Stabilization of the DNA I-Motif Structure by Incorporation of 3′-S-Phosphorothiolate Linkages

i-Motif DNA: identification, formation, and cellular functions

An i-motif (iM) is a four-stranded (quadruplex) DNA structure that folds from cytosine (C)-rich sequences. iMs can fold under many different conditions in vitro, which paves the way for their formation in living cells. iMs are thought to play key roles in various DNA transactions, notably in the regulation of genome stability, gene transcription, mRNA translation, DNA replication, telomere and centromere functions, and human diseases. We summarize the different techniques used to assess the folding of iMs in vitro and provide an overview of the internal and external factors that affect their formation and stability in vivo. We describe the possible biological relevance of iMs and propose directions towards their use as target in biology.

Stabilization of a Bimolecular Triplex by 3'-S-Phosphorothiolate Modifications: An NMR and UV Thermal Melting Investigation

Triplexes formed from oligonucleic acids are key to a number of biological processes. They have attracted attention as molecular biology tools and as a result of their relevance in novel therapeutic strategies. The recognition properties of single-stranded nucleic acids are also relevant in third-strand binding. Thus, there has been considerable activity in generating such moieties, referred to as triplex forming oligonucleotides (TFOs). Triplexes, composed of Watson-Crick (W-C) base-paired DNA duplexes and a Hoogsteen base-paired RNA strand, are reported to be more thermodynamically stable than those in which the third strand is DNA. Consequently, synthetic efforts have been focused on developing TFOs with RNA-like structural properties. Here, the structural and stability studies of such a TFO, composed of deoxynucleic acids, but with 3'-S-phosphorothiolate (3'-SP) linkages at two sites is described. The modification results in an increase in triplex melting temperature as determined by UV absorption measurements. (1) H NMR analysis and structure generation for the (hairpin) duplex component and the native and modified triplexes revealed that the double helix is not significantly altered by the major groove binding of either TFO. However, the triplex involving the 3'-SP modifications is more compact. The 3'-SP modification was previously shown to stabilise G-quadruplex and i-motif structures and therefore is now proposed as a generic solution to stabilising multi-stranded DNA structures.

Oligonucleotides forming an i-motif: the pH-dependent assembly of individual strands and branched structures containing 2'-deoxy-5-propynylcytidine

Non-branched and branched oligonucleotides incorporating consecutive runs of 2'-deoxy-5-propynylcytidine residues () instead of 2'-deoxycytidine () were synthesized. For this, phosphoramidite building blocks of 2'-deoxy-5-propynylcytidine () were prepared using acetyl, benzoyl or N,N-di-n-butylaminomethylidene protecting groups. The formation of the i-motif assemblies incorporating 2'-deoxy-5-propynylcytidine residues was confirmed by temperature-dependent CD- and UV-spectra as well as by ion-exchange chromatography. The low pK(a)-value of nucleoside (pK(a) = 3.3) compared to dC (pK(a) = 4.5) required strong acidic conditions for i-motif formation. Branched oligonucleotide residues with strands in a parallel orientation lead to a strong stabilization of the i-motif allowing aggregation even at non-optimal pH conditions (pH = 5). The immobilization of oligonucleotides incorporating multiple residues of on 15 nm gold nanoparticles generated DNA-gold nanoparticle conjugates which are able to aggregate into i-motif structures at pH 5.

Switch of Electronic Reactivity in Fullerene C60: Activation of Three trans-4 Positions via Temporary Saturation of the cis-1 Positions

[Structure: see text] The regioselective functionalization of C60 with a trans-4,trans-4,trans-4 trisaddition pattern is not feasible directly. We have found an indirect approach taking advantage of the modified electronic reactivity of cis-1 bisadducts. The cis-1 addition pattern electronically activates three trans-4 C=C bonds on the opposite hemisphere of C60, allowing further highly regioselective additions at these positions. Thermal removal of the cis-1 blocking unit results in a trans-4,trans-4,trans-4 trisadduct with C3v symmetry.