DNA Motif Recognition Modeling from Protein Sequences
Sign Up to like & getrecommendations! Published in 2018 at "iScience"
DOI: 10.1016/j.isci.2018.09.003
Abstract: Summary Although the existing works on DNA motif discovery on DNA sequences are plethoric, mechanistic knowledge to infer DNA motifs from protein sequences across multiple DNA-binding domain families without conducting any wet-lab experiments is still… read more here.
Keywords: dna; motif recognition; protein sequences; recognition modeling ... See more keywords
DNA i-motif formation at neutral pH is driven by kinetic partitioning
Sign Up to like & getrecommendations! Published in 2023 at "Nucleic Acids Research"
DOI: 10.1093/nar/gkad119
Abstract: Abstract Cytosine-rich DNA regions can form four-stranded structures based on hemi-protonated C.C+ pairs, called i-motifs (iMs). Using CD, UV absorption, NMR spectroscopy, and DSC calorimetry, we show that model (CnT3)3Cn (Cn) sequences adopt iM under… read more here.
Keywords: dna; neutral driven; dna motif; formation neutral ... See more keywords
Systematic investigation of sequence requirements for DNA i-motif formation
Sign Up to like & getrecommendations! Published in 2019 at "Nucleic Acids Research"
DOI: 10.1093/nar/gkz046
Abstract: Abstract The formation of intercalated motifs (iMs) — secondary DNA structures based on hemiprotonated C.C+ pairs in suitable cytosine-rich DNA sequences, is reflected by typical changes in CD and UV absorption spectra. By means of… read more here.
Keywords: requirements dna; investigation sequence; formation; dna motif ... See more keywords
A Method for Predicting DNA Motif Length Based On Deep Learning
Sign Up to like & getrecommendations! Published in 2022 at "IEEE/ACM Transactions on Computational Biology and Bioinformatics"
DOI: 10.1109/tcbb.2022.3158471
Abstract: A DNA motif is a sequence pattern shared by the DNA sequence segments that bind to a specific protein. Discovering motifs in a given DNA sequence dataset plays a vital role in studying gene expression… read more here.
Keywords: motif length; deep learning; motif; dna motif ... See more keywords
A transposon‐introduced G‐quadruplex motif is selectively retained and constrained to downregulate CYP321A1
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DOI: 10.1111/1744-7917.13021
Abstract: Insects utilize xenobiotic compounds to up‐ and downregulate cytochrome P450 monooxygenases (P450s) involved in detoxification of toxic xenobiotics including phytochemicals and pesticides. G‐quadruplexes (G4)‐forming DNA motifs are enriched in the promoter regions of transcription factors… read more here.
Keywords: dna; dna motif; cyp321a1; motif selectively ... See more keywords
pH-Responsive DNA Motif: From Rational Design to Analytical Applications
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DOI: 10.3389/fchem.2021.732770
Abstract: pH-responsive DNA motifs have attracted substantial attention attributed to their high designability and versatility of DNA chemistry. Such DNA motifs typically exploit DNA secondary structures that exhibit pH response properties because of the presence of… read more here.
Keywords: responsive dna; dna; chemistry; motif rational ... See more keywords