Three Pyrene-Modified Nucleotides: Synthesis and Effects in Secondary Nucleic Acid Structures

Abstract

Synthesis of three pyrene-modified nucleosides was accomplished using the CuAAC reaction. Hereby, pyrene is attached either to the 5'-position of thymidine or to the 2'-position of 2'-deoxyuridine through triazolemethylene linkers, or to the 2'-position of 2'-deoxyuridine through a more rigid triazole linker. The three nucleosides were incorporated into oligonucleotides, and these were combined in different duplexes and other secondary structures, which were analyzed by thermal stability and fluorescence studies. The three monomers were found to have different impacts on the nucleic acid complexes. Hence, pyrene attached to the 5'-position shows a tendency for intercalation into the duplex as indicated by a general decrease in fluorescence intensity followed by an increase in duplex thermal stability. Pyrene attached to the 2'-position through a rigid triazole linker also shows a tendency for intercalation but with decrease in duplex stability, whereas the pyrene attached to the 2'-position through a triazolemethylene linker is primarily situated in the minor groove as indicated by an increase in fluorescence but here in most cases leading to increase in duplex stability. All three pyrene nucleotides lead to thermal stabilization of bulged duplexes and three-way junctions. In some cases when two pyrenes were introduced into the core of these complexes, the formation or disappearance of a fluorescence excimer band can be used to indicate the hybridization process. Hereby these oligonucleotides can act as specific recognition probes.

Postsynthetic modification of peptoids via the Suzuki‐Miyaura cross‐coupling reaction

“…In addition, side chain decoration of peptoids with fluorescent dyes can provide valuable backbone structural information and altered optical property of the dyes . Among fluorescent dyes, pyrene has been one of the most frequently used for a variety of applications, such as in sensing probes and for structural study of biopolymers . In particular, its ability to form fluorescent excimers via π‐π interactions has made pyrene a molecule of choice for constructing various molecular reporter systems.…”

Double-headed nucleotides in DNA-zipper structures; base–base interactions and UV-induced cross-coupling in the minor groove

“…{ Recently, a pyrene-triazole moiety in the 59-C-position has led to some increase in thermal stability of a duplex but probably due to intercalation of the pyrene into the duplex. 38…”

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

“…A large diversity of the pyrene-modified nucleotide monomers obtained through presynthetic [ 69 , 70 , 71 , 72 , 73 , 74 , 75 ] or postsynthetic [ 76 , 77 , 78 , 79 , 80 , 81 ] conjugation of pyrene derivatives with modified nucleotides or oligonucleotides via Cu(I)-catalyzed azide alkyne Huisgen 1,3-dipolar cycloaddition (CuAAC) has been reported over the past several years.…”

“…At the same time, Nielsen and coauthors have introduced a series of pyrene-modified nucleosides ( Figure 5 ) accomplished with the use of the CuAAC reaction [ 72 , 75 ].…”

“…In case of the 2′Uapy monomer linker between pyrene and ribose being rigid, resulting in the tendency of pyrene to intercalate into the DNA:DNA duplexes, however, the thermal stability of the duplexes decreases. The pyrene moiety of the 2′Uampy monomer is most probably partly positioned in the minor groove, as the effect on fluorescence intensity varies on the nucleobase sequence, but in most cases leading to an increase in duplex stability [ 72 ]. On the other hand, the pyrene attached to the 2′-position of arabino-uridine 2′araUampy tends to intercalate into DNA:DNA duplexes, thus strongly stabilizing DNA duplexes.…”