Synthesis of oligodeoxyribonucleotides on silica gel support

Attachment of nucleosides and other linkers to solid-phase supports for oligonucleotide synthesis

Specific step-by-step instructions for conversion of 5'-O-(4,4'-dimethoxytrityl)- and base-protected nucleosides and other mono-O-(4,4'-dimethoxytrityl)-protected diols to their hemisuccinate esters and their coupling to CPG (controlled-pore glass) supports bearing aminopropyl or long chain aminoalkyl groups are presented. Additional guidelines are provided for selecting a coupling protocol and performing in-process control.

Attachment of nucleosides to solid-phase supports

Specific step-by-step instructions are given for coupling nucleosides to LCAA-CPG supports (supports consisting of a long-chain alkylamine linked to controlled-pore glass). Protocols are given for a succinic acid linker and a hydroquinone-O,O'-diacetic acid linker. The former is the most widely used linker arm, and the starting materials are widely available. The latter offers greater compatibility with base-sensitive sequence modifications and great synthetic throughput because it can be cleaved under milder and faster conditions. Additional guidelines are given for selecting a linker arm and coupling protocol. Almost any application requiring synthetic oligonucletodies can be satisfied using one of these linker arms.

Hydroquinone-O,O'-diacetic acid ('Q-linker') as a replacement for succinyl and oxalyl linker arms in solid phase oligonucleotide synthesis

When hydroquinone-O,Ooffiacetic acid is used as a linker arm in solid phase oligonucleotide synthesis, the time for NH4OH cleavage of oligodeoxy- or oligoribonucleotides is reduced to only 2 min. This allows increased productivity on automated DNA synthesizers without requiring any other modifications to existing reagents or synthesis and deprotection methods. The Q-linker may also be rapidly cleaved by milder reagents such as 5% NH4OH, potassium carbonate, anhydrous ammonia, t-butylamine or fluoride ion. However, the Q-linker is sufficiently stable for long-term storage at room temperature without degradation and no loss of material occurs during synthesis. The linker is also reasonably resistant to 20% piperidine/DMF, 0.5 M DBU/pyridine and 1:1 triethylamine/ethanol. The Q-linker can therefore serve as a general replacement for both succinyl and oxalyl linker arms.

Solid-phase synthesis of DNA fragments containing the modified base 7-hydro-8-oxo-2'-deoxyguanosine

The 5'-(4,4'-dimethoxytrityl) protected 3'-(2-cyanoethoxy)-N,N-diisopropylphosphoramidite of 7-hydro-8-oxo-2'-deoxy-guanosine, the exocyclic amino and lactam functions of which are protected with acetyl and diphenylcarbamoyl groups, respectively, has been prepared from the 8-bromo derivatives of deoxy- and riboguanosine. This synthon, in combination with standard d-nucleoside 3'-(2-cyanoethoxy)-N,N-diisopropylphosphoramidites, was applied successfully to a solid-phase synthesis. Well-defined oligodeoxyribonucleotides containing a 7-hydro-8-oxo-2'-deoxyguanosine residue at predetermined positions were obtained after deprotection with methanolic ammonia and purification by gel filtration.

Sugar modified oligonucleotides. III (1). Synthesis, nuclease resistance and base pairing properties of alpha- and beta-L-octathymidylates

Two unnatural L-oligodeoxyribonucleotides, namely alpha- and beta-L-dT8pO(CH2)3OH, have been synthesized. These oligomers are resistant towards nuclease degradation. They do not show any UV detectable base pairing with beta-D-dA8 and poly rA.

Sugar modified oligonucleotides. I. Carbo-oligodeoxynucleotides as potential antisense agents

For the first time, carbo-oligodeoxynucleotides, namely c-dT4 and c-dT12, have been synthesized. As compared to the natural oligomers these carbo-oligodeoxynucleotides are at least 5 times more stable toward enzymatic degradation and bind more strongly to complementary DNA. These preliminary data indicate that such oligomers fulfill the requirements to be considered as potential antisense agents.

Purification of synthetic oligonucleotides on a weak ion-exchange column

A weak ion-exchange column (PVDI 4000-5) was used to purify oligonucleotides of relatively large size. The purification of polynucleotides was very rapid, they were separated according to size and retained all their properties relevant to genetic engineering experiments.

Antisense RNA: effect of ribosome binding sites, target location, size, and concentration on the translation of specific mRNA molecules

A series of plasmids were constructed to generate RNA complementary to the beta-galactosidase messenger RNA under control of the phage lambda PL promoter. These plasmids generate anti-lacZ mRNA bearing or lacking a synthetic ribosome binding site adjacent to the lambda PL promoter and/or the lacZ ribosome binding site in reverse orientation. Fragments of lacZ DNA from the 5' and/or the 3' region were used in these constructions. When these anti-mRNA molecules were produced in Escherichia coli 294, maximal inhibition of beta-galactosidase synthesis occurred when a functional ribosome binding site was present near the 5' end of the anti-mRNA and the anti-mRNA synthesized was complementary to the 5' region of the mRNA corresponding to the lacZ ribosome binding site and/or the 5'-coding sequence. Anti-mRNAs producing maximal inhibition of beta-galactosidase synthesis exhibited an anti-lacZ mRNA:normal lacZ mRNA ratio of 100:1 or higher. Those showing lower levels of inhibition exhibited much lower anti-lacZ mRNA:normal lacZ mRNA ratios. A functional ribosome binding site at the 5'-end was found to decrease the decay rate of the anti-lacZ mRNAs. In addition, the incorporation of a transcription terminator just downstream of the antisense segment provided for more efficient inhibition of lacZ mRNA translation due to synthesis of smaller and more abundant anti-lacZ mRNAs. The optimal constructions produced undetectable levels of beta-galactosidase synthesis.

alpha-DNA. VII. Solid phase synthesis of alpha-anomeric oligodeoxyribonucleotides

An efficient procedure for the synthesis of unnatural alpha-anomeric oligodeoxyribonucleotides is described. This solid-phase procedure is based on the use of alpha-nucleoside phosphoramidites and alpha-nucleoside derivatized solid supports corresponding to the four natural bases and allow rapid synthesis of oligonucleotides up to 20 alpha-deoxynucleotide units in length. After HPLC purification, a 15-mer: alpha-d(CCTCTCGTTCTTTAC) and a 20-mer: alpha-d(ATACTTGAGGAAGAGGTGTT) were obtained respectively in 27 and 29% overall yields. Their purity, nucleoside composition and primary structure were ascertained by HPLC and Maxam-Gilbert sequence analyses.

Detection of human leukocyte interferon-alpha A and -alpha 2 genes in genomic DNAs by the use of deoxyoctadecyloligonucleotide probes

Two deoxyoctadecyloligonucleotides complementary to the sequence spanning a single base substitution between human leukocyte interferon (HuIFN) alpha A and alpha 2 genes were efficiently used as probes to distinguish between HuIFN-alpha A and -alpha 2 genes. At 37 degrees C or 42 degrees C under aqueous conditions (0.9 M NaCl), hybridization between both probes and the alpha A and alpha 2 genes without any mismatch was strong, whereas the hybridization with one base mismatch (alpha A probe-alpha 2 gene and alpha 2 probe-alpha A gene) was very weak or negligible. Because the single base substitution of G in the alpha 2 gene for A in the alpha A gene provides an extra HinfI site in the alpha 2 gene at the center of the sequence hybridizing to the alpha 2 probe, digestion with HinfI restriction endonuclease caused complete loss of the hybridization between the alpha 2 probe and the alpha 2 gene. PvuII digestion provides 298-bp fragments hybridizing to the probes only from the alpha A and alpha 2 genes among the known HuIFN-alpha genes. Thus, with the use of these oligonucleotide probes in combination with PvuII and PvuII-HinfI restriction endonuclease digestion, the existence of the sequences corresponding to both IFN-alpha A and IFN-alpha 2 genes in human genomic DNAs was demonstrated. The results also surprisingly indicate that these genes, formerly considered alleles because of their essential identity (1 base pair difference in the coding sequence), are not likely to be alleles, but represent closely related distinct genes.

Guanine modification during chemical DNA synthesis

Base modification during solid-phase phosphoramidite synthesis of oligodeoxynucleotides has been investigated. We have discovered chemical modification that converts dG and dG-containing oligomers to a fluorescent form. This modification has been linked to N,N-dimethylaminopyridine (DMAP), an acylation catalyst, which can displace phosphate triester adducts at the 6-position of guanine. Further, we have found that this fluorescent intermediate can be converted in ammonium hydroxide solution to 2,6 diaminopurine deoxyribonucleoside (2,6 DAP), a potentially mutagenic nucleoside analog. We have shown that N-methylimidazole (NMI) in place of DMAP eliminates the fluorescent species and reduces 2,6 DAP contamination.

Lens-specific enhancer in the third intron regulates expression of the chicken delta 1-crystallin gene

We have previously shown that the tissue specificity determinant of the chicken delta 1-crystallin gene lies 3' of position -100 (Hayashi et al. 1985). Since the promoter of the gene (delta 1-crystallin promoter) did not show any tissue specificity, we examined various segments of the delta 1-crystallin gene for a tissue-specific enhancer activity by placing each segment downstream of a heterologous transcriptional unit coding for chloramphenicol acetyltransferase (CAT) and by transfecting chicken tissues in primary culture. We found that a segment spanning the third intron bears a strong lens-specific enhancer activity. This "delta 1-crystallin enhancer" activates transcription from the delta 1-crystallin promoter 20- to 40-fold in lens cells and to various degrees with other promoters. Deletion analysis of the enhancer region indicated that it covered nearly 1 kb but did not indicate clear-cut boundaries. For its enhancer effect the core region of 120 bp and associations with certain adjoining regions were required. Removal of the enhancer from the gene totally abolished delta 1-crystallin expression, and reinsertion of the enhancer in either upstream, internal, or downstream positions restored expression. We conclude that the delta 1-crystallin enhancer is an essential and major determinant for lens-specificity of delta 1-crystallin expression.

Expression of a pseudogene for interferon-alpha L

The human leukocyte interferon-alpha L (IFN-alpha L) appears to be a pseudogene because it contains a termination codon in the DNA coding for the precursor peptide (signal peptide), but the remainder of the gene codes for an interferon protein of normal length. To determine if this gene codes for an active interferon molecule, an expression plasmid was constructed for IFN-alpha L that was produced in Escherichia coli. The IFN-alpha L is active on human and bovine cells, and exhibits a trace of activity on mouse cells.

Expression of human insulin-like growth factor I in bacteria: use of optimized gene fusion vectors to facilitate protein purification

Several fusions between the gene for human insulin-like growth factor I (IGF-I) and the genes for different IgG-binding fragments of staphylococcal protein A were assembled and compared regarding expression, secretion, and purification of the peptide hormone. After IgG affinity purification of the fusion proteins from the growth medium of Staphylococcus aureus or Escherichia coli, native IGF-I was released by cleavage of an Asn-Gly peptide bond with hydroxylamine. An optimized expression system based on a modified synthetic IgG-binding domain (z), resistant to hydroxylamine, gave the highest yield of fusion protein. After cleavage, the hormone could be separated from the IgG-binding moiety and from noncleaved fusion protein by a second passage through the IgG affinity column. The biological activity and the purity of the IGF-I obtained were confirmed by a radioreceptor assay, N-terminal sequence analysis, polyacrylamide gel electrophoresis, isoelectric focusing, and high-performance liquid chromatography.

Template-primer analogs as substrates for DNA polymerase

In order to gain more understanding about the mode of action of DNA polymerase, eight related partially self-complementary "hairpin" shaped oligodeoxynucleotides were prepared. Four of the oligomers contained either 1-beta-D-arabinofuranosyluracil (ara-U) or 1-beta-D-2'deoxyxylofuranosylthymine (dxT) nucleoside analogs at their 3' termini. We investigated the ability of the oligomers to prime DNA synthesis in relationship to the stability of the hybridized region, the nature of the sugar terminus and the DNA polymerase used (reverse transcriptase, or polymerase alpha). The results are discussed in relation to the mode of action of some nucleoside analog inhibitors of DNA polymerase. An understanding of the mechanism of DNA polymerase action was used to design template-primer analogs as polymerase inhibitors. Two of the oligodeoxynucleotide analogs prepared were found to be potent inhibitors of polymerase alpha.

Expression of an interferon-alpha gene variant in E. coli using tandemly repeated synthetic ribosomal binding sites

A human interferon-alpha 2 gene variant was expressed in Escherichia coli under the control of the tryptophan operon promoter and of a series of synthetic partially overlapping ribosomal binding sites, which control initiation of translation. Variation in the distance between the start codon and such a set of ribosomal binding sites affected the level of interferon expression much less than previously described for single ribosomal binding sites.

A system for the simultaneous chemical synthesis of different DNA fragments on solid support

A mechanical apparatus for the simultaneous synthesis of different DNA fragments on solid support is described. This new system allows the use of different kinds of supports and is amenable to automation. Utilizing this apparatus the synthesis of DNA fragments can be speeded up considerably. The effectiveness of the system is demonstrated by the simultaneous synthesis of DNA fragments up to 36 nucleotides long using phosphoamidites as building blocks and controlled pore glass as solid support.

Prevention of guanine modification and chain cleavage during the solid phase synthesis of oligonucleotides using phosphoramidite derivatives

Phosphoramidite reagents can phosphitylate guanine bases at the O6-position during solid phase synthesis and serious chain cleavage occurs if the base phosphitylation is not eliminated before the iodine/water oxidation step. This can be accomplished by blocking the O6-position with a 2-cyanoethyl protecting group for deoxyribonucleotides or with a p-nitrophenylethyl group for ribonucleotides, regenerating the guanine base with water or acetate ions, or using N-methylanilinium trifluoroacetate (TAMA) as the phosphoramidite activator. The effectiveness of these methods was demonstrated by both 31P NMR studies and by the synthesis of d(Gp)23G, (Gp)14G, and d-(Gp)13rG sequences.

Characterization of a pseudorabies virus glycoprotein gene with homology to herpes simplex virus type 1 and type 2 glycoprotein C

A pseudorabies virus (Becker strain) glycoprotein gene was located in the UL region at map position 0.40. The gene was identified by using open reading frame Escherichia coli plasmid expression vectors and specific antibody reagents. A 1.55-kilobase unspliced transcript from the gene was detected in pseudorabies virus-infected tissue culture cells. The DNA sequence revealed a single open reading frame of 1,437 base pairs encoding 479 amino acids. The predicted primary translation product has a molecular weight of 50,860 and contains features of a typical herpesvirus glycoprotein. An E. coli expression plasmid was constructed that contained essentially all of the open reading frame for this gene. Antibodies raised in rabbits against the protein expressed in bacteria by this plasmid immunoprecipitated pseudorabies virus-specific glycoproteins of 92,000 and 74,000 daltons from infected cell extracts. It is likely that these two forms represent different glycosylation states of the protein.

Modification of guanine bases by nucleoside phosphoramidite reagents during the solid phase synthesis of oligonucleotides

Nucleoside 3'-phosphoramidite and chlorophosphite reagents have been found to react with the lactam function of guanine. This reaction caused unsatisfactory results when oligodeoxyribonucleotides containing a large number of guanine bases were prepared in an automated solid phase synthesizer. The guanine modification is unstable, and leads to depurination and chain cleavage. This side reaction can be eliminated by protecting the O6-position. A new O6-p-nitrophenylethyldeoxyguanosine phosphoramidite derivative, 8, was used to prepare sequences containing up to 24 guanine bases with greatly improved results. A hexatriacontanucleotide, d(CGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCA), was also prepared using O6-protected deoxyguanosine nucleosides.