Enhanced H-bonding and π-stacking in DNA: a potent duplex-stabilizing and mismatch sensing nucleobase analogue

Abstract

Combining enhanced π-stacking, H-bonding and electrostatic attraction in a single C-monomer greatly increases DNA duplex stability and massively destabilises mismatches.

Facile functionalization at the C4 position of pyrimidine nucleosides via amide group activation with (benzotriazol-1-yloxy)tris(dimethylamino)phosphonium hexafluorophosphate (BOP) and biological evaluations of the products

“…7,8 The C4 chloro derivatives can be prepared by one of two methods, either chlorination with SOCl 2 /DMF, 9–12 or via the Appel reaction with PPh 3 /CCl 4 . 13–15 However, such chloro compounds seem labile 16 and have been used immediately upon preparation. For instance, the C4 chloro derivatives were converted to the C4 ethoxy compounds, which were then used in displacement reactions with nucleophiles.…”

Synthesis of α-PNA containing a functionalized triazine as nucleobase analogue

“…10 More recently, it has been shown that the presence of additional side-groups that enhance p-stacking interactions greatly improves the selectivity of a novel nucleobase analogue for its complementary DNA partner. 11 It is therefore important, for promoting hybridization with nucleic acids, to develop synthetic methodologies that enable the construction of biomolecular conjugates featuring functionalized nucleobases tethered to an organic scaffold.…”

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

“…Specific examples of pyrene-modified oligonucleotides reviewed here include sensitive fluorescent probes for the sequence-specific detection of nucleic acids (NAs) and discrimination of single nucleotide polymorphisms (SNPs), aptamer-based biosensors for the detection of a wide range of various targets, agents for binding of dsDNAs, building units of supramolecular complexes, and other applications. These simple synthetically-accessible molecules integrate an excellent recognition capability of oligonucleotides and ability of pyrene to act as microenvironment-sensitive fluorescent label [ 1 , 2 , 3 , 4 ], excimer- or exciplex-generating molecule [ 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 ], NA complex intercalator [ 16 , 17 , 18 , 19 ], or π-π-staking hydrophobic moiety [ 20 , 21 ]. It is worth noting that these functions of pyrene are especially brightly expressed in the NA context.…”