Abstract
In this study, the organization of genetic information in nucleic acids is defined using a novel orthogonal representation. Clearly defined base pairing in DNA allows the linear base chain and sequence to be mathematically transformed into an orthogonal representation where the G–C and A–T pairs are displayed in different planes that are perpendicular to each other. This form of base allocation enables the evaluation of any nucleic acid and predicts the likelihood of a particular region to form non-canonical motifs. The G4Hunter algorithm is currently a popular method of identifying G-quadruplex forming sequences in nucleic acids, and offers promising scores despite its lack of a substantial rational basis. The orthogonal representation described here is an effort to address this incongruity. In addition, the orthogonal display facilitates the search for other sequences that are capable of adopting non-canonical motifs, such as direct and palindromic repeats. The technique can also be used for various RNAs, including any aptamers. This powerful tool based on an orthogonal system offers considerable potential for a wide range of applications.
Highlights
Nucleic acid consists of building blocks of nucleotides that are arranged in different permutations, with the order of the nucleotides determining the sequence of DNA or RNA
The orthogonal system was applied to a series of sequences that are known to be capable of forming a G-quadruplex motif
The orthogonal system can be used for all types and sizes of nucleic acids
Summary
DNA molecules often occur in an antiparallel double-stranded structure due to Watson−Crick (WC) base pairing, with adenine and guanine bases pairing with thymine and cytosine, respectively. For canonical putative sequences adopting cruciform or G-quadruplex data over the last decade poses a considerable challenge in terms of processing and prostructures, it is more appropriate to use an application specially tailored for this purpose, vides an opportunity to develop computational analyzes that are capable of sophisticated for example, computational approaches, which study these motifs to allow for a detailed screening processes of unknown genomes, including their graphical representation [6]. The approach known as “digital signal processing” has seen increasing use in geInterestingly, the G4Hunter algorithm offers one of the highest search scores for nomic DNA research as a means of revealing genome structures and identifying hidden identifying sequences that form G-quadruplexes, but there is still a lack of a rational periodicities and features that cannot be determined using conventional DNA symbolic explanation for this success rate. The searching strategy A is and simple; each position in a sequence a score between
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