Cyanine dyes are important chemical modifications of oligonucleotides exhibiting intensive
and stable fluorescence at visible light wavelengths. When Cy3 or Cy5 dye is attached to …

Single and dual-labeled fluorescent oligodeoxynucleotides are used in many molecular
biology applications. We investigated the effects of commonly used fluorescent dyes and …

Long terminal unpaired nucleotides known as dangling ends play interesting roles in
biological systems. Previous studies, however, only dealt with the energy contributions of …

Optical spectroscopy and molecular dynamics simulations have been used to study the
interaction between a cationic cyanine dye and peptide nucleic acid (PNA)− DNA duplexes …

Locked nucleic acids (LNA; symbols of bases,+ A,+ C,+ G, and+ T) are introduced into
chemically synthesized oligonucleotides to increase duplex stability and specificity. To …

To understand the influences of the ribonucleotide on a duplex conformation and its stability,
we systematically studied the CD spectra and the thermodynamics of nucleic acid duplexes …

Peptide nucleic acid (PNA) is an oligonucleotide analogue in which the sugar− phosphate
backbone is replaced by an N-(2-aminoethyl) glycine unit to which the nucleobases are …

The geometry of the dangling base in 105 published structures (from X-ray/NMR) containing
single-stranded overhangs has been analyzed and correlated to the thermodynamic …

The thermodynamics of DNA duplex structures in the presence of high concentrations of
cosolutes in solution were investigated to discern nucleic acid structures and functions in …

Computational chemistry (B3LYP, MP2) is used to study the properties of size-expanded
DNA nucleobases generated by inserting a benzene spacer into the natural nucleobases …