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Encyclopedia > Morpholino
Segment of a Morpholino-RNA heteroduplex, 8-mer shown

In molecular biology, a Morpholino is a kind of molecule used to modify gene expression. Morpholino oligonucleotides (oligos) are an antisense technology used to block access of other molecules to specific sequences within nucleic acid. Morpholinos block small (~25 base) regions of the base-pairing surfaces of ribonucleic acid (RNA). Morpholinos are sometimes referred to as PMO (phosphorodiamidate morpholino oligo). The word "morpholino" can occur in other chemical names, referring to chemicals containing a six-membered morpholine ring; this article discusses only the Morpholino antisense oligos. Download high resolution version (455x704, 12 KB) File links The following pages link to this file: Morpholino ... Download high resolution version (455x704, 12 KB) File links The following pages link to this file: Morpholino ... Molecular biology is the study of biology at a molecular level. ... In science, a molecule is a group of atoms in a definite arrangement held together by chemical bonds. ... Gene expression, or simply expression, is the process by which a genes DNA sequence is converted into the structures and functions of a cell. ... Oligonucleotides are short sequences of nucleotides (RNA or DNA), typically with twenty or fewer base pairs. ... Antisense molecules interact with complementary strands of nucleic acids, modifying expression of genes. ... Look up nucleic acid in Wiktionary, the free dictionary. ... Ribonucleic acid (RNA) is a nucleic acid polymer consisting of nucleotide monomers, that acts as a messenger between DNA and ribosomes, and that is also responsible for making proteins out of amino acids. ...


Morpholinos are usually used as a research tool for reverse genetics by knocking down gene function. This is achieved by preventing cells from making a targeted protein[1] or by modifying the splicing of pre-mRNA.[2] These molecules have been applied to studies in several model organisms, including mice, zebrafish and frogs.[3] Reverse genetics is an approach to discovering the function of a gene that proceeds in the opposite direction of so called forward genetic screens that are more usual in classical genetics. ... A gene knockdown is either a genetically modified organism that carries one or more genes in its chromosomes that has been made less active or had its expression reduced or is the use of a reagent such as an antisense oligo to decrease expression of a specific gene, copying the... A representation of the 3D structure of myoglobin, showing coloured alpha helices. ... Pre-mRNA (preliminary mRNA) is a single strand of ribonucleic acid (RNA), synthesized from the DNA in the nucleus of a cell by the process transcription. ... A model organism is a species that is extensively studied to understand particular biological phenomena, with the expectation that discoveries made in the organism model will provide insight into the workings of other organisms. ... Feral mouse A mouse (plural mice) is a rodent that belongs to one of numerous species of small mammals. ... The name zebrafish applies to several different kinds of fish with striped bodies considered to resemble a zebra: Brachydanio rerio, also called Danio rerio or the Zebra Danio, is a commonly used model organism in studies of biological development. ... Species Xenopus amieti (volcano clawed frog) Xenopus andrei (Andres clawed frog) Xenopus borealis (Kenyan clawed frog) Xenopus boumbaensis (Mawa clawed frog) Xenopus clivii (Eritrea clawed frog) Xenopus fraseri (Frasers clawed frog) Xenopus gilli (Cape clawed frog) Xenopus laevis (African clawed frog) Xenopus largeni Xenopus longipes (savannah clawed frog...


Morpholinos are also in development as pharmaceutical therapeutics targeted against pathogenic organisms such as Mycobacterium tuberculosis and genetic diseases.[4] These synthetic oligos were conceived by James E. Summerton (Gene Tools, LLC) and developed in collaboration with Dwight D. Weller (AVI BioPharma Inc.). Pharmacology (in Greek: pharmakos (φάρμακον) meaning drug, and logos (λόγος) meaning science) is the study of how substances interact with living organisms to produce a change in function. ... A pathogen or infectious agent is a biological agent that causes disease or illness to its host. ... Binomial name Mycobacterium tuberculosis Zopf 1883 Mycobacterium tuberculosis is the bacterium that causes most cases of tuberculosis[1]. It was first described on March 24, 1882 by Robert Koch, who subsequently received the Nobel Prize in physiology or medicine for this discovery in 1905. ... A genetic disorder or a clinical phenotype. ... Gene Tools, LLC is a limited liability company located in Philomath, Oregon, United States that manufactures Morpholino antisense oligos and delivery reagents[1][2]. Gene Tools was founded in 1997 and began regularly shipping custom-sequence Morpholino oligos in 2000. ... This article or section does not cite any references or sources. ...

Contents

Structure

Morpholinos are synthetic molecules which are the product of a redesign of natural nucleic acid structure.[5] Usually 25 bases in length, they bind to complementary sequences of RNA by standard nucleic acid base-pairing. Structurally, the difference between Morpholinos and DNA is that while Morpholinos have standard nucleic acid bases, those bases are bound to morpholine rings instead of deoxyribose rings and linked through phosphorodiamidate groups instead of phosphates.[5] Replacement of anionic phosphates with the uncharged phosphorodiamidate groups eliminates ionization in the usual physiological pH range, so Morpholinos in organisms or cells are uncharged molecules. Morpholinos are not chimeric oligos; the entire backbone of a Morpholino is made from these modified subunits. Morpholinos are most commonly used as single-stranded oligos, though heteroduplexes of a Morpholino strand and a complementary DNA strand may be used in combination with cationic cytosolic delivery reagents.[6] In chemistry, chemical synthesis is purposeful execution of chemical reactions in order to get a product, or several products. ... In science, a molecule is a group of atoms in a definite arrangement held together by chemical bonds. ... Base pairs, of a DNA molecule. ... The structure of part of a DNA double helix Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions for the development and function of living organisms. ... Morpholine is an organic chemical compound having the chemical formula C4H8NO . ... Deoxyribose Deoxyribose, also known as D-Deoxyribose and 2-deoxyribose, is an aldopentose — a monosaccharide containing five carbon atoms, and including an aldehyde functional group. ... In chemistry, a phosphate is a polyatomic ion or radical consisting of one phosphorus atom and four oxygen. ... An electrostatic potential map of the nitrate ion (NO3−). Areas coloured red are lower in energy than areas colored yellow An ion is an atom or group of atoms which have lost or gained one or more electrons, making them negatively or positively charged. ... The correct title of this article is . ... On the left: nucleotides that forms the DNA and their complementary. ... The cytosol (cf. ...


Function

Morpholinos do not degrade their target RNA molecules, unlike many antisense structural types (e.g. phosphorothioates, siRNA). Instead, Morpholinos act by "steric blocking", binding to a target sequence within an RNA and simply getting in the way of molecules which might otherwise interact with the RNA.[1] Small interfering RNA (siRNA) are a class of 20-25 nucleotide-long RNA molecules that interfere with the expression of genes. ...


Morpholino oligos are often used to investigate the role of a specific mRNA transcript in an embryo. Developmental biologists inject Morpholino oligos into eggs or embryos of zebrafish,[7] African clawed frog (Xenopus),[8] chick,[9] and sea urchin,[10] producing morphant embryos. With appropriate cytosolic delivery systems, Morpholinos are effective in cell culture.[6] Binomial name Danio rerio (Hamilton-Buchanan, 1822) The Zebra Danio or Zebrafish (Brachydanio rerio or Danio rerio) is a tropical fish, commonly kept in aquaria and used for scientific research, belonging to the minnow family (Cyprinidae). ... Species Xenopus amieti (volcano clawed frog) Xenopus andrei (Andres clawed frog) Xenopus borealis (Kenyan clawed frog) Xenopus boumbaensis (Mawa clawed frog) Xenopus clivii (Eritrea clawed frog) Xenopus fraseri (Frasers clawed frog) Xenopus gilli (Cape clawed frog) Xenopus laevis (African clawed frog) Xenopus largeni Xenopus longipes (savannah clawed frog... This article or section does not adequately cite its references or sources. ... Subclasses Euechinoidea Superorder Atelostomata Order Cassiduloida Order Spatangoida (heart urchins) Superorder Diadematacea Order Diadematoida Order Echinothurioida Order Pedinoida Superorder Echinacea Order Arbacioida Order Echinoida Order Phymosomatoida Order Salenioida Order Temnopleuroida Superorder Gnathostomata Order Clypeasteroida (sand dollars) Order Holectypoida Perischoechinoidea Order Cidaroida (pencil urchins) Sea urchins are small spiny sea creatures... An organism which has been treated with a Morpholino antisense oligo to temporarily knock down expression of a targeted gene is called a Morphant. ... Epithelial cells in culture, stained for keratin (red) and DNA (green) Cell culture is the term applied when cells are grown in a synthetic environment. ...


Morpholinos are being developed as pharmaceuticals under the name "NeuGenes" by AVI BioPharma Inc. They have been used in mammals ranging from mice[11] to humans and some are currently being tested in clinical trials as anticancer therapies.[12] NeuGene is a trademark describing Morpholino antisense oligos in development as pharmaceuticals by AVI BioPharma, Inc. ... Feral mouse A mouse (plural mice) is a rodent that belongs to one of numerous species of small mammals. ... Human beings are defined variously in biological, spiritual, and cultural terms, or in combinations thereof. ... In medicine, a clinical trial (synonyms: clinical studies, research protocols, medical research) is the application of the scientific method to human health. ...


Blocking translation

Bound to the 5'-untranslated region of messenger RNA (mRNA), Morpholinos can interfere with progression of the ribosomal initiation complex from the 5' cap to the start codon. This prevents translation of the coding region of the targeted transcript (called "knocking down" gene expression). This is useful experimentally when an investigator wishes to know the function of a particular protein; Morpholinos provide a convenient means of knocking down expression of the protein and learning how that knockdown changes the cells or organism. Some Morpholinos knock down expression so effectively that after degradation of preexisting proteins the targeted proteins become undetectable by Western blot(e.g. figure 1 in:[13]). In eukaryotic genetics, the 5 UTR (read as 5 prime UnTranslated Region) is a particular section of messenger RNA (mRNA). ... Figure 1: Ribosome structure indicating small subunit (A) and large subunit (B). ... Transcript can have several meanings depending on the context used. ... A gene knockdown, is a genetically modified organism that carries one or more genes in its chromosomes that has been made less active or had its expression reduced. ... Gene expression, or simply expression, is the process by which a genes DNA sequence is converted into the structures and functions of a cell. ... A western blot with five vertical lanes, indicating proteins. ...


Modifying pre-mRNA splicing

Morpholinos can interfere with pre-mRNA processing steps, usually by preventing the splice-directing snRNP complexes from binding to their targets at the borders of introns on a strand of pre-RNA. Preventing U1 (at the donor site) or U2/U5 (at the polypyrimidine moiety and acceptor site) from binding can cause modified splicing, commonly leading to exclusions of exons from the mature mRNA. Targeting some splice targets results in intron inclusions, while activation of cryptic splice sites can lead to partial inclusions or exclusions[14]. Targets of U11/U12 snRNPs can also be blocked. Splice modification can be conveniently assayed by reverse-transcriptase polymerase chain reaction (RT-PCR) and is seen as a band shift after gel electrophoresis of RT-PCR products.[2] In genetics, splicing is a modification of genetic information after transcription, in which introns are removed and exons are joined. ... An exon is any region of DNA within a gene, that is transcribed to the final messenger RNA (mRNA) molecule, rather than being spliced out from the transcribed RNA molecule. ... Diagram of the location of introns and exons within a gene. ... RT-PCR (Reverse Transcription-PCR) is a modification of PCR in which an RNA strand is first reverse transcribed into its DNA complement or cDNA, followed by amplification of the resulting DNA using PCR. This can either be a 1 or 2 step process. ... DNA electrophoresis apparatus. ...


Blocking other mRNA sites

Morpholinos have been used to block miRNA activity,[15][16] ribozyme activity,[17] intronic splice silencers,[18] and splice enhancers.[19] U2 and U12 snRNP functions have been inhibited by Morpholinos.[20] Morpholinos targeted to "slippery" mRNA sequences within protein coding regions can induce translational frameshifts.[21] Activities of Morpholinos against this variety of targets suggest that Morpholinos can be used as a general-purpose tool for blocking interactions of proteins or nucleic acids with mRNA. In genetics, a miRNA (micro-RNA) is a form of single-stranded RNA which is typically 20-25 nucleotides long, and is thought to regulate the expression of other genes. ...


Specificity, stability and non-antisense effects

Morpholinos have become a standard knockdown tool in animal embryonic systems, which have a broader range of gene expression than adult cells and can be strongly affected by an off-target interaction. Following initial injections at the single-cell or few-cell stage, Morpholino effects have been measured at least five days later, after most of the processes of organogenesis and differentiation are past, with observed phenotypes consistent with target-gene knockdown. Control oligos with irrelevant sequences usually produce no change in embryonic phenotype, evidence of the Morpholino oligo's sequence-specificity and lack of non-antisense effects. mRNA rescue experiments, involving co-injection of a Morpholino with an mRNA having a modified UTR so it has no Morpholino target, can often restore the wild-type phenotype to the embryos; since the "rescue" mRNA would not affect phenotypic changes due to modulation of off-target gene expression by the Morpholino, this return to wild-type phenotype is further evidence of Morpholino specificity. It has been suggested that embryology be merged into this article or section. ... Drawing of the structure of cork as it appeared under the microscope to Robert Hook from Micrographia which is the origin of the word cell. POOP Cells in culture, stained for keratin (red) and DNA (green). ... Organogenesis is a stage of animal development where the ectoderm, endoderm, and mesoderm are formed. ... Embryonic stem cells differentiate into cells in various body organs. ... Individuals in the mollusk species Donax variabilis show diverse coloration and patterning in their phenotypes. ... It has been suggested that this article or section be merged with scientific control. ... In biology, a wild type is one of the major genotypes of a species that occur in nature, in contrast to induced mutations or artificial cross-breeding. ...


Because of their completely unnatural backbones, Morpholinos are not recognized by cellular proteins. Nucleases do not degrade Morpholinos[22], nor are they degraded in serum or in cells [23]. Morpholinos do not activate toll-like receptors and so they do not activate innate immune responses such as the interferon system or the NF-(kappa)B mediated inflammation response. Morpholinos are not known to modify methylation of DNA. A nuclease is an enzyme capable of cleaving the phosphodiester bonds between the nucleotide subunits of nucleic acids. ... Toll-like receptors (TLRs) are type I transmembrane proteins that serve as a key part of the innate immune system. ... Interferons (IFNs) are natural proteins produced by the cells of the immune system of most vertebrates in response to challenges by foreign agents such as viruses, bacteria, parasites and tumor cells. ... An abscess on the skin, showing the redness and swelling characteristic of inflammation. ... DNA methylation is a type of chemical modification of DNA that can be inherited without changing the DNA sequence. ...


A cause for concern in the use of Morpholinos is the potential for "off target" effects. Up to 18% of morpholinos appear to have non-target related phenotypes including cell death in the central nervous system and somite tissues of zebrafish embryos.[24] Most of these effects have been shown to be due to activation of p53-mediated apoptosis, and can be suppressed by co-injection of an anti-p53 Morpholino along with the experimental Morpholino.[25] It appears that these effects are sequence specific, as 4-base mismatch morpholinos result in a loss of non-target effects. These problems can often be overcome by the use of a second, non-overlapping morpholino or confirmation of the observed phenotypes by use of a mutant strain or dominant negative methods. As mentioned above, rescue of observed phenotypes by overexpression of the gene of interest is, when feasible, a reliable test of specificity of a morpholino.


Intellectual property

Gene Tools, LLC and AVI BioPharma Inc. claim intellectual property on aspects of Morpholino oligo.[26] Gene Tools, LLC is a limited liability company located in Philomath, Oregon, United States that manufactures Morpholino antisense oligos and delivery reagents[1][2]. Gene Tools was founded in 1997 and began regularly shipping custom-sequence Morpholino oligos in 2000. ... This article or section does not cite any references or sources. ... For the 2006 film, see Intellectual Property (film). ...


References

  1. ^ a b Summerton, J (1999). "Morpholino Antisense Oligomers: The Case for an RNase-H Independent Structural Type." (Pubmed). Biochimica et Biophysica Acta 1489: 141-58. 
  2. ^ a b Draper, BW; Morcos, PA, Kimmel, CB (2001). "Inhibition of zebrafish fgf8 pre-mRNA splicing with morpholino oligos: A quantifiable method for gene knockdown." (Pubmed). Genesis 30 (3): 154-6. 
  3. ^ Heasman J (2002). "Morpholino oligos: making sense of antisense?". Dev. Biol. 243 (2): 209-14. PMID 11884031. 
  4. ^ Geller BL (2005). "Antibacterial antisense". Curr. Opin. Mol. Ther. 7 (2): 109-13. PMID 15844617. 
  5. ^ a b Summerton, J; Weller D (1997). "Morpholino Antisense Oligomers: Design, Preparation and Properties." (Pubmed). Antisense & Nucleic Acid Drug Development 7*: 187-95. 
  6. ^ a b Morcos, PA (2001). "Achieving efficient delivery of morpholino oligos in cultured cells." (Pubmed). Genesis 30 (3): 94-102. 
  7. ^ Nasevicius, A; Ekker SC (2000). "Effective targeted gene 'knockdown' in zebrafish." (Pubmed). Nature Genetics 26 (2): 216 - 20. 
  8. ^ Heasman, J; Kofron M, Wylie C (2000). "Beta-catenin signaling activity dissected in the early Xenopus embryo: a novel antisense approach." (Pubmed). Developmental Biology 222: 124-34. 
  9. ^ Kos, R; Reedy MV, Johnson RL, Erickson CA (2001). "The winged-helix transcription factor FoxD3 is important for establishing the neural crest lineage and repressing melanogenesis in avian embryos." (Pubmed). Development 128 (8): 1467-79. 
  10. ^ Howard, EW; Newman LA, Oleksyn DW, Angerer RC, Angerer LM (2001). "SpKrl: a direct target of (beta)-catenin regulation required for endoderm differentiation in sea urchin embryos." (Pubmed). Development 128 (3): 365-75. 
  11. ^ Coonrod, SA; Bolling LC, Wright PW, Visconti PE, Herr JC (2001). "A morpholino phenocopy of the mouse MOS mutation." (Pubmed). Genesis 30 (3): 198-200. 
  12. ^ Devi GR, Beer TM, Corless CL, Arora V, Weller DL, Iversen PL (2005). "In vivo bioavailability and pharmacokinetics of a c-MYC antisense phosphorodiamidate morpholino oligomer, AVI-4126, in solid tumors". Clin. Cancer Res. 11 (10): 3930-8. PMID 15897595. 
  13. ^ Stancheva, I; Collins AL, Van den Veyver IB, Zoghbi H, Meehan RR (2003). "A mutant form of MeCP2 protein associated with human Rett syndrome cannot be displaced from methylated DNA by notch in Xenopus embryos." (Pubmed). Mol Cell 12 (2): 425-35. 
  14. ^ Morcos, PA (2007). "Achieving targeted and quantifiable alteration of mRNA splicing with Morpholino oligos." (Pubmed). Biochem Biophys Res Commun. 
  15. ^ Kloosterman, WP; Wienholds E, Ketting RF, Plasterk RH (2004). "Substrate requirements for let-7 function in the developing zebrafish embryo." (Pubmed). Nucleic Acids Res 32 (21): 6284-91. 
  16. ^ Flynt, AS; Li N, Thatcher EJ, Solnica-Krezel L, Patton JG (2007). "Zebrafish miR-214 modulates Hedgehog signaling to specify muscle cell fate." (Pubmed). Nature Genetics 39: 259-263. 
  17. ^ Yen, L; Svendsen J, Lee JS, Gray JT, Magnier M, Baba T, D'Amato RJ, Mulligan RC (2004). "Exogenous control of mammalian gene expression through modulation of RNA self-cleavage." (Pubmed). Nature 431 (7007): 471-6. 
  18. ^ Bruno, IG; Jin W, Cote GJ (2004). "Correction of aberrant FGFR1 alternative RNA splicing through targeting of intronic regulatory elements." (Pubmed). Hum Mol Genet 3 (20): 2409-20. 
  19. ^ Vetrini, F; Tammaro R, Bondanza S, Surace EM, Auricchio A, De Luca M, Ballabio A, Marigo V (2006). "Aberrant splicing in the ocular albinism type 1 gene (OA1/GPR143) is corrected in vitro by morpholino antisense oligonucleotides." (Pubmed). Hum Mutat 27 (5): 420-6. 
  20. ^ Matter, N; Konig H (2005). "Targeted 'knockdown' of spliceosome function in mammalian cells." (Pubmed). Nucleic Acids Res 33 (4): e41. 
  21. ^ Howard, MT; Gesteland RF, Atkins JF* (2004). "Efficient stimulation of site-specific ribosome frameshifting by antisense oligonucleotides." (Pubmed). RNA 10 (10): 1653-61. 
  22. ^ Hudziak, RM; Barofsky E, Barofsky DF, Weller DL, Huang SB, Weller DD (1996). "Resistance of morpholino phosphorodiamidate oligomers to enzymatic degradation." (Pubmed). Antisense Nucleic Acid Drug Dev 6 (4): 267-72. 
  23. ^ Youngblood, DS; Hatlevig SA, Hassinger JN, Iversen PL, Moulton HM (2007). "Stability of cell-penetrating peptide-morpholino oligomer conjugates in human serum and in cells." (Pubmed). Bioconjug Chem. 18 (1): 50-60. 
  24. ^ Ekker, SC; Larson JD (2001). "Morphant Technology in Model Developmental Systems." (Pubmed). Genesis 30 (3): 89-93. 
  25. ^ Robu, ME; Larson JD, Nasevicius A, Beiraghi S, Brenner C, Farber SA, Ekker SC (2007). "p53 activation by knockdown technologies." (Pubmed). PLoS Genetics in press. 
  26. ^ Gene Tools, LLC [1]

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Further reading

  • Wiley-Liss, Inc. Special Issue: Morpholino Gene Knockdowns of genesis Volume 30, Issue 3 Pages 89-200 (July 2001). A special issue of Genesis, comprised of a series of peer-reviewed short papers utilizing morpholino knock downs of gene function in various animal and tissue culture systems.
  • Moulton, Jon (2007), "Using Morpholinos to Control Gene Expression (Unit 4.30)", in Beaucage, Serge, Current Protocols in Nucleic Acid Chemistry, New Jersey: John Wiley & Sons, Inc., ISBN 978-0-471-24662-6 


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Major Families of Biochemicals
Peptides | Amino acids | Nucleic acids | Carbohydrates | Lipids | Terpenes | Carotenoids | Tetrapyrroles | Enzyme cofactors | Steroids | Flavonoids | Alkaloids | Polyketides | Glycosides
Analogues of nucleic acids: Types of Nucleic Acids Analogues of nucleic acids:
Nucleobases: Purine (Adenine, Guanine) | Pyrimidine (Uracil, Thymine, Cytosine)
Nucleosides: Adenosine/Deoxyadenosine | Guanosine/Deoxyguanosine | Uridine | Thymidine | Cytidine/Deoxycytidine
Nucleotides: monophosphates (AMP, UMP, GMP, CMP) | diphosphates (ADP, UDP, GDP, CDP) | triphosphates (ATP, UTP, GTP, CTP) | cyclic (cAMP, cGMP, cADPR)
Deoxynucleotides: monophosphates (dAMP, TMP, dGMP, dCMP) | diphosphates (dADP, TDP, dGDP, dCDP) | triphosphates (dATP, TTP, dGTP, dCTP)
Ribonucleic acids: RNA | mRNA | piRNA | tRNA | rRNA | ncRNA | sgRNA | shRNA | siRNA | snRNA | miRNA | snoRNA | LNA
Deoxyribonucleic acids: DNA | mtDNA | cDNA | plasmid | Cosmid | BAC | YAC | HAC
Analogues of nucleic acids: GNA | PNA | TNA | morpholino

  Results from FactBites:
 
Morpholino references (15432 words)
Amantana A, Iversen PL. Pharmacokinetics and biodistribution of phosphorodiamidate morpholino antisense oligomers.
Morpholino phenocopies of sqt, oep, and ntl mutations.
Morpholino phenocopies of the bmp2b/swirl and bmp7/snailhouse mutations.
Morpholino Antisense Oligos - Gene Tools, LLC (886 words)
Morpholinos can be delivered into cultured cells by a variety of methods, including scrape-loading of adherent cells, electroporation, and even microinjection.
A Morpholino oligo is radically different from natural nucleic acids, with morpholine rings replacing the ribose or deoxyribose sugar moieties and non-ionic phosphorodiamidate linkages replacing the anionic phosphates of DNA and RNA.
Because the backbone of the Morpholino oligo is not recognized by any cellular enzymes or signaling proteins, it is completely stable to nucleases and does not trigger an innate immune response through the toll-like receptors.
  More results at FactBites »

 
 

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