Studies on the stability of tritium-labeled polyuridylic acid and polyadenylic acid

Results are presented on the stability of high specific activity [uridylate-5,6-³H]polyuridylic acid and [adenylate-2,8-³H]polyadenylic acid stored under various conditions. Polyacrylamide disc gel electrophoresis in the presence of SDS was used to assess qualitatively the change in molecular weight distribution of the polynucleotides stored under different conditions. Products stored for a period of months in ethanol; water solution [1:1, $\text{v}\text{v}$] were found to have a significantly slower rate of decomposition than polynucleotides stored in frozen aqueous solution or as lyophilized solid.     

Fluorescent 2-aza-epsilon-adenosine derivatives of polyadenylic acid, polyuridylic acid, and polyinosinic acid.

A new fluorescent analog of adenosine, 1,N⁶-etheno-2-aza-adenosine, has been incorporated into polynucleotides by polynucleotide phosphorylase polymerization of 1,N⁶-etheno-2-aza-adenosine-5′-diphosphate and adenosine-5′-diphosphate, uridine-5′-diphosphate, or inosine-5′-diphosphate. These new oligonucletides possess high fluorescence when excited at 358 nm and emit at 495 nm. The ratio of the fluorescent and nonfluorescent portions of the copolymer can be controlled by the initial composition of the 2-aza-ε-adenosine-diphosphate and the corresponding nucleoside diphosphate. Fluorescent copolymers with a ratio varying from 1.6 to 35 have thus been synthesized. The physicochemical study of copolymers containing less than 10% of the 1,N⁶-etheno-2-aza-adenosine moiety showed that they are similar to poly(A), poly(U), or poly(I). Therefore, fluorescence and polarization study of the 1,N⁶-etheno-2-aza-adenosine residues that have been incorporated into the copolymer provides a sensitive indicator for the structure of the copolymer. Potentially these new copolymers may provide unique roles in probing the structure of poly(C) and poly(A) in cellular mRNA.     

Volume changes accompanying the complex formation of polyadenylic and polyuridylic acids

The complex formation of polyadenylic acid (poly A) and polyuridylic acid (poly U) in 0.1M NaCl solution containing 0.01M sodium cacodylate was followed by dilatometric measurements at various mixing ratios of poly A and poly U. The volume changes, ΔV, accompanying the formation of poly A. poly U and poly A.2poly U were + l.5 and + 2.5 ml per mole of the nucleotide residue, respectively. This increase in volume was probably due to the increased counterion binding when the single-stranded polynucleotides were converted into the double- and triple-stranded helices, since depletion of charged species from the solvent proper would lessen the effect of electrostriction, thus resulting in a positive ΔV. The conversion of a single-stranded poly A to a double-stranded helix in acidic solution led to a ΔV of + 3.8 ml per mole of the nucleotide residue. This increase in volume was attributed to the charge neutralization as a result of protonation of the adenine bases.     

Microsecond time-scale discrimination among polycytidylic acid, polyadenylic acid, and polyuridylic acid as homopolymers or as segments within single RNA molecules

Single molecules of DNA or RNA can be detected as they are driven through an alpha-hemolysin channel by an applied electric field. During translocation, nucleotides within the polynucleotide must pass through the channel pore in sequential, single-file order because the limiting diameter of the pore can accommodate only one strand of DNA or RNA at a time. Here we demonstrate that this nanopore behaves as a detector that can rapidly discriminate between pyrimidine and purine segments along an RNA molecule. Nanopore detection and characterization of single molecules represent a new method for directly reading information encoded in linear polymers, and are critical first steps toward direct sequencing of individual DNA and RNA molecules.     

Interaction of polyadenylic acid with methylated xanthines

Polyadenylic acid forms both 1 : 1 and 2 : 1 complexes with 3-methylxanthine under appropriate conditions. While the binding isotherms for formation of these complexes are typical of strongly cooperative processes, their melting profiles are anomalous and indicate that intermediate species are present during the thermal dissociation process. Theobromine and theophylline do not form complexes with polyadenylic acid under similar conditions, and they do not hydrogen-bond very strongly with 9-ethyludenine in chloroform solution.     

Triple helices formed by polyuridylic acid with some adenosine derivatives

We have prepared a variety of derivatives of adenosine which, at neutral pH's, carry protonated amine functions. These derivatives form stable helical structures with polyuridylic acid, but the melting points are not substantially higher than those of helical complexes formed by adenosine derivatives lacking cationic groups.     

The attachment of polyuridylic acid to reticulocyte ribosomes

The attachment of polyuridylic acid to reticulocyte ribosomes was studied by using polyadenylic acid, which inhibits the attachment reaction only, while permitting translation of polyuridylic acid bound to ribosomes. After addition of polyadenylic acid the amount of polyphenylalanine synthesized under standard conditions was taken as a measure of the bound polyuridylic acid. In this way certain parameters of the attachment reaction and the subsequent translation of attached polyuridylic acid were defined: (1) polyuridylic acid-ribosome interaction at 37 degrees requires only Mg(2+) at an optimum concentration of 8mm; (2) K(+) (required for translation) is a non-competitive inhibitor of the attachment reaction; (3) optimum polyphenylalanine synthesis directed by attached polyuridylic acid occurs at 5mm-Mg(2+) concentration; (4) from kinetic studies single ribosomes appear to participate in the attachment reaction.     

Triple helices formed by polyuridylic acid with some amino deoxyadenosine derivatives

Summary The stability of helical structures formed by polyuridylic acid with nucleosides and nucleotides derived from adenosine is not significantly affected by replacing hydroxyl groups by hydrogen, amino, or azido functions. Stability is affected by the position of the phosphate group.