Automated Chemical Synthesis of PNA and PNA-DNA Chimera on a Nucleic Acid Synthesizer

Vinayak, Ravi; Laan, Alexander C. van der; Brill, Rick; Otteson, Ken; Andrus, Alex; Kuyl‐Yeheskiely, E.; Boom, Jacques H. van

doi:10.1080/07328319708006248

Cited by 13 publications

(18 citation statements)

References 8 publications

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“…Another promising modification is the introduction of peptide nucleic acid (PNA) units into the nucleic acid backbone leading to PNA-DNA hybrids, the so-called PNA-DNA chimeras [108,109]. In the PNA, a 2-aminoethylglycine linkage replaces the normal sugar-phosphate backbone and the bases are attached to the backbone by methylene carbonyl groups as shown in Fig.…”

Section: Modified Aptamersmentioning

confidence: 99%

Quadruplex-Forming Oligonucleotides as Tools in Anticancer Therapy and Aptamers Design: Energetic Aspects

Petraccone

Barone²,

Giancola³

2005

CMCACA

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Recent investigations on the G-quadruplex motif propose a new strategy for the making of antitumour drugs. Quadruplex-drug complexes have been suggested to inhibit telomerase activity; further, aptamers based on the quadruplex motif have been proved useful as tools aimed at binding and inhibiting particular proteins, thus serving as pharmaceutically active agents. However, the design of new aptamers is difficult because many factors affecting their activity and stability have not still been clarified. The knowledge of the energetics of quadruplex formation is a crucial point in view of their potential therapeutic utilization both as targets as well as therapeutic agents. In this review the energetic aspects of both quadruplex assembly and quadruplex-ligand interactions are discussed together with a summary of recent studies on physico-chemical properties in solution of quadruplex structures obtained from synthetic aptamers, including PNA-DNA chimeras.

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Section: Modified Aptamersmentioning

confidence: 99%

Quadruplex-Forming Oligonucleotides as Tools in Anticancer Therapy and Aptamers Design: Energetic Aspects

Petraccone

Barone²,

Giancola³

2005

CMCACA

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“…The assembled PNA fragments ( Table 2, IVϪVII) were detached from the solid support and the nucleobases deprotected by ammonolysis. [32] The oligomers were then purified by HPLC and analyzed by mass spectrometry.…”

Section: Resultsmentioning

confidence: 99%

A Novel N-(Pyrrolidinyl-2-methyl)glycine-Based PNA with a Strong Preference for RNA over DNA

Slaitas

Yeheskiely

2002

Eur. J. Org. Chem.

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A novel, N-(pyrrolidinyl-2-methyl)glycine-based (Pmgbased) PNA is introduced. The synthesis of the backbone was accomplished in good yield, starting from prolinol. Thymine (S)-and (R)-Pmg and adenine-and cytosine-derived (R)-Pmg monomers were prepared. Five different fragments − two with either the (R) or the (S) isomer of the thymine Pmg monomer, two oligomers with two consecutive (R)-or (S)-thymine Pmg units, and fully modified (R)-Pmg decamer − were assembled on a solid support. UV thermal melting experiments with complementary DNA and RNA were performed in order to determine the effects of conformational restriction, steric hindrance, and chirality on the

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“…After the last elongation step, the oligomers were cleaved from the solid support and deprotected by treatment with 1.5 mL methanolic ammonia at 50 °C for 16 h [34].…”

Section: Methodsmentioning

confidence: 99%

Molecular interactions with nuclear factor κB (NF‐κB) transcription factors of a PNA–DNA chimera mimicking NF‐κB binding sites

Romanelli¹,

Pedone²,

Saviano³

et al. 2001

European Journal of Biochemistry

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The decoy approach against nuclear factor kB (NF-kB) is a useful tool to alter NF-kB dependent gene expression using synthetic oligonucleotides (ODNs) carrying NF-kB specific cis-elements. Unfortunately, ODNs are not stable and need to be extensively modified to be used in vivo or ex vivo. We have previously evaluated the possible use of peptide nucleic acids (PNAs) as decoy molecules. The backbone of PNAs is composed of N-(2-aminoethyl)glycine units, rendering these molecules resistant to both nucleases and proteases. We found that the binding of NF-kB transcription factors to PNAs was either very low (binding to PNA-PNA hybrids) or exhibited low stability (binding to PNA-DNA hybrids). The main consideration of the present paper was to determine whether PNA-DNA chimeras mimicking NF-kB binding sites are capable of stable interactions with proteins belonging to the NF-kB family. Molecular modeling was employed for the design of PNA -DNA chimeras; prediction of molecular interactions between chimeras and NF-kB nuclear proteins were investigated by molecular dynamics simulations, and interactions between PNA -DNA chimeras and NF-kB proteins were studied by gel shifts. We found significant differences between the structure of duplex NF-kB PNA-DNA chimera and duplex NF-kB DNA-DNA. However, it was found that these differences do not prevent the duplex PNA -DNA chimera from binding to NF-kB transcription factors, being able to suppress the molecular interactions between HIV-1 LTR and p50, p52 and nuclear factors from B-lymphoid cells. Therefore, these results demonstrate that the designed NF-kB DNA-PNA chimeras could be used for a decoy approach in gene therapy.

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Automated Chemical Synthesis of PNA and PNA-DNA Chimera on a Nucleic Acid Synthesizer

Cited by 13 publications

References 8 publications

Quadruplex-Forming Oligonucleotides as Tools in Anticancer Therapy and Aptamers Design: Energetic Aspects

Quadruplex-Forming Oligonucleotides as Tools in Anticancer Therapy and Aptamers Design: Energetic Aspects

A Novel N-(Pyrrolidinyl-2-methyl)glycine-Based PNA with a Strong Preference for RNA over DNA

Molecular interactions with nuclear factor κB (NF‐κB) transcription factors of a PNA–DNA chimera mimicking NF‐κB binding sites

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