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Base Pair Mismatch

The Experts below are selected from a list of 171 Experts worldwide ranked by ideXlab platform

Hui Li – 1st expert on this subject based on the ideXlab platform

  • cytosine cytosine Base Pair Mismatch and chirality in nucleotide supramolecular coordination complexes
    Chemistry: A European Journal, 2017
    Co-Authors: Pei Zhou, Leilei Gu, Hui Li

    Abstract:

    : The BasePair sequences are the foundation for the biological processes of DNA or RNA, and BasePair Mismatch is very important to reveal genetic diseases and DNA rearrangements. However, the lack of well-defined structural information about BasePair Mismatch is obstructing the investigation of this issue. The challenge is to crystallize the materials containing the BasePair Mismatch. Engineering the small-molecule mimics or model is an effective strategy to solve this issue. Here, six cytidine-5′-monophosphate (CMP) and 2′-deoxycytidine-5′-monophosphate (dCMP) coordination polymers were reported containing cytosine-cytosine BasePair Mismatch (i-motif), and their single-crystal structures and chiralities were studied. The precise control over the formation of the i-motif was demonstrated, in which the regulating of supramolecular interactions was achieved Based on molecular design. In addition, the chiralities of these coordination polymers were investigated according to their crystal structures and solution- and solid-state circular dichroism spectroscopy.

  • Cytosine–Cytosine BasePair Mismatch and Chirality in Nucleotide Supramolecular Coordination Complexes
    Chemistry: A European Journal, 2017
    Co-Authors: Pei Zhou, Leilei Gu, Hui Li

    Abstract:

    : The BasePair sequences are the foundation for the biological processes of DNA or RNA, and BasePair Mismatch is very important to reveal genetic diseases and DNA rearrangements. However, the lack of well-defined structural information about BasePair Mismatch is obstructing the investigation of this issue. The challenge is to crystallize the materials containing the BasePair Mismatch. Engineering the small-molecule mimics or model is an effective strategy to solve this issue. Here, six cytidine-5′-monophosphate (CMP) and 2′-deoxycytidine-5′-monophosphate (dCMP) coordination polymers were reported containing cytosine-cytosine BasePair Mismatch (i-motif), and their single-crystal structures and chiralities were studied. The precise control over the formation of the i-motif was demonstrated, in which the regulating of supramolecular interactions was achieved Based on molecular design. In addition, the chiralities of these coordination polymers were investigated according to their crystal structures and solution- and solid-state circular dichroism spectroscopy.

J Crain – 2nd expert on this subject based on the ideXlab platform

  • Base Pair Mismatch identification with dna nanoswitch and long lifetime acridine fluorophore
    Sensors and Actuators B-chemical, 2010
    Co-Authors: Colin D Mcguinness, J Crain, David Keszenmanpereyra, Paul Dickinson, Colin Campbell, Beatrice A Maltman, Till T Bachmann, Peter Ghazal

    Abstract:

    Detection of single Base Pair mutations in an unlabelled nucleic acid target sequence is demonstrated using the time-resolved measurement of the Forster Resonance Energy Transfer (FRET) between a long lifetime acridine-Based fluorophore and a non-fluorescent quencher molecule covalently bound to a DNA Holliday junction-Based nanoswitch.

David A. Stahl – 3rd expert on this subject based on the ideXlab platform

  • optimization of single Base Pair Mismatch discrimination in oligonucleotide microarrays
    Applied and Environmental Microbiology, 2003
    Co-Authors: Hidetoshi Urakawa, Peter A Noble, Said El Fantroussi, John J. Kelly, Hauke Smidt, James C Smoot, Erik H Tribou, David A. Stahl

    Abstract:

    The discrimination between perfect-match and single-BasePairMismatched nucleic acid duplexes was investigated by using oligonucleotide DNA microarrays and nonequilibrium dissociation rates (melting profiles). DNA and RNA versions of two synthetic targets corresponding to the 16S rRNA sequences of Staphylococcus epidermidis (38 nucleotides) and Nitrosomonas eutropha (39 nucleotides) were hybridized to perfect-match probes (18-mer and 19-mer) and to a set of probes having all possible single-BasePair Mismatches. The melting profiles of all probe-target duplexes were determined in parallel by using an imposed temperature step gradient. We derived an optimum wash temperature for each probe and target by using a simple formula to calculate a discrimination index for each temperature of the step gradient. This optimum corresponded to the output of an independent analysis using a customized neural network program. These results together provide an experimental and analytical framework for optimizing Mismatch discrimination among all probes on a DNA microarray.

  • single Base Pair discrimination of terminal Mismatches by using oligonucleotide microarrays and neural network analyses
    Applied and Environmental Microbiology, 2002
    Co-Authors: Hidetoshi Urakawa, Peter A Noble, Said El Fantroussi, John J. Kelly, David A. Stahl

    Abstract:

    The effects of single-BasePair near-terminal and terminal Mismatches on the dissociation temperature (Td) and signal intensity of short DNA duplexes were determined by using oligonucleotide microarrays and neural network (NN) analyses. Two perfect-match probes and 29 probes having a single-BasePair Mismatch at positions 1 to 5 from the 5′ terminus of the probe were designed to target one of two short sequences representing 16S rRNA. Nonequilibrium dissociation rates (i.e., melting profiles) of all probe-target duplexes were determined simultaneously. Analysis of variance revealed that position of the Mismatch, type of Mismatch, and formamide concentration significantly affected the Td and signal intensity. Increasing the concentration of formamide in the washing buffer decreased the Td and signal intensity, and it decreased the variability of the signal. Although Tds of probe-target duplexes with Mismatches in the first or second position were not significantly different from one another, duplexes with Mismatches in the third to fifth positions had significantly lower Tds than those with Mismatches in the first or second position. The trained NNs predicted the Td with high accuracies (R2 = 0.93). However, the NNs predicted the signal intensity only moderately accurately (R2 = 0.67), presumably due to increased noise in the signal intensity at low formamide concentrations. Sensitivity analysis revealed that the concentration of formamide explained most (75%) of the variability in Tds, followed by position of the Mismatch (19%) and type of Mismatch (6%). The results suggest that position of the Mismatch at or near the 5′ terminus plays a greater role in determining the Td and signal intensity of duplexes than the type of Mismatch.