Journal of Biomolecular Structure and Dynamics
ISSN: 0739-1102 (Print) 1538-0254 (Online) Journal homepage: http://www.tandfonline.com/loi/tbsd20
24 Interference of PNA binding to the nontemplate strand with transcription supports the general model for transcription blockage by R-loop formation Boris P. Belotserkovskii & Philip C. Hanawalt To cite this article: Boris P. Belotserkovskii & Philip C. Hanawalt (2015) 24 Interference of PNA binding to the non-template strand with transcription supports the general model for transcription blockage by R-loop formation, Journal of Biomolecular Structure and Dynamics, 33:sup1, 14-14, DOI: 10.1080/07391102.2015.1032564 To link to this article: http://dx.doi.org/10.1080/07391102.2015.1032564
Published online: 23 Jun 2015.
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Date: 25 January 2016, At: 13:39
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Journal of Biomolecular Structure and Dynamics Vol. 33, Supplement, 2015
24
Interference of PNA binding to the non-template strand with transcription supports the general model for transcription blockage by R-loop formation
Boris P. Belotserkovskii* and Philip C. Hanawalt
Downloaded by [50.67.208.23] at 13:39 25 January 2016
Department of Biology, Stanford University, Stanford, CA 94305, USA *Email:
[email protected], Phone: (650) 723 2425
Transcription blockage can strongly affect various DNA and RNA transactions (reviewed in Hanawalt & Spivak, 2008; Belotserkovskii, Mirkin, & Hanawalt, 2013). Thus, it is of interest to study the various factors that can cause transcription blockage and to elucidate mechanisms of their action. Peptide Nucleic Acids (PNAs) are artificial DNA mimics with superior nucleic acid binding capabilities. The effect of PNA binding to the (GAA/CTT)n sequence within the transcribed DNA region upon T7 RNA polymerase transcription was studied in vitro. In the case of the PNA binding to the template strand, the blockage signals concentrated primarily in the narrow area close to the upstream flank of the PNA-bound sequence, consistent with the blockage being caused by RNA polymerase “bumping” into the PNA/DNA hybrid (Belotserkovskii, Liu, & Hanawalt, 2009). In contrast, for PNA binding to the non-template strand, a characteristic pattern of blockage signals was observed, extending downstream from the PNA binding site (Belotserkovskii & Hanawalt, 2014), similar to that produced by G-rich homopurine-homopyrimidine sequences (Belotserkovskii et al., 2010, 2013). This striking similarity between transcription blockage patterns caused by two seemingly unrelated factors suggests a common mechanism of blockage. This common mechanism likely involves R-loop formation, which is facilitated both by PNA binding to the non-template strand and by G-rich homopurine-homopyrimidine sequences, due to sequestration of the non-template strand or due to formation of an extrastable RNA/DNA hybrid, respectively. We suggest that there is a general mechanism of transcription blockage by R-loop formation, which presumably involves destabilization of the transcription complex, making it more prone to spontaneous pausing or termination. This research was supported by an NIH grant, CA077712, from the National Cancer Institute to P.C.H.
References Belotserkovskii, B. P., & Hanawalt, P. C. (2014). PNA binding to the non-template DNA strand interferes with transcription, suggesting a blockage mechanism mediated by R-loop
formation. Molecular Carcinogenesis. (Epub ahead of print). Belotserkovskii, B. P., Liu, R., & Hanawalt, P. C. (2009). Peptide nucleic acid (PNA) binding and its effects on in vitro transcription in Friedreich’s ataxia triplet repeats. Molecular Carcinogenesis, 48, 299–308. Belotserkovskii, B. P., Liu, R., Tornaletti, S., Krasilnikova, M. M., Mirkin, S. M., & Hanawalt, P. C. (2010). Mechanisms and implications of transcription blockage by guanine-rich DNA sequences. Proceedings of the National Academy of Sciences, 107, 12816–12821. Belotserkovskii, B. P., Mirkin, S. M., & Hanawalt, P. C. (2013). DNA sequences that interfere with transcription: Implications for genome function and stability. Chemical Reviews, 113, 8620–8637. Belotserkovskii, B. P., Neil, A. J., Saleh, S. S., Shin, J. H., Mirkin, S. M., & Hanawalt, P. C. (2013). Transcription blockage by homopurine DNA sequences: Role of sequence composition and single-strand breaks. Nucleic Acids Res, 41, 1817–1828. Hanawalt, P. C., & Spivak, G. (2008). Transcription-coupled DNA repair: Two decades of progress and surprises. Nature Reviews Molecular Cell Biology, 9, 958–970.
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New insights on nucleic acids – protein interfaces revealed by VLDM, a geometrical approach
A. Elbahnsia,b*, O. Mauffreta, D. Perahiaa, B. Hartmanna and C. Ogueyb a
LBPA, UMR 8113 CNRS, ENS de Cachan, 61 avenue du Président Wilson, 94235 Cachan Cedex, France; bLPTM, Université de Cergy-Pontoise, 2 avenue Adolphe Chauvin, 95031 Cergy-Pontoise, France *Email:
[email protected], Phone: (+33)147407752
Complexes involving nucleic acids and proteins are ubiquitous and fundamental for cell life. Deciphering the interface between nucleic acids and proteins is crucial for better understanding the stabilities of the complexes and the mechanisms underlying their formation. To describe the interface between nucleic acids and proteins, we developed a geometrical method, called VLDM (Voronoi Laguerre Delauney for Macromolecules). VLDM is based on the representation of molecules by a collection of polyhedra filling space without overlaps or gaps (Esque & Oguey, 2010). On the basis of this diagram, the topology of complex systems can be explored systematically without any need of empirical or subjective adjustments. In this work, VLDM was applied to two systems of major biological interest. The nucleocapsid protein NCp7 of HIV-1 is a small basic protein with a chaperone activity on nucleic acids, RNA and DNA. The latter binds to two non equivalent Zn-fingers. A series of NMR structures of RNA and DNA-containing complexes (Darlix et al., 2011) were analyzed by VLDM. The results showed
