Self-duplex formation of an A(py)-substituted oligodeoxyadenylate and its unique fluorescence

Probe for i-motif structure and G-rich strands using end-stacking ability

We suggest a novel method for probing human i-motif structure based on a pi-stacking interaction between a base pair of two cytosines and a non-polar aromatic fluorophore, PyA, at the end position.

Homoadenine signalling system for SNP typing

We report a homoadenine-based fluorescent probing system containing two pyrene-modified deoxyadenosine units for SNP typing in homoadenine and homothymine.

Detection of structure-switching in G-quadruplexes using end-stacking ability

G-quadruplex-forming ODNs containing nonpolar aromatic fluorophore moiety, A(PY) at the dangling ends undergo pi-stacking on surface of G-quadruplex, and the fluorescence change can be used to distinguish the structure-switching between the mixed parallel/antiparallel structure and antiparallel structure.

Quencher-free molecular beacons: a new strategy in fluorescence based nucleic acid analysis

Molecular beacons (MBs) have been used as viable fluorescent probes in nucleic acid analysis. Many researchers around the world continue to modify the MBs to suit their needs. As a result, a number of nucleic acid probing systems with close resemblance to the MBs are being reported from time to time. Quencher-free molecular beacons (QF-MBs) are a significant modification of the conventional MB; in QF-MBs the quencher part has been eliminated. Despite the absence of the quencher, the QF-MBs can identify specific target DNA. They can also be used in SNP typing and in real-time PCR analysis for quantification of DNAs. The design, factors behind functioning and applications of different types of QF-MBs and closely related quencher-free nucleic acid probing systems (QF-NAPs) have been described in this tutorial review.

Probing the stable G-quadruplex transition using quencher-free end-stacking ethynyl pyrene-adenosine

Pyrene-modified adenosines in the dangling positions of G-rich oligodeoxynucleotides undergo pi-stacking in their G-quadruplex formation, but not in their single strands, which can be characterized by fluorescence lambda(max) changes that occur on stacking.