Molecular interactions between nuclear factor κB (NF-κB) transcription factors and a PNA-DNA chimera mimicking NF-κB binding sites(431 views) Romanelli A, Pedone C, Saviano M, Bianchi N, Borgatti M, Mischiati C, Gambari R
Keywords: Aids, Nf-κb, Peptide Nucleic Acids, Pna-Dna Chimeras, Transcription Factors, Glycine Derivative, Hybrid Protein, Immunoglobulin Enhancer Binding Protein, Isoprotein, Nuclear Factor, Oligonucleotide, Protein P50, Proteinase, Article, Binding Site, Gene Expression, Gene Therapy, Human Immunodeficiency Virus 1, Long Terminal Repeat, Lymphoid Cell, Molecular Dynamics, Molecular Interaction, Molecular Model, Prediction, Priority Journal, Protein Determination, Protein Protein Interaction, Protein Stability, Protein Structure, Simulation, Animals, Circular Dichroism, Drug Stability, Hiv-1, Macromolecular Substances, Nf-Kappa B, Nucleic Acid Conformation, Protein Conformation, Recombinant Fusion Proteins, Thermodynamics,
Affiliations: *** IBB - CNR ***
Biocrystallography Research Center, CNR, Ferrara University, Napoli, Italy
Department of Biochemistry and Molecular Biology, Ferrara University, Ferrara, Italy
Biotechnology Centre, Ferrara University, Ferrara, Italy
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Kozlov, I. A., Kubareva, E. A., Ivanovskaya, M. G., Shabarova, Z. A., Design of new reagents on the base of DNA duplexes for irreversible inhibition of transcription factor NF-kappa B (1997) Antisense Nucleic Acid Drug Dev., 7, pp. 279-289
Cho-Chung, Y. S., Park, Y. G., Nesterova, M., Lee, Y. N., Cho, Y. S., CRE-decoy oligonucleotide-inhibition of gene expression and tumor growth (2000) Mol. Cell. Biochem., 212, pp. 29-34
Lee, Y. N., Park, Y. G., Choi, Y. H., Cho, Y. S., Cho-Chung, Y. S., CRE-transcription factor decoy oligonucleotide inhibition of MCF-7 breast cancer cells: Cross-talk with p53 signaling pathway (2000) Biochemistry, 39, pp. 4863-4868
Khaled, A. R., Butfiloski, E. J., Sobel, E. S., Schiffenbauer, J., Functional consequences of the SHP-1 defect in motheaten viable mice: Role of NF-kappa B (1998) Cell. Immunol., 185, pp. 49-58
Sharma, H. W., Perez, J. R., Higgins-Sochaski, K., Hsiao, R., Narayanan, R., Transcription factor decoy approach to decipher the role of NF-kappa B in oncogenesis (1996) Anticancer Res., 16, pp. 61-69
Vos, I. H., Govers, R., Grone, H. J., Kleij, L., Schurink, M., De Weger, R. A., Goldschmeding, R., Rabelink, T. J., NF kappaB decoy oligodeoxynucleotides reduce monocyte infiltration in renal allografts (2000) FASEB J., 14, pp. 815-822
Larsen, H. J., Nielsen, P. E., Transcription-mediated binding of peptide nucleic acid (PNA) to double-stranded DNA: Sequence-specific suicide transcription (1996) Nucleic Acids Res., 24, pp. 458-463
Hanvey, J. C., Peffer, N. J., Bisi, J. E., Thomson, S. A., Cadilla, R., Josey, J. A., Ricca, D. J., Babiss, L. E., Antisense and antigene properties of peptide nucleic acids (1992) Science, 258, pp. 1481-1485
Demidov, V. V., Potaman, V. N., Frank-Kamenetsk, M. D., Egholm, M., Buchard, O., Sonnichsen, S. H., Nielsen, P. E., Stability of peptide nucleic acids in human serum and cellular extracts (1994) Biochem. Pharmacol., 48, pp. 1310-1313
Misra, H. S., Pandey, P. K., Modak, M. J., Vinayak, R., Pandey, V. N., Polyamide nucleic acid-DNA chimera lacking the phosphate backbone are novel primers for polymerase reaction catalyzed by DNA polymerases (1998) Biochemistry, 37, pp. 1917-1925
Will, D. W., Breipohl, G., Langner, D., Knolle, J., Uhlmann, E., The synthesis of polyamide nucleic acids using a novel monomethoxytrityl protecting-group strategy (1995) Tetrahedron, 51, pp. 12069-12082
Dignam, J. D., Lebovitz, R. M., Roeder, R. G., Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei (1983) Nucleic Acids Res., 11, pp. 1475-1489
Chen, F. E., Huang, D., Chen, Y., Ghosh, G., Crystal structure of p50/p65 heterodimer of transcription factor NF-kappaB bound to DNA (1998) Nature, 391, pp. 410-413
Bloomfield, V. A., Crothers, D. M., Tinoco I. T., Jr., Nucleic Acids: structures, properties and functions, , University Science Book, Sausalito, CA
McShean, W. M., Rossen, R. D., Laughter, A. H., Trial, J., Kessler, D. J., Zendegui, J. G., Hogan, M. E., Orson, F. M., Inhibition of transcription of HIV-1 in infected human cells by oligodeoxy-nucleotides designed to form DNA triple helices (1992) J. Biol. Chem., 267, pp. 5712-5721
Molecular interactions between nuclear factor κB (NF-κB) transcription factors and a PNA-DNA chimera mimicking NF-κB binding sites
The decoy approach against nuclear factor κB (NF-κB) is a useful tool to alter NF-κB dependent gene expression using synthetic oligonucleotides (ODNs) carrying NF-κB 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-κB 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-κB binding sites are capable of stable interactions with proteins belonging to the NF-κB family. Molecular modeling was employed for the design of PNA-DNA chimeras; prediction of molecular interactions between chimeras and NF-κB nuclear proteins were investigated by molecular dynamics simulations, and interactions between PNA-DNA chimeras and NF-κB proteins were studied by gel shifts. We found significant differences between the structure of duplex NF-κB PNA-DNA chimera and duplex NF-κB DNA-DNA. However, it was found that these differences do not prevent the duplex PNA-DNA chimera from binding to NF-κB 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-κB DNA-PNA chimeras could be used for a decoy approach in gene therapy.
Molecular interactions between nuclear factor κB (NF-κB) transcription factors and a PNA-DNA chimera mimicking NF-κB binding sites