Abstract
The non-covalent interaction of achiral porphyrins with nucleic acids has been extensively studied, and various macrocycles have been indeed utilized as reporters of different sequences of DNA bases. Nevertheless, few studies have been published on the capability of these macrocycles to discriminate among the various nucleic acid conformations. Circular dichroism spectroscopy allowed to characterize the binding of several cationic and anionic mesoporphyrins and metallo derivatives with Z–DNA, in order to exploit the functionality of these systems as probes, storing system, and logic gate.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Belmont P, Constant JF, Demeunyck M (2001) Nucleic acid conformation diversity: from structure to function and regulation. Chem Soc Rev 30:70–81
Jovin TM, Soumpasis DM, McIntosh LP (1987) The transition between B-DNA and Z-DNA. Annu Rev Phys Chem 38:521–558
Rich A, Nordheim A, Wang AH (1984) The chemistry and biology of left-handed Z-DNA. Annu Rev Biochem 53:791–842
Rich A, Zhang S (2003) Timeline: Z-DNA: the long road to biological function. Nat Rev Genet 4:566–572
Herbert A, Alfken J, Kim Y--G, Mian IS, Nishikura K, Rich A (1997) A Z-DNA binding domain present in the human editing enzyme, double-stranded RNA adenosine deaminase. Proc Natl Acad Sci U S A 94:8421–8426
Kim Y--G, Lowenhaupt K, Maas S, Herbert A, Schwartz T, Rich A (2000) The Zab domain of the human RNA editing enzyme ADAR1 recognizes Z-DNA when surrounded by B-DNA. J Biol Chem 275:26828–26833
Kim Y--G, Lowenhaupt K, Oh D--B, Kim KK, Rich A (2004) Evidence that vaccinia virulence factor E3L binds to Z-DNA in vivo: implications for development of a therapy for poxvirus infection. Proc Natl Acad Sci U S A 101:1514–1518
Schwartz T, Rould MA, Lowenhaupt K, Herbert A, Rich A (1999) Crystal structure of the Zalpha domain of the human editing enzyme ADAR1 bound to left-handed Z-DNA. Science 284:1841–1845
Berova N, Nakanishi K, Woody RW (2000) Circular dichroism principles and application. Wiley-VCH, New York
Kypr J, Kejnovská I, Renčiuk D, Vorlíčková M (2009) Circular dichroism and conformational polymorphism of DNA. Nucleic Acids Res 37:1713–1725
Mammana A, De Napoli M, Lauceri R, Purrello R (2005) Induction and memory of chirality in porphyrin hetero-aggregates: the role of the central metal ion. Bioorg Med Chem 13:5159–5163
Pasternack RF, Francesconi L, Raff D, Spiro E (1973) Aggregation of nickel(II), copper(II), and zinc(II) derivatives of water-soluble porphyrins. Inorg Chem 12:2606–2611
Choi JK, D’Urso A, Balaz M (2013) Chiroptical properties of anionic and cationic porphyrins and metalloporphyrins in complex with left-handed Z-DNA and right-handed B-DNA. J Inorg Biochem 127:1–6
D’Urso A, Choi JK, Shabbir--Hussain M, Ngwa FN, Lambousis MI, Purrello R, Balaz M (2010) Recognition of left-handed Z-DNA of short unmodified oligonucleotides under physiological ionic strength conditions. Biochem Biophys Res Commun 397:329–332
Parkinson A, Hawken M, Hall M, Sanders KJ, Rodger A (2000) Amine induced Z-DNA in poly(dG-dC)·poly(dG-dC): circular dichroism and gel electrophoresis study. Phys Chem Chem Phys 2:5469–5478
Schoenknecht T, Diebler H (1993) Spectrophotometric and kinetic studies of the binding of Ni2+, Co2+, and Mg2+ to poly(dG-dC) · poly(dG-dC). Determination of the stoichiometry of the Ni2+-induced B → Z transition. J Inorg Biochem 50:283–298
Fuertes MA, Cepeda V, Alonso C, Perez JM (2006) Molecular mechanisms for the B-Z transition in the example of poly[d(G-C)d(G-C)] polymers. A critical review. Chem Rev 106:2045–2064
D’Urso A, Mammana A, Balaz M, Holmes AE, Berova N, Lauceri R, Purrello R (2009) Interactions of a Tetraanionic porphyrin with DNA: from a Z-DNA sensor to a versatile supramolecular device. J Am Chem Soc 131:2046–2047
(a) D’Urso A, Holmes AE, Berova N, Balaz M, Purrello R (2011) Z-DNA recognition in B-Z-B sequences by a cationic zinc porphyrin. Chem Asian J 6:3104–3109; (b) Ha SC, Lowenhaupt K, Rich A, Kim YG, Kim KK (2005) Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases. Nature 437:1183–1186
(a) Moller A, Nordheim A, Kozlowski SA, Patel DJ, Rich A (1984) Bromination stabilizes poly(dG-dC) in the Z-DNA form under low-salt conditions. Biochemistry 23:54–62; (b) Nadler A, Diederichsen U (2008) Guanosine analog with respect to Z-DNA stabilization: nucleotide with combined C8-Bromo and C2′-Ethynyl modifications. Eur J Org Chem 9:1544–1549; (c) Kimura T, Kawai K, Tojo S, Majima T (2004) One-electron attachment reaction of B- and Z-DNA modified by 8-Bromo-2′-deoxyguanosine. J Org Chem 69:1169–1173
Gangemi CMA, D’Urso A, Tomaselli GA, Berova N, Purrello R (2017) A novel porphyrin-based molecular probe ZnTCPPSpm4 with catalytic, stabilizing and chiroptical diagnostic power towards DNA B-Z transition. J Inorg Biochem 173:141–143
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
D’Urso, A. (2023). Chiroptical Properties of Z-DNA Using Ionic Porphyrins and Metalloporphyrins. In: Kim, K.K., Subramani, V.K. (eds) Z-DNA. Methods in Molecular Biology, vol 2651. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3084-6_9
Download citation
DOI: https://doi.org/10.1007/978-1-0716-3084-6_9
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-3083-9
Online ISBN: 978-1-0716-3084-6
eBook Packages: Springer Protocols