A rellable mapping method for sequence determination of oligodeoxyribonucleotides by mobility shift analysis

The method for sequence analysis of large oligodeoxyribonucleotides based on the characteristic mobility shifts of their sequential partial degradation products on two-dimensional homochromatography has been perfected using a large number of synthetic oligodeoxyribonucleotides of defined sequences as standards. Flat bed electrophoresis with careful temperature control gave entirely reproducible mobilities in the first dimension. Using this information, an accurate formula has been derived for calculating the relative electrophoretic mobilities of oligodeoxyribonucleotides of any composition. This formula is used to calculate the mobility shifts between two consecutive oligodeoxyribonucleotides in a series of partial products of an unknown oligomer distributed in the two-dimensional homochromatogram which differ by one nucleotide in length. This is compared with the observed mobility shift value to identify the added nucleotide. This provides a direct and rapid method for obtaining the unambiguous sequence of an entire oligodeoxyribonucleotide up to 15 nucleotides in length.     

Biotin-Labeled Synthetic Oligodeoxyribonucleotides: Chemical Synthesis and Uses as Hybridization Probes

Abstract

Several biotinylated synthetic oligodeoxyribonucleotides have been selectively prepared by a simple and efficient chemical method. This procedure allows the specific and covalent coupling of one biotinmoiety to any 5′-kinased unprotected oliqodeoxyribonucleotide through an aminoalkylphosphoramide linker arm. The reactions are performed in aqueous solutions on unprotected oligonucleotides and proceed cleanly with good yields. This method is insensitive of the length of the polynucleotide, of the nucleotide sequence and of the nature of the 5′-terminal nucleotide.     

Interaction of Complementary Oligonucleotides with the 3′-End of Yeast tRNAPHE

Abstract

Interaction of yeast tRNA^Phe with oligodeoxyribonucleotides (ONs), complementary to the nucleotides 62–76 was investigated. Results of gel-mobility shift assay and RNase A probing evidence that the ONs containing the sequence complementary to the tRNA ACCA end can easily invade the hairpin structure under physiological conditions. The limiting step of association process is the tRNA unfolding.     

DNA sequence organization in theThysanura Thermobia domestica

Summary Cot and chemical analysis show that the haploid genome size of Thermobia domestica is 3–4×10⁹ nucleotide pairs. Of this DNA 33% is single copy sequences and 67% is repetitive sequences. The repetitive sequences are predominantly 300 nucleotides in length and are interspersed among the single copy sequences in a short period interspersion pattern similar to that observed in Xenopus and many other higher eucaryotes. The DNA sequence organization observed in Thermobia is compared with that of other more highly evolved insects.Abbrevations HAP-hydroxyapatite, Cot mole nucleotides × liter^–1 s. - N sodium phosphate, pH 6.8     

CHARACTERIZATION OF POLY(A) SEQUENCES IN BRAIN RNA

—Nuclear and polysomal brain RNA from the rabbit bind to Millipore filters and oligo(dT)-cellulose suggesting the presence of poly(A) sequences. The residual polynucleotide produced after RNase digestion of ³²P pulse-labelled brain RNA is 95% adenylic acid and 200-250 nucleotides in length. After longer isotope pulses the polysomal poly(A) sequence appears heterodisperse in size and shorter than the nuclear poly (A). Poly(A) sequences of brain RNA are located at the 3′-OH termini as determined by the periodate-[³H]NaBH₄ labelling technique. Cordycepin interferes with the processing of brain mRNA as it inhibits in vivo poly(A) synthesis by about 80% and decreases the appearance of rapidly labelled RNA in polysomes by about 45%. A small poly(A) molecule 10-30 nucleotides in length is present in rapidly labelled RNA. It appears to be less sensitive to cordycepin than the larger poly(A) and is not found in polysomal RNA.     

Correction for non-uniform phosphate labeling of E. coli and phage RNAs synthesized in vivo

$\text{E. coli}$ cells grown to phosphate starvation incorporate ³²PO₄ unequally into the α position of the four ribonucleotide triphosphates during a short period of labeling. A method for determining the relative specific activities of nucleotides in RNA molecules synthesized under these conditions and correcting sequence data is described.     

Rapid analysis of 3'-ends of DNA fragments by terminal 32P-labeling

A fast method of analysis of the 3′ ends of oligodeoxyribonucleotides is described. Basically the method involves: (a) Labeling of the 3′ ends of oligodeoxyribonucleotides with the terminal deoxynucleotidyl transferase and [α-³²P] ATP as donor; (b) hydrolysis of the labeled fragments to 3′ deoxymononucleotides by acid DNase and spleen exonuclease; (c) unidimensional separation on polyethylene imine cellulose thin-layer plates of the four 3′ deoxyribomononucleotides, 3′ riboadenylic acid, and ATP.     

An improved method for assaying pyrophosphate exchange measuring Cerenkov radiation

The determination of the amount of radioactivity in ³²P-labeled nucleotides absorbed to charcoal is greatly simplified when the same medium is used for extraction and for counting the secondary Cerenkov radiation. Addition of 4-methylumbelliferone increases the efficiency and decreases quenching caused by charcoal particles. With regard to reproducibility and amount of background the method is comparable to other published methods. Its application in a pyrophosphate exchange assay is described.     

Improved synthesis of 32P-labelled 3′,5′-cyclic AMP, 3′,5′-cyclic GMP and other 3′,5′cyclic ribo- and deoxyribonucletodies of high specific activity

A general procedure is described for the two-step chemical synthesis from [³²P]orthophosphoric acid of the eight common ribo- and deoxyribonucleoside 3′,5′-cyclic monophosphates. The method is simple and reliable and both steps are carried out in the same reaction flask without an intermediate purification step. ³²P-labelled cyclic nucleotides are obtained after paper chromatography in yields of 20–60% relative to starting [³²P]orthophosphoric acid and with a specific activity of greater than 1 mCi/μmole. Alternative methods for the purification of reaction mixtures and for the preparation of ³²P-labelled 3′,5′-cyclic AMP and 3,′,5′-cyclic GMP are described.     

Characterization of bacteriophage T4 and D RNA, a low-molecular-weight RNA of unknown function

The nucleotide sequence of T4 band D RNA, a stable RNA species encoded by bacteriophage T4, has been deduced from analysis of the ³²P-labeled RNA and comparison with the DNA sequence of the T4 genome in the region encoding the RNA. The sequence is: pA-U-G-A-G-A-A-A-C-C-G-G-G-U-C-G-C-U-A-C-C-G-G-U-A-A-G-U-C-G-U-C-G-G-A-C-U-G-A-U-G-G-U-U-C-C-C-U-G-A-G-U-A-A-G-G-A-A-U-U-G-C-G-U-U-A-A-U-A-A -U-C-U-U-U-G-C-G-U-U-U-A-U-U-G-A-U-G-C-C-C-U-C-U-U-A-C-A-U-C-A-C-A-G-C-A-G-A-A-A-C-G-G-C-G-C-A-C-C-A_OH. Band D RNA is 120 nucleotides long, and contains no modified nucleotides. The sequence can be arranged in a secondary structure consistent with the results of limited digestion with nuclease S1, but shows no striking similarities to tRNAs. While a biological function for band D RNA is unknown, similar molecules are encoded by bacteriophages T2 and T6, indicating that the molecule has been preserved during evolution. This retention may reflect a significant function for the RNA.     

H-phosphonate method in the synthesis of structural gene of human interleukin-4

A modified H-phosphonate method was used to synthesize 32 oligodeoxyribonucleotides ranging in length from 23 to 28, which were enzymatically joined together to give the human interleukin 4 gene. The high degree of the oligonucleotide purity, achieved through the application of anion-exchange and reverse phase HPLC, ensures the high percentage of the desired sequence (about 75%) in the cloned DNA.     

N2-Substituted-2′-deoxyguanosine 5′-Triphosphates as Substrates for E. coli DNA Polymerase I

Abstract

Several N²-alkyl and N²-phenyl 2′-deoxyguanosine 5′-triphosphates and 2-bromo-2′-deoxyinosine 5′-triphosphate were synthesized and tested as substrates for E. coli DNA polymerase I with a template: primer system requiring incorporation of 85 nucleotides. N²-Methyl-dGTP and N²-ethyl-dGTP were found to be efficiently incorporated in place of dGTP to give full length product. N²-n-Hexyl-dGTP supported limited full length synthesis at high concentration, but N²-phenyl- and N²-(p-n-butylphenyl)-dGTP were poor substrates. 2-Bromo-2′-deoxyinosine 5′-triphosphate was a good substrate for pol I, and it was a replacement only for dGTP. Melting temperatures of oligodeoxyribonucleotides containing N²-alkyl-dG residues, annealed to complementary single stranded DNA, were lower than that of the normal oligomer.     

Adenylate cyclase assay with [alpha-32P]ATP as substrate. A simple modification for lowering blanks

In the assay of adenylate cyclase using [α-³²P]ATP as the substrate and alumina chromatography as the separating procedure for labeled nucleotides, blank levels are dependent on the quality of the labeled ATP and also on that of the alumina. In order to lower the blanks by eliminating the radioactive material contaminating the commercial [α-³²P]ATP preparations, the following treatment is proposed: The reaction mixture resulting from the incubation is heated for 4 min at 95°C in 0.165 n HCl, then it is chromatographed on a selected alumina (Woelm) column. In the conditions used, cyclic AMP was unaffected, while blank values were low. The detection limit of [³²P]cyclic AMP was thus higher and the precision of enzyme activity determination was improved, while the advantages of one-step chromatography were retained.     

Synthesis of a modified gene encoding human ornithine transcarbamylase for expression in mammalian mitochondrial and universal translation systems: a novel approach towards correction of a genetic defect

The mitochondrial (mt) genome is a potential means of gene delivery to human cells for therapeutic expression. As a first step towards this, we have synthesised a gene coding for mature human ornithine transcarbamylase (OTC) by recursive PCR using 18 oligodeoxyribonucleotides, each 70–80 nucleotides in length, with codons which should allow translation in accordance with both mammalian mt and universal codon usage. Flanking mt DNA sequences were incorporated which are designed to facilitate site-specific cloning into the mt genome. Expression of this human gene in Escherichia coli leads to an immunoreactive OTC product of the correct size and N-terminal amino-acid sequence, but which forms inclusion bodies and lacks enzymatic activity     

Sequence organization in Xenopus DNA studied by the electron microscope.

Xenopus laevis DNA was extracted from red blood cells and sheared to a mean length of 2780 nucleotides. The DNA was stripped of foldback-containing fragments and incubated to C₀t 10 (mol · s · l⁻¹), allowing most repetitive sequences to form duplex structures. Duplex-containing fragments were eluted from an hydroxylapatite column and visualized for electron microscopy by spreading from 57% formamide according to the modified Kleinschmidt technique of Davis et al. (1971). The mean length of the fragments observed was 2445 nucleotides. A total of 1700 DNA strands were photographed and studied. Less than 5% of the total strand length was in uninterpretable structures. Every molecule falling within the confines of the plates was included in the sample. Over 50% of the total strand length in the sample was found in structures bearing at least one interspersed repetitive sequence duplex terminated by four single-strand regions. The fraction of DNA present in duplex regions was almost exactly that predicted if the duplex regions represent all the interspersed middle repetitive sequence in the Xenopus genome. Direct measurement of visualized duplexes shows that the mean length of interspersed repetitive sequence elements in this genome is 345 nucleotides. Duplex length was shown to be independent of the length of the strands bearing the duplexes. These observations provide direct confirmation of the length of approximately 300 nucleotides indicated for interspersed repetitive sequences by earlier physical-chemical studies 011 Xenopus DNA. In strands carrying two duplexes terminated by single-strand regions the interduplex, or single-copy sequence element length could be measured. Sequence interspersion curves generated from these data are roughly consistent with those derived earlier from measurements of hydroxylapatite binding as a function of fragment length.     

32P-base analysis of DNA

A ³²P-labeling method for the base composition analysis of nonradioactive DNA was developed consisting of the digestion of DNA to deoxynucleoside 3′-monophosphates by incubation with a mixture of micrococcal nuclease and spleen phosphodiesterase, transfer of ³²P-label from [γ-³²P]ATP to the 5′-hydroxyl groups of the mononucleotides by T4 polynucleotide kinase, two-dimensional anion-exchange thin-layer chromatography on PEI-cellulose of the resultant [5′-³²P]deoxynucleoside 3′,5′-bisphosphates, autoradiography, and scintillation counting. The method was standardized to afford quantitative digestion of DNA to mononucleotides as well as to give quantitative incorporation of ³²P-label into the nucleotides in the DNA hydrolysate so as to make the method an accurate means for determining the base composition of eucaryotic DNA containing adenine, guanine, thymine, cytosine, and 5-methylcytosine.     

In vitro generation of specific deletions in DNA cloned in M13 vectors using synthetic oligodeoxyribonucleotides: mutants in the 5''-flanking region of the yeast alcohol dehydrogenase II gene.

Deletion mutants are particularly useful in defining the boundaries of noncoding genetic functions. Such mutants can be precisely generated using synthetic oligodeoxyribonucleotides as mutagens. In this paper we describe the application of this method to recombinant DNA cloned in a phage M13-derived vector. The mutagenic oligodeoxyribonucleotides, 20 and 21 nucleotides in length, were used to delete a tract of 20 dA-dT base-pairs and an adjacent 22 base-pair perfect dyad from the ADR3 locus, the 5'-flanking regulatory region of the ADR2 gene, of Saccharomyces cerevisiae with high efficiency.     

Complexity of RNA in Eggs of DROSOPHILA MELANOGASTER and MUSCA DOMESTICA

Comparative measurements are presented of the sequence complexity of the RNA stored in the eggs of two dipteran flies, Musca domestica and Drosophila melanogaster. The genome of Musca is about five times the size of the Drosophila genome and contains about 3.6 times as much single-copy sequence. As shown earlier, the interspersion of repetitive and single-copy sequence is of the short-period form in Musca, and is of the long-period form in Drosophila. The egg RNA complexities were determined by hybridization of excess RNA with radioactively labeled single-copy DNA. Complexity is expressed as the length (in nucleotides) of diverse single-copy sequence represented in the RNA. The complexity of the RNA of the Musca egg is about 2.4 x 10⁷ nucleotides, and that of the Drosophila egg is about 1.2 x 10⁷ nucleotides. The RNA of the Musca egg is similar to or very slightly lower in complexity than that of other egg RNAs, e.g., those of Xenopus and sea urchin. Compared to all previously measured egg RNAs, Drosophila egg RNA is low in sequence complexity.