Structured Review

Roche gc rich solution
Bisulfite footprinting by deep-sequencing across the <t>FMR1</t> repeats in wild-type (WT) hESCs. (A) DNA bisulfite footprinting by deep-sequencing was carried out using unconverted primers in WT XY hESC (WT-ES-4). This was followed by a bioinformatic analysis which separated the reads into nontemplate <t>(G-rich;</t> left panel) and template (C-rich; right panel) strands, according to conversion patterns. Next, the reads were clustered into heatmaps. For simplicity, the template strand is presented in an opposite orientation (from 3′ to 5′ similar to the nontemplate strand orientation). The total read count appears on the y -axis. The length of the analyzed region is 250 bp with 80 C sites for the nontemplate and 100 C sites for the template strand. Dark gray and blue represent double-strand DNA (dsDNA) at the nontemplate and template strands, respectively, red represents single-strand DNA (ssDNA), and black represents sequencing errors. The TSS site and the repeats are designated with yellow lines. (B) DNA bisulfite footprinting by deep-sequencing was carried out using unconverted primers in a FXS XX hESC lines with an unmethylated full expansion (uFM) with skewed X-inactivation of the WT allele (uFM-ES-2), which allowed the selective amplification of a methylated WT allele. This was followed by a bioinformatic analysis, which separated the reads into nontemplate (G-rich; left panel) and template (C-rich; right panel) strands, according to conversion patterns.
Gc Rich Solution, supplied by Roche, used in various techniques. Bioz Stars score: 89/100, based on 62 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Images

1) Product Images from "The G-rich Repeats in FMR1 and C9orf72 Loci Are Hotspots for Local Unpairing of DNA"

Article Title: The G-rich Repeats in FMR1 and C9orf72 Loci Are Hotspots for Local Unpairing of DNA

Journal: Genetics

doi: 10.1534/genetics.118.301672

Bisulfite footprinting by deep-sequencing across the FMR1 repeats in wild-type (WT) hESCs. (A) DNA bisulfite footprinting by deep-sequencing was carried out using unconverted primers in WT XY hESC (WT-ES-4). This was followed by a bioinformatic analysis which separated the reads into nontemplate (G-rich; left panel) and template (C-rich; right panel) strands, according to conversion patterns. Next, the reads were clustered into heatmaps. For simplicity, the template strand is presented in an opposite orientation (from 3′ to 5′ similar to the nontemplate strand orientation). The total read count appears on the y -axis. The length of the analyzed region is 250 bp with 80 C sites for the nontemplate and 100 C sites for the template strand. Dark gray and blue represent double-strand DNA (dsDNA) at the nontemplate and template strands, respectively, red represents single-strand DNA (ssDNA), and black represents sequencing errors. The TSS site and the repeats are designated with yellow lines. (B) DNA bisulfite footprinting by deep-sequencing was carried out using unconverted primers in a FXS XX hESC lines with an unmethylated full expansion (uFM) with skewed X-inactivation of the WT allele (uFM-ES-2), which allowed the selective amplification of a methylated WT allele. This was followed by a bioinformatic analysis, which separated the reads into nontemplate (G-rich; left panel) and template (C-rich; right panel) strands, according to conversion patterns.
Figure Legend Snippet: Bisulfite footprinting by deep-sequencing across the FMR1 repeats in wild-type (WT) hESCs. (A) DNA bisulfite footprinting by deep-sequencing was carried out using unconverted primers in WT XY hESC (WT-ES-4). This was followed by a bioinformatic analysis which separated the reads into nontemplate (G-rich; left panel) and template (C-rich; right panel) strands, according to conversion patterns. Next, the reads were clustered into heatmaps. For simplicity, the template strand is presented in an opposite orientation (from 3′ to 5′ similar to the nontemplate strand orientation). The total read count appears on the y -axis. The length of the analyzed region is 250 bp with 80 C sites for the nontemplate and 100 C sites for the template strand. Dark gray and blue represent double-strand DNA (dsDNA) at the nontemplate and template strands, respectively, red represents single-strand DNA (ssDNA), and black represents sequencing errors. The TSS site and the repeats are designated with yellow lines. (B) DNA bisulfite footprinting by deep-sequencing was carried out using unconverted primers in a FXS XX hESC lines with an unmethylated full expansion (uFM) with skewed X-inactivation of the WT allele (uFM-ES-2), which allowed the selective amplification of a methylated WT allele. This was followed by a bioinformatic analysis, which separated the reads into nontemplate (G-rich; left panel) and template (C-rich; right panel) strands, according to conversion patterns.

Techniques Used: Footprinting, Sequencing, Amplification, Methylation

Proposed model for the formation of noncanonical structures by the G/C-rich repeats at the FMR1 and C9orf72 loci. Four potential configurations can be formed at the repeats in FMR1 and C9orf72 ). Such G-rich hybrid structures are expected to be particularly stable and difficult for the cell to resolve, thus providing a potent source of repeat instability. Blue, red, and green lines designate the DNA (paired and unpaired), the CGG/GGGGCC repeats on the nontemplate/template strand, and the newly synthesized RNA molecules, respectively. FM, full mutation; WT, wild type.
Figure Legend Snippet: Proposed model for the formation of noncanonical structures by the G/C-rich repeats at the FMR1 and C9orf72 loci. Four potential configurations can be formed at the repeats in FMR1 and C9orf72 ). Such G-rich hybrid structures are expected to be particularly stable and difficult for the cell to resolve, thus providing a potent source of repeat instability. Blue, red, and green lines designate the DNA (paired and unpaired), the CGG/GGGGCC repeats on the nontemplate/template strand, and the newly synthesized RNA molecules, respectively. FM, full mutation; WT, wild type.

Techniques Used: Synthesized, Mutagenesis

2) Product Images from "The G-rich Repeats in FMR1 and C9orf72 Loci Are Hotspots for Local Unpairing of DNA"

Article Title: The G-rich Repeats in FMR1 and C9orf72 Loci Are Hotspots for Local Unpairing of DNA

Journal: Genetics

doi: 10.1534/genetics.118.301672

Bisulfite footprinting by deep-sequencing across the FMR1 repeats in wild-type (WT) hESCs. (A) DNA bisulfite footprinting by deep-sequencing was carried out using unconverted primers in WT XY hESC (WT-ES-4). This was followed by a bioinformatic analysis which separated the reads into nontemplate (G-rich; left panel) and template (C-rich; right panel) strands, according to conversion patterns. Next, the reads were clustered into heatmaps. For simplicity, the template strand is presented in an opposite orientation (from 3′ to 5′ similar to the nontemplate strand orientation). The total read count appears on the y -axis. The length of the analyzed region is 250 bp with 80 C sites for the nontemplate and 100 C sites for the template strand. Dark gray and blue represent double-strand DNA (dsDNA) at the nontemplate and template strands, respectively, red represents single-strand DNA (ssDNA), and black represents sequencing errors. The TSS site and the repeats are designated with yellow lines. (B) DNA bisulfite footprinting by deep-sequencing was carried out using unconverted primers in a FXS XX hESC lines with an unmethylated full expansion (uFM) with skewed X-inactivation of the WT allele (uFM-ES-2), which allowed the selective amplification of a methylated WT allele. This was followed by a bioinformatic analysis, which separated the reads into nontemplate (G-rich; left panel) and template (C-rich; right panel) strands, according to conversion patterns.
Figure Legend Snippet: Bisulfite footprinting by deep-sequencing across the FMR1 repeats in wild-type (WT) hESCs. (A) DNA bisulfite footprinting by deep-sequencing was carried out using unconverted primers in WT XY hESC (WT-ES-4). This was followed by a bioinformatic analysis which separated the reads into nontemplate (G-rich; left panel) and template (C-rich; right panel) strands, according to conversion patterns. Next, the reads were clustered into heatmaps. For simplicity, the template strand is presented in an opposite orientation (from 3′ to 5′ similar to the nontemplate strand orientation). The total read count appears on the y -axis. The length of the analyzed region is 250 bp with 80 C sites for the nontemplate and 100 C sites for the template strand. Dark gray and blue represent double-strand DNA (dsDNA) at the nontemplate and template strands, respectively, red represents single-strand DNA (ssDNA), and black represents sequencing errors. The TSS site and the repeats are designated with yellow lines. (B) DNA bisulfite footprinting by deep-sequencing was carried out using unconverted primers in a FXS XX hESC lines with an unmethylated full expansion (uFM) with skewed X-inactivation of the WT allele (uFM-ES-2), which allowed the selective amplification of a methylated WT allele. This was followed by a bioinformatic analysis, which separated the reads into nontemplate (G-rich; left panel) and template (C-rich; right panel) strands, according to conversion patterns.

Techniques Used: Footprinting, Sequencing, Amplification, Methylation

Proposed model for the formation of noncanonical structures by the G/C-rich repeats at the FMR1 and C9orf72 loci. Four potential configurations can be formed at the repeats in FMR1 and C9orf72 ). Such G-rich hybrid structures are expected to be particularly stable and difficult for the cell to resolve, thus providing a potent source of repeat instability. Blue, red, and green lines designate the DNA (paired and unpaired), the CGG/GGGGCC repeats on the nontemplate/template strand, and the newly synthesized RNA molecules, respectively. FM, full mutation; WT, wild type.
Figure Legend Snippet: Proposed model for the formation of noncanonical structures by the G/C-rich repeats at the FMR1 and C9orf72 loci. Four potential configurations can be formed at the repeats in FMR1 and C9orf72 ). Such G-rich hybrid structures are expected to be particularly stable and difficult for the cell to resolve, thus providing a potent source of repeat instability. Blue, red, and green lines designate the DNA (paired and unpaired), the CGG/GGGGCC repeats on the nontemplate/template strand, and the newly synthesized RNA molecules, respectively. FM, full mutation; WT, wild type.

Techniques Used: Synthesized, Mutagenesis

Related Articles

Polymerase Chain Reaction:

Article Title: The G-rich Repeats in FMR1 and C9orf72 Loci Are Hotspots for Local Unpairing of DNA
Article Snippet: .. For ssDNA displacement at FMR1 , GC-RICH solution was added to the PCR mix, according to the manufacturer’s instructions (Roche). .. Amplified products were cloned, and single colonies were analyzed for cytosine conversions by direct sequencing (ABI 3130), using the BigDye Terminator v3.1 Cycle Sequencing Kit.

Article Title: The Scope for Thalassemia Gene Therapy by Disruption of Aberrant Regulatory Elements
Article Snippet: .. Sequencing Purified plasmids and PCR products were sequenced using the BigDye Terminator v1.1 Cycler sequencing kit (Applied Biosystems, Foster City, CA, USA), including 1 × GC-RICH solution (Roche, Basel, Switzerland). .. DNA sequencing products were purified using Performa® DTR Gel Filtration Cartridges Performa® DTR Gel Filtration Cartridges (Edge Biosystems, Gaithersburg, MD, USA, USA) and analyzed on a Hitachi 3031xl Genetic Analyzer with the Sequence Detection Software version 5.2 (Applied Biosystems, Foster City, MA, USA).

Article Title: Simple Repeat-Primed PCR Analysis of the Myotonic Dystrophy Type 1 Gene in a Clinical Diagnostics Environment
Article Snippet: .. Each 25 μ L PCR comprised FastStart Reaction Buffer without MgCl2 (Roche), 2 mM MgCl2 (Roche), GC-rich solution (Roche), 10 mM dNTP mix, 20 μ M forward and reverse primers, 1U FastStart Taq DNA Polymerase (Roche), and 50 ng of genomic DNA. .. The PCR amplification conditions comprised an initial denaturation of 94°C for five minutes then 35 cycles of denaturation at 94°C for 45 seconds, annealing at 70°C for 30 seconds with extension at 72°C for 30 seconds and a final extension at 72°C for 10 minutes.

Article Title: The G-rich Repeats in FMR1 and C9orf72 Loci Are Hotspots for Local Unpairing of DNA
Article Snippet: .. For ssDNA displacement at FMR1 , GC-RICH solution was added to the PCR mix, according to the manufacturer’s instructions (Roche). .. Amplified products were cloned, and single colonies were analyzed for cytosine conversions by direct sequencing (ABI 3130), using the BigDye Terminator v3.1 Cycle Sequencing Kit.

Article Title: New species of Ophiostomatales from Scolytinae and Platypodinae beetles in the Cape Floristic Region, including the discovery of the sexual state of Raffaelea.
Article Snippet: .. For DNA amplification, the reaction mixture for the Polymerase Chain Reaction (PCR) was 25 µL, consisting of 11.3 µL ddH2O, 2 µL DNA, 2.5 µL 10X PCR reaction buffer (with MgCl2), 2.5 µL deoxyribonucleotide triphosphate mix (dNTP) (5mM), 5 µL GC rich solution (Roche Applied Science, Mannheim, Germany), 0.5 µL of each primer (10mM), 0.5 µL extra MgCl2 (25mM) and 0.2 µL FastStart Taq DNA Polymerase (Roche Applied Science, Mannheim, Germany). .. For the relevant fungal morpho-types, primers T10 (O’Donnell and Cigelnik 1997) and Bt2b (Glass and Donaldson 1995) were used to amplify part of the Beta-tubulin (Bt) gene region and where amplification did not work, Bt2a (Glass and Donaldson 1995) replaced T10.

Sequencing:

Article Title: The Scope for Thalassemia Gene Therapy by Disruption of Aberrant Regulatory Elements
Article Snippet: .. Sequencing Purified plasmids and PCR products were sequenced using the BigDye Terminator v1.1 Cycler sequencing kit (Applied Biosystems, Foster City, CA, USA), including 1 × GC-RICH solution (Roche, Basel, Switzerland). .. DNA sequencing products were purified using Performa® DTR Gel Filtration Cartridges Performa® DTR Gel Filtration Cartridges (Edge Biosystems, Gaithersburg, MD, USA, USA) and analyzed on a Hitachi 3031xl Genetic Analyzer with the Sequence Detection Software version 5.2 (Applied Biosystems, Foster City, MA, USA).

Amplification:

Article Title: Multimarker RT-PCR assay for the detection of minimal residual disease in sentinel lymph nodes of breast cancer patients
Article Snippet: .. Cytokeratin-19 and NY-BR-1 were amplified in a 50 μ l reaction mixture containing 5 pmol of both primers, 2 mM MgCl2 , 200 μ mol l−1 of each deoxyribonucleoside triphosphate, and 2.5 U of the recombinant FastStart Taq DNA Polymerase in 1 × GC-RICH solution (Roche, Mannheim, Germany). ..

Article Title: New species of Ophiostomatales from Scolytinae and Platypodinae beetles in the Cape Floristic Region, including the discovery of the sexual state of Raffaelea.
Article Snippet: .. For DNA amplification, the reaction mixture for the Polymerase Chain Reaction (PCR) was 25 µL, consisting of 11.3 µL ddH2O, 2 µL DNA, 2.5 µL 10X PCR reaction buffer (with MgCl2), 2.5 µL deoxyribonucleotide triphosphate mix (dNTP) (5mM), 5 µL GC rich solution (Roche Applied Science, Mannheim, Germany), 0.5 µL of each primer (10mM), 0.5 µL extra MgCl2 (25mM) and 0.2 µL FastStart Taq DNA Polymerase (Roche Applied Science, Mannheim, Germany). .. For the relevant fungal morpho-types, primers T10 (O’Donnell and Cigelnik 1997) and Bt2b (Glass and Donaldson 1995) were used to amplify part of the Beta-tubulin (Bt) gene region and where amplification did not work, Bt2a (Glass and Donaldson 1995) replaced T10.

Recombinant:

Article Title: Multimarker RT-PCR assay for the detection of minimal residual disease in sentinel lymph nodes of breast cancer patients
Article Snippet: .. Cytokeratin-19 and NY-BR-1 were amplified in a 50 μ l reaction mixture containing 5 pmol of both primers, 2 mM MgCl2 , 200 μ mol l−1 of each deoxyribonucleoside triphosphate, and 2.5 U of the recombinant FastStart Taq DNA Polymerase in 1 × GC-RICH solution (Roche, Mannheim, Germany). ..

Purification:

Article Title: The Scope for Thalassemia Gene Therapy by Disruption of Aberrant Regulatory Elements
Article Snippet: .. Sequencing Purified plasmids and PCR products were sequenced using the BigDye Terminator v1.1 Cycler sequencing kit (Applied Biosystems, Foster City, CA, USA), including 1 × GC-RICH solution (Roche, Basel, Switzerland). .. DNA sequencing products were purified using Performa® DTR Gel Filtration Cartridges Performa® DTR Gel Filtration Cartridges (Edge Biosystems, Gaithersburg, MD, USA, USA) and analyzed on a Hitachi 3031xl Genetic Analyzer with the Sequence Detection Software version 5.2 (Applied Biosystems, Foster City, MA, USA).

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    Roche gc rich solution
    Bisulfite footprinting by deep-sequencing across the <t>FMR1</t> repeats in wild-type (WT) hESCs. (A) DNA bisulfite footprinting by deep-sequencing was carried out using unconverted primers in WT XY hESC (WT-ES-4). This was followed by a bioinformatic analysis which separated the reads into nontemplate <t>(G-rich;</t> left panel) and template (C-rich; right panel) strands, according to conversion patterns. Next, the reads were clustered into heatmaps. For simplicity, the template strand is presented in an opposite orientation (from 3′ to 5′ similar to the nontemplate strand orientation). The total read count appears on the y -axis. The length of the analyzed region is 250 bp with 80 C sites for the nontemplate and 100 C sites for the template strand. Dark gray and blue represent double-strand DNA (dsDNA) at the nontemplate and template strands, respectively, red represents single-strand DNA (ssDNA), and black represents sequencing errors. The TSS site and the repeats are designated with yellow lines. (B) DNA bisulfite footprinting by deep-sequencing was carried out using unconverted primers in a FXS XX hESC lines with an unmethylated full expansion (uFM) with skewed X-inactivation of the WT allele (uFM-ES-2), which allowed the selective amplification of a methylated WT allele. This was followed by a bioinformatic analysis, which separated the reads into nontemplate (G-rich; left panel) and template (C-rich; right panel) strands, according to conversion patterns.
    Gc Rich Solution, supplied by Roche, used in various techniques. Bioz Stars score: 89/100, based on 62 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/gc rich solution/product/Roche
    Average 89 stars, based on 62 article reviews
    Price from $9.99 to $1999.99
    gc rich solution - by Bioz Stars, 2020-07
    89/100 stars
      Buy from Supplier

    85
    Roche gc rich solution buffer
    Bisulfite footprinting by deep-sequencing across the <t>FMR1</t> repeats in wild-type (WT) hESCs. (A) DNA bisulfite footprinting by deep-sequencing was carried out using unconverted primers in WT XY hESC (WT-ES-4). This was followed by a bioinformatic analysis which separated the reads into nontemplate <t>(G-rich;</t> left panel) and template (C-rich; right panel) strands, according to conversion patterns. Next, the reads were clustered into heatmaps. For simplicity, the template strand is presented in an opposite orientation (from 3′ to 5′ similar to the nontemplate strand orientation). The total read count appears on the y -axis. The length of the analyzed region is 250 bp with 80 C sites for the nontemplate and 100 C sites for the template strand. Dark gray and blue represent double-strand DNA (dsDNA) at the nontemplate and template strands, respectively, red represents single-strand DNA (ssDNA), and black represents sequencing errors. The TSS site and the repeats are designated with yellow lines. (B) DNA bisulfite footprinting by deep-sequencing was carried out using unconverted primers in a FXS XX hESC lines with an unmethylated full expansion (uFM) with skewed X-inactivation of the WT allele (uFM-ES-2), which allowed the selective amplification of a methylated WT allele. This was followed by a bioinformatic analysis, which separated the reads into nontemplate (G-rich; left panel) and template (C-rich; right panel) strands, according to conversion patterns.
    Gc Rich Solution Buffer, supplied by Roche, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/gc rich solution buffer/product/Roche
    Average 85 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    gc rich solution buffer - by Bioz Stars, 2020-07
    85/100 stars
      Buy from Supplier

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    Bisulfite footprinting by deep-sequencing across the FMR1 repeats in wild-type (WT) hESCs. (A) DNA bisulfite footprinting by deep-sequencing was carried out using unconverted primers in WT XY hESC (WT-ES-4). This was followed by a bioinformatic analysis which separated the reads into nontemplate (G-rich; left panel) and template (C-rich; right panel) strands, according to conversion patterns. Next, the reads were clustered into heatmaps. For simplicity, the template strand is presented in an opposite orientation (from 3′ to 5′ similar to the nontemplate strand orientation). The total read count appears on the y -axis. The length of the analyzed region is 250 bp with 80 C sites for the nontemplate and 100 C sites for the template strand. Dark gray and blue represent double-strand DNA (dsDNA) at the nontemplate and template strands, respectively, red represents single-strand DNA (ssDNA), and black represents sequencing errors. The TSS site and the repeats are designated with yellow lines. (B) DNA bisulfite footprinting by deep-sequencing was carried out using unconverted primers in a FXS XX hESC lines with an unmethylated full expansion (uFM) with skewed X-inactivation of the WT allele (uFM-ES-2), which allowed the selective amplification of a methylated WT allele. This was followed by a bioinformatic analysis, which separated the reads into nontemplate (G-rich; left panel) and template (C-rich; right panel) strands, according to conversion patterns.

    Journal: Genetics

    Article Title: The G-rich Repeats in FMR1 and C9orf72 Loci Are Hotspots for Local Unpairing of DNA

    doi: 10.1534/genetics.118.301672

    Figure Lengend Snippet: Bisulfite footprinting by deep-sequencing across the FMR1 repeats in wild-type (WT) hESCs. (A) DNA bisulfite footprinting by deep-sequencing was carried out using unconverted primers in WT XY hESC (WT-ES-4). This was followed by a bioinformatic analysis which separated the reads into nontemplate (G-rich; left panel) and template (C-rich; right panel) strands, according to conversion patterns. Next, the reads were clustered into heatmaps. For simplicity, the template strand is presented in an opposite orientation (from 3′ to 5′ similar to the nontemplate strand orientation). The total read count appears on the y -axis. The length of the analyzed region is 250 bp with 80 C sites for the nontemplate and 100 C sites for the template strand. Dark gray and blue represent double-strand DNA (dsDNA) at the nontemplate and template strands, respectively, red represents single-strand DNA (ssDNA), and black represents sequencing errors. The TSS site and the repeats are designated with yellow lines. (B) DNA bisulfite footprinting by deep-sequencing was carried out using unconverted primers in a FXS XX hESC lines with an unmethylated full expansion (uFM) with skewed X-inactivation of the WT allele (uFM-ES-2), which allowed the selective amplification of a methylated WT allele. This was followed by a bioinformatic analysis, which separated the reads into nontemplate (G-rich; left panel) and template (C-rich; right panel) strands, according to conversion patterns.

    Article Snippet: For ssDNA displacement at FMR1 , GC-RICH solution was added to the PCR mix, according to the manufacturer’s instructions (Roche).

    Techniques: Footprinting, Sequencing, Amplification, Methylation

    Proposed model for the formation of noncanonical structures by the G/C-rich repeats at the FMR1 and C9orf72 loci. Four potential configurations can be formed at the repeats in FMR1 and C9orf72 ). Such G-rich hybrid structures are expected to be particularly stable and difficult for the cell to resolve, thus providing a potent source of repeat instability. Blue, red, and green lines designate the DNA (paired and unpaired), the CGG/GGGGCC repeats on the nontemplate/template strand, and the newly synthesized RNA molecules, respectively. FM, full mutation; WT, wild type.

    Journal: Genetics

    Article Title: The G-rich Repeats in FMR1 and C9orf72 Loci Are Hotspots for Local Unpairing of DNA

    doi: 10.1534/genetics.118.301672

    Figure Lengend Snippet: Proposed model for the formation of noncanonical structures by the G/C-rich repeats at the FMR1 and C9orf72 loci. Four potential configurations can be formed at the repeats in FMR1 and C9orf72 ). Such G-rich hybrid structures are expected to be particularly stable and difficult for the cell to resolve, thus providing a potent source of repeat instability. Blue, red, and green lines designate the DNA (paired and unpaired), the CGG/GGGGCC repeats on the nontemplate/template strand, and the newly synthesized RNA molecules, respectively. FM, full mutation; WT, wild type.

    Article Snippet: For ssDNA displacement at FMR1 , GC-RICH solution was added to the PCR mix, according to the manufacturer’s instructions (Roche).

    Techniques: Synthesized, Mutagenesis