The Experts below are selected from a list of 291 Experts worldwide ranked by ideXlab platform

Luke Masson - One of the best experts on this subject based on the ideXlab platform.

  • designing better Probes effect of Probe Size mismatch position and number on hybridization in dna oligonucleotide microarrays
    Journal of Microbiological Methods, 2004
    Co-Authors: Jaroslaw Letowski, Roland Brousseau, Luke Masson
    Abstract:

    Abstract DNA microarrays represent a powerful technology whose use has been hampered by the uncertainty of whether the same principles, established on a scale typical for membrane hybridizations, apply when using the smaller, rigid support of microarrays. Our goal was to understand how the number and position of base pair mismatches, Probe length and their G+C content affect the intensity and specificity of the hybridization signal. One set of oligonucleotides (50-mers) based on three regions of the Bacillus thuringiensis cry1Aa1 gene possessing 30%, 42%, and 56% G+C content, a second set with similar G+C content (37% to 40%) but different lengths (30 to 100 bases), and finally amplicon Probes (101 to 3000 base pairs) with G+C contents of 37% to 39%, were used. Probes with mismatches distributed over their entire length were the most specific, while those with mismatches grouped at either the 3′ or 5′-end were the least specific. Hybridizations done at 8 to 13 °C below the calculated Tm of perfectly matched Probes, as compared to the widely used lower temperatures of 20 to 25 °C, enhanced Probe discrimination. Longer Probes produced higher fluorescent hybridization signals than shorter ones. These results should help to optimize the design of oligonucleotide-based DNA microarrays.

  • designing better Probes effect of Probe Size mismatch position and number on hybridization in dna oligonucleotide microarrays
    Journal of Microbiological Methods, 2004
    Co-Authors: Jaroslaw Letowski, Roland Brousseau, Luke Masson
    Abstract:

    DNA microarrays represent a powerful technology whose use has been hampered by the uncertainty of whether the same principles, established on a scale typical for membrane hybridizations, apply when using the smaller, rigid support of microarrays. Our goal was to understand how the number and position of base pair mismatches, Probe length and their G+C content affect the intensity and specificity of the hybridization signal. One set of oligonucleotides (50-mers) based on three regions of the Bacillus thuringiensis cry1Aa1 gene possessing 30%, 42%, and 56% G+C content, a second set with similar G+C content (37% to 40%) but different lengths (30 to 100 bases), and finally amplicon Probes (101 to 3000 base pairs) with G+C contents of 37% to 39%, were used. Probes with mismatches distributed over their entire length were the most specific, while those with mismatches grouped at either the 3' or 5'-end were the least specific. Hybridizations done at 8 to 13 degrees C below the calculated T(m) of perfectly matched Probes, as compared to the widely used lower temperatures of 20 to 25 degrees C, enhanced Probe discrimination. Longer Probes produced higher fluorescent hybridization signals than shorter ones. These results should help to optimize the design of oligonucleotide-based DNA microarrays.

Jaroslaw Letowski - One of the best experts on this subject based on the ideXlab platform.

  • designing better Probes effect of Probe Size mismatch position and number on hybridization in dna oligonucleotide microarrays
    Journal of Microbiological Methods, 2004
    Co-Authors: Jaroslaw Letowski, Roland Brousseau, Luke Masson
    Abstract:

    Abstract DNA microarrays represent a powerful technology whose use has been hampered by the uncertainty of whether the same principles, established on a scale typical for membrane hybridizations, apply when using the smaller, rigid support of microarrays. Our goal was to understand how the number and position of base pair mismatches, Probe length and their G+C content affect the intensity and specificity of the hybridization signal. One set of oligonucleotides (50-mers) based on three regions of the Bacillus thuringiensis cry1Aa1 gene possessing 30%, 42%, and 56% G+C content, a second set with similar G+C content (37% to 40%) but different lengths (30 to 100 bases), and finally amplicon Probes (101 to 3000 base pairs) with G+C contents of 37% to 39%, were used. Probes with mismatches distributed over their entire length were the most specific, while those with mismatches grouped at either the 3′ or 5′-end were the least specific. Hybridizations done at 8 to 13 °C below the calculated Tm of perfectly matched Probes, as compared to the widely used lower temperatures of 20 to 25 °C, enhanced Probe discrimination. Longer Probes produced higher fluorescent hybridization signals than shorter ones. These results should help to optimize the design of oligonucleotide-based DNA microarrays.

  • designing better Probes effect of Probe Size mismatch position and number on hybridization in dna oligonucleotide microarrays
    Journal of Microbiological Methods, 2004
    Co-Authors: Jaroslaw Letowski, Roland Brousseau, Luke Masson
    Abstract:

    DNA microarrays represent a powerful technology whose use has been hampered by the uncertainty of whether the same principles, established on a scale typical for membrane hybridizations, apply when using the smaller, rigid support of microarrays. Our goal was to understand how the number and position of base pair mismatches, Probe length and their G+C content affect the intensity and specificity of the hybridization signal. One set of oligonucleotides (50-mers) based on three regions of the Bacillus thuringiensis cry1Aa1 gene possessing 30%, 42%, and 56% G+C content, a second set with similar G+C content (37% to 40%) but different lengths (30 to 100 bases), and finally amplicon Probes (101 to 3000 base pairs) with G+C contents of 37% to 39%, were used. Probes with mismatches distributed over their entire length were the most specific, while those with mismatches grouped at either the 3' or 5'-end were the least specific. Hybridizations done at 8 to 13 degrees C below the calculated T(m) of perfectly matched Probes, as compared to the widely used lower temperatures of 20 to 25 degrees C, enhanced Probe discrimination. Longer Probes produced higher fluorescent hybridization signals than shorter ones. These results should help to optimize the design of oligonucleotide-based DNA microarrays.

Rajarshi Chakrabarti - One of the best experts on this subject based on the ideXlab platform.

  • transport of Probe particles in a polymer network effects of Probe Size network rigidity and Probe polymer interaction
    Soft Matter, 2019
    Co-Authors: Praveen Kumar, Ligesh Theeyancheri, Subhasish Chaki, Rajarshi Chakrabarti
    Abstract:

    Fundamental understanding of the effect of microscopic parameters on the dynamics of Probe particles in different complex environments has wide implications. Examples include diffusion of proteins in biological hydrogels, porous media, polymer matrix, etc. Here, we use extensive molecular dynamics simulations to investigate the dynamics of the Probe particle in a polymer network on a diamond lattice, which provides substantial crowding to mimic the cellular environment. Our simulations show that the dynamics of the Probe increasingly becomes restricted, non-Gaussian and subdiffusive on increasing the network rigidity, binding affinity and Probe Size. In addition, the velocity autocorrelation functions show negative dips owing to the viscoelasticity and caging due to the surrounding network. These observations go with the general experimental findings. Importantly, for a Probe particle of Size comparable to the mesh Size, unrestricted motion engulfing large length scales has been observed. This happens with a more flexible polymer network, which is easily pushed by the bigger Probe. On increasing the rigidity of the network, the bigger Probe can not efficiently push the network and as a result the long tail disappears. Our study gives a general qualitative picture of the transport of Probes in a gel-like medium, as encountered in different contexts.

  • Transport of Probe particles in a polymer network: effects of Probe Size, network rigidity and Probe–polymer interaction
    Soft matter, 2019
    Co-Authors: Praveen Kumar, Ligesh Theeyancheri, Subhasish Chaki, Rajarshi Chakrabarti
    Abstract:

    Fundamental understanding of the effect of microscopic parameters on the dynamics of Probe particles in different complex environments has wide implications. Examples include diffusion of proteins in biological hydrogels, porous media, polymer matrix, etc. Here, we use extensive molecular dynamics simulations to investigate the dynamics of the Probe particle in a polymer network on a diamond lattice, which provides substantial crowding to mimic the cellular environment. Our simulations show that the dynamics of the Probe increasingly becomes restricted, non-Gaussian and subdiffusive on increasing the network rigidity, binding affinity and Probe Size. In addition, the velocity autocorrelation functions show negative dips owing to the viscoelasticity and caging due to the surrounding network. These observations go with the general experimental findings. Importantly, for a Probe particle of Size comparable to the mesh Size, unrestricted motion engulfing large length scales has been observed. This happens with a more flexible polymer network, which is easily pushed by the bigger Probe. On increasing the rigidity of the network, the bigger Probe can not efficiently push the network and as a result the long tail disappears. Our study gives a general qualitative picture of the transport of Probes in a gel-like medium, as encountered in different contexts.

  • Transport of Probe particles in polymer network: effects of Probe Size, network rigidity and Probe-polymer interaction.
    arXiv: Soft Condensed Matter, 2019
    Co-Authors: Praveen Kumar, Ligesh Theeyancheri, Subhasish Chaki, Rajarshi Chakrabarti
    Abstract:

    Fundamental understanding of the effect of microscopic parameters on the dynamics of Probe particles in different complex environments has wide implications. Examples include diffusion of proteins in the biological hydrogels, porous media, polymer matrix, etc. Here, we use extensive molecular dynamics simulations to investigate the dynamics of the Probe particle in a polymer network on a diamond lattice which provides substantial crowding to mimic the cellular environment. Our simulations show that the dynamics of the Probe increasingly becomes restricted, non-Gaussian and subdiffusive on increasing the network rigidity, binding affinity and the Probe Size. In addition, the velocity autocorrelation functions show negative dips owing to the viscoelasticity and caging due to surrounding network. These observations go with general experimental findings. Surprisingly for a Probe particle of Size comparable to the mesh Size, unrestricted motion engulfing large length scales has been observed. This happens with the more flexible polymer network, which is easily pushed by the bigger Probe. Our study gives a general qualitative picture of transport of Probes in gel like medium, as encountered in different contexts.

Roland Brousseau - One of the best experts on this subject based on the ideXlab platform.

  • designing better Probes effect of Probe Size mismatch position and number on hybridization in dna oligonucleotide microarrays
    Journal of Microbiological Methods, 2004
    Co-Authors: Jaroslaw Letowski, Roland Brousseau, Luke Masson
    Abstract:

    Abstract DNA microarrays represent a powerful technology whose use has been hampered by the uncertainty of whether the same principles, established on a scale typical for membrane hybridizations, apply when using the smaller, rigid support of microarrays. Our goal was to understand how the number and position of base pair mismatches, Probe length and their G+C content affect the intensity and specificity of the hybridization signal. One set of oligonucleotides (50-mers) based on three regions of the Bacillus thuringiensis cry1Aa1 gene possessing 30%, 42%, and 56% G+C content, a second set with similar G+C content (37% to 40%) but different lengths (30 to 100 bases), and finally amplicon Probes (101 to 3000 base pairs) with G+C contents of 37% to 39%, were used. Probes with mismatches distributed over their entire length were the most specific, while those with mismatches grouped at either the 3′ or 5′-end were the least specific. Hybridizations done at 8 to 13 °C below the calculated Tm of perfectly matched Probes, as compared to the widely used lower temperatures of 20 to 25 °C, enhanced Probe discrimination. Longer Probes produced higher fluorescent hybridization signals than shorter ones. These results should help to optimize the design of oligonucleotide-based DNA microarrays.

  • designing better Probes effect of Probe Size mismatch position and number on hybridization in dna oligonucleotide microarrays
    Journal of Microbiological Methods, 2004
    Co-Authors: Jaroslaw Letowski, Roland Brousseau, Luke Masson
    Abstract:

    DNA microarrays represent a powerful technology whose use has been hampered by the uncertainty of whether the same principles, established on a scale typical for membrane hybridizations, apply when using the smaller, rigid support of microarrays. Our goal was to understand how the number and position of base pair mismatches, Probe length and their G+C content affect the intensity and specificity of the hybridization signal. One set of oligonucleotides (50-mers) based on three regions of the Bacillus thuringiensis cry1Aa1 gene possessing 30%, 42%, and 56% G+C content, a second set with similar G+C content (37% to 40%) but different lengths (30 to 100 bases), and finally amplicon Probes (101 to 3000 base pairs) with G+C contents of 37% to 39%, were used. Probes with mismatches distributed over their entire length were the most specific, while those with mismatches grouped at either the 3' or 5'-end were the least specific. Hybridizations done at 8 to 13 degrees C below the calculated T(m) of perfectly matched Probes, as compared to the widely used lower temperatures of 20 to 25 degrees C, enhanced Probe discrimination. Longer Probes produced higher fluorescent hybridization signals than shorter ones. These results should help to optimize the design of oligonucleotide-based DNA microarrays.

Praveen Kumar - One of the best experts on this subject based on the ideXlab platform.

  • transport of Probe particles in a polymer network effects of Probe Size network rigidity and Probe polymer interaction
    Soft Matter, 2019
    Co-Authors: Praveen Kumar, Ligesh Theeyancheri, Subhasish Chaki, Rajarshi Chakrabarti
    Abstract:

    Fundamental understanding of the effect of microscopic parameters on the dynamics of Probe particles in different complex environments has wide implications. Examples include diffusion of proteins in biological hydrogels, porous media, polymer matrix, etc. Here, we use extensive molecular dynamics simulations to investigate the dynamics of the Probe particle in a polymer network on a diamond lattice, which provides substantial crowding to mimic the cellular environment. Our simulations show that the dynamics of the Probe increasingly becomes restricted, non-Gaussian and subdiffusive on increasing the network rigidity, binding affinity and Probe Size. In addition, the velocity autocorrelation functions show negative dips owing to the viscoelasticity and caging due to the surrounding network. These observations go with the general experimental findings. Importantly, for a Probe particle of Size comparable to the mesh Size, unrestricted motion engulfing large length scales has been observed. This happens with a more flexible polymer network, which is easily pushed by the bigger Probe. On increasing the rigidity of the network, the bigger Probe can not efficiently push the network and as a result the long tail disappears. Our study gives a general qualitative picture of the transport of Probes in a gel-like medium, as encountered in different contexts.

  • Transport of Probe particles in a polymer network: effects of Probe Size, network rigidity and Probe–polymer interaction
    Soft matter, 2019
    Co-Authors: Praveen Kumar, Ligesh Theeyancheri, Subhasish Chaki, Rajarshi Chakrabarti
    Abstract:

    Fundamental understanding of the effect of microscopic parameters on the dynamics of Probe particles in different complex environments has wide implications. Examples include diffusion of proteins in biological hydrogels, porous media, polymer matrix, etc. Here, we use extensive molecular dynamics simulations to investigate the dynamics of the Probe particle in a polymer network on a diamond lattice, which provides substantial crowding to mimic the cellular environment. Our simulations show that the dynamics of the Probe increasingly becomes restricted, non-Gaussian and subdiffusive on increasing the network rigidity, binding affinity and Probe Size. In addition, the velocity autocorrelation functions show negative dips owing to the viscoelasticity and caging due to the surrounding network. These observations go with the general experimental findings. Importantly, for a Probe particle of Size comparable to the mesh Size, unrestricted motion engulfing large length scales has been observed. This happens with a more flexible polymer network, which is easily pushed by the bigger Probe. On increasing the rigidity of the network, the bigger Probe can not efficiently push the network and as a result the long tail disappears. Our study gives a general qualitative picture of the transport of Probes in a gel-like medium, as encountered in different contexts.

  • Transport of Probe particles in polymer network: effects of Probe Size, network rigidity and Probe-polymer interaction.
    arXiv: Soft Condensed Matter, 2019
    Co-Authors: Praveen Kumar, Ligesh Theeyancheri, Subhasish Chaki, Rajarshi Chakrabarti
    Abstract:

    Fundamental understanding of the effect of microscopic parameters on the dynamics of Probe particles in different complex environments has wide implications. Examples include diffusion of proteins in the biological hydrogels, porous media, polymer matrix, etc. Here, we use extensive molecular dynamics simulations to investigate the dynamics of the Probe particle in a polymer network on a diamond lattice which provides substantial crowding to mimic the cellular environment. Our simulations show that the dynamics of the Probe increasingly becomes restricted, non-Gaussian and subdiffusive on increasing the network rigidity, binding affinity and the Probe Size. In addition, the velocity autocorrelation functions show negative dips owing to the viscoelasticity and caging due to surrounding network. These observations go with general experimental findings. Surprisingly for a Probe particle of Size comparable to the mesh Size, unrestricted motion engulfing large length scales has been observed. This happens with the more flexible polymer network, which is easily pushed by the bigger Probe. Our study gives a general qualitative picture of transport of Probes in gel like medium, as encountered in different contexts.