A direct selection strategy for isolating aptamers with pH-sensitive binding activity

2018 ◽  
Author(s):  
Zhang-He Goh
Keyword(s):  
Binding Activity ◽  
Ph Sensitive ◽  
Direct Selection ◽  
Selection Strategy

scholarly journals Direct Selection Strategy for Isolating Aptamers with pH-Sensitive Binding Activity

ACS Sensors ◽  
2018 ◽  
Vol 3 (12) ◽  
pp. 2574-2580 ◽  
Author(s):  
Chelsea K. L. Gordon ◽  
Michael Eisenstein ◽  
Hyongsok Tom Soh
Keyword(s):  
Binding Activity ◽  
Ph Sensitive ◽  
Direct Selection ◽  
Selection Strategy

scholarly journals A direct selection strategy for isolating aptamers with pH-sensitive binding activity

2018 ◽  
Author(s):  
Chelsea K. L. Gordon ◽  
Michael Eisenstein ◽  
Hyongsok Tom Soh
Keyword(s):  
A Priori ◽  
Binding Activity ◽  
Switching Behavior ◽  
Direct Selection ◽  
Selection Strategy ◽  
Dependent Manner ◽  
Ph Responsive ◽  
Dna Motif ◽  
Ph Conditions ◽  
Streptavidin Binding

AbstractAn aptamer reagent that can switch its binding affinity in a pH-responsive manner would be highly valuable for many biomedical applications including imaging and drug delivery. Unfortunately, the discovery of such aptamers is difficult and only a few have been reported to date. Here we report the first experimental strategy for generating pH-responsive aptamers through direct selection. As an exemplar, we report streptavidin-binding aptamers that retain nanomolar affinity at pH 7.4 but exhibit a ~100-fold decrease in affinity at pH 5.2. These aptamers were generated by incorporating a known streptavidin-binding DNA motif into an aptamer library and performing FACS-based screening at multiple pH conditions. Upon structural analysis, we found that one aptamer’s affinity-switching behavior is driven by a non-canonical G-A base-pair that controls its folding in a highly pH-dependent manner. We believe our strategy could be readily extended to other aptamer-target systems because it does not require a priori structural knowledge of the aptamer or the target.

scholarly journals Early generation selection strategy for yield and yield components in white oat

2005 ◽  
Vol 62 (4) ◽  
pp. 357-365 ◽  
Author(s):  
Giovani Benin ◽  
Fernando Irajá Félix de Carvalho ◽  
Antônio Costa de Oliveira ◽  
Claudir Lorencetti ◽  
Igor Pires Valério ◽  
...  
Keyword(s):  
Grain Yield ◽  
Indirect Selection ◽  
Grain Weight ◽  
Yield Potential ◽  
High Yield ◽  
Direct Selection ◽  
Selection Strategy ◽  
Breeding Method ◽  
Growing Seasons ◽  
Selection For

Several studies have searched for higher efficiency on plant selection in generations bearing high frequency of heterozygotes. This work aims to compare the response of direct selection for grain yield, indirect selection through average grain weight and combined selection for higher yield potential and average grain weight of oat plants (Avena sativa L.), using the honeycomb breeding method. These strategies were applied in the growing seasons of 2001 and 2002 in F3 and F4 populations, respectively, in the crosses UPF 18 CTC 5, OR 2 <FONT FACE=Symbol>´</FONT> UPF 7 and OR 2 <FONT FACE=Symbol>´</FONT> UPF 18. The ten best genetic combinations obtained for each cross and selection strategy were evaluated in greenhouse yield trials. Selection of plants with higher yield and average grain weight might be performed on early generations with high levels of heterozygosis. The direct selection for grain yield and indirect selection for average grain weight enabled to increase the average of characters under selection. However, genotypes obtained through direct selection presented lower average grain weight and those obtained through the indirect selection presented lower yield potential. Selection strategies must be run simultaneously to combine in only one genotype high yield potential and large grain weight, enabling maximum genetic gain for both characters.

Nucleotides flanking a conserved TAAT core dictate the DNA binding specificity of three murine homeodomain proteins

1993 ◽  
Vol 13 (4) ◽  
pp. 2354-2365
Author(s):  
K M Catron ◽  
N Iler ◽  
C Abate
Keyword(s):  
Dna Binding ◽  
Binding Sites ◽  
Target Genes ◽  
Equilibrium Constants ◽  
Binding Specificity ◽  
Binding Activity ◽  
Selection Strategy ◽  
Homeodomain Proteins ◽  
Control Regions

Murine homeobox genes play a fundamental role in directing embryogenesis by controlling gene expression during development. The homeobox encodes a DNA binding domain (the homeodomain) which presumably mediates interactions of homeodomain proteins with specific DNA sites in the control regions of target genes. However, the bases for these selective DNA-protein interactions are not well defined. In this report, we have characterized the DNA binding specificities of three murine homeodomain proteins, Hox 7.1, Hox 1.5, and En-1. We have identified optimal DNA binding sites for each of these proteins by using a random oligonucleotide selection strategy. Comparison of the sequences of the selected binding sites predicted a common consensus site that contained the motif (C/G)TAATTG. The TAAT core was essential for DNA binding activity, and the nucleotides flanking this core directed binding specificity. Whereas variations in the nucleotides flanking the 5' side of the TAAT core produced modest alterations in binding activity for all three proteins, perturbations of the nucleotides directly 3' of the core distinguished the binding specificity of Hox 1.5 from those of Hox 7.1 and En-1. These differences in binding activity reflected differences in the dissociation rates rather than the equilibrium constants of the protein-DNA complexes. Differences in DNA binding specificities observed in vitro may contribute to selective interactions of homeodomain proteins with potential binding sites in the control regions of target genes.

scholarly journals Nucleotides flanking a conserved TAAT core dictate the DNA binding specificity of three murine homeodomain proteins.

1993 ◽  
Vol 13 (4) ◽  
pp. 2354-2365 ◽  
Author(s):  
K M Catron ◽  
N Iler ◽  
C Abate
Keyword(s):  
Dna Binding ◽  
Binding Sites ◽  
Target Genes ◽  
Equilibrium Constants ◽  
Binding Specificity ◽  
Binding Activity ◽  
Selection Strategy ◽  
Homeodomain Proteins ◽  
Control Regions

Murine homeobox genes play a fundamental role in directing embryogenesis by controlling gene expression during development. The homeobox encodes a DNA binding domain (the homeodomain) which presumably mediates interactions of homeodomain proteins with specific DNA sites in the control regions of target genes. However, the bases for these selective DNA-protein interactions are not well defined. In this report, we have characterized the DNA binding specificities of three murine homeodomain proteins, Hox 7.1, Hox 1.5, and En-1. We have identified optimal DNA binding sites for each of these proteins by using a random oligonucleotide selection strategy. Comparison of the sequences of the selected binding sites predicted a common consensus site that contained the motif (C/G)TAATTG. The TAAT core was essential for DNA binding activity, and the nucleotides flanking this core directed binding specificity. Whereas variations in the nucleotides flanking the 5' side of the TAAT core produced modest alterations in binding activity for all three proteins, perturbations of the nucleotides directly 3' of the core distinguished the binding specificity of Hox 1.5 from those of Hox 7.1 and En-1. These differences in binding activity reflected differences in the dissociation rates rather than the equilibrium constants of the protein-DNA complexes. Differences in DNA binding specificities observed in vitro may contribute to selective interactions of homeodomain proteins with potential binding sites in the control regions of target genes.

Genetic parameters, selection gains and genotypic correlations in kale half-siblings progenies

2020 ◽  
pp. 591
Author(s):  
Orlando Gonçalves Brito ◽  
Valter Carvalho de Andrade Júnior ◽  
Alcinei Mistico Azevedo ◽  
Natália Oliveira Silva ◽  
José Sebastião Cunha Fernandes ◽  
...  
Keyword(s):  
Plant Height ◽  
Genetic Parameters ◽  
Correlation Study ◽  
Indirect Selection ◽  
Leaf Length ◽  
Direct Selection ◽  
Selection Strategy ◽  
Leaf Yield ◽  
Number Of Leaves ◽  
Genotypic Correlations

The objective of this work is to estimate genetic parameters, direct and indirect selection gains and to study the genotypic correlations in kale half-siblings. A number of 33 half-siblings progenies of kale were evaluated in the years 2015/2016 in Diamantina, state of Minas Gerais, Brazil. The characteristics evaluated were number of shoots, number of leaves, fresh mass per leaf, leaf yield, plant height, stem diameter, leaf length, limb length, petiole length, diameter of petiole base, diameter of petiole medium and leaf width. The analyzes were performed using mixed models (REML / BLUP) estimating the genetic parameters and the direct and indirect predicted genetic selection gains. A genetic correlation matrix was obtained from the additive genetic values. Genetic variability was observed in the population. The highest predicted gains are obtained by direct selection in the number of leaves. The best indirect selection strategy was based on leaf productivity, as it avoided unfavorable indirect selection gains for the other characteristics, except for plant height. It was also found that the simultaneous selection, based on ranks average, can be efficient, with favorable gain estimates for all characteristics. The correlation study indicated that the associations of higher intensity were established between the number of leaves with the leaf yield and the diameter of the stem.

Genomic analysis of C-type lectins

2002 ◽  
Vol 69 ◽  
pp. 59-72 ◽  
Author(s):  
Kurt Drickamer ◽  
Andrew J. Fadden
Keyword(s):  
Biological Effects ◽  
Cell Signalling ◽  
Genomic Analysis ◽  
Binding Activity ◽  
Immunoglobulin Superfamily ◽  
Carbohydrate Binding ◽  
Carbohydrate Recognition ◽  
Calcium Dependent ◽  
Binding Domains ◽  
Carbohydrate Recognition Domains

Many biological effects of complex carbohydrates are mediated by lectins that contain discrete carbohydrate-recognition domains. At least seven structurally distinct families of carbohydrate-recognition domains are found in lectins that are involved in intracellular trafficking, cell adhesion, cell–cell signalling, glycoprotein turnover and innate immunity. Genome-wide analysis of potential carbohydrate-binding domains is now possible. Two classes of intracellular lectins involved in glycoprotein trafficking are present in yeast, model invertebrates and vertebrates, and two other classes are present in vertebrates only. At the cell surface, calcium-dependent (C-type) lectins and galectins are found in model invertebrates and vertebrates, but not in yeast; immunoglobulin superfamily (I-type) lectins are only found in vertebrates. The evolutionary appearance of different classes of sugar-binding protein modules parallels a development towards more complex oligosaccharides that provide increased opportunities for specific recognition phenomena. An overall picture of the lectins present in humans can now be proposed. Based on our knowledge of the structures of several of the C-type carbohydrate-recognition domains, it is possible to suggest ligand-binding activity that may be associated with novel C-type lectin-like domains identified in a systematic screen of the human genome. Further analysis of the sequences of proteins containing these domains can be used as a basis for proposing potential biological functions.

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