DOI: 10.1002/chem.200902029 Role of Environmental Factors on the Structure and Spectroscopic Response of 5’-DNA–Porphyrin Conjugates Caused by Changes in the Porphyrin– Porphyrin Interactions Angela Mammana, [a] Gennaro Pescitelli, [c] Tomohiro Asakawa, [a] Steffen Jockusch, [a] Ana G. Petrovic, [a] Regina R. Monaco, [a] Roberto Purrello, [d] Nicholas J. Turro, [a] Koji Nakanishi, [a] George A. Ellestad,* [a] Milan Balaz,* [b] and Nina Berova* [a] Abstract: We have explored the utility, strength, and limitation of through- space exciton-coupled circular dichro- ism in determination of the secondary structure of optically active chromo- phoric nanoarrays using the example of end-capped porphyrin– and metallo- porphyrin–oligodeoxynucleotide conju- gates. We put special emphasis on the explanation of the origin and signifi- cance of the distinctive multiple bands in the CD spectra (trisignate and tetra- signate CD bands). Such CD profiles are often observed in chiral aggregates or multichromophoric arrays but have never before been studied in detail. We found that variation of temperature and ionic strength has a profound effect on the geometry of the porphy- rin–DNA conjugates and thus the nature of electronic interactions. At lower temperatures and in the absence of NaCl all three 5’-DNA–porphyrin conjugates display negative bisignate CD exciton couplets of variable inten- sity in the Soret region resulting from through-space interaction between the electric transition dipole moments of the two end-capped porphyrins. As the temperature is raised these exciton couplets are transformed into single positive bands originating from the porphyrin–single-strand DNA interac- tions. At higher ionic strengths and low temperatures, multisignate CD bands are observed in the porphyrin Soret region. These CD signature bands orig- inate from a combination of intermo- lecular, end-to-end porphyrin–porphy- rin stacking between duplexes and por- phyrin–DNA interactions. The inter- molecular aggregation was confirmed by fluorescence and absorption spec- troscopy and resonance light scattering. DeVoe theoretical CD calculations, in conjunction with molecular dynamics simulations and Monte Carlo confor- mational searches, were used to mimic the observed bisignate exciton-coupled CD spectra as well as multiple CD bands. Calculations correctly predicted the sign and shape of the experimental- ly observed CD spectra. These studies reveal that the exciton-coupled circular dichroism is a very useful technique for the determination of the structure of optically active arrays. Keywords: circular dichroism · DNA aggregation · helical struc- tures · molecular modeling · porphyrinoids [a] Dr. A. Mammana, Dr. T. Asakawa, Dr. S. Jockusch, Dr. A. G. Petrovic, Dr. R. R. Monaco, Prof. N. J. Turro, Prof. K. Nakanishi, Dr. G. A. Ellestad, Prof. N. Berova Department of Chemistry, Columbia University 3000 Broadway, New York, NY 10027 (USA) Fax: (+ 1) 212-932-8273 E-mail : ndb1@columbia.edu gae2104@columbia.edu [b] Prof. M. Balaz Department of Chemistry, University of Wyoming 1000 E. University Avenue, Laramie, WY 82071 (USA) Fax: (+ 1) 307-766-2807 E-mail: mbalaz@uwyo.edu [c] Dr. G. Pescitelli Dipartimento di Chimica e Chimica Industriale Universita degli Studi di Pisa, 56126 Pisa (Italy) [d] Prof. R. Purrello Department of Chemical Sciences, University of Catania Viale Andrea Doria 6, 95125 Catania (Italy) Supporting information for this article is available on the WWW under http://dx.doi.org/10.1002/chem.200902029. Chem. Eur. J. 2009, 15, 11853 – 11866 # 2009 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim 11853 FULL PAPER