Mechanism of oligonucleotide loop formation in solution

Roy, Siddhartha ; Weinstein, Shulamith ; Borah, Babul ; Nickol, Joanne ; Appella, Ettore ; Sussman, Joel L. ; Miller, Maria ; Shindo, Heisaburo ; Cohen, Jack S. (1986) Mechanism of oligonucleotide loop formation in solution Biochemistry, 25 (23). pp. 7417-7423. ISSN 0006-2960

Full text not available from this repository.

Official URL:

Related URL:


We have studied the tridecadeoxynucleotide CGCGAATTACGCG (I), which contains an additional A at position 9 compared to the dodecanucleotide of which the crystal structure has been determined. Sequence I exhibits no distinct melting curve and also has a concentration-dependent pattern of peaks on reverse-phase chromatography. This behavior is explained by a slow equilibration between loop and duplex forms in solution. We have characterized this equilibrium by proton NMR spectroscopy and shown that it is fully reversible by monitoring the two thymine methyl resonances, each of which occurs in two environments. Lower temperature and higher concentration favor the duplex; the midpoint of the transition is such that the loop predominates at room temperature. We have measured the van't Hoff enthalpy of formation of the duplex and the activation energy by temperature-jump and saturation-transfer experiments. The results are compared with those for the 17-mer sequence CGCGCGAATTACGCGCG (II), which contains two additional base pairs in the stem of the loop. The thermodynamic parameters and the effect of increasing salt concentration on the rate of conversion of the loop and duplex forms lead us to presume that the mechanism of interconversion involves complete strand separation and re-formation rather than cruciform formation and branch migration.

Item Type:Article
Source:Copyright of this article belongs to American Chemical Society.
ID Code:43131
Deposited On:10 Jun 2011 05:54
Last Modified:10 Jun 2011 05:54

Repository Staff Only: item control page