Extended Target Sequence Specificity of PNA–Minor‐Groove Binder Conjugates

Nielsen, Peter E.; Frederiksen, Karin; Behrens, Carsten

doi:10.1002/cbic.200400251

Cited by 9 publications

(4 citation statements)

References 28 publications

(28 reference statements)

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“…Indeed, we observe only limited differences of binding efficiency when targeting decamer, dodecamer and pentadecamer dsDNA targets by a pentadecamer homopyrimidine PNA via helix invasion (unpublished data). Such extended dsDNA sequences may, however, be targeted using modular constructs containing PNA oligomer conjugated to small molecule DNA binding agents such as the minor groove binder Hoechst ( 39 ). In this approach, the sequence preference of the minor groove binder selects a subset of targets via equilibrium interactions with its own target, which is followed by PNA helix invasion at sites that contain an adjacent PNA target.…”

Section: Discussionmentioning

confidence: 99%

Structural diversity of target-specific homopyrimidine peptide nucleic acid–dsDNA complexes

Bentin¹,

Hansen²,

Nielsen³

2006

Nucleic Acids Research

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Sequence-selective recognition of double-stranded (ds) DNA by homopyrimidine peptide nucleic acid (PNA) oligomers can occur by major groove triplex binding or by helix invasion via triplex P-loop formation. We have compared the binding of a decamer, a dodecamer and a pentadecamer thymine–cytosine homopyrimidine PNA oligomer to a sequence complementary homopurine target in duplex DNA using gel-shift and chemical probing analyses. We find that all three PNAs form stable triplex invasion complexes, and also conventional triplexes with the dsDNA target. Triplexes form with much faster kinetics than invasion complexes and prevail at lower PNA concentrations and at shorter incubation times. Furthermore, increasing the ionic strength strongly favour triplex formation over invasion as the latter is severely inhibited by cations. Whereas a single triplex invasion complex is formed with the decameric PNA, two structurally different target-specific invasion complexes were characterized for the dodecameric PNA and more than five for the pentadecameric PNA. Finally, it is shown that isolated triplex complexes can be converted to specific invasion complexes without dissociation of the Hoogsteen base-paired triplex PNA. These result demonstrate a clear example of a ‘triplex first’ mechanism for PNA helix invasion.

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Section: Discussionmentioning

confidence: 99%

Structural diversity of target-specific homopyrimidine peptide nucleic acid–dsDNA complexes

Bentin¹,

Hansen²,

Nielsen³

2006

Nucleic Acids Research

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“…Although no clear structure/activity relationships are apparent from the present results, it is noteworthy that both 9-aminoacridine and “Hoechst” which are the most active ligands in terms of uptake potentiation are also nucleic acid binding ligands. Furthermore, dsDNA targeted PNA oligomers conjugated to acridine or Hoechst have superior properties that can be exploited in the discovery of antigene agents ( , ). Therefore, these ligands may serve a dual role for PNA activity.…”

Section: Discussionmentioning

confidence: 99%

Cellular Delivery of Polyheteroaromate−Peptide Nucleic Acid Conjugates Mediated by Cationic Lipids

2005

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In the search of facile and efficient methods for PNA cellular delivery, we have tested a series of PNA conjugates based on (hetero) aromatic, lipophilic compounds such as 9-aminoacridine, benzimidazoles, carbazole, anthraquinone, porphyrine, psoralen, pyrene, and phenyl-bis-benzimidazole ("Hoechst"). These chemically modified PNAs were delivered to cultured pLuc705HeLa cells mediated by cationic liposomes (LipofectAMINE or LiofectAMINE2000), and their nuclear delivery was inferred from induced luciferase activity as a consequence of pre-mRNA splicing correction by the antisense-PNA. PNAs modified with 9-aminoacridine, "Hoechst", or acetyl-"Hoechst" showed highest antisense activities (while unmodified PNA failed to show any significant antisense activity). In particular, bis-acridine-conjugated PNA showed nearly 60% splicing correction at 250 nM concentration in combination with LipofectAMINE2000. Interestingly, relative differences between the derivatives were observed when LipofectAMINE was used as compared to LipofectAMINE2000, but in general the latter yielded the higher antisense activity. The most active modifications of these PNA constructs were further tested for antisense down-regulation of luciferase in p53R cells in order to evaluate the cytoplasmic activity (uptake) of the PNAs. A dose-dependent down regulation of luciferase was demonstrated also in this system. The PNA conjugated to acetyl-Hoechst caused a reduction of luciferase activity to less than 40% of the control at a concentration of 1 muM. These results indicate that conjugation of (hetero) polyaromatic compounds to PNA can dramatically improve liposome-mediated cellular delivery both to cytoplasm as well as to the nucleus. However, no clear structure/activity relations are apparent from the present results, except that both 9-aminoacridine and "Hoechst" are also nucleic acid binding ligands.

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“…These types of conjugates have potential for developing transcription factor inhibitor. A deoxynucleic guanidine (DNG)−Hoechst 33258 conjugate and PNA−bisbenzimidazole conjugate have also been used to stabilize triple helix and double helix , . It has been reported that minor groove binders are comparable with the intercalators in the degree of stabilization of the triple helix, especially when two ligand molecules are attached in a parallel orientation to the same terminal phosphate of a triplex-forming ODN .…”

Section: Triple Helicesmentioning

confidence: 99%

Groove Binding Ligands for the Interaction with Parallel-Strandedps-Duplex DNA and Triplex DNA

Jain

Bhattacharya

2010

Bioconjugate Chem.

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DNA adopts different conformations not only based on novel base pairs, but also with different chain polarities. Besides several duplex structures (A, B, Z, parallel stranded (ps)-DNA, etc.), DNA also forms higher-order structures like triplex, tetraplex, and i-motif. Each of these structures has its own biological significance. The ps-duplexes have been found to be resistant to certain nucleases and endonucleases. Molecules that promote triple-helix formation have significant potential. These investigations have many therapeutic advantages which may be useful in the regulation of the expression of genes responsible for certain diseases by locking either their transcription (antigene) or translation (antisense). Each DNA minor groove binding ligand (MGBL) interacts with DNA through helical minor groove recognition in a sequence-specific manner, and this interferes with several DNA-associated processes. Incidentally, these ligands interact with some non-B-DNA and with higher-order DNA structures including ps-DNA and triplexes. While the design and recognition of minor grooves of duplex DNA by specific MGBLs have been a topic of many reports, limited information is available on the binding behavior of MGBLs with nonduplex DNA. In this review, we summarize various attempts of the interaction of MGBLs with ps-DNA and DNA triplexes.

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Extended Target Sequence Specificity of PNA–Minor‐Groove Binder Conjugates

Cited by 9 publications

References 28 publications

Structural diversity of target-specific homopyrimidine peptide nucleic acid–dsDNA complexes

Structural diversity of target-specific homopyrimidine peptide nucleic acid–dsDNA complexes

Cellular Delivery of Polyheteroaromate−Peptide Nucleic Acid Conjugates Mediated by Cationic Lipids

Groove Binding Ligands for the Interaction with Parallel-Strandedps-Duplex DNA and Triplex DNA

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