Separation and chain-length determination of polynucleotides by gel filtration

Oligomerization of uridine phosphorimidazolides on montmorillonite: a model for the prebiotic synthesis of RNA on minerals

The 5'-phosphorimidazolide of uridine reacts on Na(+)-montmorillonite 22A in aqueous solution to give oligomers as long as 7 mers. The maximum chain length increases to 9 mers and the overall oligomer yield increases when 9:1 ImpU, A5' ppA mixtures react under the same conditions. The oligomer yield and maximum chain length decreases with the structure of the added pyrophosphate in the order A5' ppA > A5' ppU > U5' ppU. Structure analysis of individual oligomer fractions was performed by selective enzymatic hydrolyses followed by HPLC analysis of the products. The regioselectivity for 3',5'-bond formation is 80-90% in the 9:1 ImpU, A5' ppA reaction, a percentage comparable to that observed in the 9:1 ImpA, A5' ppA reaction. Oligomerization of ImpU is inhibited by addition of dA5' ppdA, and MeppA. No oligomers containing A5' ppU were products of the 9:1 ImpU,A5' ppA reaction, a finding consistent with the simple addition of the ImpU to the A5' ppA and not the rearrangement of an ImpU-A5' ppA adduct. Concentrations of lysine or arginine which were close to that of the ImpU did not inhibit oligomer formation. Treatment of Na(+)-montmorillonite with 1 M arginine yielded arginine-montmorillonite, an amino acid-mineral adduct which did not catalyze ImpU oligomerization. Neither the 4-9 mers formed in the 9:1 ImpU, A5' ppA reaction nor the 4-9 mers formed by the base hydrolysis of poly(U) served as templates for the formation of oligo(A)s.

Operational variables in high-performance gel filtration of DNA fragments and RNAs

Double-stranded DNA fragments and ribosomal and transfer RNAs were measured by high-performance gel filtration on TSK-GEL G2000SW, G3000SW, G4000SW and G5000PW columns to investigate the separation range and resolution of these columns and the effects of eluent ionic strength and flow-rate on retention and resolution. These columns could separate double-stranded DNA fragments up to ca 1 X 10(6) and rRNAs up to ca 5 X 10(6) daltons in molecular weight. However, it was found that the selection of the column is very important to achieve optimum separation, depending on the molecular weight of the sample. Elution is delayed as the eluent ionic strength is increased. An eluent ionic strength of 0.3-0.5 seemed appropriate in most cases. Resolution is greatly increased as the flow-rate is decreased.

Complex population of nonpolyadenylated messenger RNA in mouse brain

The complexity of nonadenylated mRNA [poly(A)-mRNA] has been determined by hybridization with single-copy DNA (scDNA) and cDNA. Our results show that poly(A)- and poly(A)+ mRNA are essentially nonoverlapping (nonhomologous) sequence populations of similar complexity. The sum of the complexities of poly(A)+ mRNA and poly(A)- mRNA is equal to that of total polysomal RNA or total mRNA, or the equivalent of approximately 1.7 x 10(5) different sequences 1.5 kb in length. Poly(A)- mRNA, isolated from polysomal RNA by benzoylated cellulose chromatography, hybridized with 3.6% of the scDNA, corresponding to a complexity of 7.8 x 10(4) different 1.5 kb sequences. The equivalent of only one adenosine tract of approximately 20 nucleotides per 100 poly(A)- mRNA molecules 1.5 kb in size was observed by hybridization with poly(U). cDNA was transcribed from poly(A)- mRNA using random oligonucleotides as primers. Only 1-2% of the single-copy fraction of this cDNA was hybridized using poly(A)+ mRNA as a driver. These results show that poly(A)- mRNA shares few sequences with poly(A)+ mRNA and thus constitutes a separate, complex class of messenger RNA. These measurements preclude the presence of a complex class of bimorphic mRNAs [that is, species present in both poly(A)+ and poly(A)- forms] in brain polysomes.

Partitioning of amino acids and nucleotides between water and micellar hexadecyltrimethylammonium halides. The prebiotic significance of cationic surfaces

Using quantitative gel filtration techniques partition coefficients, Kp-values, have been determined between aqueous cationic micellar hexadecyltrimethylammonium bromide, CTAB, and several biomonomer. Kp-values for 5'-adenylic acid, 5'-cytidylic acid, 5'-guanylic acid, 5'-uridylic acid and 5'-thymidylic acid are 1,400 +/- 150. Nucleotides bind to CTAB micelles effectively, but nonselectively. Conversely, the binding of tRNAs to micellar CTAB is selective. Kp-values for glutamic acid II, tyrosine and phenylalanine tRNAs (in 1.0MNaCl) are 520, 3,100 and 5,600, respectively. Kp-values for the binding of alanine, arginine, aspartic acid, glutamic acid, glycine, histidine, phenylalanine, serine, threonine and tryptophan to micellar CTAB are less than 8. Conversion of unitless Kp-values for the binding of amino acids, nucleotides and nucleosides to both anionic and cationic micelles, to K (in 1/g) values allows the comparison of clays and micelles as prebiotic concentrating media. Using correlations between surface densities of the biomonomers and their binding constants, it is shown that aqueous micelles (at pH = 8) are a better concentrating media than are clays.

Polyribonucleotides containing thiopurines. Synthesis and properties of poly(1-methyl-6-thioguanylic acid)

The synthesis of 1-methyl-6-thioguanosine 5'-diphosphate and its conversion to poly(1-methyl-6-thioguanylic acid) by means of polynucleotide phosphorylase are described. The polymer exhibited cooperative behavior (Tm = 294 K in the absence of added NaCl) characteristic of a highly stacked single-stranded helical array. In a high salt environment (0.5 M NaCl) the melting was much less cooperative and gave a higher Tm (313 K); this is suggestive of interstrand aggregation involving hydrogen bonding. The polynucleotide exhibited a remarkably high pKa (6.2) compared to that of the mononucleotide (2.6), and formed a very stable acid structure (Tm = 356 K in 50% ethylene glycol). Comparisons with poly(1-methyl-6-thioinosinic acid) and poly(6-thioguanylic acid) establish that both the 2-amino group and the 1-methyl group are required for the formation of the stable acid structure.

Differential partitioning of tRNAs between micellar and aqueous phases: a convenient gel filtration method for separation of tRNAs

Partition coefficients (Kp) of phenylalanine, glutamic acid-II and tyrosine tRNAs between water and micellar cetyltrimethylammonium chloride (CTACl) have been determined to be 5600, 520 and 3100, respectively, by gel filtration on Sephadex G-100-120. Equations for obtaining Kp values from quantitative gel filtration have also been derived. The use of this method for the separation of tRNAs is demonstrated.

The influence of salt on the aggregation state of spectrin from bovine erythrocyte membranes

Sedimentation velocity and gel filtration experiments have been performed with bovine spectrin over a wide range of neutral salt concentrations. Increasing salt concentrations tend to increase both the sedimentation coefficient of spectrin and the elution volume of the protein from 4% agarose columns. No conformation change can be detected by means of optical rotation measurements as the salt concentration is raised. The results are incompatible with the hypothesis that salt causes the aggregation of spectrin, but are consistent with the existence of marked charge effects operative at low salt concentrations. In support of the charge effect hypothesis, acidic groups have been detected on the agarose gels, and ion-exclusion behaviour on the column has been observed with other proteins of similar size.

Incorporation of 5'-amino-5'-deoxythymidine5'-phosphate in polynucleotides by use of DNA polymerase I and a phiX174 DNA template

An aqueous solution of 5'-amino-5'-deoxythymidine 5'-triphosphate, prepared by incubation of equimolar solutions of 5'-amino-5'-deoxythymidine and sodium trimetaphosphate, stimulates synthesis of acid-precipitable polynucleotides in a system containing single-strand phiX174 DNA template, random oligonucleotide primers, dATP, dCTP,dGTP, Escherichia coli DNA polymerase I, and either magnesium or manganese ion. Approximately onefold synthesis on the template can be achieved and each of the indicated reagents is essential for extensive synthesis. The reaction is slower than the corresponding reaction of dTTP as a consequence of a lower V max and a higher Km for the amino analogue. That aminodeoxythymidine phosphate is incorporated into the synthetic polynucleotides was shown by a double-labeling experiment with [14C]dATP and [32P]-5'-amino-5'-deoxythymidine 5'-triphosphate and by the unusually high lability of the phosphoramidate polynucleotides toward acid. The phosphoramidate polynucleotides range in size from about 100 nucleotide units to well over a thousand nucleotide units, and the size is increased by addition of DNA ligase to the system. These experiments indicate that synthetic polynucleotides in which oligonucleotide blocks have been joined by means of phosphoramidate bonds should prove useful as primers for enzymatic syntheses with DNA polymerase I.

Nucleotide sequence of an RNA polymerase binding site from the DNA of bacteriophage fd

The primary structure of a strong RNA polymerase binding site in the replicative form DNA of phage fd has been determined by direct DNA sequencing. It is: (see article). The molecule contains regions with 2-fold symmetry and sequence homologies to promoter regions from other DNAs. The startpoint of transcription is located in the center of the binding site.

Oligothymidylates: formation by thermal condensation of O 2 ,5'-cyclothymidine 3'-phosphate

Thermal activation of O(2),5'-cyclothymidine 3'-phosphate in solution and in the solid state led to the formation of thymidine oligonucleotides containing up to approximately 12 nucleotide units. Only the 3',5' internucleotide diester bonds were formed. This polymerization occurs without the addition of any activating agent or catalyst.

Genetic assay for small fragments of bacteriophage phi X174 deoxyribonucleic acid

The double-stranded replicative form deoxyribonucleic acid (RF-DNA) of bacteriophage phiX174 was fragmented by pancreatic deoxyribonuclease, and the complementary strand fragments were then annealed to intact viral single strands. When such complexes infected Escherichia coli spheroplasts, some of the progeny virus bore genetic markers derived from the RF-DNA fragments. In this way, genetic markers have been salvaged from DNA fragments less than 50 nucleotides in length. This method is potentially useful as a specific assay to aid in the purification of genetically defined DNA fragments and also as a mechanism for the incorporation of small chemically synthesized DNA sequences into viral genomes.