695:(RNAi). The primary problem with using RNAi in gene modulation is drug delivery to target cells. RNAi gene modulation has been successfully applied to mice toward the treatment of a mouse model for inflammatory bowel disease. This treatment utilized liposome-based beta-7 integrin-targeted, stabilized nanoparticles entrapping short interfering RNAs (siRNAs). There are several other forms of RNAi delivery, including: polyplex delivery, ligand-siRNA conjugates, naked delivery, inorganic particle deliver using gold nanoparticles, and site specific local delivery.
404:
384:
376:
286:
538:
546:
400:
to inhibit transcription of the downstream 5S RNA. In contrast, if the regulator is a repressor, this will increase transcriptional levels. As an example, SPA targeting to the host factor LSF, which represses expression of the human immunodeficiency virus (HIV) type 1 long terminal repeat (LTR), blocks binding of LSF and consequently de-represses expression of LTR .
311:. This occurs through hydrogen bonding within the minor groove of DNA. The amide pairs Py/Im, Py/Hp, Hp/Py, and Im/Py recognize the Watson-Crick base pairs C-G, A-T, T-A, and G-C, respectively (Table 1). See figure for a graphical representation of 5'-GTAC-3' recognition by a SPA. SPAs have low toxicity, but have not yet been used in human gene modulation.
636:
level - can influence the accessibility of sequences of DNA to transcription machinery, thereby influencing the rate at which it can be transcribed. If, instead of impacting the DNA strand directly, as described above, a designer zinc-finger protein instead affects epigenetic modification state for a
399:
SPAs may also modulate transcription by targeting a transcription regulator binding site. If the regulator is an activator of transcription, this will decrease transcriptional levels. As an example, SPA targeting to the binding site for the activating transcription factor TFIIIA has been demonstrated
618:
in that region will subsequently result. Transcription rates of genes so-affected will be reduced. Many of the effector domains function to modulate either the DNA directly - e.g. via methylation, cleaving, or recombination of the target DNA sequence - or by modulating its transcription rate - e.g.
366:
The major structural drawback to unmodified SPAs as gene modulators is that their recognition sequence cannot be extended beyond 5 Watson-Crick base pairings. The natural curvature of the DNA minor groove is too tight a turn for the hairpin structure to match. There are several groups with proposed
137:
631:
state and the ability of transcriptional machinery to access the affected genes. Epigenetic modification is a major theme in determining varying expression levels for genes, as explained by the idea that how tightly-wound the DNA strand is - from histones at the local level up to chromatin at the
243:
complexes are assembled on the targeted sequence, the DNA is repaired. Damage of the intramolecular recombination substrate can then be repaired and detected if resection goes far enough to produce compatible ends on both sides of the cleavage site and then 3' overhangs are ligated leading to the
416:
SPAs have not been shown to directly modify DNA or have activity other than direct blocking of other factors or processes. However, modifying agents can be bound to the tail ends of the hairpin structure. The specific binding of the SPA to DNA allows for site-specific targeting of the conjugated
420:
SPAs have been paired with the DNA-alkylating moieties cyclopropylpyrroloindole and chlorambucil that were able to damage and crosslink SV40 DNA. This effect inhibited cell cycling and growth. Chlorambucil, a chemotherapeutic agent, was more effective when conjugated to an SPA than without.
79:
variants. In contrast, traditional gene therapy typically introduces a gene which can express only one transcript, rather than a set of stoichiometrically-expressed spliced transcript variants. Additionally, virally-introduced genes can be targeted for gene silencing by methylation which can
424:
In 2012, SPAs were conjugated to SAHA, a potent histone deacetylase (HDAC) inhibitor. SPAs with conjugated SAHA were targeted to Oct-3/4 and Nanog which induced epigenetic remodeling and consequently increased expression of multiple pluripotency related genes in mouse embryonic fibroblasts.
247:
In model systems TFOs can inhibit gene expression at the DNA level as well as induce targeted mutagenesis in the model. TFO-induced inhibition of transcription elongation on endogenous targets have been tested on cell cultures with success. However, despite much
63:
level. The advantage to this approach over modulation at the mRNA or protein level is that every cell contains only a single gDNA copy. Thus the target copy number is significantly lower allowing the drugs to theoretically be administered at much lower doses.
27:
in that gene modulation seeks to alter the expression of an endogenous gene (perhaps through the introduction of a gene encoding a novel modulatory protein) whereas gene therapy concerns the introduction of a gene whose product aids the recipient directly.
2258:
Snowden, AW.; Zhang, L.; Urnov, F.; Dent, C.; Jouvenot, Y.; Zhong, X.; Rebar, EJ.; Jamieson, AC.; et al. (December 2003). "Repression of vascular endothelial growth factor A in glioblastoma cells using engineered zinc finger transcription factors".
609:
Effector domains bound to the zinc-finger can also have comparable effects. It is the function of these effector domains which are arguably the most important with respect to the use of designer zinc-finger proteins for therapeutic gene modulation. If a
281:
of DNA. They can exert an effect either directly, by binding a regulatory region or transcribed region of a gene to modify transcription, or indirectly, by designed conjugation with another agent that makes alterations around the DNA target site.
259:
by targeting transcription initiation or elongation, arresting at the triplex binding sites, or introducing permanent changes in a target sequence via stimulating a cell's inherent repair pathways. These applications can be relevant in creating
104:
in duplex DNA which creates a third strand or a triple helix. The binding occurs at polypurine or polypyrimidine regions via
Hoogsteen hydrogen bonds to the purine (A / G) bases on the double stranded DNA that is already in the form of the
486:
371:
which relaxes the structure. Another approach to extending the recognition length is to use several short hairpins in succession. This approach has increased the recognition length to up to eleven Watson-Crick base pairs.
2096:
Urnov, FD.; Miller, JC.; Lee, YL.; Beausejour, CM.; Rock, JM.; Augustus, S.; Jamieson, AC.; Porteus, MH.; et al. (June 2005). "Highly efficient endogenous human gene correction using designed zinc-finger nucleases".
298:
Specific bases in the minor groove of DNA can be recognized and bound by small synthetic polyamides (SPAs). DNA-binding SPAs have been engineered to contain three polyamide amino acid components: hydroxypyrrole (Hp),
678:
were able to demonstrate that their engineered protein could block transcription of the oncogene in vivo. Leukemia cells became dependent on regular growth factors, bringing the cell cycle back under the control of
264:
that inhibit gene expression at the DNA level. Since aberrant gene expression is a hallmark of cancer, modulating these endogenous genes' expression levels could potentially act as a therapy for multiple
289:
Cartoon representation of a synthetic polyamide to DNA sequence recognition. The DNA sequence 5'-GTAC-3' is recognized by the amino acid pairs Py/Im, Py/Hp, Hp/Py, and Im/Py. See for chemical structure
133:(A / G), or mixed purine and pyrimidine bind to the same purine-rich strand via reverse Hoogsteen bonds in an anti-parallel fashion. TFO's can recognize purine-rich target strands for duplex DNA.
172:
gene target sites to polypurine-polypyrimidine stretches in duplex DNA. If a method to also allow TFOs to bind to pyrimidine bases was generated, this would enable TFOs to target any part of the
239:. If a target sequence is located between two inactive copies of a gene, DNA ligands, such as TFOs, can bind to the target site and would be recognized as DNA lesions. To fix these lesions,
307:(Py). Chains of these amino acids loop back on themselves in a hairpin structure. The amino acids on either side of the hairpin form a pair which can specifically recognize both sides of a
619:
inhibiting transcription via repressor domains that block transcriptional machinery, promoting transcription with activation domains that recruit transcriptional machinery to the site, or
121:
orientation to target polypurine or polypyrimidine regions. Since the DNA-recognition codes are different for the parallel and the anti-parallel fashion of TFO binding, TFOs composed of
2481:"Identifier NCT00080392.Modulation of Vascular Endothelial Growth Factor (VEGF) Using an Engineered Zinc-Finger Transcription Factor to Treat Lower Limb Intermittent Claudication"
478:
atom, which serves to stabilize the protein domain as a whole. This stabilization particularly benefits the Ξ±-helix in its function as the DNA-recognition and -binding domain.
396:
SPAs may inhibit transcription through binding within a transcribed region of a target gene. This inhibition occurs through blocking of elongation by an RNA polymerase.
100:
Triplex-forming oligonucleotides (TFO) are one potential method to achieve therapeutic gene modulation. TFOs are approximately 10-40 base pairs long and can bind in the
522:), thereby ensuring that the protein motif is highly selective of its target. In engineering a designer zinc-finger protein, researchers can utilize techniques such as
83:
There are three major categories of agents that act as transcriptional gene modulators: triplex-forming oligonucleotides (TFOs), synthetic polyamides (SPAs), and
195:
and specificity, in vivo stability, and uptake into cells. Researchers are attempting to overcome these limitations by improving TFO characteristics through
948:
Simon, P.; Cannata, F.; Concordet, JP.; Giovannangeli, C. (August 2008). "Targeting DNA with triplex-forming oligonucleotides to modify gene sequence".
80:
counteract the effect of traditional gene therapy. This is not anticipated to be a problem for transcriptional modulation as it acts on endogenous DNA.
203:
between the TFO and the DNA duplex. Also due to their high molecular weight, uptake into cells is limited and some strategies to overcome this include
590:- the binding site for naturally-occurring transcription factors will be obscured, leading to a corresponding decrease or increase, respectively, in
2337:
Dykxhoorn, DM.; Lieberman, J. (2006). "Running interference: prospects and obstacles to using small interfering RNAs as small molecule drugs".
1791:
2554:
1298:
Lown JW (1988). "Lexitropsins: rational design of DNA sequence reading agents as novel anti-cancer agents and potential cellular probes".
59:
An approach to therapeutic modulation utilizes agents that modulate endogenous transcription by specifically targeting those genes at the
562:
in a number of ways. Ultimately, two factors are primarily responsible for the result on expression: whether the targeted sequence is a
180:
of TFO to bind to a target DNA region. An approach to overcome this limitation is to develop TFOs with modified nucleotides that act as
2207:
Lara, H.; Wang, Y.; Beltran, AS.; JuΓ‘rez-Moreno, K.; Yuan, X.; Kato, S.; Leisewitz, AV.; Cuello Fredes, M.; et al. (August 2012).
117:
TFOs can be either polypurine or polypyrimidine molecules and bind to one of the two strands in the double helix in either parallel or
788:"Chimeric retroviral helper virus and picornavirus IRES sequence to eliminate DNA methylation for improved retroviral packaging cells"
223:
and much of this revolves around their potential applications in antigene therapy. In particular they have been used as inducers of
614:
domain is bound to the designer zinc-finger protein, when the zinc-finger protein binds to the target DNA sequence an increase in
739:
have been completed which identify this zinc-finger protein as a promising and safe potential therapeutic agent for treatment of
36:
752:
983:
Zhou, Y.; Kierzek, E.; Loo, ZP.; Antonio, M.; Yau, YH.; Chuah, YW.; Geifman-Shochat, S.; Kierzek, R.; Chen, G. (July 2013).
1035:
Guntaka, RV.; Varma, BR.; Weber, KT. (January 2003). "Triplex-forming oligonucleotides as modulators of gene expression".
674:
with the tri-domain zinc-finger protein in order to facilitate binding of the protein to genomic DNA in the nucleus, Choo
261:
232:
732:
659:
1541:"Targeted derepression of the human immunodeficiency virus type 1 long terminal repeat by pyrrole-imidazole polyamides"
1070:
Faria, M.; Wood, CD.; Perrouault, L.; Nelson, JS.; Winter, A.; White, MR.; Helene, C.; Giovannangeli, C. (April 2000).
740:
736:
671:
177:
118:
1488:
Gottesfeld JM, Neely L, Trauger JW, Baird EE, Dervan PB (1997). "Regulation of gene expression by small molecules".
244:
formation of a single active copy of the gene and the loss of all the sequences between the two copies of the gene.
640:
In the first case to successfully demonstrate the use of designer zinc-finger proteins to modulate gene expression
1742:
Papworth, M.; Kolasinska, P.; Minczuk, M. (January 2006). "Designer zinc-finger proteins and their applications".
2564:
2559:
1809:"Use of a zinc-finger consensus sequence framework and specificity rules to design specific DNA binding proteins"
1325:
Trauger JW, Baird EE, Dervan PB (1996). "Recognition of DNA by designed ligands at subnanomolar concentrations".
523:
224:
106:
44:
591:
168:
Another limitation is that TFOs can only bind to purine-rich target strands and this would limit the choice of
32:
1680:"A synthetic small molecule for rapid induction of multiple pluripotency genes in mouse embryonic fibroblasts"
367:
workarounds to this problem. SPAs can be made to better follow the curvature of the minor groove by inserting
252:
success, there has been limited achievement in cellular applications potentially due to target accessibility.
1132:
Reddy BS, Sharma SK, Lown JW (2001). "Recent developments in sequence selective minor groove DNA effectors".
185:
1868:"A rapid, generally applicable method to engineer zinc fingers illustrated by targeting the HIV-1 promoter"
2346:
531:
680:
192:
1072:"Targeted inhibition of transcription elongation in cells mediated by triplex-forming oligonucleotides"
846:"Therapeutic modulation of endogenous gene function by agents with designed DNA-sequence specificities"
2161:
2106:
2050:
1936:
1820:
1691:
1497:
1334:
1263:
Dervan PB, Edelson BS (2003). "Recognition of the DNA minor groove by pyrrole-imidazole polyamides".
1221:
1083:
2351:
1206:
723:
that prompts the patient to produce an engineered transcription factor, the target of which is the
708:
648:
designed a protein consisting of three zinc-finger domains that targeted a specific sequence on a
579:
447:
403:
383:
375:
181:
141:
126:
84:
1922:"In vivo repression by a site-specific DNA-binding protein designed against an oncogenic sequence"
534:
of motifs with known target specificity to produce a library of sequence-specific final proteins.
176:. Also the human genome is rich in polypurine and polypyrimidine sequences which could affect the
2130:
1970:
1921:
1521:
1358:
1245:
716:
228:
220:
235:. One such gene sequence modification method is through the targeting DNA with TFOs to active a
2384:"Systemic leukocyte-directed siRNA delivery revealing cyclin D1 as an anti-inflammatory target"
1639:"Cell-free and cellular activities of a DNA sequence selective hairpin polyamide-CBI conjugate"
2529:
2462:
2413:
2364:
2319:
2268:
2240:
2189:
2122:
2078:
2019:
1962:
1897:
1848:
1787:
1759:
1717:
1660:
1619:
1570:
1513:
1470:
1447:
1428:
1393:
1350:
1307:
1280:
1237:
1207:"Recognition of the four Watson-Crick base pairs in the DNA minor groove by synthetic ligands"
1184:
1149:
1111:
1052:
1014:
965:
927:
875:
817:
757:
563:
285:
2519:
2452:
2444:
2403:
2395:
2356:
2309:
2299:
2230:
2220:
2209:"Targeting serous epithelial ovarian cancer with designer zinc finger transcription factors"
2179:
2169:
2114:
2068:
2058:
2009:
2001:
1952:
1944:
1887:
1879:
1838:
1828:
1751:
1707:
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1609:
1601:
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1505:
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1385:
1342:
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1229:
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1141:
1101:
1091:
1044:
1004:
996:
957:
917:
909:
865:
857:
807:
799:
767:
707:. The efficacy and safety of EW-A-401, an engineered zinc-finger transcription factor, as a
692:
575:
571:
527:
510:
on the Ξ±-helix gives the motif its target sequence specificity. The domain binds to a seven-
507:
204:
48:
2360:
606:
transcription complexes, resulting in a truncated or otherwise nonfunctional gene product.
277:
Synthetic polyamides are a set of small molecules that form specific hydrogen bonds to the
615:
587:
559:
519:
515:
379:
Synthetic polyamide blocking of RNA transcription by binding within the transcribed region
196:
20:
719:
ailment, has been investigated in clinical trials. The protein consists of an engineered
23:
at one of various stages, with a view to alleviate some form of ailment. It differs from
2165:
2150:"Positive and negative regulation of endogenous genes by designed transcription factors"
2110:
2054:
1990:"Site-selective in vivo targeting of cytosine-5 DNA methylation by zinc-finger proteins"
1940:
1824:
1695:
1590:"DNA crosslinking and biological activity of a hairpin polyamide-chlorambucil conjugate"
1501:
1411:
Kers I, Dervan PB (2002). "Search for the optimal linker in tandem hairpin polyamides".
1338:
1225:
1087:
537:
2457:
2432:
2408:
2383:
2314:
2287:
2235:
2208:
1892:
1867:
1712:
1679:
1556:
1009:
984:
922:
897:
704:
652:
603:
256:
236:
200:
40:
2014:
1989:
1614:
1589:
1565:
1540:
1424:
1276:
1180:
1048:
870:
845:
812:
787:
545:
2548:
2184:
2149:
2073:
2038:
1843:
1808:
1389:
1249:
1106:
1071:
985:"Recognition of RNA duplexes by chemically modified triplex-forming oligonucleotides"
803:
567:
154:
1974:
898:"Oligo/polynucleotide-based gene modification: strategies and therapeutic potential"
703:
Designer zinc-finger proteins, on the other hand, have undergone some trials in the
140:
Triple
Stranded DNA: TFOs bind in a similar fashion to the double stranded DNA as a
2134:
1588:
Wang YD, Dziegielewski J, Wurtz NR, Dziegielewska B, Dervan PB, Beerman TA (2003).
1525:
1362:
762:
728:
712:
368:
76:
68:
24:
2480:
637:
target DNA region, modulation of gene expression could similarly be accomplished.
961:
2304:
1678:
Pandian NG, Nakano Y, Sato S, Morinaga H, Bando T, Nagase H, Sugiyama H (2012).
624:
463:
451:
208:
158:
2382:
Peer, D.; Park, EJ.; Morishita, Y.; Carman, CV.; Shimaoka, M. (February 2008).
1755:
458:. In both designer and natural zinc-finger motifs, the protein consists of two
666:
cells to proliferate in the absence of specific growth factors, a hallmark of
633:
574:
are bound to the zinc-finger domain. If the target sequence for an engineered
511:
503:
459:
240:
122:
1145:
2399:
2225:
628:
611:
583:
467:
308:
300:
2533:
2466:
2417:
2368:
2323:
2272:
2244:
2193:
2174:
2126:
2063:
2023:
1901:
1833:
1763:
1721:
1664:
1655:
1638:
1623:
1574:
1474:
1432:
1397:
1284:
1188:
1153:
1115:
1096:
1056:
1018:
969:
931:
879:
821:
2082:
2039:"Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain"
1966:
1852:
1517:
1354:
1311:
1241:
913:
2005:
1605:
1000:
861:
663:
655:
471:
439:
249:
169:
72:
2448:
2118:
485:
482:
is an example of a naturally-occurring protein with zinc-finger motifs.
2524:
2507:
720:
649:
641:
620:
304:
2508:"VEGF gene therapy: therapeutic angiogenesis in the clinic and beyond"
1957:
1703:
1539:
Coull JJ, He G, Melander C, Rucker VC, Dervan PB, Margolis DM (2002).
1466:
157:, the nitrogen atom at position 3 on the cytosine residue needs to be
125:(C / T) bind to the purine-rich strand of the target double helix via
1948:
1509:
1448:"Recognition of ten base pairs of DNA by head-to-head hairpin dimers"
1376:
Wemmer DE (2000). "Designed sequence-specific minor groove ligands".
1346:
1167:
Dervan PB (2001). "Molecular
Recognition of DNA by Small Molecules".
724:
667:
479:
455:
266:
173:
130:
60:
1883:
1637:
Wang YD, Dziegielewski J, Chang AY, Dervan PB, Beerman TA (2002).
1233:
691:
The major approach to post-transcriptional gene modulation is via
219:
Scientists are still refining the technology to turn TFOs into a
153:
In order for TFO motifs to bind in a parallel fashion and create
599:
595:
475:
136:
499:
443:
278:
101:
67:
This approach also offers several advantages over traditional
31:
Modulation of gene expression can be mediated at the level of
1205:
White S, Szewcxyk JW, Turner JM, Baird EE, Dervan PB (1998).
162:
602:, the designer zinc-finger will obscure the sequence from
75:
transcription should yield correct relative expression of
1786:. San Francisco: Pearson/Benjamin Cummings. p. 595.
315:
Table 1. Amide pair to nucleotide pair recognition code.
47:. It may also be mediated post-transcriptionally through
1920:
Choo, Y.; SΓ‘nchez-GarcΓa, I.; Klug, A. (December 1994).
165:
levels it is not, which could prevent parallel binding.
2037:
Kim, YG.; Cha, J.; Chandrasegaran, S. (February 1996).
129:
hydrogen bonds in a parallel fashion. TFOs composed of
2487:. U.S. National Institutes of Health. 30 December 2011
2148:
Beerli, RR.; Dreier, B.; Barbas, CF. (February 2000).
1988:
Carvin, CD.; Parr, RD.; Kladde, MP. (November 2003).
387:
Synthetic polyamide blocking of transcription factors
731:development. Although not yet approved by the U.S.
313:
207:, coupling of the TFO to hydrophobic residues like
454:domains to modulate specific target areas of the
407:Synthetic polyamide conjugated to modifying agent
1737:
1735:
1733:
1731:
199:, such as modifying the TFO backbone to reduce
1777:
1775:
1773:
1030:
1028:
891:
889:
514:sequence of DNA (positions 1 through 6 on the
1200:
1198:
896:Sargent, RG.; Kim, S.; Gruenert, DC. (2011).
725:vascular endothelial growth factor-A (VEGF-A)
438:Designer zinc-finger proteins are engineered
227:, reagents that selectively and specifically
191:Other limitations include concerns regarding
8:
1915:
1913:
1911:
1866:Isalan, M.; Klug, A.; Choo, Y. (July 2001).
1127:
1125:
943:
941:
558:Designer zinc-finger proteins can modulate
2433:"Progress toward in vivo use of siRNAs-II"
839:
837:
835:
833:
831:
658:. This specific oncogene is implicated in
598:. Similarly, if the target sequence is an
188:of the TFO for specific target sequences.
2523:
2456:
2407:
2350:
2313:
2303:
2234:
2224:
2183:
2173:
2072:
2062:
2013:
1956:
1891:
1842:
1832:
1807:Desjarlais, JR.; Berg, JM. (March 1993).
1711:
1654:
1613:
1564:
1105:
1095:
1008:
921:
869:
811:
474:residues on the Ξ²-sheets are bonded to a
2288:"Progress towards in vivo use of siRNAs"
544:
536:
484:
402:
382:
374:
284:
135:
2506:Giacca, M.; Zacchigna, S. (June 2012).
2431:Rettig, GR.; Behlke, MA. (March 2012).
778:
19:refers to the practice of altering the
2361:10.1146/annurev.bioeng.8.061505.095848
570:of DNA, and whether and what types of
554:Effects and impacts on gene modulation
518:of DNA, plus positions 0 and 3 on the
7:
687:Post-transcriptional gene modulation
35:by DNA-binding agents (which may be
844:Uil TG, Haisma HJ, Rots MG (2003).
446:. These proteins capitalize on the
255:TFOs have the potential to silence
211:, or cell permeabilization agents.
1557:10.1128/jvi.76.23.12349-12354.2002
1378:Annu. Rev. Biophys. Biomol. Struct
727:gene, which positively influences
627:-modification domains that affect
14:
662:. The oncogene typically enables
578:is a regulatory domain - e.g., a
498:Zinc-finger motifs bind into the
442:used to target specific areas of
231:target DNA, and as modulators of
1390:10.1146/annurev.biophys.29.1.439
804:10.1128/JVI.74.11.5242-5249.2000
541:Zinc fingers binding a DNA helix
470:residues on the Ξ±-helix and two
91:Triplex-forming oligonucleotides
37:artificial transcription factors
1446:Weyermann P, Dervan PB (2002).
753:Artificial transcription factor
55:Transcriptional gene modulation
1:
1784:Molecular biology of the gene
1425:10.1016/s0968-0896(02)00221-3
1277:10.1016/s0959-440x(03)00081-2
1181:10.1016/s0968-0896(01)00262-0
1049:10.1016/s1357-2725(02)00165-6
530:for binding capacity, or the
489:Example of zinc-finger motifs
429:Designer zinc-finger proteins
149:Complications and limitations
962:10.1016/j.biochi.2008.04.004
733:Food and Drug Administration
660:acute lymphoblastic leukemia
2555:Therapeutic gene modulation
2305:10.1016/j.ymthe.2006.01.001
741:peripheral arterial disease
672:nuclear localization signal
480:Transcription factor TFIIIA
362:Limitations and workarounds
142:triplex helix configuration
17:Therapeutic gene modulation
2581:
2286:Behlke, MA. (April 2006).
1756:10.1016/j.gene.2005.09.011
786:Young WB, Link CJ (2000).
502:of helical DNA, where the
45:synthetic oligonucleotides
1782:Watson, James D. (2008).
524:site-directed mutagenesis
2154:Proc Natl Acad Sci U S A
2043:Proc Natl Acad Sci U S A
1813:Proc Natl Acad Sci U S A
1265:Curr. Opin. Struct. Biol
1146:10.2174/0929867003373292
1076:Proc Natl Acad Sci U S A
737:Phase I clinical studies
616:methylation state of DNA
201:electrostatic repulsions
2400:10.1126/science.1149859
2226:10.1074/jbc.M112.360768
1037:Int J Biochem Cell Biol
434:What they are/structure
225:site-specific mutations
2175:10.1073/pnas.040552697
2064:10.1073/pnas.93.3.1156
1834:10.1073/pnas.90.6.2256
1656:10.1074/jbc.M207179200
1594:Nucleic Acids Research
1097:10.1073/pnas.97.8.3862
850:Nucleic Acids Research
550:
542:
532:in vitro recombination
490:
408:
388:
380:
309:Watson-Crick base pair
290:
197:chemical modifications
145:
914:10.1089/oli.2010.0273
699:Clinical significance
549:Epigenetic mechanisms
548:
540:
488:
406:
386:
378:
288:
205:DNA condensing agents
139:
71:. Directly targeting
520:complementary strand
450:capacity of natural
412:Conjugate modulation
273:Synthetic polyamides
182:locked nucleic acids
85:DNA binding proteins
21:expression of a gene
2449:10.1038/mt.2011.263
2339:Annu Rev Biomed Eng
2166:2000PNAS...97.1495B
2119:10.1038/nature03556
2111:2005Natur.435..646U
2055:1996PNAS...93.1156K
1941:1994Natur.372..642C
1825:1993PNAS...90.2256D
1696:2012NatSR...2E.544P
1649:(45): 42431β42437.
1551:(23): 12349β12354.
1502:1997Natur.387..202G
1339:1996Natur.382..559T
1300:Anticancer Drug Des
1226:1998Natur.391..468W
1088:2000PNAS...97.3862F
792:Journal of Virology
709:pharmacologic agent
594:for the associated
316:
221:therapeutic product
2525:10.1038/gt.2012.17
2485:ClinicalTrials.gov
2006:10.1093/nar/gkg853
1684:Scientific Reports
1606:10.1093/nar/gkg215
1001:10.1093/nar/gkt352
862:10.1093/nar/gkg815
551:
543:
491:
409:
389:
381:
314:
291:
146:
107:Watson-Crick helix
1994:Nucleic Acids Res
1793:978-0-8053-9592-1
1704:10.1038/srep00544
1600:(21): 1208β1215.
1496:(6629): 202β205.
1467:10.1021/ja020258k
1461:(24): 6872β6878.
1419:(10): 3339β3349.
1413:Bioorg. Med. Chem
1333:(6591): 559β561.
1220:(6666): 468β471.
1169:Bioorg. Med. Chem
989:Nucleic Acids Res
856:(21): 6064β6078.
798:(11): 5242β5249.
758:Antisense therapy
681:normal regulation
670:. By including a
564:regulatory region
560:genome expression
528:randomized trials
417:modifying agent.
392:Direct modulation
359:
358:
2572:
2565:Applied genetics
2560:Medical genetics
2538:
2537:
2527:
2503:
2497:
2496:
2494:
2492:
2477:
2471:
2470:
2460:
2428:
2422:
2421:
2411:
2394:(5863): 627β30.
2379:
2373:
2372:
2354:
2334:
2328:
2327:
2317:
2307:
2283:
2277:
2276:
2255:
2249:
2248:
2238:
2228:
2219:(35): 29873β86.
2204:
2198:
2197:
2187:
2177:
2145:
2139:
2138:
2105:(7042): 646β51.
2093:
2087:
2086:
2076:
2066:
2034:
2028:
2027:
2017:
2000:(22): 6493β501.
1985:
1979:
1978:
1960:
1949:10.1038/372642a0
1926:
1917:
1906:
1905:
1895:
1863:
1857:
1856:
1846:
1836:
1804:
1798:
1797:
1779:
1768:
1767:
1739:
1726:
1725:
1715:
1675:
1669:
1668:
1658:
1634:
1628:
1627:
1617:
1585:
1579:
1578:
1568:
1536:
1530:
1529:
1510:10.1038/387202a0
1485:
1479:
1478:
1455:J. Am. Chem. Soc
1452:
1443:
1437:
1436:
1408:
1402:
1401:
1373:
1367:
1366:
1347:10.1038/382559a0
1322:
1316:
1315:
1295:
1289:
1288:
1260:
1254:
1253:
1211:
1202:
1193:
1192:
1175:(9): 2215β2235.
1164:
1158:
1157:
1129:
1120:
1119:
1109:
1099:
1067:
1061:
1060:
1032:
1023:
1022:
1012:
980:
974:
973:
945:
936:
935:
925:
902:Oligonucleotides
893:
884:
883:
873:
841:
826:
825:
815:
783:
768:RNA interference
693:RNA interference
576:designer protein
572:effector domains
323:Nucleotide Pair
317:
262:cancer therapies
215:What can they do
193:binding affinity
184:to increase the
163:physiological pH
49:RNA interference
2580:
2579:
2575:
2574:
2573:
2571:
2570:
2569:
2545:
2544:
2541:
2505:
2504:
2500:
2490:
2488:
2479:
2478:
2474:
2430:
2429:
2425:
2381:
2380:
2376:
2336:
2335:
2331:
2285:
2284:
2280:
2267:(24): 8968β76.
2257:
2256:
2252:
2206:
2205:
2201:
2160:(4): 1495β500.
2147:
2146:
2142:
2095:
2094:
2090:
2036:
2035:
2031:
1987:
1986:
1982:
1935:(6507): 642β5.
1924:
1919:
1918:
1909:
1865:
1864:
1860:
1806:
1805:
1801:
1794:
1781:
1780:
1771:
1741:
1740:
1729:
1677:
1676:
1672:
1636:
1635:
1631:
1587:
1586:
1582:
1538:
1537:
1533:
1487:
1486:
1482:
1450:
1445:
1444:
1440:
1410:
1409:
1405:
1375:
1374:
1370:
1324:
1323:
1319:
1297:
1296:
1292:
1262:
1261:
1257:
1209:
1204:
1203:
1196:
1166:
1165:
1161:
1134:Curr. Med. Chem
1131:
1130:
1123:
1069:
1068:
1064:
1034:
1033:
1026:
995:(13): 6664β73.
982:
981:
977:
947:
946:
939:
895:
894:
887:
843:
842:
829:
785:
784:
780:
776:
749:
701:
689:
556:
496:
436:
431:
414:
394:
364:
296:
275:
233:gene expression
217:
151:
115:
98:
93:
57:
41:small molecules
12:
11:
5:
2578:
2576:
2568:
2567:
2562:
2557:
2547:
2546:
2540:
2539:
2498:
2472:
2443:(3): 483β512.
2423:
2374:
2352:10.1.1.418.758
2329:
2278:
2250:
2199:
2140:
2088:
2049:(3): 1156β60.
2029:
1980:
1907:
1872:Nat Biotechnol
1858:
1819:(6): 2256β60.
1799:
1792:
1769:
1727:
1670:
1629:
1580:
1531:
1480:
1438:
1403:
1368:
1317:
1290:
1271:(3): 284β299.
1255:
1194:
1159:
1140:(5): 475β508.
1121:
1062:
1024:
975:
956:(8): 1109β16.
937:
885:
827:
777:
775:
772:
771:
770:
765:
760:
755:
748:
745:
717:cardiovascular
705:clinical arena
700:
697:
688:
685:
604:RNA polymerase
555:
552:
516:primary strand
495:
492:
435:
432:
430:
427:
413:
410:
393:
390:
363:
360:
357:
356:
353:
349:
348:
345:
341:
340:
337:
333:
332:
329:
325:
324:
321:
295:
292:
274:
271:
216:
213:
155:hydrogen bonds
150:
147:
114:
111:
97:
94:
92:
89:
56:
53:
13:
10:
9:
6:
4:
3:
2:
2577:
2566:
2563:
2561:
2558:
2556:
2553:
2552:
2550:
2543:
2535:
2531:
2526:
2521:
2517:
2513:
2509:
2502:
2499:
2486:
2482:
2476:
2473:
2468:
2464:
2459:
2454:
2450:
2446:
2442:
2438:
2434:
2427:
2424:
2419:
2415:
2410:
2405:
2401:
2397:
2393:
2389:
2385:
2378:
2375:
2370:
2366:
2362:
2358:
2353:
2348:
2344:
2340:
2333:
2330:
2325:
2321:
2316:
2311:
2306:
2301:
2298:(4): 644β70.
2297:
2293:
2289:
2282:
2279:
2274:
2270:
2266:
2262:
2254:
2251:
2246:
2242:
2237:
2232:
2227:
2222:
2218:
2214:
2210:
2203:
2200:
2195:
2191:
2186:
2181:
2176:
2171:
2167:
2163:
2159:
2155:
2151:
2144:
2141:
2136:
2132:
2128:
2124:
2120:
2116:
2112:
2108:
2104:
2100:
2092:
2089:
2084:
2080:
2075:
2070:
2065:
2060:
2056:
2052:
2048:
2044:
2040:
2033:
2030:
2025:
2021:
2016:
2011:
2007:
2003:
1999:
1995:
1991:
1984:
1981:
1976:
1972:
1968:
1964:
1959:
1954:
1950:
1946:
1942:
1938:
1934:
1930:
1923:
1916:
1914:
1912:
1908:
1903:
1899:
1894:
1889:
1885:
1884:10.1038/90264
1881:
1878:(7): 656β60.
1877:
1873:
1869:
1862:
1859:
1854:
1850:
1845:
1840:
1835:
1830:
1826:
1822:
1818:
1814:
1810:
1803:
1800:
1795:
1789:
1785:
1778:
1776:
1774:
1770:
1765:
1761:
1757:
1753:
1749:
1745:
1738:
1736:
1734:
1732:
1728:
1723:
1719:
1714:
1709:
1705:
1701:
1697:
1693:
1689:
1685:
1681:
1674:
1671:
1666:
1662:
1657:
1652:
1648:
1644:
1643:J. Biol. Chem
1640:
1633:
1630:
1625:
1621:
1616:
1611:
1607:
1603:
1599:
1595:
1591:
1584:
1581:
1576:
1572:
1567:
1562:
1558:
1554:
1550:
1546:
1542:
1535:
1532:
1527:
1523:
1519:
1515:
1511:
1507:
1503:
1499:
1495:
1491:
1484:
1481:
1476:
1472:
1468:
1464:
1460:
1456:
1449:
1442:
1439:
1434:
1430:
1426:
1422:
1418:
1414:
1407:
1404:
1399:
1395:
1391:
1387:
1383:
1379:
1372:
1369:
1364:
1360:
1356:
1352:
1348:
1344:
1340:
1336:
1332:
1328:
1321:
1318:
1313:
1309:
1305:
1301:
1294:
1291:
1286:
1282:
1278:
1274:
1270:
1266:
1259:
1256:
1251:
1247:
1243:
1239:
1235:
1234:10.1038/35106
1231:
1227:
1223:
1219:
1215:
1208:
1201:
1199:
1195:
1190:
1186:
1182:
1178:
1174:
1170:
1163:
1160:
1155:
1151:
1147:
1143:
1139:
1135:
1128:
1126:
1122:
1117:
1113:
1108:
1103:
1098:
1093:
1089:
1085:
1082:(8): 3862β7.
1081:
1077:
1073:
1066:
1063:
1058:
1054:
1050:
1046:
1042:
1038:
1031:
1029:
1025:
1020:
1016:
1011:
1006:
1002:
998:
994:
990:
986:
979:
976:
971:
967:
963:
959:
955:
951:
944:
942:
938:
933:
929:
924:
919:
915:
911:
907:
903:
899:
892:
890:
886:
881:
877:
872:
867:
863:
859:
855:
851:
847:
840:
838:
836:
834:
832:
828:
823:
819:
814:
809:
805:
801:
797:
793:
789:
782:
779:
773:
769:
766:
764:
761:
759:
756:
754:
751:
750:
746:
744:
742:
738:
734:
730:
726:
722:
718:
714:
711:for treating
710:
706:
698:
696:
694:
686:
684:
682:
677:
673:
669:
665:
661:
657:
654:
651:
647:
643:
638:
635:
630:
626:
622:
617:
613:
607:
605:
601:
597:
593:
592:transcription
589:
585:
581:
577:
573:
569:
568:coding region
565:
561:
553:
547:
539:
535:
533:
529:
525:
521:
517:
513:
509:
505:
501:
494:How they work
493:
487:
483:
481:
477:
473:
469:
465:
461:
457:
453:
449:
445:
441:
433:
428:
426:
422:
418:
411:
405:
401:
397:
391:
385:
377:
373:
370:
361:
354:
351:
350:
346:
343:
342:
338:
335:
334:
330:
327:
326:
322:
319:
318:
312:
310:
306:
302:
293:
287:
283:
280:
272:
270:
268:
263:
258:
253:
251:
245:
242:
238:
234:
230:
226:
222:
214:
212:
210:
206:
202:
198:
194:
189:
187:
183:
179:
175:
171:
166:
164:
160:
156:
148:
143:
138:
134:
132:
128:
124:
120:
113:How they work
112:
110:
108:
103:
96:What are they
95:
90:
88:
86:
81:
78:
74:
70:
65:
62:
54:
52:
50:
46:
42:
38:
34:
33:transcription
29:
26:
22:
18:
2542:
2518:(6): 622β9.
2515:
2511:
2501:
2489:. Retrieved
2484:
2475:
2440:
2436:
2426:
2391:
2387:
2377:
2342:
2338:
2332:
2295:
2291:
2281:
2264:
2260:
2253:
2216:
2212:
2202:
2157:
2153:
2143:
2102:
2098:
2091:
2046:
2042:
2032:
1997:
1993:
1983:
1932:
1928:
1875:
1871:
1861:
1816:
1812:
1802:
1783:
1750:(1): 27β38.
1747:
1743:
1690:(544): 544.
1687:
1683:
1673:
1646:
1642:
1632:
1597:
1593:
1583:
1548:
1544:
1534:
1493:
1489:
1483:
1458:
1454:
1441:
1416:
1412:
1406:
1381:
1377:
1371:
1330:
1326:
1320:
1306:(1): 25β40.
1303:
1299:
1293:
1268:
1264:
1258:
1217:
1213:
1172:
1168:
1162:
1137:
1133:
1079:
1075:
1065:
1043:(1): 22β31.
1040:
1036:
992:
988:
978:
953:
949:
908:(2): 55β75.
905:
901:
853:
849:
795:
791:
781:
763:Gene therapy
729:blood vessel
713:claudication
702:
690:
675:
645:
639:
608:
557:
526:followed by
500:major groove
497:
437:
423:
419:
415:
398:
395:
369:beta-alanine
365:
297:
279:minor groove
276:
257:silence gene
254:
246:
218:
190:
167:
152:
119:antiparallel
116:
102:major groove
99:
82:
69:gene therapy
66:
58:
30:
25:gene therapy
16:
15:
2345:: 377β402.
2213:J Biol Chem
1384:: 439β461.
743:in humans.
735:(FDA), two
721:plasmid DNA
634:chromosomal
623:- or other
588:replication
452:zinc-finger
448:DNA-binding
237:target gene
209:cholesterol
178:specificity
123:pyrimidines
2549:Categories
2261:Cancer Res
1958:10261/6295
774:References
625:epigenetic
512:nucleotide
504:amino acid
320:Amide Pair
303:(Im), and
241:DNA repair
170:endogenous
159:protonated
73:endogenous
2512:Gene Ther
2347:CiteSeerX
1250:205023593
950:Biochimie
629:chromatin
612:methylase
584:repressor
468:histidine
301:imidazole
294:Structure
161:, but at
127:Hoogsteen
2534:22378343
2467:22186795
2437:Mol Ther
2418:18239128
2369:16834561
2324:16481219
2292:Mol Ther
2273:14695215
2245:22782891
2194:10660690
2127:15806097
2024:14602907
1975:12701336
1902:11433278
1764:16298089
1722:22848790
1665:12196541
1624:12582240
1575:12414976
1545:J. Virol
1475:12059208
1433:12150881
1398:10940255
1285:12831879
1189:11553460
1154:11281837
1116:10760257
1057:12467644
1019:23658228
970:18460344
932:21417933
880:14576293
822:10799600
747:See also
664:leukemia
656:oncogene
580:promoter
508:sequence
506:residue
472:cysteine
462:and one
460:Ξ²-sheets
440:proteins
250:in vitro
186:affinity
2491:25 July
2458:3293614
2409:2490797
2388:Science
2315:7106286
2236:3436144
2162:Bibcode
2135:4390010
2107:Bibcode
2083:8577732
2051:Bibcode
1967:7990954
1937:Bibcode
1893:2677679
1853:8460130
1821:Bibcode
1713:3408130
1692:Bibcode
1526:4358491
1518:9144294
1498:Bibcode
1363:4335955
1355:8700233
1335:Bibcode
1312:2838035
1242:9461213
1222:Bibcode
1084:Bibcode
1010:3711454
923:3078494
650:BCR-ABL
644:, Choo
642:in vivo
621:histone
464:Ξ±-helix
305:pyrrole
269:types.
131:purines
2532:
2465:
2455:
2416:
2406:
2367:
2349:
2322:
2312:
2271:
2243:
2233:
2192:
2182:
2133:
2125:
2099:Nature
2081:
2071:
2022:
2015:275549
2012:
1973:
1965:
1929:Nature
1900:
1890:
1851:
1841:
1790:
1762:
1720:
1710:
1663:
1622:
1615:150233
1612:
1573:
1566:136904
1563:
1524:
1516:
1490:Nature
1473:
1431:
1396:
1361:
1353:
1327:Nature
1310:
1283:
1248:
1240:
1214:Nature
1187:
1152:
1114:
1104:
1055:
1017:
1007:
968:
930:
920:
878:
871:275457
868:
820:
813:110878
810:
676:et al.
668:cancer
653:fusion
646:et al.
466:. Two
456:genome
267:cancer
229:cleave
174:genome
77:splice
2185:26462
2131:S2CID
2074:40048
1971:S2CID
1925:(PDF)
1844:46065
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