Evaluating the Binding Affinities of NF-κB Protein to the Single-Nucleotide Mismatch DNA Binding Sites by Using Double-Stranded DNA Microarray

2006 ◽  
Vol 6 (4) ◽  
pp. 1014-1018 ◽  
Author(s):  
Yunfei Bai ◽  
Qinyu Ge ◽  
Quanjun Liu ◽  
Tongxiang Li ◽  
Jinke Wang ◽  
...  
Keyword(s):  
Dna Binding ◽  
Dna Microarray ◽  
Binding Sites ◽  
Binding Affinities ◽  
Single Nucleotide ◽  
Double Stranded Dna ◽  
Dna Binding Sites ◽  
Nucleotide Mismatch ◽  
Single Nucleotide Mismatch

An improved gel-based DNA microarray method for detecting single nucleotide mismatch

2006 ◽  
Vol 27 (19) ◽  
pp. 3904-3915 ◽  
Author(s):  
Peng Feng Xiao ◽  
Lu Cheng ◽  
Yuan Wan ◽  
Bei Li Sun ◽  
Zao Zao Chen ◽  
...  
Keyword(s):  
Dna Microarray ◽  
Single Nucleotide ◽  
Nucleotide Mismatch ◽  
Single Nucleotide Mismatch

scholarly journals Antisense Oligonucleotide Screening to Optimize the Rescue of the Splicing Defect Caused by the Recurrent Deep-Intronic ABCA4 Variant c.4539+2001G>A in Stargardt Disease

Genes ◽  
2019 ◽  
Vol 10 (6) ◽  
pp. 452 ◽  
Author(s):  
Alejandro Garanto ◽  
Lonneke Duijkers ◽  
Tomasz Z. Tomkiewicz ◽  
Rob W. J. Collin
Keyword(s):  
Pluripotent Stem Cells ◽  
Antisense Oligonucleotides ◽  
Autosomal Recessive ◽  
Stargardt Disease ◽  
Single Nucleotide ◽  
Significant Correction ◽  
Nucleotide Mismatch ◽  
Single Nucleotide Mismatch ◽  
Splicing Defects ◽  
Induced Pluripotent

Deep-sequencing of the ABCA4 locus has revealed that ~10% of autosomal recessive Stargardt disease (STGD1) cases are caused by deep-intronic mutations. One of the most recurrent deep-intronic variants in the Belgian and Dutch STGD1 population is the c.4539+2001G>A mutation. This variant introduces a 345-nt pseudoexon to the ABCA4 mRNA transcript in a retina-specific manner. Antisense oligonucleotides (AONs) are short sequences of RNA that can modulate splicing. In this work, we designed 26 different AONs to perform a thorough screening to identify the most effective AONs to correct splicing defects associated with c.4539+2001G>A. All AONs were tested in patient-derived induced pluripotent stem cells (iPSCs) that were differentiated to photoreceptor precursor cells (PPCs). AON efficacy was assessed through RNA analysis and was based on correction efficacy, and AONs were grouped and their properties assessed. We (a) identified nine AONs with significant correction efficacies (>50%), (b) confirmed that a single nucleotide mismatch was sufficient to significantly decrease AON efficacy, and (c) found potential correlations between efficacy and some of the parameters analyzed. Overall, our results show that AON-based splicing modulation holds great potential for treating Stargardt disease caused by splicing defects in ABCA4.

scholarly journals Analysis of two distinct single-stranded DNA binding sites on the recA nucleoprotein filament.

1993 ◽  
Vol 268 (30) ◽  
pp. 22525-22530
Author(s):  
A Zlotnick ◽  
R.S. Mitchell ◽  
R.K. Steed ◽  
S.L. Brenner
Keyword(s):  
Dna Binding ◽  
Binding Sites ◽  
Single Stranded Dna ◽  
Dna Binding Sites
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