Effect of solution composition upon poly U

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

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.

Base pairing in 5-chlorouridine

5-Chlorouridine has been found to crystallize from water with the molecules of the nucleoside arranged in a base-paired, parallel-stranded ribbon. This type of polymer structure has not been previously considered for nucleic acids. We have constructed a model of polyuridylic acid based upon the 5-chlorouridine crystal structure and wish to suggest it as a plausible molecular complex for this and perhaps other polynucleotides.The crystals are monoclinic, space group P2(1), with a = 7.536 A,b = 5.790 A, c = 13.219 A, and beta = 99.89 degrees . There are two 5-chlorouridine molecules per cell. The nucleoside bases are linked across a 2(1) axis with hydrogen bonds between N(3) and O(4). The hydrogen bond length is 2.85 A. The conformation of the base with the ribose about the beta-glycosidic bond is anti, with a torsion angle relative to O (1') of -59.8 degrees . The sugar puckering is C(2')-endo, and the conformation about the C(4')-C(5') bond is gauche-gauche. To build the polymer model, the C(4')-C(5') bond was rotated 100 degrees and the sugar-base torsion angle adjusted to -30 degrees . This brought O(3') and O(5') of adjacent sugars close enough to make the phosphate ester linkage found in polynucleotides.