Development of Gene‐Targeted Polypyridyl Triplex‐Forming Oligonucleotide Hybrids

Fantoni, Nicolò Zuin; McGorman, Bríonna; Molphy, Zara; Singleton, Daniel; Walsh, Sarah; El‐Sagheer, Afaf H.; McKee, Vickie; Brown, Tom; Kellett, Andrew

doi:10.1002/cbic.202000408

Cited by 18 publications

(27 citation statements)

References 54 publications

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“…[21,25] To help address this limitation, we recently developed discrete and targeted mononuclear copper(II) complexes using caged tris-(2-pyridyl-methyl)amine (TMPA) or di-(2pycolylamine) (DPA) ligands and explored their cutting mechanisms using radicalt rapping experiments. [26] Oxidativec utting by the Cu II -phenanthrene TFO hybrids reported here are, most likely,m ediated through as imilar superoxide (O 2 C À )r adical mechanism that is outlined in Figure 8-II.…”

Section: Discussionmentioning

confidence: 85%

A Click Chemistry Approach to Developing Molecularly Targeted DNA Scissors

Lauria

Slator

McKee

et al. 2020

Chemistry A European J

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Nucleic acid click chemistry was used to prepare a family of chemically modified triplex forming oligonucleotides (TFOs) for application as a new gene‐targeted technology. Azide‐bearing phenanthrene ligands—designed to promote triplex stability and copper binding—were ‘clicked’ to alkyne‐modified parallel TFOs. Using this approach, a library of TFO hybrids was prepared and shown to effectively target purine‐rich genetic elements in vitro. Several of the hybrids provide significant stabilisation toward melting in parallel triplexes (>20 °C) and DNA damage can be triggered upon copper binding in the presence of added reductant. Therefore, the TFO and ‘clicked’ ligands work synergistically to provide sequence‐selectivity to the copper cutting unit which, in turn, confers high stabilisation to the DNA triplex. To extend the boundaries of this hybrid system further, a click chemistry‐based di‐copper binding ligand was developed to accommodate designer ancillary ligands such as DPQ and DPPZ. When this ligand was inserted into a TFO, a dramatic improvement in targeted oxidative cleavage is afforded.

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Section: Discussionmentioning

confidence: 85%

A Click Chemistry Approach to Developing Molecularly Targeted DNA Scissors

Lauria

Slator

McKee

et al. 2020

Chemistry A European J

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“…Recently, the ClickGene consortium [229] applied click chemistry to conjugate various copper‐based AMNs to triplex‐forming oligonucleotides. Using this strategy, wide libraries of TFO‐targeted AMNs were efficiently generated and evaluated for their copper‐complex structure‐activity relationship and sequence‐directed oxidative damage [230–232] . The artificial nuclease Clip–Phen machinery was coupled by Hocek and co‐workers to different positions (i. e., 5′‐end, 36 a and 36 b ; 3′‐end, 36 c ; or internal, 36 d – f ) of TFO probes using various linkers differing in length, flexibility and polarity (Figure 14).…”

Section: Gene Editingmentioning

confidence: 99%

“… A) Clicked AMN−TFO hybrids developed by Hocek and co‐workers ( 36 ) [230] and Kellett and co‐workers ( 37 – 43 ) [231,232] as sequence–targeted gene‐knockout agents. B) Alkyne spacers used to conjugate the AMN to the oligonucleotide strand.…”

Section: Gene Editingmentioning

confidence: 99%

“…In parallel, two studies carried out by Kellett and co‐workers focused on conjugating either phenanthrene ( 37 – 41 ) [231] or TPMA ( 42 , 43 ) [232] derivatives (Figure 14) to TFOs of various length by click chemistry. The extended aromaticity of phenanthrene dsDNA intercalators covalently attached to the TFO significantly stabilized the triplex structure upon hybridization and increased its melting temperature with Δ T M up to 22 °C [231] .…”

Section: Gene Editingmentioning

confidence: 99%

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DNA‐Targeted Metallodrugs: An Untapped Source of Artificial Gene Editing Technology

2021

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DNA binding metal complexes are synonymous with anticancer drug discovery. Given the array of structural and chemical reactivity properties available through careful design, metal complexes have been directed to bind nucleic acid structures through covalent or noncovalent binding modes. Several recognition modes – including crosslinking, intercalation, and oxidation – are central to the clinical success of broad‐spectrum anticancer metallodrugs. However, recent progress in nucleic acid click chemistry coupled with advancement in our understanding of metal complex–nucleic acid interactions has opened up new avenues in genetic engineering and targeted therapies. Several of these applications are enabled by the hybridisation of oligonucleotide or polyamine probes to discrete metal complexes, which facilitate site‐specific reactivity at the nucleic acid interface under the guidance of the probe. This Review focuses on recent advancements in hybrid design and, by way of an introduction to this topic, we provide a detailed overview of nucleic acid structures and metal complex–nucleic acid interactions. Our aim is to provide readers with an insight on the rational design of metal complexes with DNA recognition properties and an understanding of how the sequence‐specific targeting of these interactions can be achieved for gene engineering applications.

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“…39 Several intercalator-type modifications have been introduced in TFOs leading to formation of stable parallel triplexes at neutral pH. [40][41][42][43][44][45][46][47][48][49][50][51] Modifications of the DNA/RNA phosphate backbone, especially charge neutral modifications, have gained attention in recent years because such modifications not only improve the nuclease resistance of ONs, but also enhance their affinity towards complementary DNA/RNA/dsDNA as well as their cell permeability. The lack of a negatively charged backbone also improved the binding of PNA to DNA or RNA strands.…”

Section: Introductionmentioning

confidence: 99%

DNA with zwitterionic and negatively charged phosphate modifications: formation of DNA triplexes, duplexes and cell permeability studies

Su¹,

Bayarjargal²,

Hale³

et al. 2020

Preprint

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Two phosphate modifications were introduced into the DNA backbone using Staudinger reaction between the 3’,5’-dinucleoside β-cyanoethyl phosphite triester formed during DNA synthesis and the sulfonyl azides, 4-(azidosulfonyl)-N,N,N-trimethylbutan-1-aminium iodide (N+ azide) or p-toluenesulfonyl (tosyl or Ts) azide, to provide either a zwitterionic phosphoramidate with N+ modification or a negatively charged phosphoramidate for Ts- modification in the DNA sequence. Incorporation of these N+ and Ts- modifications led to the formation of thermally stable parallel DNA triplexes, regardless of the number of modifications incorporated into the oligodeoxynucleotides (ONs). For both N+ and Ts- modified ONs, the antiparallel duplexes formed with complementary RNA were more stable than those formed with complementary DNA (except for ONs where the modification is in the middle of the sequence). Incorporation of N+ modifications led to the formation of duplexes whose thermal stability was less dependent on ionic strength than native DNA duplexes. Thermodynamic analysis of melting curves revealed that it is a reduction in unfavourable entropy, despite the decrease in favourable enthalpy, which is responsible for the stabilisation of duplexes with N+ modification. N+ ONs also demonstrated greater resistance to nuclease digestion by snake venom phosphodiesterase I than the corresponding Ts-ONs. Cell permeability studies showed that Ts- ONs diffuse into the nucleus of mouse fibroblast NIH3T3 cells without the need for transfection reagents. In contrast, N+ ONs were concentrated in vesicles within the cytoplasm. These results indicate that both N+ and Ts- modified ONs are promising for various in vivo applications.

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Development of Gene‐Targeted Polypyridyl Triplex‐Forming Oligonucleotide Hybrids

Cited by 18 publications

References 54 publications

A Click Chemistry Approach to Developing Molecularly Targeted DNA Scissors

A Click Chemistry Approach to Developing Molecularly Targeted DNA Scissors

DNA‐Targeted Metallodrugs: An Untapped Source of Artificial Gene Editing Technology

DNA with zwitterionic and negatively charged phosphate modifications: formation of DNA triplexes, duplexes and cell permeability studies

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