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ID: 206981.0, MPI für biophysikalische Chemie / Molekulare Biologie (Dr. Thomas M. Jovin)
Parallel DNA double helices incorporating isoG or m⁵ isoC bases studied by FTIR, CD and molecular modeling
Authors:Geingenaud, F.; Mondragon-Sanchez, J. A.; Liquier, J.; Shchyolkina, A. K.; Klement, R.; Arndt-Jovin, D. J.; Jovin, T. M.; Tallandier, E.
Date of Publication (YYYY-MM-DD):2005-02
Title of Journal:Spectrochimica Acta A
Start Page:579
End Page:587
Sequence Number of Article:doi:10.1016/j.saa.2004.05.037
Review Status:Peer-review
Audience:Not Specified
Abstract / Description:FTIR spectroscopy has been used to follow the formation of parallel stranded DNA duplexes incorporating isoG or m⁵isoC bases and determine their base pairing scheme. The results are discussed in comparison with data concerning anti-parallel duplexes with comparable base composition and sequence. In duplexes containing A–T and isoG–C or m⁵isoC–G base pairs shifts of the thymine C2=O2 and C4=O4 carbonyl stretching vibrations (to lower and higher wavenumbers, respectively, when compared to their positions in classical cis Watson–Crick (WC) base pairs) reflect the formation of transWatson–Crick A–T base pairs. All carbonyl groups of cytosines, m⁵isocytosines, guanines and isoguanines are found to be involved in hydrogen bonds, indicative of the formation of isoG–C and m⁵isoC–G base pairs with three hydrogen bonds. Molecular modeling shows that both structures form regular right handed helices with C2'endo sugar puckers. The role of the water content on the helical conformation of the parallel duplexes has been studied by FTIR and CD. It is found that a conformational transition similar to the B->A transition observed for anti-parallel duplexes induced by a decrease of the water content of the samples can occur for these parallel duplexes. Their helical flexibility has been evidenced by FTIR studies on hydrated films by the emergence of absorption bands characteristic of A type geometry, in particular by an S-type->N-type repuckering of the deoxyribose. All sugars in the parallel duplex with alternating d(isoG–A)/d(C–T) sequence can adopt an N-type geometry in low water content conditions. The conformational transition of the parallel hairpin duplex with alternating d(isoG-A)/d(C-T) sequence was followed by circular dichroism in water / trifluoroethanol solutions and its free energy at 0°C was estimated to be 6.6±0.3 kcal mol ⁻¹.
Free Keywords:parallel-DNA; isoguanine; m5isocytosine; FTIR; CD; modeling
Last Change of the Resource (YYYY-MM-DD):2005-01-18
External Publication Status:published
Document Type:Article
Communicated by:N. N.
Affiliations:MPI für biophysikalische Chemie/Abt. Thomas Jovin / 060/AG Donna Arndt-Jovin
External Affiliations:Equipe de Spectroscopie Biomoleculaire, UFR de Medecine, Universite Paris 13, 74 rue Marcel Cachin, F93017 Bobigny Cedex, France; Engelhardt Institute of Molecular Biology, Russian Academy of Science, Vavilova 32, 119991 Moscow, Russia
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