title: Effect of LNA- and OMeN-modified oligonucleotide probes on the stability and discrimination of  mismatched base pairs of duplexes.
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.
authors.affiliation: Department of Biochemistry and Molecular Biology, Key Laboratory of Medical Cell Biology of Minister of Education, China Medical University, Shenyang, Liaoning, 110001, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Yan
authors.forename: Jing
authors.initials: J
authors.lastname: Yan
authors.forename: Xianyu
authors.initials: X
authors.lastname: Piao
authors.forename: Tianbiao
authors.initials: T
authors.lastname: Zhang
authors.forename: Yifu
authors.initials: Y
authors.lastname: Guan
mesh_terms: D020137:Base Pair Mismatch; D004247:DNA / Q000737:chemistry / Q000235:genetics; D018076:DNA, Complementary / Q000737:chemistry / Q000235:genetics; D009691:Nucleic Acid Denaturation; D009693:Nucleic Acid Hybridization / Q000379:methods*; D009711:Nucleotides / Q000737:chemistry; D015345:Oligonucleotide Probes / Q000737:chemistry*; D009841:Oligonucleotides / Q000737:chemistry*; D013696:Temperature
chemical_list: D018076:DNA, Complementary; D009711:Nucleotides; D015345:Oligonucleotide Probes; D009841:Oligonucleotides; C477371:locked nucleic acid; D004247:DNA