Influence of Tetra(ethylene glycol) (EG4) Substitution at the Loop Region on the Intramolecular DNA i-Motif
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In this research, we employed tetra(ethylene glycol) (EG4) to substitute bases at the loop region of the intramolecular DNA i-motif formed by (CCCTAA)3CCC, and systematically studied the influence of such nonbase components on the stability and conformation of the formed structures by circular dichroism (CD), UV–vis spectroscopy and gel electrophoresis. We found that with all loop bases substituted, the i-motif structure can still form. The stability of the i-motif generally got weaker with the increase of the substitution number. Substitution at different positions might lead to different topologies. The findings above demonstrate that bases at the loop region play an important role on the stability and topology of the intramolecular DNA i-motif.Keywords:
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DNA contains the information of structure and function of different molecules of any living being. Short repeating patterns in a DNA sequence, called Motifs, are useful to understand and analyze this information. Recent advancements in gene expression analysis already prompt the scientists to introduce a number of motif finding algorithms. Among different motif search problems, one of them is Planted Motif Search (PMS). In this paper, we have proposed an approximate algorithm for Planted Motif Search which at first generates all possible motif set and use a bucketing concept to find out the proper motifs from the whole dataset. Two benchmark datasets of DNA sequences are used to evaluate the performance of the proposed method and its comparative analysis with other approaches. Experimental results demonstrate that proposed bucketing approach is more robust than the other approximate algorithms providing more amounts of motifs within less amount of time. Most of the time, above 80% of the possible motifs of the given input set are found within a reasonable time.
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