4 research outputs found

    Effects of sodium ions on melting temperatures of DNA–DNA and LNA–DNA duplexes

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    <p><b>Copyright information:</b></p><p>Taken from "Design of LNA probes that improve mismatch discrimination"</p><p>Nucleic Acids Research 2006;34(8):e60-e60.</p><p>Published online 2 May 2006</p><p>PMCID:PMC1456327.</p><p>© The Author 2006. Published by Oxford University Press. All rights reserved</p> Duplexes were investigated that had a T•A base pair in the X•Y mismatch site. All duplexes had the same base sequence, 5′-ggtcctttcttggtg-3′/3′-ccaggaaagaaccac-5′, where LNA modifications were introduced at various positions (). Solid lines were calculated using a published salt correction ()

    Dependence of melting temperature and mismatch discrimination on oligomer length

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    <p><b>Copyright information:</b></p><p>Taken from "Design of LNA probes that improve mismatch discrimination"</p><p>Nucleic Acids Research 2006;34(8):e60-e60.</p><p>Published online 2 May 2006</p><p>PMCID:PMC1456327.</p><p>© The Author 2006. Published by Oxford University Press. All rights reserved</p> Average melting temperatures were calculated for 50% g•c DNA duplex oligomers that did not contain any mismatched base pairs as well as oligomers with single g•t or a•c mismatches. Predictions assumed total single strand concentration of 400 nM in 1 M Na buffer

    Fluorescence emission spectra of target oligomer, 5′-gcgaggpggctt-3′, with single 2-aminopurine (p) reveal the magnitude of stacking interactions

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    <p><b>Copyright information:</b></p><p>Taken from "Design of LNA probes that improve mismatch discrimination"</p><p>Nucleic Acids Research 2006;34(8):e60-e60.</p><p>Published online 2 May 2006</p><p>PMCID:PMC1456327.</p><p>© The Author 2006. Published by Oxford University Press. All rights reserved</p> Duplexes containing a H-bonded t•p base pair are compared with mismatched g•p base pair duplexes. Both unmodified DNA probes (blue lines) and probes with a LNA triplet at the mismatch site (red lines) were studied. UV melting experiments in 1 M Na buffer showed that LNA triplets increased mismatch discrimination for these sequences

    Difference of Δ values between LNA and DNA probes for various mismatches

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    <p><b>Copyright information:</b></p><p>Taken from "Design of LNA probes that improve mismatch discrimination"</p><p>Nucleic Acids Research 2006;34(8):e60-e60.</p><p>Published online 2 May 2006</p><p>PMCID:PMC1456327.</p><p>© The Author 2006. Published by Oxford University Press. All rights reserved</p> Sequence Set 1 (panel A and B), and Sets 2 and 3 (panel C) are plotted. Positions of LNA residues and set names are shown in Figure 1. A positive difference indicates improved mismatch discrimination for the LNA probe relative to the DNA probe. Dashed lines denote the range (±0.8°C), which is within the experimental error of the measurements
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