Synthesis and characterization of oligodeoxyribonucleotides modified with 2′-thio-2′-deoxy-2′-S-(pyren-1-yl)methyluridine

Abstract

Pyrene-functionalized oligonucleotides are intensively explored for applications in materials science and diagnostics. Here, we describe a short synthetic route to 2′-S-(pyren-1-yl)methyl-2′-thiouridine monomer S, its incorporation into oligodeoxyribonucleotides (ONs), and biophysical characterization thereof. Pseudorotational analysis reveals that the furanose ring of this monomer has a slight preference for South-type conformations. ONs modified with monomer S display high cDNA affinity but decreased binding specificity. Hybridization is associated with bathochromic shifts of pyrene absorption bands and quenching of pyrene fluorescence consistent with an intercalative binding mode of the pyrene moiety. Monomer S was also evaluated as a building block for mixed-sequence recognition of double-stranded DNA via the Invader strategy. However, probes with +1 interstrand arrangements of monomer S were found to be less efficient than Invader probes based on 2′-O-(pyren-1-yl)methyluridine or 2′-N-(pyren-1-yl)methyl-2′-N-methyl-2′-aminouridine.

Recognition of mixed-sequence DNA using double-stranded probes with interstrand zipper arrangements of O2′-triphenylene- and coronene-functionalized RNA monomers

“…20 In fact, we have shown that Invader probes based on the 2′- O -(pyren-1-yl)methyl-RNA chemistry can be used for recognition of mixed-sequence chromosomal DNA targets at non-denaturing conditions. 26 Recently, we have carried out a series of systematic structure-property studies aiming at improving the dsDNA-recognition efficiency of Invader probes and have thus examined the impact of different nucleobases, 27 relative intercalator orientations, 28 intercalator-sugar linkers, 20 sugar skeletons, 20,29 backbones and probe architectures. 26,30–32 …”

Recent Advances in Nucleic Acid Targeting Probes and Supramolecular Constructs Based on Pyrene-Modified Oligonucleotides

“…Owing to these unique predictable properties, the 2′- O -(pyrene-1-yl)methyl-modified nucleotide monomers have been used as components of highly sensitive probes in a number of fluorescent approaches to RNA detection [ 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 47 ], as SNP-discriminating RNA-specific fluorescent probes [ 48 , 49 ], as key components in highly-fluorescent pyrene π-stack arrays on RNA ( Figure 2 b) ( Section 2.3.6 ) [ 46 , 50 , 51 , 52 , 53 , 54 , 55 ], and also as intercalating units efficiently stabilizing DNA:DNA duplexes ( Section 3.2 ) [ 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 ]. The properties and applications of the oligonucleotides comprising 2′- O -(pyren-1-yl)methylribonucleotides monomers have been discussed in detail in the just published review [ 64 ].…”

“…Hrdlicka and coworkers have introduced so-called Invader probes, i.e., short dsDNA probes that are energetically activated through modification with one or more +1 interstrand zipper arrangements of pyrene-modified nucleotides ( Figure 36 ) [ 17 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 237 , 238 , 239 , 240 ].…”

“…Later, various variants of the second generation of dsDNA Invader probes with interstrand zipper arrangements based on 2′-pyrene-modified RNA or DNA monomers were thoroughly studied. They are synthetically more readily accessible and tend to intercalate into DNA duplexes (monomers K , W and Z , i.e., diverse 2′-heteroatoms, linkers, affecting the orientation of intercalator or internucleotidic linkage, Figure 37 ) [ 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 238 , 239 , 240 ].…”

“…As a result, the Invader probes with +1 interstrand zipper arrangements of monomers K1 , K4 , and W1 were found to recognize dsDNA with efficiencies similar to the Invader LNA probes [ 60 , 61 ]. However, probes with +1 interstrand arrangements of monomer W4 were proved to be significantly less efficient than Invader probes based on monomer K4 or W1 [ 62 ]. The Invader probes comprising monomers Z1 or Z2 with a phosphorothioate backbone are more stable towards nucleolytic degradation, although they display less efficient recognition of dsDNA targets [ 239 ].…”