| Targeta | Multiplexb | Triplex Proofc | Transcription Assayd | Maxium Effecte | Controlsf | Ref. |
|---|---|---|---|---|---|---|
| Drosophila hsp26 promoter -89, chromosome | 25 bp mirror repeat, H | oligo hybrid., DEPC FP, S1 nuclease/ DEPC FP | in vivo, Drosophila, hsp26-lacZ transgene, β-gal | -67% del. H, +2% mut. H-, -68% H'+ | del. H, mut. H-, H' | 92 |
| syn., promoter, plasmid | (G• C)n, H' | CAA FP | in vivo, LTK-cells, TK CAT, direct & competitions | +970% (G)30, +90% (G)18, +50% (G)35 | number of repeats | 15 |
| syn., +120, plasmid | 38 bp mirror repeat, H or H'? | chloroquine 2D gel electro- phoresis | in vivo, E. coli, lacZ, β-gal | -80% | mut. H- | 93 |
| murine c-Ki-ras promoter, plasmid | 27 bp mirror repeat, H | CAA FP | in vivo, HepG2 cells, CAT | -50% mut. H-, -50% mut. H+ | mut. H-, multi mut. H+ | 94 |
| syn., +17, plasmid | 69 bp mirror repeat, stabilized with BePI, Hy-5 | CAA FP, mung-bean nuclease | in vivo, E. coli, viability | -53% (-74% @ 5 μM BePI) | H- / tetR | 95 |
| chicken malic enzyme promoter, plasmid | 49 bp Py/ Pu, H' | S1 & P1 nuclease | in vivo, chicken hepatocytes, CAT | +900%, (+0% reversed orientation) | H-, H+ reversed | 96 |
| murine metallothionein-1 promoter, plasmid | 128 bp, H-y3 | CAA, DEPC, DMS FP | in vivo, NIH 3T3 cells, luciferase | no effect, basal or Cd2+ -induced | H-, reverse orientation | 97 |
| syn., human frataxin 1st intron GAA repeat, +100? plasmid | (GAA• TTC)n repeats, H'? | n.s. | in vivo, COS-7 cells, RNase Not protection, β-gal | -91% @ n = 230 repeats | number of repeats, reverse orientation | 98 |
| syn., human frataxin 1st intron GAA repeat, +100? plasmid | (GAA• TTC)n repeats, H'? | DEPC (ss DNA tested!) | in vitro, T7 RNA pol., runoff | -90% @ n = 88 repeats | number of repeats | 99 |
| syn., human frataxin 1st intron GAA repeat, +100? plasmid | (GAA)88, H'? | n.s. | in vitro, T7 RNA pol., runoff | -90% (-25% @ 2.5 μM complement [TTC]7 ODN) | (GGA)7 ODN / (CUG)88 template | 100 |
| syn.,human frataxin 1st intron GAA repeat, +100? plasmid | (GAA)150, (multi-H'(sticky DNA) | gel mobility/ gel mobility | in vitro, T7 or SP6 RNA pol. or HeLa NE, runoff | -99% r[UUC]150, -95% co-transcribed control | number of repeats, orientation / co-transcribed control template | 101 |
| human HMGA2 promoter, -25, plasmid | 60 bp Py/Pu, H? | S1 nuclease, EMSA | in vivo, NIH 3T3, luciferase | +400% H+ supercoiled, (+200% mut. H-) | mut. H-, linear or supercoiled/ CMV β-gal | 102 |
| syn., E. coli PIT sequences, promoter & downstream, plasmid | 33 nt multimers, H' | n.s. | in vivo, E. coli, lacZ, β-gal | -0% (promoter PIT); +300% (downstream 2 x PIT), mRNA translation effect | PIT-, mut. PIT | 103 |
| Drosophila hsp26 promoter, chromosome | 25 bp mirror repeat, H | DMS, kethoxal, CMCT, KMnO4 & UV FP / REPA | in vivo, Drosophila, hsp26-lacZ transgene, β-gal | -0% H-, -40% mut. H+ | mut. H- & multi-mut. H+ | 104 |
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.
b Triplex information is indicated as length of the triplex-forming region, sequence of repeating element, auxiliary compounds (“stabilized with...”), and triplex motif (H or H'). BePI, (3-methoxy- 7H-8-methyl-11-[(3'-amino-propyl) amino] benzo[e]pyrido [4,3-b]indole.
c Assays used to demonstrate triplex formation include electrophoretic mobility shift assays (EMSA), oligonucleotide hybridization, footprinting (FP) with enzymes like S1 nuclease or with chemicals including chloroacetaldehyde (CAA), 1-cyclohexyl-3-(2-morpholinoethyl)-carbodiimide metho- p-toluene sulfonate (CMCT), diethylpyrocarbonate (DEPC), and dimethyl sulfate (DMS), or with ultraviolet radiation (UV) and restriction endonuclease protection assays (REPA). Assays indicated after a slash (e.g., UV FP / REPA) indicate those assays performed after transcription has occurred or in vivo.
d Transcription assay information is presented as extract (e.g., nuclear, NE) or polymerase (e.g., T7 RNA pol.), template, assay type (e.g., runoff) for in vitro studies, and cell type, template, and assay type for in vivo studies. In vivo assays include RNA-based (e.g., RNase protection) and enzymatic activity assays (e.g., chloramphenicol acetyltransferase [CAT], β-galactosidase [β-gal.], luciferase [luc]).
e Maximum effect of triplex on transcription. Minus and plus sign preceding percentage effect indicate triplex-dependent transcription inhibition and stimulation, respectively. Hand H+ refer to mutations that either disrupt or promote H(H')-DNA formation. Del., deletion. Mut., mutation. Unexpected or unusual findings are indicated in parentheses.
f Controls used to demonstrate specificity of triplex effects on transcription. Controls involving template DNA are shown before the slash, while controls involving alternative targets are shown after (e.g., H- / tetR).
From: Do DNA Triple Helices or Quadruplexes Have a Role in Transcription?
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