Use of EDTA derivatization to characterize interactions between oligodeoxyribonucleoside methylphosphonates and nucleic acids.

EDTA-derivatized oligonucleoside methylphosphonates were prepared and used to characterize hybridization between the oligomers and single-stranded DNA or RNA. The melting temperatures of duplexes formed between an oligodeoxyribonucleotide 35-mer and complementary methylphosphonate 12-mers were 4-12 degrees C higher than those of duplexes formed by oligodeoxyribonucleotide 12-mers as determined by spectrophotometric measurements. Derivatization of the methylphosphonate oligomers with EDTA reduced the melting temperature by 5 degrees C. Methylphosphonate oligomer-nucleic acid complexes were stabilized by base stacking interactions between the terminal bases of the two oligomers binding to adjacent binding sites on the target. In the presence of Fe2+ and DTT, the EDTA-derivatized oligomers produce hydroxyl radicals that cause degradation of the sugar-phosphate backbone of both targeted DNA and RNA. Degradation occurs specifically in the region of the oligomer binding site and is approximately 20-fold more efficient for single-stranded DNA than for RNA. In comparison to the presence of one oligomer, the extent of target degradation was increased considerably by additions of two oligomers that bind at adjacent sites on the target. For example, the extent of degradation of a single-stranded DNA 35-mer caused by two contiguously binding oligomers, one of which was derivatized by EDTA, was approximately 2 times greater than that caused by the EDTA-derivatized oligomer alone. Although EDTA-derivatized oligomers are stable for long periods of time in aqueous solution, they undergo rapid autodegradation in the presence of Fe2+ and DTT with half-lives of approximately 30 min. This autodegradation reaction renders the EDTA-derivatized oligomers unable to cause degradation of their complementary target nucleic acids.(ABSTRACT TRUNCATED AT 250 WORDS)

Photochemical cross-linking of psoralen-derivatized oligonucleoside methylphosphonates to rabbit globin messenger RNA.

Antisense oligodeoxyribonucleoside methylphosphonates targeted against various regions of mRNA or precursor mRNA are selective inhibitors of mRNA expression both in cell-free systems and in cells in culture. The efficiency with which methylphosphonate oligomers interact with mRNA, and thus inhibit translation, can be considerably increased by introducing photoactivatable psoralen derivatives capable of cross-linking with the mRNA. Oligonucleoside methylphosphonates complementary to coding regions of rabbit alpha- or beta-globin mRNA were derivatized with 4'-(aminoalkyl)-4,5',8-trimethylpsoralens by attaching the psoralen group to the 5' end of the oligomer via a nuclease-resistant phosphoramidate linkage. The distance between the psoralen group and the 5' end of the oligomer can be adjusted by changing the number of methylene groups in the aminoalkyl linker arm. The psoralen-derivatized oligomers specifically cross-link to their complementary sequences on the targeted mRNA. For example, an oligomer complementary to nucleotides 56-67 of alpha-globin mRNA specifically cross-linked to alpha-globin mRNA upon irradiation of a solution of the oligomer and rabbit globin mRNA at 4 degrees C. Oligomers derivatized with 4'-[[N-(2-amino-ethyl)amino]methyl]-4,5',8-trimethylpsoralen gave the highest extent of cross-linking to mRNA. The extent of cross-linking was also determined by the chain length of the oligomer and the structure of the oligomer binding site. Oligomers complementary to regions of mRNA that are sensitive to hydrolysis by single-strand-specific nucleases cross-linked to an approximately 10-30-fold greater extent than oligomers complementary to regions that are insensitive to nuclease hydrolysis.(ABSTRACT TRUNCATED AT 250 WORDS)

Interaction of psoralen-derivatized oligodeoxyribonucleoside methylphosphonates with synthetic DNA containing a promoter for T7 RNA polymerase.

The interaction of 4'-N(2-aminoethyl)aminomethyl-4,5',8-trimethylpsoralen-modified oligonucleoside methylphosphonates with synthetic ds-DNA containing a T7 RNA polymerase promoter was studied. The oligomers effectively crosslinked with either coding or noncoding ss-DNA when irradiated at 365 nm, but not with ds-DNA. The extent of the crosslinking reaction, which was complete within 16 min: (a) reached its maximum at an oligomer concentration of 3 microM; (b) remained constant below the Tm of the duplex and then rapidly decreased; and (c) appeared to depend upon the sequence surrounding the psoralen crosslinking site. An oligomer crosslinked to the template strand inhibited transcription by T7 RNA polymerase whereas an oligomer crosslinked to the non-template strand had only a small inhibitory effect. Oligomers did not crosslink to ds-DNA undergoing transcription nor did they inhibit the transcription reaction.

Interaction of psoralen-derivatized oligodeoxyribonucleoside methylphosphonates with single-stranded DNA.

Oligodeoxyribonucleoside methylphosphonates derivatized at the 5' end with 4'-(amino-alkyl)-4,5',8-trimethylpsoralen were prepared. The interaction of these psoralen-derivatized methylphosphonate oligomers with synthetic single-stranded DNAs 35 nucleotides in length was studied. Irradiation of a solution containing the 35-mer and its complementary methylphosphonate oligomer at 365 nm gave a cross-linked duplex produced by cycloaddition between the psoralen pyrone ring of the derivatized methylphosphonate oligomer and a thymine base of the DNA. Photoadduct formation could be reversed by irradiation at 254 nm. The rate and extent of cross-linking were dependent upon the length of the aminoalkyl linker between the trimethylpsoralen group and the 5' end of the methylphosphonate oligomer. Methylphosphonate oligomers derivatized with 4'-[[N-(2-aminoethyl)amino]methyl]- 4,5',8-trimethylpsoralen gave between 70% and 85% cross-linked product when irradiated for 20 min at 4 degrees C. Further irradiation did not increase cross-linking, and preirradiation of the psoralen-derivatized methylphosphonate oligomer at 365 nm reduced or prevented cross-linking. These results suggest that the methylphosphonate oligomers undergo both cross-linking and deactivation reactions when irradiated at 365 nm. The extent of cross-linking increased up to 10 microM oligomer concentration and dramatically decreased at temperatures above the estimated Tm of the methylphosphonate oligomer-DNA duplex. The cross-linking reaction was dependent upon the fidelity of base-pairing interactions between the methylphosphonate oligomers and the single-stranded DNA. Noncomplementary oligomers did not cross-link, and the extent of cross-linking of oligomers containing varying numbers of noncomplementary bases was greatly diminished or eliminated.(ABSTRACT TRUNCATED AT 250 WORDS)

Inhibition of vesicular stomatitis virus protein synthesis and infection by sequence-specific oligodeoxyribonucleoside methylphosphonates.

Oligodeoxyribonucleoside methylphosphonates which have sequences complementary to the initiation codon regions of N, NS, and G vesicular stomatitis virus (VSV) mRNAs were tested for their ability to inhibit translation of VSV mRNA in a cell-free system and in VSV-infected mouse L cells. In a rabbit reticulocyte lysate cell-free system, the oligomers complementary to N (oligomer I) and NS (oligomer II) mRNAs inhibited translation of VSV N and NS mRNAs whereas oligomer III had only a slight inhibitory effect on N protein synthesis. At 100 and 150 microM, oligomer I specifically inhibited N protein synthesis in the lysate. In contrast, at 150 microM, oligomer II inhibited both N and NS protein synthesis. This reduced specificity of inhibition may be due to the formation of partial duplexes between oligomer II and VSV N mRNA. The oligomers had little or no inhibitory effects on the synthesis of globin mRNA in the same lysate system. Oligomers I-III specifically inhibited the synthesis of all five viral proteins in VSV-infected cells in a concentration-dependent manner. The oligomers had no effects on cellular protein synthesis in uninfected cells nor on cell growth. An oligothymidylate which forms only weak duplexes with poly(rA) had just a slight effect on VSV protein synthesis and yield of virus. Oligomers I-III have extensive partial complementarity with the coding regions of L mRNA. The nonspecific inhibition of viral protein synthesis in infected cells may reflect the role of N, NS, and/or L proteins in the replication and transcription of viral RNA or result from duplex formation between the oligomers and complementary, plus-strand viral RNA.(ABSTRACT TRUNCATED AT 250 WORDS)

Solid-phase syntheses of oligodeoxyribonucleoside methylphosphonates.

Oligodeoxyribonucleoside methylphosphonates of defined sequence of the type d-Np(NP)nN, where n is 6-13, are readily prepared on insoluble polystyrene supports by use of protected 5'-(dimethoxytrityl)deoxyribonucleoside 3'-(methylphosphonic imidazolides) as synthetic intermediates. The imidazolides are prepared in situ by reaction of protected 5'-(dimethoxytrityl)deoxyribonucleoside with methylphosphonic bis(imidazolide) and can be stores in the reaction solution for up to 2 weeks at 4 degrees C with no loss in activity. The condensation reaction is accelerated by the presence of tetrazole, which appears to act as an acid catalyst. The half-life for dimer formation on the polystyrene support is 5 min, and the reaction is 95% complete after 60 min. Although similar kinetics are observed when controlled pore glass is used as the support, the extent of the reaction does not go beyond 78%, even after prolonged incubation. In order to simplify purification and sequence analysis of the oligomer, the 5'-terminal nucleoside unit is linked via a phosphodiester bond. This linkage may be introduced by either an o-chlorophenyl phosphotriester method or a cyanoethyl phosphoramidite method. The latter procedure simplifies the deprotection step, since the cyanoethyl group is readily cleaved by ethylenediamine, which also removes the base protecting groups and cleaves the oligomer from the support. The singly charged oligomers are easily purified by affinity chromatography on DEAE-cellulose. The chain lengths of the oligomers were confirmed after 5'-end labeling with polynucleotide kinase by partial hydrolysis of the methylphosphonate linkages with 1 M aqueous piperidine followed by polyacrylamide gel electrophoresis of the hydrolysate.(ABSTRACT TRUNCATED AT 250 WORDS)

Inhibition of rabbit globin mRNA translation by sequence-specific oligodeoxyribonucleotides.

Oligodeoxyribonucleotides 8-12 nucleotides in length whose sequences are complementary to the 5' end, the initiation codon regions, or the coding regions of rabbit globin mRNA were tested for their ability to inhibit translation in a rabbit reticulocyte lysate and in a wheat germ extract. The oligomers interact specifically with their target mRNAs as shown by their ability to serve as primers with reverse transcriptase. In the reticulocyte lysate, oligomers complementary to the 5' end or the initiation codon regions inhibit translation of both alpha- and beta-globin mRNA, whereas oligomers complementary to the coding regions have little or no effect. This suggests that reticulocyte ribosomes are able to displace the oligomers from the mRNA during the elongation but not the initiation step of translation. In the wheat germ system, translation was effectively inhibited by all oligomers regardless of their binding site on the message. In contrast to their behavior in the reticulocyte system, the oligomers inhibited alpha- and beta-globin synthesis in a specific manner. This observation suggests that control of alpha- and beta-globin mRNA translation is coordinated in the reticulocyte lysate system but not in the wheat germ extract. The results of our studies indicate that oligodeoxyribonucleotides may be useful probes for studying control of mRNA translation in cell-free systems.

Hybridization arrest of globin synthesis in rabbit reticulocyte lysates and cells by oligodeoxyribonucleoside methylphosphonates.

Oligodeoxyribonucleoside methylphosphonates which are complementary to the 5' end, the initiation codon regions, or the coding regions of rabbit globin mRNA were synthesized. These oligomers were shown to interact with their complementary mRNA binding sites by their ability to serve as primers for reverse transcriptase. In several cases, the priming efficiency of the oligomers was enhanced when the oligomer was preannealed with the mRNA. This behavior correlates with the predicted secondary structure of the mRNA and suggests that some oligomer binding sites occur in hydrogen-bonded stem regions of the mRNA. Methylphosphonate oligomers inhibit translation of globin mRNA in reticulocyte lysates. Inhibition is due to the interaction of the oligomers with mRNA. The extent of inhibition is affected by the sequence and chain length of the oligomer, the location of the oligomer binding site on the mRNA, and the secondary structure of the binding site. Oligomers which bind to the 5' end and initiation codon regions of beta-globin mRNA inhibit both alpha- and beta-globin synthesis whereas oligomers which bind to the coding region of alpha-globin mRNA or the coding region of beta-globin mRNA inhibit translation of their target mRNA in a specific manner. Oligodeoxyribonucleoside methylphosphonates inhibit globin synthesis in rabbit reticulocytes. The effects of various oligomers on cellular globin synthesis are similar to those in the lysate system and suggest that the conformation of globin mRNA is the same in both systems during translation.

Characterization of sequence-specific oligodeoxyribonucleoside methylphosphonates and their interaction with rabbit globin mRNA.

Oligodeoxynucleoside methylphosphonates, nucleic acid analogues that contain nonionic, 3'-5'-linked methylphosphonate internucleotide bonds, can be used to control mRNA function in living cells. In order to use analogues of defined sequence in biochemical and biological experiments, methods have been developed to characterize the chain length and sequence of oligodeoxyribonucleoside methylphosphonates and to study their interaction with mRNA. Methylphosphonate oligomers that terminate at the 5' end with a 3'-5' internucleotide phosphodiester bond are readily phosphorylated by polynucleotide kinase. Treatment of these 32P end labeled oligomers with aqueous piperidine randomly hydrolyzes the methylphosphonate linkage and upon gel electrophoresis produces a ladder of oligomers, which allows the chain length of the oligomer to be determined. The sequence of 32P end labeled oligonucleoside methylphosphonates can be determined by a modified chemical sequencing procedure. The interaction of the oligomers with rabbit globin mRNA was studied. The oligomers hybridize with mRNA in agarose gels. The stability of the hybrids increases with increasing chain length of the oligomer. The binding site of the oligomers on mRNA can be determined by using the oligomer as a primer for reverse transcriptase. The length of the resulting transcript is determined by polyacrylamide gel electrophoresis after removal of the methylphosphonate primer by treatment with piperidine. The results indicate that binding and priming ability of the oligonucleoside methylphosphonates are affected by the secondary structure of the mRNA.

Control of ribonucleic acid function by oligonucleoside methylphosphonates.

Oligodeoxyribonucleoside methylphosphonates contain nonionic 3'-5' linked methylphosphonate internucleotide bonds in place of the normal charged phosphodiester linkage of natural nucleic acids. These oligomers are resistant to nuclease hydrolysis, can pass through the membranes of mammalian cells in culture and can form stable hydrogen-bonded complexes with complementary nucleotide sequences of cellular RNAs such as mRNA. The oligomers are readily synthesized on insoluble polymer supports. Their chainlength and nucleotide sequence can be determined by chemical sequencing procedures. Oligonucleoside methylphosphonates which are complementary to the 5'-end, initiation codon region, or coding region of rabbit globin mRNA inhibit translation of the mRNA in rabbit reticulocyte lysates and globin synthesis in rabbit reticulocytes. This inhibition is due to the interaction of the oligomers with mRNA and the extent of inhibition is influenced by the secondary structure of the mRNA and the location of oligomer binding site on the mRNA. Oligomers complementary to the initiation codon regions of N, NS and G protein mRNAs of Vesicular stomatitis virus (VSV) inhibit virus protein synthesis in VSV-infected Mouse L-cells. These oligomers do not affect L-cell protein synthesis or growth. Virus protein synthesis and growth can also be selectively inhibited by oligonucleoside methylphosphonates which are complementary to the donor or acceptor splice junctions of virus pre mRNA. An oligomer complementary to the donor splice junction of SV40 large T antigen mRNA inhibits T-antigen synthesis in SV40-infected African green monkey kidney cells but does not inhibit overall cellular protein synthesis.(ABSTRACT TRUNCATED AT 250 WORDS)

Phosphorylation and inactivation of rat liver glycogen synthase by cAMP-dependent protein kinase and cAMP-independent synthase (casein) kinase-1.

Phosphorylation of liver glycogen synthase by cAMP-dependent protein kinase (A-kinase) results in the incorporation of approximately 0.7 to 1.0 mol of PO4/subunit. Analyses of the tryptic peptides by isoelectric focusing and peptide mapping reveal the presence of a single 32P-labeled peptide. This extent of phosphorylation does not result in a significant reduction of the synthase activity ratio. Phosphorylation of the liver synthase by cAMP-independent synthase (casein) kinase-1 results in the incorporation of 1.6 to 2.2 mol of PO4/subunit. Although at least 4 tryptic peptides have been found to be labeled with 32P, no significant reduction of the synthase activity ratio was observed. Under the same assay conditions, the muscle synthase is effectively inactivated by either kinase alone or in combination. Inactivation of liver synthase can be achieved after phosphorylation by A-kinase and followed by synthase (casein) kinase-1. However, the inactivation becomes less effective if the order of the addition of these two kinases is reversed. Under the latter assay condition, the phosphate incorporation is less than additive in the presence of both kinases. Prior phosphorylation of the synthase by A-kinase transforms the synthase to become a better substrate for synthase (casein) kinase-1 as evidenced by a 3- to 5-fold increase in the rate of phosphorylation. This increased rate of phosphorylation of the synthase by synthase (casein) kinase-1 results from the rapid phosphorylation of a site neighboring to that previously phosphorylated by A-kinase.

Phosphorylation of troponin and myosin light chain by cAMP-independent casein kinase-2 from rabbit skeletal muscle.

Casein kinase-2 from rabbit skeletal muscle was found to phosphorylate, in addition to glycogen synthase, troponin from skeletal muscle, and myosin light chain from smooth muscle. Troponin T and the 20,000 Mr myosin light chain are phosphorylated by casein kinase-2 at much greater rates than glycogen synthase. The V values for the phosphorylation of troponin and myosin light chain are nearly an order of magnitude greater than that of glycogen synthase; however, the Km values for these two substrates are greater than that for glycogen synthase. The kinase activities with the various protein substrates are stimulated approximately three- and fivefold by 5 mM spermidine and 3 mM spermine, respectively. Heparin is a potent inhibitor of the kinase when casein, glycogen synthase, or myosin light chain is the substrate. However, with troponin as substrate the kinase is relatively insensitive to inhibition by heparin. The amount of heparin required for 50% inhibition with troponin as substrate is at least 10 times greater than with casein as substrate. The phosphorylation of troponin by casein kinase-2 results in the incorporation of phosphate into two major tryptic peptides, which are different from those phosphorylated by casein kinase-1. The site in myosin light chain phosphorylated by casein kinase-2 is different from that phosphorylated by myosin light chain kinase.