Synthesis and properties of oligonucleotides bearing a pendant pyrene group

Two hexathymidine oligonucleotide derivatives bearing a pyrenylbutyl substituent at a designated internucleotide phosphorus were prepared by solid phase syntheses using 5'-O-(di-p-methoxytrityl)thymidyl-3'-4-(1-pyrenyl)butyl phosphorochloridite and 5'-O-(di-p-methoxytrityl)thymidyl-3'2,2,2-trichloro-1,1-dimethylet hyl phosphorochloridite as phosphitylating agents. Spectrophotometric studies showed that these oligomers bind to Poly A, but not to Poly C, Poly G, or Poly U, and that the complexes with Poly A are somewhat more stable than the duplex formed between hexathymidine pentaphosphate and Poly A.     

Chemical synthesis of diastereomeric diadenosine boranophosphates (ApbA) from 2'-O-(2-cyanoethoxymethyl)adenosine by the boranophosphotriester method

We have synthesized diastereomerically pure diadenosine 3',5'-boranophosphates (Ap(b)A) by using the boranophosphotriester method from ribonucleosides protected with the 2'-hydroxy protecting group 2-cyanoethoxymethyl (CEM). Melting curves of the triple-helical complex of the dimer Ap(b)A and 2poly(U) at high ionic strength revealed that presumptive (Sp)-Ap(b)A had a much higher affinity and presumptive (Rp)-Ap(b)A a much lower affinity for poly(U) than the natural dimer ApA did. In contrast, the affinities of these dimers for poly(dT) were similar. Both the (Rp)- and the (Sp)-boranophosphate diastereomers showed much higher resistance to digestion by snake venom phosphodiesterase and nuclease P1 than ApA did. They have potential for use as synthons to be incorporated into boranophosphate oligonucleotides. In particular, because oligonucleotides containing Sp boranophosphate nucleotides are expected to bind more strongly and specifically to RNA than natural oligoribonucleotides do, they may find application in the isolation and detection of functional RNA in basic research and diagnostics.     

The role of a template sugar-phosphate backbone in the ribosomal decoding mechanism. Comparative study of poly(U) and poly(dT) template activity

To study the role of a template sugar-phosphate backbone in the ribosomal decoding process, poly(U), poly(dT) and poly(dU)-directed cell-free amino acid incorporation was investigated under the influence of neomycin and high concentrations of Mg2+. The specificity of a factor-dependent translation system of Escherichia coli was shown to change according to the principle: "either ribo- or deoxyribopolynucleotide messenger". Poly(dT) is shown to be effectively translated in the absence of elongation factors, both at low (2 degrees C) and high (37 degrees C) temperature. Neomycin inhibits factor-free poly(dT) translation. Little or no poly(U) translation is observed in this system. A chromatographic analysis of the oligophenylalanine residues synthesized seems to show that translocation is the main step responsible for ribosome specificity to the ribo- or deoxyribopolynucleotide template in both factor-dependent and factor-free translation systems.     

A homopolymer of the potent antitumor drug 2'-deoxy-5-fluorouridylate

Poly(5-fluoro-2'-deoxyuridylic acid) was synthesized and its properties were compared with those of poly(dT) and poly(dU). It readily complexed with poly(dA). The 1:1 complex melted at about 20 degrees C lower than poly(dA) . poly(dT). A triple-stranded helix, poly(dA) . 2 poly(dF5U) was formed only in high salt (2.0 M NaCl).     

A homopolymer of the potent antitumor drug 2′-deoxy-5-fluorouridylate

Poly(5-fluoro-2′-deoxyuridylic acid) was synthesized and its properties were compared with those of poly(dT) and poly(dU). It readily complexed with poly(dA). The 1:1 complex melted at about 20°C lower than poly(dA) · poly(dT). A triple-stranded helix, poly(dA)·2 poly(dF⁵U) was formed only in high salt (2.0 M NaCl).     

Inhibition of UDP-glucuronosyltransferase activity by possible transition-state analogues in rat-liver microsomes

A series of possible transition state analogues of the glucuronidation reaction catalyzed by UDP-glucuronosyltransferase were tested for their inhibitory effect on glucuronidation of various substrates in a rat liver microsomal fraction. In general 4-nitrophenol glucuronidation was more effectively inhibited than that of 1-naphthol, bilirubin or testosterone. 2-(1-Naphthyl)ethyl-UDP and 2,2,2-(triphenyl)ethyl-UDP were the most effective inhibitors. Their inhibitory effect was competitive towards both UDP-glucuronic acid and 4-nitrophenol. These compounds were much more effective inhibitors than UDP; therefore addition of a lipophilic group enhances the inhibitory potency of UDP. The various UDP derivatives showed differences in their abilities to inhibit the glucuronidation of the four acceptor substrates, supporting the concept that the different forms of UDP-glucuronosyl transferase have different active sites.     

Nonionic nucleic acid analogues. Synthesis and characterization of dideoxyribonucleoside methylphosphonates.

A series of dideoxyribonucleoside methylphosphonate analogues, dNpN and dNpNp, which contain a nonionic 3'--5' methylphosphonyl internucleoside linkage were prepared. The two diastereoisomers, designated isomers 1 and 2, of each dimer differ in configuration of the methylphosphonate group and were separated by column chromatography. The diastereoisomers of each dimer have different conformations in solution as shown by ultraviolet hypochromicity data and their circular dichroism spectra. For example, dApA isomer 1 is more highly stacked than isomer 2, although both isomers are less stacked than the dinucleoside monophosphate, dApA. The circular dichroism spectrum of isomer 1 is very similar to that of dApA, while the CD spectrum of isomer 2 shows a loss of molecular ellipticity, [theta], at 270 nm and a greatly diminished [theta] at 250 nm. These results suggest that the stacked bases of dApA isomer 1 tend to orient in an oblique manner, while those in isomer 2 tend to orient in a parallel manner. This interpretation is verified by the 1H NMR study of these dimers (L. S. Kan, D. M. Cheng, P. S. Miller, J. Yano, and P. O. P. Ts'o, unpublished experiments). Both diastereoisomers of dAaA form 2U:1A and 2T:1A complexes with poly(U) and poly(dT), respectively. The higher Tm (Tm of poly(U)--isomer 1, 15.4 degrees C; Tm of poly(U)--isomer 2, 19.8 degrees C; Tm of poly(dT)--isomer 1, 18.7 degrees C; Tm of poly(dT)--isomer 2, 18.4 degrees C) values of these complexes vs. those of the corresponding dApA--polynucleotide complexes (Tm of poly(U)--dApA, 7.0 degrees C; Tm of poly(dT)--DApA, 9.2 degrees C) result from decreased charge repulsion between the nonionic dimer backbone and the negatively charged polymer backbone. The difference in conformations between dApA isomer 1 and dApA isomer 2 is reflected in the Tm of the isomer 1-poly(U) complex which is 4.4 degrees C lower than that of the isomer 2-poly(U) complex. Since these nonionic oligonucleotide analogues are taken up by cells in culture, they show promise as molecular probes for the function and structure of nucleic acids inside living cells.     

Novel properties of DNA polymerase beta with poly(rA).oligo(dT) template-primer.

Purified DNA polymerase beta of calf thymus can utilize poly(rA).oligo(dT) as efficiently as poly(dA).oligo(dT) or activated DNA as a template primer. The poly(rA).oligo(dT)-dependent activity of DNA polymerase beta was found to differ markedly from the DNA-dependent activity of the same enzyme (with either activated calf thymus DNA or poly(dA).(dT)10) in the following respects. 1) Poly(rA)-dependent activity was strongly inhibited by natural DNA from various sources or synthetic deoxypolymer duplexes at very low concentrations (less than 0.5 microgram/ml) at which the DNA-dependent activity was affected to a much smaller extent, if at all. 2) Poly(rA)-dependent activity was inhibited by N-ethylmaleimide more strongly than DNA-dependent activity measured at 37 degrees C, while it was resistant to this reagent at 26 degrees C. 3) The curves of the activity versus substrate concentration were sigmoidal in the poly(rA)-dependent reaction but hyperbolic in the activated DNA-dependent reaction. A kinetic study suggested that the association of beta-enzyme protomers may be required to copy the poly(rA) strand.     

Double-stranded RNA

Summary High molecular weight, fully double-stranded RNA (dsRNA) has been recognized as the genetic material of many plant, animal, fungal, and bacterial viruses (Diplomaviruses); virus-specific dsRNA is also found in cells infected with single-stranded RNA viruses.DsRNA has been identified in a variety of apparently normal eucaryotic cells and is associated with the killer character of certain strains of Saccaromyces cerevisiae.The properties and significance of these various dsRNA species are described and discussed, as well as the available information concerning the biosynthesis of such RNA in virus-infected cells, its degradation by a variety of enzymes, and some problems concerning the variables which may control this process.Finally, the biological functions of dsRNA are briefly considered, as well as the structural properties important for its activity as an inducer of interferon and an inhibitor of protein synthesis.Abbreviations dsRNA for double-stranded RNA - ssRNA for single-stranded RNA - SSC for 0.15 m sodium chloride, 0.015 m sodium citrate, pH 7 - Poly(A), poly(C), poly(U) for polyadenylate, polycytidylate and polyuridylate, respectively - Poly(A).poly(U), poly(G).poly(C), poly(I).poly(C) for double-stranded complexes formed between polyadenylate and polyuridylate, polyguanylate and polycytidylate, and polyinosinate and polycytidylate, respectively. - Poly(rA).poly(dT) for the complex formed between polyriboadenylate and polydeoxyribothymidylate - Poly(A-U), poly(G-C) for the alternating copolymers containing AMP and UMP, or GMP and CMP, respectively - Poly(rA).poly(dUz) for the complex formed between polyadenylate and poly 2-azido-2deoxyuridylate - (I)_n.(br⁵C)_n for the complex formed between polyinosinate and poly 5-bromocytidylate - (I)_n.(s²C)_n for the complex formed between polyinosinate and poly 2-thiocytidylate - (dI_n3)_n.(C)_n for the complex formed between poly 2-azido-2-deoxyinosinate and polycytidylate - MW for molecular weight     

Synthesis and its properties of oligonucleotide analogue containing thiocarbamate interlinkages.

Novel nucleotide analogues have been synthesized from morpholine subunits with thiocarbamate linkages. They indicated much stronger interaction with poly U or poly dT than the corresponding natural oligodeoxyribonucleotides. Solubility of the analogues in water was greatly enhanced by introducing sulfate groups at their both ends.     

Parallel-stranded duplex DNA containing dA · dU base pairs

DNA oligonucleotides with dA and dU residues can form duplexes with trans d(A · U) base pairing and the sugar-phosphate backbone in a parallel-stranded orientation, as previously established for oligonucleotides with d(A · T) base pairs. The properties of such parallel-stranded DNA (ps-DNA) 25-mer duplexes have been characterized by absorption (uv), CD, ir, and fluorescence spectroscopy, as well as by nuclease sensitivity. Comparisons were made with duplex molecules containing (a) dT in both strands, (b) dU in one strand and dT in the second, and (c) the same base combinations in reference antiparallel-stranded (aps) structures. Thermodynamic analysis revealed that total replacement of deoxythymine by deoxyuridine was accompanied by destabilization of the ps-helix (reduction in T_m by −13°C in 2 mM MgGl₂, 10 mM Na-cacodylate). The U-containing ps-helix (U1 · U2) also melted 14°C lower than the corresponding aps-helix under the same ionic conditions; this difference was very close to that observed between ps and aps duplexes with d(A · T) base pairs. Force field minimized structures of the various ps and aps duplexes with either d(A · T) or d(A · U) base pairs ps/aps and dT/dU combinations are presented. The energy-minimized helical parameters did not differ significantly between the DNAs containing dT and dU. © 1996 John Wiley & Sons, Inc.     

Enhancement of peptide bond formation by polyribonucleotides on clay surfaces in fluctuating environments

Summary The condensation of glycine to form oligoglycine during temperature and moisture fluctuations on clay surfaces was enhanced up to fourfold by polyribonucleotides. Polydeoxyribonucleotides gave no enhancement. Yields were greatly reduced in the absence of clay. A small preference was observed among the polyribonucleotide bases with enhancements in the order of Poly G > Poly A = Poly U > Poly C at high density of polynucleotide on the clay surface and Poly G > Poly U > Poly C > Poly A at low density. This and other experiments seem to indicate a codonic bias in the interaction of polynucleotides with amino acids reacting to form peptide bonds. A mechanism is proposed which involves (1) activation of glycine on the clay surface, (2) formation of esters between glycine and the 2-OH groups of the polyribonucleotide, and (3) formation of peptide bonds between adjacent amino acyl esters. If this mechanism is correct, it may provide the basis for a simple, direct-template translation process.Abbreviations Poly A Polyadenylic acid - Poly C Polycytidylic acid - Poly G Polyguanylic acid - Poly U Polyuridylic acid - Poly dA Polydeoxyadenylic acid     

Synthesis of a dA-dT base pair analogue and its effects on DNA-ligand binding

Two nucleoside derivatives containing the base analogues 3-deazaadenine and 3-methyl-2-pyridone have been prepared as analogues of dA and dT, respectively. After conversion into the appropriately protected phosphoramidites, DNA sequences were prepared with site-specifically placed analogues. When present in a duplex DNA sequence, the analogues result in the deletion of one or both of the hydrogen bonding functional groups (the N3-nitrogen of dA and the O2-carbonyl of dT) present in the minor groove. Binding by two ligands, 4',6-diamidine-2-phenyl indole (DAPI) and Hoechst 33258 in the minor groove has been probed using a variety of DNA sequences. These sequences contain a d(GAATTC)2 core with analogue nucleosides substituted for one or more of the dA and dT residues. DAPI bound strongly to any sequence that contained both O2-carbonyls of the central two dT residues. The presence of a dc3A residue did in some cases enhance binding. With one of the central O2-carbonyls deleted, the binding was noticeably reduced, and with both absent, no significant binding could be detected. Similar although less dramatic results were observed with Hoechst 33258 binding to analogue sequences.     

Thermodynamics-structure relationship of single mismatches in RNA/DNA duplexes

Thermodynamics of 66 RNA/DNA duplexes containing single mismatches were measured by UV melting methods. Stability enhancements for rG. dT mismatches were the largest of all mismatches examined here, while rU.dG mismatches were not as stable. The methyl group on C5 of thymine enhanced the stability by 0.12 approximately 0.53 kcal mol(-)(1) depending on the identity of adjacent Watson-Crick base pairs, whereas the 2'-hydroxyl group in ribouridine stabilized the duplex by approximately 0.6 kcal mol(-)(1) regardless of the adjacent base pairs. Stabilities induced by the methyl group in thymine, the 2'-hydroxyl group of ribouridine, and an nucleotide exchange at rG.dT and rU.dG mismatches were found to be independent of each other. The order for the mismatch stabilities is rG.dT > rU. dG approximately rG.dG > rA.dG approximately rG.dA approximately rA. dC > rA.dA approximately rU.dT approximately rU.dC > rC.dA approximately rC.dT, although the identity of the adjacent base pairs slightly altered the order. The pH dependence stability and structural changes were suggested for the rA.dG but not for rG.dA mismatches. Comparisons of trinucleotide stabilities for G.T and G.U pairs in RNA, DNA, and RNA/DNA duplexes indicate that stable RNA/DNA mismatches exhibit a stability similar to RNA mismatches while unstable RNA/DNA mismatches show a stability similar to that of DNA mismatches. These results would be useful for the design of antisense oligonucleotides.     

A 5'----3' exoribonuclease of Saccharomyces cerevisiae: size and novel substrate specificity

The purification scheme for a 5'----3' exoribonuclease of Saccharomyces cerevisiae has been modified to facilitate purification of larger amounts of enzyme and further extended to yield highly purified enzyme by use of poly(A)-agarose chromatography. As determined by either sodium dodecyl sulfate-polyacrylamide gel electrophoresis or physical characterization, the enzyme has a molecular weight of about 160,000. Further studies of its substrate specificity show that poly(C) and poly(U) preparations require 5' phosphorylation for activity and that poly(A) with a 5'-triphosphate end group is hydrolyzed at only 12% of the rate of poly(A) with a 5'-monophosphate end group. DNA is not hydrolyzed, but synthetic polydeoxyribonucleotides are strong competitive inhibitors of the hydrolysis of noncomplementary ribopolymers. Poly(A).poly(U) and poly(A).poly(dT) are hydrolyzed at 60 and 50%, respectively, of the rate of poly(A) at 37 degrees C. The RNase H activity of the enzyme can also be demonstrated using an RNA X M13 DNA hybrid as a substrate. When poly(dT).poly(dA) with a 5'-terminal poly(A) segment on the poly(dA) is used as a substrate, the enzyme hydrolyzes the poly(A) "tail," removing the last ribonucleotide, but does not hydrolyze the poly(dA).