Carbazole modified oligonucleotides: synthesis, hybridization studies and fluorescence properties (original) (raw)
Related papers
2′-O-Carbamate-containing oligonucleotides: synthesis and properties
Tetrahedron Letters, 2001
In order to evaluate the effect of a new 2%-carbohydrate modification on the hybridization properties of oligonucleotides, uridine 2%-O-carbamates were synthesized and incorporated into DNA strands. The key intermediate in the synthesis, a mixed succinimide carbonate 2, was treated with various amines to give 2%-O-carbamates 3. Thermal melting studies of modified oligonucleotides revealed that the presence of the 2%-O-carbamate modification significantly destabilized DNA/RNA duplexes. A molecular-modeling study indicated that unfavorable steric interactions between the hydrogen of the NH group from the carbamate substituent and the anomeric hydrogen of the sugar residue on the same strand of the duplex may be the contributing factor causing destabilization.
Tetrahedron, 1998
The synthesis of modified oligonucleotides (ODNs), tethered with phenazine (pzn) at CI' of 1-(Ydeoxypsicofuranosyl)uracil, the thermal stability, and fluorescence properties of their duplexes and triplexes are described. The key intermediates, the psicofuranosyluracil derivatives 7 and 8 with phenazine l'-tethered through a tinker composed of a phosphate and two methylene groups, were synthesized from 1-(3'-deoxypsicofuranosyl)umcil 5 [5-~ 6 (26%)-* 7 (62%) or 8 (70%)]. Compound 7 was converted into the corresponding 6'-O-DMTr protected 4'-phosphocamidite block 13 in three steps [7-~ 9 (83%) ~ 11 (83%)-~ 13 (83%)], whereas compound 8 was used in the preparation of the modified solid support 14 in four steps [8 ~ 10 (28%)-* 12 (70%)-~ 14]. Modified 9-mer ODNs 28-31 and 18-mer ODNs 22-25 were then assembled in a usual manner using automated solid-phase DNA synthesis protocol. The phenazine-tethered 9-mers (28-31) were tested for their ability to form stable duplexes with target DNA-strands (19-20). The phenazine-tethered 18-reefs (22-25) were tested for their ability to form stable triplexes with 24-met and 29-mer duplex targets (15.16 and 17.18). Triplexes consisting of modified ODNs with pzn at the 5'-terminal (as in 24) and at 3',5'-terminals (as in 25) were more stable than the unmodified parent triplex. No triplex was found to have formed with modified ODNs with pzn attached at 3'-or at the middle of the strand at neutral pH (7.3), but triplex formation was observed at acidic pH (6.0) although they were less stable than the unmodified parent triplex. The same Irend was observed for duplexes. The fluorescence intensity of pzn in the modified triplexes was enhanced and blue-shifted by-13 nm relative to the single strand. In contrast, the changes in fluorescence intensities ofpzn in the modified duplexes were relatively less compared to the triplexes. The fluorescence intensity increased proportionally as the thermal stabilities of the triplexes increased. A comparison of the fluorescent intensity changes (AF) shows that the fluorophore in duplexes (AF =-1.2 to +1.5) experiences relatively minor change in the microenvironment compared to that of the triplexes (AF 91.5 to 4.5). Nevertheless, in both cases the phenazine residue most probably interacts with the neighbouring nucleobases as a weak exterior binder.
A Fluorescent Carbazole Derivative: High Sensitivity for Quadruplex DNA
Analytical Chemistry, 2003
We have synthesized a novel molecule, 3,6-bis(1-methyl-4-vinylpyridium)carbazole diiodide (BMVC), for recognizing specific quadruplex structures, particularly the quadruplex of human telomeric sequence d(T 2 AG 3) 4. The fluorescence intensity of the BMVC molecule increases from 1 to almost 2 orders of magnitude upon interacting with various DNAs. At a concentration of BMVC of 10 µM, fluorescence bands with different colors of BMVC in electrophoresis gels of various DNAs can be observed. The fluorescence of BMVC can be used to discriminate between duplex and quadruplex DNAs. At the low concentration of 0.1 µM BMVC in prestained gels, the fluorescence is observed in the presence of quadruplexes with anti-anti-anti-anti and anti-anti-syn-syn arrangements. However, no fluorescence band is detected upon interacting with duplexes and quadruplexes with antisyn-anti-syn arrangement. Moreover, the sensitivity assays show that as little as 0.2 pmol of quadruplex of d(T 2 AG 3) 4 can be revealed by BMVC.
Pharmaceutics, 2021
Oligonucleotides with the sequences 5′-GTG AUPA TGC, 5′-GCA TAUP CAC and 5′-GUPG ATA UPGC, where UP is 2′-O-propargyl uridine, were subjected to post-synthetic Cu(I)-catalyzed azide–alkyne cycloaddition to attach 1,4,7,10-tetraazacyclododecane (cyclen) and two well-known DNA intercalating dyes: thioxanthone and 1,8-naphthalimide. We propose a convenient cyclen protection–deprotection strategy that allows efficient separation of the resulting polyamine–oligonucleotide conjugates from the starting materials by RP-HPLC to obtain high-purity products. In this paper, we present hitherto unknown macrocyclic polyamine–oligonucleotide conjugates and their hybridization properties reflected in the thermal stability of thirty-two DNA duplexes containing combinations of labeled strands, their unmodified complementary strands, and strands with single base pair mismatches. Circular dichroism measurements showed that the B-conformation is retained for all dsDNAs consisting of unmodified and modif...
Nucleosides, Nucleotides and Nucleic Acids, 2011
Carboxyalkyl derivative of the intercalating agent imidazo[4,5-b]phenazine was used for the post-synthetic oligonucleotide modification. Model pentadecathymidylate-imidazophenazine conjugate was prepared from 5'-aminoalkyl-modified (dT) 15 using phosphonium coupling reagent BOP in the presence of 1-hydroxybenzotriazole. Spectral-fluorescent properties of the conjugate were studied. The attachment of the dye was found to increase the thermal stability of (dT) 15 duplex with poly(dA) by more than 4°C, probably by intercalation mechanism.
Proceedings of The 15th International Electronic Conference on Synthetic Organic Chemistry, 2011
A novel class of backbone-modified oligonucleotide analogs has emerged since the discovery of Cu I-catalyzed 3+2 azide-alkyne cycloaddition. These are oligonucleotide analogs with 1,4-substituted 1,2,3-triazoles in internucleotide linkages. Of all such analogs known to date, only the triazole-linked deoxythymidine decamer has been reported to show enhanced binding affinity to complementary DNA. Importantly, it is a fully modified (dT) 10 analog. Irregular oligonucleotides bearing the same backbone modification have not been described so far. With a goal of investigating sequence and regularity dependence of the effect of this modification on duplex stability, we have designed sequentially heterogenous modified oligonucleotides, which can be prepared using a modified dinuleoside block. In this paper we report on the synthesis of the dithymidine phosphoramidite block with the triazole linker, its utilization in oligonucleotide synthesis and hybridization data of thus obtained oligonucleotide analogs. The effect of single and multiple modifications on stability of irregular sequence duplexes is assessed and compared with published data for the oligo(T)/oligo(A) duplex. We also compare the effect of the linker concerned with that of a shorter triazole linker.
Tetrahedron Letters, 1994
Oligonucleotides containing noiel N24midazolyl~ro ylguanine and N2-Imidazolylpropyl-2-amiadenine moieties wem synthesked and studxxl F or their hybridization and biophysical propertk. Intemstingly, these hetcmcyle modified oli on~leotides showed a remakable enhancement of heteroduplcx binding affdty when hybn '&ed to complementary DNA. Modified oligonucleotides are of interest as antiscnse therapeutic agents.1 Although this relatively new drug discovery concept is presently thought to be of gzeat therapeutic potential. a number of problems have yet to be sokd.1 For example. the precise event(s) that terminates or in some way interferes with an essential RNA function after sequcncc-specifii binding of an oEgonucleutide to a target RNA is unclear_ Antisense effects are bust to result as a consequence of simply binding of the olig~~l~ti& to targekd RNA or binding and subsequent cleavage of targeted RNA by endogenous RNase ~1.2 Both mechanisms require nucleasc resistant-oligonucelotides which effectively bind to target RNA. Unfortunately, first generation modifxations such aa phosphorottdoates, methylphosphanates, and phoaphoramidates, although providing n&ease resistance, compromised heteroduplex binding affinity.1 The RNase H mode of action requires that the heteroduplex formed between the RNA target and the DNA be bound and cleaved by the enzyme. However, all reported modificati~ of the sugar-phosphate backbone, with the exception of phosphorothioates and phosphorodithioates, obliterate the RNase H terminating event, 1~3 We m pursuing several amhes to develop antisense oligonucleotides with precise terminating events. One is based on the concept that antisense oligonuckotides containing ~~~~-rn~fi~ti~, rather than ~~-p~~ rn~~~, can be resistant to nucleolytic &gradation, yet on h~~tion to target RNA provides a heteroduplex &at supports RNase H-mediated cleavage.7 Another approach is directed to the development of sequence-specific chemical cleavers of RNA. This concept requires the attachment of pendent groups with acid/base properties to oligonucleotides; when hybridized to RNA, the pendent groups of the oligonucleotides would be accessible, via the minor groove, to the a'-hydroxyl and ~~~Of~~~A Obviously, pendent groups designed to support eitherenzymatic orchemical cleavage of RNA must be compatible with the requisite hybridization step. We have focused on pendcnt groups on the N2-position of guanine and 2-aminoadenine as these groups should protrude into the minor groove of a DNA-RNA
Bioscience reports, 2007
2'-O,4'-C-methylene-linked ribonucleotide derivatives, named LNA (locked nucleic acid) and BNA (bridged nucleic acid) are nucleic acid analogoues that have shown high-affinity recognition of DNA and RNA, and the employment of LNA oligomers for antisense activity, gene regulation and nucleic acid diagnostics seems promising. Here we show kinetic and thermodynamic results on the interaction of a series of 10 bases long LNA-DNA mixmers, gabmers as well as full length LNA's with the complementary DNA, RNA and LNA oligonucleotides in the presence and absence of 10 mM Mg(2+)- ions. Our results show no significant differences in the reaction thermodynamics and kinetics between the LNA species, only a tendency to stronger duplex formation with the gabmer and mixmer. Introduction of a few LNA's thus may be a better strategy, than using full length LNA's to obtain an oligonucleotide that markedly increases the strength of duplexes formed with the complementary DNA and RNA.