title: Pyrenemethyl ara-uridine-2'-carbamate: a strong interstrand excimer in the major groove of a DNA duplex.
abstract: The synthesis of new nucleoside derivatives, ara-uridine-2'-carbamates, and their incorporation into synthetic DNA oligomers is described. The modification directs ligands into the major groove of duplex DNA and somewhat destabilizes the duplexes of modified oligonucleotides with complementary DNA or RNA. In the case of pyrenemethyl carbamate modification in DNA-DNA duplexes, the destabilization is considerably reduced. The pyrenemethyl derivative also shows remarkable spectral properties: a "reversed" absorbance change for pyrene at 350 nm in the course of denaturation of the DNA duplex, as compared to the change seen in the nucleotide absorbance at 260 nm. This derivatization also causes pronounced sequence-dependent excimer formation in the major groove.
authors.affiliation: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia.
authors.forename: Natalia N
authors.initials: NN
authors.lastname: Dioubankova
authors.forename: Andrei D
authors.initials: AD
authors.lastname: Malakhov
authors.forename: Dmitry A
authors.initials: DA
authors.lastname: Stetsenko
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Gait
authors.forename: Pavel E
authors.initials: PE
authors.lastname: Volynsky
authors.forename: Roman G
authors.initials: RG
authors.lastname: Efremov
authors.forename: Vladimir A
authors.initials: VA
authors.lastname: Korshun
mesh_terms: D004247:DNA / Q000737:chemistry*; D004355:Drug Stability; D005453:Fluorescence; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry*; D015345:Oligonucleotide Probes; D009841:Oligonucleotides / Q000138:chemical synthesis* / Q000737:chemistry; D012313:RNA / Q000737:chemistry; D012833:Siloxanes / Q000138:chemical synthesis* / Q000737:chemistry; D013050:Spectrometry, Fluorescence; D013696:Temperature; D014529:Uridine / Q000031:analogs & derivatives / Q000138:chemical synthesis* / Q000737:chemistry
chemical_list: C484719:2'-O-(pyren-1-ylmethylaminocarbonyl)-3',5'-O-(tetraisopropyldisiloxan-1,3-diyl)uracil-1-arabinofuranoside; D009692:Nucleic Acid Heteroduplexes; D015345:Oligonucleotide Probes; D009841:Oligonucleotides; D012833:Siloxanes; D012313:RNA; D004247:DNA; D014529:Uridine