (T_m), Fourier transform infrared spectroscopy (FTIR), and restriction endonuclease protection assays (REPA). Assays shown after a slash (e.g., PCR/PCR) indicate those assays performed after transcription has occurred.
: ^d Transcription assay information is presented as extract (e.g., nuclear, NE) or polymerase (pol.), template, and assay type for in vitro studies and cell type, assay type, and TFO administration method for in vivo studies. In vitro assays include runoff, G-free cassette, primer extension, and truncated transcript. In vivo assays include RNA-based (e.g., northern, reverse transcriptase PCR [RT-PCT]), immunological (e.g., enzyme-linked immunosorption [ELISA], immunofluorescence microscopy [IFM], fluorescence-activated cell sorting [FACS]), and enzymatic activity assays (e.g., chloramphenicol acetyltransferase [CAT], β-galactosidase [β-gal.], luciferase [luc.]). Preformed triplexes (pre. 3plx).
: ^e Maximum effect of triplex on transcription. Minus and plus signs indicate triplex-dependent transcription inhibition and stimulation, respectively. Unexpected or unusual findings are indicated in parentheses. Mut., mutant.
: ^f Controls used to demonstrate specificity of triplex effects on transcription. Controls involving oligonucleotides are shown before the slash, while controls involving targets are shown after (e.g., scrambled ODN/mutant promoter). Additional abbreviations include: unmodified (unmod.), cytomegalovirus immediate-early promoter (CMV IE), and unsubstituted (unsub.).

From: Do DNA Triple Helices or Quadruplexes Have a Role in Transcription?

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