Thermal stability of G-rich anti-parallel DNA triplexes upon insertion of LNA and α-L-LNA.

Tamer R Kosbar,Erik B Pedersen,Mamdouh A Sofan,Laila Abou-Zeid

doi:10.1039/c5ob00535c

Tamer R Kosbar, Erik B Pedersen + Show 2 more

Open Access

https://doi.org/10.1039/c5ob00535c

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Abstract

G-rich anti-parallel DNA triplexes were modified with LNA or α-L-LNA in their Watson-Crick and TFO strands. The triplexes were formed by targeting a pyrimidine strand to a putative hairpin formed by Hoogsteen base pairing in order to use the UV melting method to evaluate the stability of the triplexes. Their thermal stability was reduced when the TFO strand was modified with LNA or α-L-LNA. The same trend was observed when the TFO strand and the purine Watson-Crick strand both were modified with LNA. When all triad components were modified with α-L-LNA and LNA in the middle of the triplex, the thermal melting was increased. When the pyrimidine sequence was modified with a single insertion of LNA or α-L-LNA the ΔTm increased. Moreover, increasing the number of α-L-LNA in the pyrimidine target sequence to six insertions, leads to a high increase in the thermal stability. The conformational S-type structure of α-L-LNA in anti-parallel triplexes is preferable for triplex stability.

Highlights

DNA triplexes are formed when a DNA duplex containing a polypurine tract interacts with a third strand by means of specific hydrogen bonds in the major groove of the duplex
The results showed that, multi insertion of α-L-LNA (Tα and Cα) in the pyrimidine target sequence increase the stacking between the nucleobases in the three strands of the anti-parallel triplex which reflects the high thermal stability of ON25 (Fig. 5a)
When the TFO, Watson–Crick and the target strands were modified with Tα, AL and Tα, respectively (Fig. 5b), the triplex structure was undisturbed and the Tαnucleobase in the TFO strand hybridized nicely to the nucleobase AL in the Watson–Crick duplex, thereby explaining the increase in stability when the three strands were modified with α-L-LNA and LNA (ON12)

Summary

Introduction

DNA triplexes are formed when a DNA duplex containing a polypurine tract interacts with a third strand by means of specific hydrogen bonds in the major groove of the duplex. One insertion of Tα in the pyrimidine target sequence and in the TFO part decreased the thermal stability of the anti-parallel triplex by only 0.5 °C (ON14).

Results

Conclusion