Polycytosine regions contained in DNA hairpin loops interact via a four-stranded, parallel structure similar to the i-motif.
Thermal denaturation profiles of an oligodeoxynucleotide that forms a hairpin structure with a cytidine-rich loop show an unexpected transition at 60 degrees C at pH 5.0 but not at pH 8.0. Analytical ultracentrifugation shows that this transition reflects dimer formation via the interaction of loops from two molecules to form a novel structure termed the h-dimer. The dependence of this structure on low pH implies the formation of cytosine-protonated cytosine base pairs. NMR spectroscopy, thermal denaturation and ultraviolet absorption spectral analysis suggest a similarity to the i-motif structure recently proposed for the interaction of deoxycytidine oligomers. The use of hairpin loops to form i-motif-like structures may prove useful in searches for cognate proteins and possibly in the production of antibodies.
Rohozinski
J
J
Research School of Biological Sciences, Australian National University, Canberra.
Hancock
J M
JM
Keniry
M A
MA
D001483:Base Sequence; D002499:Centrifugation, Density Gradient; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry*; D006863:Hydrogen-Ion Concentration; D009682:Magnetic Resonance Spectroscopy; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D011066:Poly C / Q000737:chemistry*; D011089:Polydeoxyribonucleotides / Q000737:chemistry; D013056:Spectrophotometry, Ultraviolet; D013696:Temperature
D011089:Polydeoxyribonucleotides; D011066:Poly C; D004247:DNA