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Effect of LNA- and OMeN-modified oligonucleotide probes on the stability and discrimination of mismatched base pairs of duplexes

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Abstract

Locked nucleic acid (LNA) and 2′-O-methyl nucleotide (OMeN) are the most extensively studied nucleotide analogues. Although both LNA and OMeN are characterized by the C3′-endo sugar pucker conformation, which is dominant in A-form DNA and RNA nucleotides, they demonstrate different binding behaviours. Previous studies have focused attention on their properties of duplex stabilities, hybridization kinetics and resistance against nuclease digestion; however, their ability to discriminate mismatched hybridizations has been explored much less. In this study, LNA- and OMeN-modified oligonucleotide probes have been prepared and their effects on the DNA duplex stability have been examined: LNA modifications can enhance the duplex stability, whereas OMeN modifications reduce the duplex stability. Next, we studied how the LNA:DNA and OMeN:DNA mismatches reduced the duplex stability. Melting temperature measurement showed that different LNA:DNA or OMeN:DNA mismatches indeed influence the duplex stability differently. LNA purines can discriminate LNA:DNA mismatches more effectively than LNA pyrimidines as well as DNA nucleotides. Furthermore, we designed five LNA- and five OMeN-modified oligonucleotide probes to simulate realistic situations where target–probe duplexes contain a complementary LNA:DNA or OMeN:DNA base pairs and a DNA:DNA mismatch simultaneously. The measured collective effect showed that the duplex stability was enhanced by the complementary LNA:DNA base pair but decreased by the DNA:DNA mismatch in a position-dependent manner regardless of the chemical identity and position of the complementary LNA:DNA base pair. On the other hand, the OMeN-modified probes also showed that the duplex stability was reduced by both the OMeN modification and the OMeN:DNA mismatch in a position-dependent manner.

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Abbreviations

LNA:

locked nucleic acid

MM:

mismatch

OMeN:

2′-O-methyl nucleotide

PM:

perfect match

RT-PCR:

real-time polymerase chain reaction

SNP:

single nucleotide polymorphism

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Acknowledgements

The authors are grateful for the financial support to YG from the National Natural Science Foundation of China (No. 31070705) and to YY from the Postdoctoral Research Grant of Ministry of Education (20081042).

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  1. Ying Yan

    Present address: Department of Radiotherapy, Shenyang Northern Hospital, Shenyang, Liaoning, 110016, China

Authors and Affiliations

  1. Department of Biochemistry and Molecular Biology, Key Laboratory of Medical Cell Biology of Minister of Education, China Medical University, Shenyang, Liaoning, 110001, China

    Ying Yan, Jing Yan, Xianyu Piao, Tianbiao Zhang & Yifu Guan

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  1. Ying Yan
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  2. Jing Yan
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  3. Xianyu Piao
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  4. Tianbiao Zhang
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  5. Yifu Guan
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Corresponding author

Correspondence to Yifu Guan.

Additional information

Corresponding editor: Basuthkar J Rao

[Yan Y, Yan J, Piao X, Zhang T and Guan Y 2012 Effect of LNA- and OMeN-modified oligonucleotide probes on the stability and discrimination of mismatched base pairs of duplexes. J. Biosci. 37 XXX–XXX] DOI 10.1007/s12038-012-9196-4

[Yan Y Yan J, Piao X, Zhang T and Guan Y 2012 Effect of LNA- and OMeN-modified oligonucleotide probes on the stability and discrimination of mismatched base pairs of duplexes. J. Biosci. 37 DOI 10.1007/s12038-012-9196-4]

Ying Yan and Jing Yan contributed equally.

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Yan, Y., Yan, J., Piao, X. et al. Effect of LNA- and OMeN-modified oligonucleotide probes on the stability and discrimination of mismatched base pairs of duplexes. J Biosci 37, 233–241 (2012). https://doi.org/10.1007/s12038-012-9196-4

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  • DOI: https://doi.org/10.1007/s12038-012-9196-4

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