Structural transitions in poly(A), poly(C), poly(U), and poly(G) and their possible biological roles

Abstract

The homopolynucleotide (homo-oligonucleotide) tracts function as regulatory elements at various stages of mRNAs life cycle. Numerous cellular proteins specifically bind to these tracts. Among them are the different poly(A)-binding proteins, poly(C)-binding proteins, multifunctional fragile X mental retardation protein which binds specifically both to poly(G) and poly(U) and others. Molecular mechanisms of regulation of gene expression mediated by homopolynucleotide tracts in RNAs are not fully understood and the structural diversity of these tracts can contribute substantially to this regulation. This review summarizes current knowledge on different forms of homoribopolynucleotides, in particular, neutral and acidic forms of poly(A) and poly(C), and also biological relevance of homoribopolynucleotide (homoribo-oligonucleotide) tracts is discussed. Under physiological conditions, the acidic forms of poly(A) and poly(C) can be induced by proton transfer from acidic amino acids of proteins to adenine and cytosine bases. Finally, we present potential mechanisms for the regulation of some biological processes through the formation of intramolecular poly(A) duplexes. Communicated by Ramaswamy H. Sarma.

Dual-Color Emissive AIEgen for Specific and Label-Free Double-Stranded DNA Recognition and Single-Nucleotide Polymorphisms Detection

“…The above results testified that the dual-color emission of TPBT was directly related to the double-helix structure of dsDNA, exhibiting a high specificity to dsDNA. Moreover, RNA has an additional non-Watson–Crick base pair (G·U pair) compared with DNA, which makes ssRNA easy to form intra/intermolecular RNA duplexes . Such RNA duplexes can also activate the 537 nm emission peak.…”

Short PolyA RNA Homopolymers Undergo Mg2+-Mediated Kinetically Arrested Condensation

“…The length and presence of these sequences have been functionally associated with mRNA half-life, degradation machinery, and transcriptional processes. , From a chemical perspective, polyrA, despite its simplicity of sequence, has a complex array of structural forms. Due to its potential for self-interaction, polyrA has the potential to transition between random coils, single-stranded helices, and double-stranded structures depending on environmental conditions. − Furthermore, recent studies indicate that polyrA interacts with Mg 2+ in a manner distinct from polyrU and polydA with respect to both hydration and binding preference compared to Na + . , …”

Auxiliary domains of the HrpB bacterial DExH-box helicase shape its RNA preferences

“…Thus, it is more likely that HrpB would prefer some RNA structures over others. For example, under physiological conditions poly(G) adopts quadruplex structures that could impair the recognition by HrpB [33,34]. Of note, poly(I) does not form quadruplexes and indeed stimulates HrpB ATPase similarly to poly(A) (data not shown).…”

“…However, it is not unprecedented as SrmB, a DEAD-box helicase from E. coli, has been also shown to be stimulated by poly(A) and poly(C), but not by poly(U) [32]. Importantly, homopolyribonucleotides differ not only by their primary RNA sequence but also by their secondary and higher order structures [33]. Thus, it is more likely that HrpB would prefer some RNA structures over others.…”

“…Of note, poly(I) does not form quadruplexes and indeed stimulates HrpB ATPase similarly to poly(A) (data not shown). Likewise, poly(U) could be a poor activator of HrpB ATPase because it occurs as a singlestranded molecule adopting random coils, whereas poly(A) and poly(C) good activator because they exist as single-stranded molecules with ordered helical and coiled structures [33].…”