Base Pair Mismatch

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Hui Li - One of the best experts 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 Base-Pair sequences are the foundation for the biological processes of DNA or RNA, and Base-Pair Mismatch is very important to reveal genetic diseases and DNA rearrangements. However, the lack of well-defined structural information about Base-Pair Mismatch is obstructing the investigation of this issue. The challenge is to crystallize the materials containing the Base-Pair 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 Base-Pair 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 Base-Pair sequences are the foundation for the biological processes of DNA or RNA, and Base-Pair Mismatch is very important to reveal genetic diseases and DNA rearrangements. However, the lack of well-defined structural information about Base-Pair Mismatch is obstructing the investigation of this issue. The challenge is to crystallize the materials containing the Base-Pair 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 Base-Pair 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 - One of the best experts on this subject based on the ideXlab platform.

David A. Stahl - One of the best experts 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, Said El Fantroussi, James C Smoot, Erik H Tribou, Peter A Noble, John J. Kelly, Hauke Smidt, David A. Stahl
    Abstract:

    The discrimination between perfect-match and single-Base-Pair-Mismatched 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-Base-Pair 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, Said El Fantroussi, Peter A Noble, John J. Kelly, David A. Stahl
    Abstract:

    The effects of single-Base-Pair 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-Base-Pair 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.

Pei Zhou - One of the best experts 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 Base-Pair sequences are the foundation for the biological processes of DNA or RNA, and Base-Pair Mismatch is very important to reveal genetic diseases and DNA rearrangements. However, the lack of well-defined structural information about Base-Pair Mismatch is obstructing the investigation of this issue. The challenge is to crystallize the materials containing the Base-Pair 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 Base-Pair 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 Base-Pair sequences are the foundation for the biological processes of DNA or RNA, and Base-Pair Mismatch is very important to reveal genetic diseases and DNA rearrangements. However, the lack of well-defined structural information about Base-Pair Mismatch is obstructing the investigation of this issue. The challenge is to crystallize the materials containing the Base-Pair 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 Base-Pair 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.

Jiyoun Jeong - One of the best experts on this subject based on the ideXlab platform.

  • Base Pair Mismatch can destabilize small dna loops through cooperative kinking
    Physical Review Letters, 2019
    Co-Authors: Jiyoun Jeong
    Abstract:

    : Base-Pair Mismatch can relieve mechanical stress in highly strained DNA molecules, but how it affects their kinetic stability is not known. Using single-molecule fluorescence resonance energy transfer, we measured the lifetimes of tightly bent DNA loops with and without Base-Pair Mismatch. Surprisingly, for loops captured by stackable sticky ends which leave single-stranded DNA breaks (or nicks) upon annealing, the Mismatch decreased the loop lifetime despite reducing the overall bending stress, and the decrease was largest when the Mismatch was placed at the DNA midpoint. These findings suggest that Base-Pair Mismatch increases bending stress at the opposite side of the loop through an allosteric mechanism known as cooperative kinking. Based on this mechanism, we present a three-state model that explains the apparent dichotomy between thermodynamic and kinetic stability.

  • Base Pair Mismatch can destabilize small dna loops through cooperative kinking
    bioRxiv, 2019
    Co-Authors: Jiyoun Jeong
    Abstract:

    Base Pair Mismatch can relieve mechanical stress in highly strained DNA molecules, but how it affects their kinetic stability is not known. Using single-molecule Fluorescence Resonance Energy Transfer (FRET), we measured the lifetimes of tightly bent DNA loops with and without Base Pair Mismatch. Surprisingly, for loops captured by stackable sticky ends, the Mismatch decreased the loop lifetime despite reducing the overall bending stress, and the decrease was largest when the Mismatch was placed at the DNA midpoint. These findings show that Base Pair Mismatch transfers bending stress to the opposite side of the loop through an allosteric mechanism known as cooperative kinking. Based on this mechanism, we present a three-state model that explains the apparent dichotomy between thermodynamic and kinetic stability of DNA loops.