New Code for DNA Nucleotide Sequences

Abstract

DNA nucleotides consist of the complementary base pairs of Adenine-Thymine (A-T) and Cytosine-Guanine (C-G) that encode as a sequence for genes, and encode for an upstream initiation site that enables transcription. Recently, this lab has shown that steroid hormones are structurally symmetric with each of the four DNA nucleotide pairs and through an ionic binding process may enable gene transcription. Here, a new code is developed for DNA nucleotide sequences that relates to the initiation site for gene transcription. The structural code consists of the orientation of steroid molecules in binding to DNA nucleotides and the class of steroid molecules that form an intermolecular hydrogen bond with an available functional group of Thymine. This later class thereby describes a steroid hormone-DNA nucleotide-ion complex with three hydrogen bonds for A-T and T-A, which thereby matches the three internal hydrogen bonds associated with C-G and G-C. The code consists of two binary vectors to characterize the four configurations of DNA nucleotides and is shown to be consistent with known regulatory elements of DNA sequences associated with gene transcription, including the TATA box and the E-Box, along with other promoters. In addition, the code, which is bijective, is applied to analyze the DNA sequence associated with SARS-CoV-2 to identify regions with relevant structural characteristics.

Intermolecular Enzymatic Encoding of Nucleic Acid, Steroid Complexes: A New Theory on the Chemical Origin of Life Based on Evidence of Structural Symmetry

“…Thus, it is apparent that this representation is still conserved to this date, which includes the relationship with steroid hormones, the orientation, the intermolecular bonds, the connection to the phosphodiester backbone, and even the configuration of the end groups. Moreover, together, the orientation and class of steroid hormone correspondence form a new code for DNA as shown in Figure 2(c), which is further described in the preprint [23]. Moreover, this is consistent with the indication in Section 2.2 which noted that the nucleotide pairs with pyrimidines along left (5') side had to be flipped in order to achieve their proper orientation consistent with the double helix.…”

“…An evaluation of the structural symmetry of cortisol and the adenine-thymine base pair was determined, noting the intermolecular binding. Thus the symmetry of steroid molecules and DNA nucleotides was discovered [21,22,23]. This structural symmetry of steroid molecules and DNA nucleotides then led to the current results to define a basis for the transcription results perceived of cortisol on adenine-thymine, and other potential interactions between RNA nucleotide and other functional cyclic compounds.…”

Direct Binding of Complementary Symmetric Ligands to DNA Nucleotide Pairs by Means of Transcription Factors

“…To develop the new mechanism for transcription, a fundamental result begins the analysis on the basic structure of DNA nucleotides and the characteristics of ligands that are capable of directly coupling with the DNA nucleotide pairs. I first presented these results in the preprints [9,10,23] and my books pertaining to the design of DNA and the genetic codes, and the origin of life [11].…”