Intermolecular Binding of Functional Cyclic Compounds to RNA Nucleotides by an Ionic Process

Abstract

Exogenous RNA comprises the genetic material associated with several diseases which require immediate treatment, and thus mechanisms to hinder intracellular translation and reproduction of RNA viral agents are of great importance. Applying recent developments from this lab in methods relating to the interaction of DNA with steroid hormones, cyclic compounds are presented for intermolecular binding to nucleic acids. The requirements to achieve binding with RNA nucleotide pairs are described, which involve at a minimum functional elements positioned to interact with the lateral phosphate groups for each of the RNA strands through coupling with a positively charged ion, such as Mg2+, Ca2+, or Zn2+ ions; and an intermolecular hydrogen bond with the oxygen element of uracil at the carbon two location. Additional features of the binding molecules are examined for enhancements and differentiation in binding capability and include aromatic groups that have both a structural role of steric hindrance and a functional role to stabilize the binding mechanisms. Several categories of cyclic compounds are associated to have specific binding capabilities, and the interaction of these structures with potential receptor molecules are evaluated for assessment in delivery and binding of the compound to nucleic acids.

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

“…Furthermore, the backside elements of the steroid hormones, such as an OH group, can influence the transcription process. Indeed, these concepts have been applied to RNA based applications in forming an intermolecular bond with uracil in a like manner of thymine [28].…”

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

“…Moreover, this newly identified structure is in perfect harmony with the four fused-ring structure of a steroid molecule, thereby establishing the potential for a symmetric relationship with ligands that also consist of four fused rings, or have similar positional arrangements of its composite functional groups. Moreover, not only is this relationship relevant to transcription, this discovery and concept forms the premise in the development of mechanisms for the design of DNA and the biological cell, as described in my recent research monograph on the origin of life [12].…”