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Mechanism of oligonucleotide loop formation in solution.

Abstract：

: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.

journal_name

Biochemistry

journal_title

Biochemistry

authors

Roy S,Weinstein S,Borah B,Nickol J,Appella E,Sussman JL,Miller M,Shindo H,Cohen JS

doi

10.1021/bi00371a025

subject

Has Abstract

pub_date

1986-11-18 00:00:00

pages

7417-23

issue

23

eissn

0006-2960

issn

1520-4995

journal_volume

25

pub_type

杂志文章

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