2003
DOI: 10.1002/cbic.200300678
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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" absorba… Show more

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Cited by 63 publications
(49 citation statements)
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“…We speculate that the intense excimer emission of +2 zipper duplex P1:P4 is a result of pyrene-pyrene stacking interactions in the grooves, in a similar manner as observed for DNA duplexes with +2 zipper arrangements of pyrene-functionalized ara -uridine monomers. 41-43 Interestingly, +1 zipper duplexes X2:X5 and S2:S5 , which are comprised of (pyren-1-yl)carbonyl-functionalized monomers, do not display excimer emission, but instead feature monomer emission that is considerably more intense than in duplexes with other interstrand arrangements.…”
Section: Resultsmentioning
confidence: 99%
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“…We speculate that the intense excimer emission of +2 zipper duplex P1:P4 is a result of pyrene-pyrene stacking interactions in the grooves, in a similar manner as observed for DNA duplexes with +2 zipper arrangements of pyrene-functionalized ara -uridine monomers. 41-43 Interestingly, +1 zipper duplexes X2:X5 and S2:S5 , which are comprised of (pyren-1-yl)carbonyl-functionalized monomers, do not display excimer emission, but instead feature monomer emission that is considerably more intense than in duplexes with other interstrand arrangements.…”
Section: Resultsmentioning
confidence: 99%
“…There are many reports of duplexes with interstrand zipper arrangements of pyrene-functionalized monomers in which excimer-emitting pyrene dimers are formed in the grooves 41-50 or duplex core. 26,29,31,52-54 Considering that intercalation of the pyrene moieties is expected to be the primary binding mode for the monomers reported herein, 32,34,36,39 stacking of the pyrenes inside the duplex core appears to be the most plausible binding mode for double-stranded probes with +1 interstrand monomer arrangements.…”
Section: Resultsmentioning
confidence: 99%
“…S7), implying a coplanar arrangement of the pyrene moieties with an interplanar separation of ~3.4 Å. 20,27,28,31,40-45 …”
Section: Resultsmentioning
confidence: 99%
“…The starting compound 1 31 was trans formed into the N(3) (2,4 dinitrophenylsulfenyl) deriva tive with transient trimethylsilylation of the 2´ OH group. 32 Allylation of N(3) protected arabinouridine 2 was carried out in the presence of 2 tert butylimino 2 diethylamino 1,3 dimethylperhydro 1,3,2 diazaphos phorine (BDDDP).…”
Section: Resultsmentioning
confidence: 99%