Metal ions cause the isomerization of certain intramolecular triplexes.

S M Kang,F Wohlrab,R D Wells

doi:10.1016/s0021-9258(18)48423-2

S M Kang, F Wohlrab + Show 1 more

Open Access

https://doi.org/10.1016/s0021-9258(18)48423-2

Copy DOI

Abstract

The influence of cations on the capacity of five oligopurine.oligopyrimidine mirror repeat sequences to adopt intramolecular triplexes (the usual H-y3 isomer and/or the rare H-y5 isomer) in recombinant plasmids was investigated. Unexpectedly, the presence of certain metal ions (magnesium, zinc, manganese, and calcium) stabilized the (GAA)4TTCGC(GAA)4 insert in the rare H-y5 when cloned into either of two different sequence backgrounds. Alternatively, either shortening or lengthening the sequence at the central interruption, which becomes the loop of the triplex, led to the formation of the canonical H-y3 under all conditions tested. Similarly, other oligopurine.oligopyrimidine mirror repeat sequences (i.e. (GAA)8 or (GGA)8) formed only the H-y3 under all experimental conditions. All triplexes were stabilized by negative supercoiling at pH 5.0; chemical probe and primer extension analyses served as critical structural tools. Hence, the nature of the central interruption sequence (the loop) of the mirror repeat is important for the stabilization of the H-y5. This region may be important for metal ion binding in the initial stages of triplex formation and thus may play a critical role in determining which isomer is formed. The possible biological role of a DNA sequence adopting three different conformations is discussed.

Highlights

The influence of cations on the capacity offive oli- [9] demonstrated that an AG repeat sequence interrupted by gopurine.oligopyrimidine mirror repeat sequences to a 12-nucleotide non-pur .pyr spacer adopted two different adopt intramoleculartriplexes
Sequences (i.e. (GAA)s or (GGA)s) formed only the H- An intramolecular triplex may exist in one of two isomers y 3 under all experimentalconditions.All triplexes (Fig. 1).In one isomer, the 5’ half of the purine strand is the were stabilized by negative supercoilingat pH 5.0; single strand, and the 3’ junction of the pyrimidine strand chemical probe and primerextension analyses served between B-DNA and the triplex may be unpaired (H-y3)
The nature of the the other, the3‘ half of the purine strand is single stranded, central interruption sequence(the loop) of the mirror and the5’ junction of the pyrimidine strand may be unpaired repeat is important for the stabilization of the H-y5. (H-y5)

Summary

Metal Ions Cause the Isomerizationof Certain Intramolecular Triplexes*

The nature of the the other, the3‘ half of the purine strand is single stranded, central interruption sequence(the loop) of the mirror and the5’ junction of the pyrimidine strand may be unpaired repeat is important for the stabilization of the H-y5. It appears that isomerization can be influenced by more than one factor since some pur .pyr sequences were reported not to form the H-y5 at DNA adopts various conformations as dictated by its sequence Several types of mirror repeat pur-pyr sequences form intramolecular triplexes inwhich one half of the pyrimidine strand folds back and hydrogen bonds via Hoogsteen base pairswith half of the purine strand in thWe atson-Crick duplex resulting in C+GCand TATbase triads anda singlestranded region (the “other” half of the purine-rich strand) (reviewed in 4).

Isomerization of ITnrtripalmexoelescular

RESULTS

DISCUSSION