A PNA-DNA linker synthesis of N-((4,4′-dimethoxytrityloxy)ethyl)-N-(thymin-1-ylacetyl)glycine

Petersen, Kenneth H.; Jensen, Dorte K.; Egholm, Michael; Nielsen, Peter E.; Buchardt, Ole

doi:10.1016/0960-894x(95)00177-u

Cited by 43 publications

(35 citation statements)

References 9 publications

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“…Modified PNAs should be designed, synthesized, and tested to find DNA-PNA and PNA-PNA hybrids able to generate highly stable complexes with NF-B, in order to obtain efficient decoy activity. Of interest, from this point of view, are the recently described PNA-DNA chimeras (58) or the structural variant PHONA, in which the peptide bond is replaced by a phosphonic acid ester bridge (56).…”

Section: Discussionmentioning

confidence: 99%

Interaction of the Human NF-κB p52 Transcription Factor with DNA-PNA Hybrids Mimicking the NF-κB Binding Sites of the Human Immunodeficiency Virus Type 1 Promoter

Mischiati¹,

Borgatti²,

Bianchi³

et al. 1999

Journal of Biological Chemistry

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We determined whether peptide nucleic acids (PNAs) are able to interact with NF-B p52 transcription factor. The binding of NF-B p52 to DNA-DNA, DNA-PNA, PNA-DNA, and PNA-PNA hybrid molecules carrying the NF-B binding sites of human immunodeficiency type 1 long terminal repeat was studied by (i) biospecific interaction analysis (BIA) using surface plasmon resonance technology, (ii) electrophoretic mobility shift, (iii) DNase I footprinting, and (iv) UV cross-linking assays. Our results demonstrate that NF-B p52 does not efficiently bind to PNA-PNA hybrids. However, a DNA-PNA hybrid molecule was found to be recognized by NF-B p52, although the molecular complexes generated exhibited low stability. From the theoretical point of view, our results suggest that binding of NF-B p52 protein to target DNA motifs is mainly due to contacts with bases; interactions with the DNA backbone are, however, important for stabilization of the protein-DNA complex. From the practical point of view, our results suggest that DNA-PNA hybrid can be recognized by NF-B p52 protein, although with an efficiency lower than DNA-DNA NF-B target molecules; therefore, our results should encourage studies on modified PNAs in order to develop potential agents for the decoy approach in gene therapy.It is well established that both constitutive and tissue-specific regulation of gene expression is operated at the transcriptional level by the interaction between nuclear proteins (transcription factors) and promoter regions containing DNA elements (transcription signals) that exhibit specific nucleotide sequences (1-4). Several reviews reporting the nucleotide sequences of transcription signals and the relative binding proteins have been published (5-7). The requirement of protein-

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Section: Discussionmentioning

confidence: 99%

Interaction of the Human NF-κB p52 Transcription Factor with DNA-PNA Hybrids Mimicking the NF-κB Binding Sites of the Human Immunodeficiency Virus Type 1 Promoter

Mischiati¹,

Borgatti²,

Bianchi³

et al. 1999

Journal of Biological Chemistry

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“…monomeric building blocks. The successful synthesis of PNA/ DNA chimeras by the block condensation approach is fraught with difficulties, which include insufficient solubility and low yields, [77] and has not been realized so far. The on-line solidphase synthesis strategy has proven to be the most successful and flexible method for the synthesis of PNA/DNA chimeras.…”

Section: Synthesis Of Pna/dna Chimerasmentioning

confidence: 99%

PNA: Synthetic Polyamide Nucleic Acids with Unusual Binding Properties

Uhlmann¹,

Peyman²,

Breipohl³

et al. 1998

Angewandte Chemie International Edition

397

217

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The astonishing discovery that peptide nucleic acids (PNAs, B=nucleobase), in spite of their drastic structural difference to natural DNA, are better nucleic acid mimetics than many other oligonucleotides has resulted in an explosion of research into this class of compounds. The synthesis, physical properties, and biological interactions of PNAs as well as their chimeras with DNA and RNA are summarized here.

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“…In this strategy the monomethoxytrityl (MeOTr) group is used for the temporary protection of the backbone amino function and acyl protecting groups are used for the protection of the exocyclic amino functions of the nucleobases [24][25][26][27]. The MeOTr is removed under mild conditions (3% trichloroacetic acid in dichloromethane), and the nucleobase protecting groups are removed using concentrated aqueous ammonia.…”

mentioning

confidence: 99%

“…The synthesis of PNA-DNA chimeras 3 and 4 were performed using the methodology described previously [24][25][26][27]. In this strategy the monomethoxytrityl (MeOTr) group is used for the temporary protection of the backbone amino function and acyl protecting groups are used for the protection of the exocyclic amino functions of the nucleobases [24][25][26][27].…”

mentioning

confidence: 99%

“…These conditions are similar to those employed in DNA synthesis allowing the preparation of molecules carrying both PNA and DNA moieties. The connexion of the PNA and the DNA part was done using a thymine PNA linker molecule carrying an OH protected with the MeOTr group [25,27,28]. The oligonucleotide part was assembled on an automatic DNA synthesizer using standard protocols.…”

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confidence: 99%

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Hybridization and Melting Behavior of Peptide Nucleic Acid (PNA) Oligonucleotide Chimeras Conjugated to Gold Nanoparticles

Murphy

Redmond

Torre

et al. 2004

Helvetica Chimica Acta

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In this study, Peptide Nucleic Acids (PNA) and PNA-DNA chimeras carrying thiol groups were used for surface functionalization of gold nanoparticles. Conjugation of PNA to citrate stabilized gold nanoparticles destabilized the nanoparticles causing them to precipitate. Addition of a tail of glutamic acid to the PNA prevented destabilisation of the nanoparticles but resulted in loss of interaction with complementary sequences.Importantly, PNA-DNA chimeras gave stable conjugates with gold nanoparticles. The hybridisation and melting properties of complexes formed from chimera-nanoparticle conjugates and oligonucleotide-nanoparticle conjugates are described for first time.Similar to oligonucleotide-nanoparticle conjugates, conjugates with PNA-DNA chimeras gave sharper and more defined melting profiles than those obtained using unmodified oligonucleotides. In addition, mismatch discrimination was found to be more efficient than with unmodified oligonucleotides

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A PNA-DNA linker synthesis of N-((4,4′-dimethoxytrityloxy)ethyl)-N-(thymin-1-ylacetyl)glycine

Cited by 43 publications

References 9 publications

Interaction of the Human NF-κB p52 Transcription Factor with DNA-PNA Hybrids Mimicking the NF-κB Binding Sites of the Human Immunodeficiency Virus Type 1 Promoter

Interaction of the Human NF-κB p52 Transcription Factor with DNA-PNA Hybrids Mimicking the NF-κB Binding Sites of the Human Immunodeficiency Virus Type 1 Promoter

PNA: Synthetic Polyamide Nucleic Acids with Unusual Binding Properties

Hybridization and Melting Behavior of Peptide Nucleic Acid (PNA) Oligonucleotide Chimeras Conjugated to Gold Nanoparticles

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