Hybridization of nucleic acids immobilized on solid supports

Synthetic oligonucleotide probes deduced from amino acid sequence data. Theoretical and practical considerations

Synthetic probes deduced from amino acid sequence data are widely used to detect cognate coding sequences in libraries of cloned DNA segments. The redundancy of the genetic code dictates that a choice must be made between (1) a mixture of probes reflecting all codon combinations, and (2) a single longer "optimal" probe. The second strategy is examined in detail. The frequency of sequences matching a given probe by chance alone can be determined and also the frequency of sequences closely resembling the probe and contributing to the hybridization background. Gene banks cannot be treated as random associations of the four nucleotides, and probe sequences deduced from amino acid sequence data occur more often than predicted by chance alone. Probe lengths must be increased to confer the necessary specificity. Examination of hybrids formed between unique homologous probes and their cognate targets reveals that short stretches of perfect homology occurring by chance make a significant contribution to the hybridization background. Statistical methods for improving homology are examined, taking human coding sequences as an example, and considerations of codon utilization and dinucleotide frequencies yield an overall homology of greater than 82%. Recommendations for probe design and hybridization are presented, and the choice between using multiple probes reflecting all codon possibilities and a unique optimal probe is discussed.

Temporal regulation of baculovirus RNA: overlapping early and late transcripts

Analysis of the temporal sequence of RNA transcription within the Autographa californica nuclear polyhedrosis virus genome revealed individual transcription units composed of overlapping early or late RNAs, or both. High-resolution S1 nuclease mapping within the 3.0-kilobase HindIII-K fragment located five overlapping RNAs (1.07, 1.38, 2.63, 3.16, and 3.50 kilobases) transcribed in the same direction and terminated at a common 3' site. The smallest RNAs appeared early but were replaced in time by successively larger RNAs initiated further upstream. Primer extension analysis supported the contention that this temporal regulation involved the sequential activation of upstream promoters and the coordinate deactivation of downstream promoters. As such, transcription from upstream genes may suppress that of downstream genes via transcriptional interference (promoter occlusion) and thereby facilitate sequential expression of different viral functions. In contrast, overlapping RNAs with extended 3' ends were transcribed from the abundantly expressed p10 and polyhedrin genes mapping to the HindIII-Q,P/EcoRI-P and HindIII-V/EcoRI-I fragments, respectively. These RNAs were synthesized maximally during the very late occlusion phase and consisted of a major small transcript and several larger but less abundant transcripts.

Studies on four cellular proto-oncogenes and their expression in PCC4 embryonal carcinoma cells: amplification of c-Ki-ras oncogene

We examined the expression of four cellular proto-oncogenes in two teratocarcinoma cell lines, one undifferentiated and malignant (PCC4), one differentiated and non malignant (PCD1). In this paper we report that transcript levels of c-Ki-ras, c-myc and c-fos are significantly higher in PCC4 cells whereas transcripts of c-Ha-ras are unchanged. Southern blot analysis does not reveal any structural alteration of c-myc and c-fos in PCC4 cells. On the contrary, the c-Ki-ras proto-oncogene is amplified 10 to 20 fold in PCC4 cells.

Oncogene expression in rat hepatomas and during hepatocarcinogenesis

In this study we examined oncogene expression in several Morris hepatomas. We found elevated transcripts for Ha-ras, Ki-ras, and the myc oncogenes, while the src oncogene was not increased. Northern analysis revealed transcript sizes of 1.4 kb for Ha-ras and 2.5 kb for myc. Analysis of primary tumors induced by the carcinogen 3'-methyl-4-dimethylaminoazobenzene (3'-MDAB) showed increasing oncogene transcript production with increasing length of diet. The results show enhanced ras and myc expression in rat hepatocellular carcinomas and during hepatocarcinogenesis.

Relationship of M protein genes in group A streptococci

The M protein of group A streptococci is considered one of the primary virulence determinants of this organism because it prevents phagocytosis. All of the 56 different M protein types of group A streptococci tested contain a DNA region that hybridizes with a labeled probe consisting of DNA encoding the type 6 M protein (emm6 gene). In addition, 2 of 3 functionally M- group A strains (strains that are successfully phagocytized) also contain this gene, but this DNA is not present in 1 M- strain. Of the other streptococcal groups, only groups C and G, which are closely related to group A, contain DNA that hybridizes with emm6. None of the non-streptococcal Gram-positive bacteria tested contains emm6-related DNA. In the strain from which emm6 was cloned, there appears to be only a single copy of this gene.

Dot-blot procedure with [32P]DNA probes for the sensitive detection of avocado sunblotch and other viroids in plants

Avocado sunblotch viroid (ASBV) has been detected down to a level of about 20 pg per gram fresh weight of leaves by the use of a dot-blot hybridization procedure and partially purified nucleic acid extracts. Three [32P]DNA probes were compared, two prepared from full-length ASBV clones in the single-strand M13mp93 vector and the other by primer extension on purified ASBV. All three probes gave the same sensitivity of detection of ASBV. The methods developed have also been used successfully for the routine detection of potato spindle tuber viroid, citrus exocortis viroid, and coconut cadang cadang viroid.

Rapid induction of the expression of proto-oncogene fos during human monocytic differentiation

The differentiation into macrophages of the monocytic cell line U-937 or the monomyelocytic cell line HL-60 induced by phorbol esters is accompanied by a rapid induction of the expression of the proto-oncogene c-fos. Maximal levels of c-fos gene transcripts accumulate within 20-30 min following induction. By 2 hr, the c-fos-specific mRNA level drops 5 to 10 fold below that detected at 30 min after induction. The concentration of c-fos mRNA remains unchanged for the next 5 days, at which time over 99% of the viable precursor cells are converted to adherent macrophages. c-fos protein can be detected within 20 min of induction, reaching maximal levels by 40-60 min. Little or no c-fos protein is detected by 120-150 min after induction, even though c-fos mRNA remains detectable. Presence of cycloheximide leads to superinduction of c-fos mRNA transcripts. No c-fos gene transcripts are detected when the HL-60 cell line is induced with Me2SO to differentiate to granulocytes. A role for the c-fos protein is envisaged in the monocyte differentiation pathway.

Interferon-mediated regulation of myc and Ki-ras oncogene expression in long-term-treated murine viral transformed cells

Long-term treatment of a murine retroviral-transformed cell line (Ki-Balb) with 50 units/ml of interferon (IFN) resulted in a morphological reversion. The effects of IFN on myc and Ki-ras oncogene expression were examined after 6 months of treatment. mRNA dot and Northern blots hybridization analysis reveal that the expression of c-myc at the RNA level decreases by about fourfold. This reduction in the c-myc mRNA appears to be selective since in the same cells v-Ki-ras and an endogenous retroviral gene, intracisternal A particles (IAP), are increased four- and threefold, respectively. No significant inhibition of cellular growth and cell-cycle distribution was observed in IFN-Ki-Balb-treated cells.

Gene encoding human growth hormone-releasing factor precursor: structure, sequence, and chromosomal assignment

We have isolated and characterized overlapping clones from phage lambda and cosmid human genomic libraries that predict the entire structure of the gene encoding the precursor to human growth hormone-releasing factor. The gene includes five exons spanning 10 kilobase pairs of human genomic DNA. There appears to be a segregation of distinct functional regions of the GRF precursor and its mRNA into the five exons of the gene. The DNA sequences of all exons, intron/exon boundaries, and 5' and 3' flanking regions are presented. Dot-blot analysis of DNA from high resolution dual-laser-sorted human chromosomes indicates that the single-copy growth hormone-releasing factor gene is located on human chromosome 20.

Detection of sickle-cell mutation by electrophoresis of partial RNA:DNA hybrids following solution hybridization

We have developed a method in which partially single-stranded (ss) DNA molecules containing a defined region of duplex RNA:DNA are electrophoretically separated in agarose gels. The partial hybrids are formed by solution hybridization with a uniform length RNA probe complementary to part of the DNA sequence of interest. Following hybridization, the RNA/DNA mixture is fractionated by agarose gel electrophoresis at high temperature to minimize intrastrand base pairing which causes mobility heterogeneity. Not requiring the steps of DNA transfer from the gel to a solid support and subsequent probing, pre-electrophoretic hybridization allows the direct identification of single-copy fragments. Conditions for the detection of single-copy genes in human DNA digested with specific restriction endonucleases were developed and applied to the diagnosis of sickle-cell disease. This method should be applicable for the analysis of DNAs of high complexity where the presence of DNA polymorphisms and interspersed repeated DNA sequences often make impossible the creation of complete RNA:DNA hybrids.

Regulation of mRNA levels of rat liver carbamoylphosphate synthetase by glucocorticosteroids and cyclic AMP as estimated with a specific cDNA

The construction and cloning of a cDNA complementary to the mRNA of rat liver carbamoylphosphate synthetase (ammonia) is described. Using this cDNA, the size of the mature, cytosolic carbamoylphosphate synthetase (ammonia) mRNA is estimated to be 6.0 Kb. The levels of carbamoylphosphate synthetase (ammonia) mRNA in liver are shown to be regulated by glucocorticosteroids and cyclic AMP. By studying mRNA levels of carbamoylphosphate synthetase, albumin and phosphoenolpyruvate carboxykinase, using specific cDNA clones, we show that carbamoylphosphate synthetase gene expression, like that of albumin is liver-specific.

Efficient in vitro synthesis of biologically active RNA and RNA hybridization probes from plasmids containing a bacteriophage SP6 promoter

A simple and efficient method for synthesizing pure single stranded RNAs of virtually any structure is described. This in vitro transcription system is based on the unusually specific RNA synthesis by bacteriophage SP6 RNA polymerase which initiates transcription exclusively at an SP6 promoter. We have constructed convenient cloning vectors that contain an SP6 promoter immediately upstream from a polylinker sequence. Using these SP6 vectors, optimal conditions have been established for in vitro RNA synthesis. The advantages and uses of SP6 derived RNAs as probes for nucleic acid blot and solution hybridizations are demonstrated. We show that single stranded RNA probes of a high specific activity are easy to prepare and can significantly increase the sensitivity of nucleic acid hybridization methods. Furthermore, the SP6 transcription system can be used to prepare RNA substrates for studies on RNA processing (1,5,9) and translation (see accompanying paper).