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Molecular modeling of new permanently charged phenanthridinium-nucleobase conjugates in complexes with double stranded polynucleotides


Grabar, Marina; Tomić, Sanja; Tumir Marija, Lidija; Piantanida, Ivo
Molecular modeling of new permanently charged phenanthridinium-nucleobase conjugates in complexes with double stranded polynucleotides // Ninth Triennial Congress of the World Association ot Theoretical and Computational Chemists - Book of Abstracts / Yáñez, Manuel ; Mó, Otilia (ur.).
Santiago de Compostela, 2011. (poster, nije recenziran, sažetak, znanstveni)


Naslov
Molecular modeling of new permanently charged phenanthridinium-nucleobase conjugates in complexes with double stranded polynucleotides

Autori
Grabar, Marina ; Tomić, Sanja ; Tumir Marija, Lidija ; Piantanida, Ivo

Vrsta, podvrsta i kategorija rada
Sažeci sa skupova, sažetak, znanstveni

Izvornik
Ninth Triennial Congress of the World Association ot Theoretical and Computational Chemists - Book of Abstracts / Yáñez, Manuel ; Mó, Otilia - Santiago de Compostela, 2011

Skup
Ninth Triennial Congress of the world association of Theoretical and Computational chemists

Mjesto i datum
Santiago se Compostela, Španjolska, 17-22.07.2011

Vrsta sudjelovanja
Poster

Vrsta recenzije
Nije recenziran

Ključne riječi
Molecular modelling; AMBER; phenanthridinium conjugates; DNA; RNA

Sažetak
Small molecules targeting DNA/RNA have attracted significant scientific interest due to the medicine, biochemical and biological implications of such molecular recognition events. Most often these small molecules rely on the dominant non-covalent binding mode for their interacion with double stranded (ds) DNA/RNA (e.g. intercalation, minor groove binding). The combination of different binding modes within one molecules as well as additional steric and structural features controlling three-dimensional recognition drew some attention over the last few years with the aim of developing new more selective drugs or biochemical markers as well as research tools on a molecular level. Since many of the antitumor drugs act by modifying (i.e. alkylating) nucleobases in DNA, molecules that bind specifically at such lesions and inhibit the DNA repair system may potentiate the action of antitumor drugs. In this work we shall present our molecular modelling results in combination with spectroscopic measurements for a series of new permanently charged phenanthridinium-nucleobase conjugates in complexes with polynucleotides. Specifically, the complexes with double stranded DNA (poly dAdT – poly dAdT) and double stranded RNA ( poly AH+) were studied. Since here we are dealing with protonated adenine in RNA, we had to implement a special procedure of parameterization. The calculations required for parametrization of the nucleotide with protonated adenine were carried out using the Gaussian033 program at the HF/6-31G(d) level of theory. The molecular modelling was performed with AMBER101 suite. AMBER ff99SB2 and GAFF1 force field were used to parameterize molecules.

Izvorni jezik
Engleski

Znanstvena područja
Fizika, Kemija



POVEZANOST RADA


Projekt / tema
098-1191344-2860 - Proučavanje biomakromolekula računalnim metodama i razvoj novih algoritama (Sanja Tomić, )

Ustanove
Institut "Ruđer Bošković", Zagreb