Analysis of the 3'-terminal nucleotide sequence of vesicular stomatitis virus N protein mRNA

Transcriptional control of the RNA-dependent RNA polymerase of vesicular stomatitis virus

The nonsegmented negative strand (NNS) RNA viruses include some of the mosr problematic human, animal and plant pathogens extant: for example, rabies virus, Ebola virus, respiratory syncytial virus, the parainfluenza viruses, measles and infectious hemapoietic necrosis virus. The key feature of transcriptional control in the NNS RNA viruses is polymerase entry at a single 3' proximal site followed by obligatory sequential transcription of the linear array of genes. The levels of gene expression are primarily regulated by their position on the genome. The promoter proximal gene is transcribed in greatest abundance and each successive downstream gene is synthesized in progressively lower amounts due to attenuation of transcription at each successive gene junction. In addition, NNS RNA virus gene expression is regulated by cis-acting sequences that reside at the beginning and end of each gene and the intergenic junctions. Using vesicular stomatitis virus (VSV), the prototypic NNS, many of these control elements have been identified.The signals for transcription initiation and 5' end modification and for 3' end polyadenylation and termination have been elucidated. The sequences that determine the ability of the polymerase to slip on the template to generate polyadenylate have been identified and polyadenylation has been shown to be template dependent and integral to the termination process. Transcriptional termination is a key element in control of gene expression of the negative strand RNA viruses and a means by which expression of individual genes may be silenced or regulated within the framework of a single transcriptional promoter. In addition, the fundamental question of the site of entry of the polymerase during transcription has been reexamined and our understanding of the process altered and updated. The ability to engineer changes into infectious viruses has confirmed the action of these elements and as a consequence, it has been shown that transcriptional control is key to controlling the outcome of a viral infection. Finally, the principles of transcriptional regulation have been utilized to develop a new paradigm for systematic attenuation of virulence to develop live attenuated viral vaccines.

Developmentally regulated transporter in Leishmania is encoded by a family of clustered genes

We have previously cloned a gene for a developmentally regulated transport protein from the trypanosomatid protozoan Leishmania enriettii. We demonstrate here that this transporter is encoded by a single family of tandemly clustered genes containing approximately 8 copies of the 3.6 kilobase repeat unit. Transcriptional mapping defines a contiguous 3.3 kilobase region of the repeat unit that encodes the mRNA. The 5' end of the mature mRNA contains the spliced leader or mini-exon previously identified in kinetoplastid protozoa, while the 3' ends of the mRNA are heterogeneous in sequence and in location of the polyadenylation site. We have identified genomic restriction fragments that flank the tandem repeat on the 5' and 3' sides and which may be linked to sequences required for expression of the gene family. Other species of Leishmania also contain sequences that hybridize to the cloned L. enriettii gene at high stringency.

Mitotic recombination in germ cells generated two major histocompatibility complex mutant genes shown to be identical by RNA sequence analysis: Kbm9 and Kbm6

RNA sequencing represents a major procedural simplification for nucleotide sequence analysis of a transcribed gene. Using newly adapted mRNA and cDNA sequencing procedures, we have sequenced 855 nucleotides of Kbm9 mRNA, corresponding to the codons for the aminoterminal 285 amino acids. The inferred DNA sequence of the Kbm9 gene differs from the parental Kb sequence by single nucleotide alterations in each of codons 116 and 121, resulting in Tyr----Phe and Cys----Arg substitutions, respectively. The Kbm9 sequence is identical to that of another independently arising MHC mutant gene, Kbm6. As both the Kbm9 and Kbm6 genes were generated by recombination between the Kb and Q4 genes, our data indicate that the identical genetic interactions have occurred at least twice. The relatively large extent of identity between Q4 and Kb may be responsible for frequent recombination between the two genes. The parents of the original bm9 mutant mice had five identical mutant offspring, which can be explained by mitotic recombination in the germ cells, producing gonadal mosaicism in the C57BL/6 mother. Thus, mitotic recombination, and not meiotic recombination, appears to be responsible for the formation of at least some of the Kb mutants. Such a mechanism probably plays a major role in the generation of diversity in the major histocompatibility complex.

"Dideoxy" RNA sequencing: a rapid method for studying genetic information

The chain termination sequencing technique on RNA is a very rapid, direct method for the analysis of genetic information. It is particularly suitable for analysing systems on which microgram amounts of 50% pure RNA can be made available and for which numerous data are needed in order to derive genetic or structural information. The usefulness and limitations of the technique are discussed.

Precursor nucleotides at the 5' end are not required for processing by RNase E at the 3' end of 5-S rRNA

7-S RNA, a single-site substrate for the processing enzyme RNase E of Escherichia coli, consists of p5 rRNA (the precursors of 5-S RNA) and the 3'-end region of the rRNA transcript which is mainly a termination stem and loop. The 7-S RNA studied here was derived mainly from the rRNA gene cluster rrnD, carried in a multicopy plasmid. It contains four different populations of molecules that differ from each other at their 5' ends only: the shortest species has the 5' end of the mature 5-S rRNA, while the others are one, two and three nucleotides longer. The four different 5'-end forms were separated in a long sequencing gel. Processing of these forms and unfractionated 7-S RNA by RNase E in vitro, showed that all forms, even the shortest one, can be processed to p5 rRNA. Since the extra nucleotides at the 5' end of the molecule could be base-paired with the region of 7-S RNA where RNase E cuts, it is concluded that this double-stranded structure is not required for the action of RNase E in separating the 3' end of p5 rRNA from the termination stem.

Activation of the genes for variant surface glycoproteins 117 and 118 in Trypanosoma brucei

We have studied the activation of genes for VSGs (variant surface glycoproteins) in Trypanosoma brucei (strain 427) in six independently isolated trypanosome clones; four expressing the gene for VSG 118 and two the gene for VSG 117. In all cases, gene activation is brought about by a duplicative transposition of the gene to an expression site located close to the end of a chromosome. The DNA segments flanking the expression-linked extra gene copy are nearly devoid of restriction enzyme recognition sites and their lengths vary by more than 10,000 base-pairs among different variants. From the correspondence of five upstream restriction sites, we conclude that the same expression site is used in each case. The transposition event does not lead to detectable alterations in the sequence coding for the mature protein. All restriction enzyme recognition sites detected in the basic copy gene are present also in each of the expression-linked copies. This argues against the introduction of mutations by an error-prone polymerase during the synthesis of the expression-linked copy. In five of the six variants, the 3' end of the VSG messenger RNA differs from that of the corresponding basic copy gene by multiple point mutations, insertions and deletions, starting at positions varying from 16 nucleotides upstream to 113 downstream of the last codon of the mature protein. We attribute this end alteration to the recombination process that introduces the gene into the expression site. We confirm that the expression-linked gene copy is more sensitive to DNase I than the corresponding basic copy gene. This appears to be due to its activated state and not to its location near the end of a chromosome, because another basic copy VSG gene permanently located near a chromosome end is not hypersensitive to DNase I. The mature transcripts of the 117 and 118 genes all possess the same 35 nucleotides at their 5' ends and these are not encoded contiguously in the basic gene copies with the remainder of the mRNAs. This extends our previous conclusion, that mature VSG mRNAs are formed by a splicing process in which the 35-nucleotide sequence encoded in the expression site is fused onto the body of the mRNA contributed by the transposed gene.

Sequence of the nucleocapsid gene from murine coronavirus MHV-A59

The nucleotide sequence of the RNA encoding the nucleocapsid protein of coronavirus MHV-A59 has been determined. Copy DNA was prepared from mRNA isolated from virally infected cells, fragmented and cloned in the phage vector M13 mp8 for direct sequence determination. A sequence of 1817 nucleotides, adjacent to the viral poly-A tail, was obtained. It contains a single long open reading frame encoding a protein of mol. wt. 49660, which is enriched in basic residues.

RNA splicing is required to make the messenger RNA for a variant surface antigen in trypanosomes

The expression of the gene for variant surface glycoprotein (VSG) 118 in Trypanosoma brucei is activated by transposing a DNA segment containing the gene and 1-2 kb in front of it to an expression site elsewhere in the genome. By S1 nuclease protection and RNA blotting experiments we show here the presence of several minor transcripts in trypanosomes synthesizing VSG 118, one of which covers the entire transposed segment. Comparison of the sequence of the 5' terminal segment of VSG 118 messenger RNA (mRNA), determined by primed reverse transcription, and the corresponding region of the 118 VSG gene, shows that the 5' terminal 34 nucleotides of the mRNA are not encoded in the 118 VSG gene contiguous with the remainder of the mRNA. We conclude that synthesis of a VSG mRNA involves splicing of a much longer primary transcript, which may start outside the transposed segment.

Aberrant glycoprotein mRNA synthesized by the internal deletion mutant of vesicular stomatitis virus

The internal deletion mutant (DI-LT) derived from the heat-resistant strain of vesicular stomatitis virus synthesized an aberrant polyadenylated mRNA in vivo and in vitro. No normal glycoprotein message could be detected among the in vivo transcription products. The abnormal RNA contained a transcript of the partially deleted polymerase gene covalently linked to the 3' end of the glycoprotein message. The polyadenylate is located at the 3' end of the molecule and is most probably encoded by the remnant polymerase gene polyadenylation signal. This aberrant RNA may be synthesized because of either a failure to terminate transcription at the end of the glycoprotein gene or an inability to process an abnormal polycistronic precursor.

Nucleotide sequences of the mRNA's encoding the vesicular stomatitis virus N and NS proteins

The complete nucleotide sequences of the vesicular stomatitis virus (VSV) mRNA's encoding the N and NS proteins have been determined from the sequences of cDNA clones. The mRNA encoding the N protein is 1,326 nucleotides long, excluding polyadenylic acid. It contains an open reading frame for translation which extends from the 5'-proximal AUG codon to encode a protein of 422 amino acids. The N and mRNA is known to contain a major ribosome binding site at the 5'-proximal AUG codon and two other minor ribosome binding sites. These secondary sites have been located unambiguously at the second and third AUG codons in the N mRNA sequence. Translational initiation at these sites, if it in fact occurs, would result in synthesis of two small proteins in a second reading frame. The VSV and mrna encoding the NS protein is 815 nucleotides long, excluding polyadenylic acid, and encodes a protein of 222 amino acids. The predicted molecular weight of the NS protein (25,110) is approximately one-half of that predicted from the mobility of NS protein on sodium dodecyl sulfate-polyacrylamide gels. Deficiency of sodium dodecyl sulfate binding to a large negatively charged domain in the NS protein could explain this anomalous electrophoretic mobility.

Enhanced mutability associated with a temperature-sensitive mutant of vesicular stomatitis virus

Temperature-sensitive (ts) mutant tsD1 of vesicular stomatitis virus, New Jersey serotype, is the sole representative of complementation group D. Clones derived from this mutant exhibited three different phenotypes with respect to electrophoretic mobility of the G and N polypeptides of the virion in sodium dodecyl sulfate-polyacrylamide gel. Analysis of non-ts pseudorevertants showed that none of the three phenotypes was associated with the temperature sensitivity of mutant tsD1. Additional phenotypes, some also involving the NS polypeptide, appeared during sequential cloning, indicating that mutations were generated at high frequency during replication of tsD1. Furthermore, mutations altering the electrophoretic mobility of the G, N, NS, and M polypeptides were induced in heterologous viruses multiplying in the same cells as tsD1. These heterologous viruses included another complementing ts mutant of vesicular stomatitis virus New Jersey and ts mutants of vesicular stomatitis virus Indiana and Chandipura virus. Complete or incomplete virions of tsD1 appeared to be equally efficient inducers of mutations in heterologous viruses. Analysis of the progeny of a mixed infection of two complementing ts mutants of vesicular stomatitis virus New Jersey with electrophoretically distinguishable G, N, NS, and M proteins yielded no recombinants and excluded recombination as a factor in the generation of the electrophoretic mobility variants. In vitro translation of total cytoplasmic RNA from BHK cells indicated that post-translational processing was not responsible for the aberrant electrophoretic mobility of the N, NS, and M protein mutants. Aberrant glycosylation could account for three of four G protein mutants, however. Some clones of tsD1 had an N polypeptide which migrated faster in sodium dodecyl sulfate-polyacrylamide gel than did the wild type, suggesting that the polypeptide might be shorter by about 10 amino acids. Determination of the nucleotide sequence to about 200 residues from each terminus of the N gene of one of these clones, a revertant, and the wild-type parent revealed no changes compatible with synthesis of a shorter polypeptide by premature termination or late initiation of translation. The sequence data indicated, however, that the N-protein mutant and its revertant differed from the parental wild type in two of the 399 nucleotides determined. These sequencing results and the phenomenon of enhanced mutability associated with mutant tsD1 reveal that rapid and extensive evolution of the viral genome can occur during the course of normal cytolytic infection of cultured cells.

Polycistronic vesicular stomatitis virus RNA transcripts

A procedure to enrich for the sequences present at the junction between the linked messages in the polycistronic RNAs symthesized in vitro by vesicular stomatitis virus (VSV) is described. Analyses of these sequences show that they contain a precise transcript of both the intercistronic dinucleotide and the pentanucleotide 5'--C-U-G-U-U--3', common to the 5'-end of all VSV cistrons, covalently linked to the 3'-side of the intervening poly(A). The data strongly suggest that the VSV transcriptase polyadenylylates the mRNAs and can then resume direct and precise transcription of the genome-without reinitiation and without skipping nucleotides.

Site on the vesicular stomatitis virus genome specifying polyadenylation and the end of the L gene mRNA

The 5'-terminal nucleotide sequence from positions 50 to 130 of vesicular stomatitis virus RNA was determined indirectly by using a defective interfering particle RNA which contains covalently linked genomic minus and antigenomic plus sense RNAs. The last 18 nucleotides of the L gene coding for in the viral polymerase were identified and isolated by specific duplex formation between 5' terminally labeled oligonucleotides from a small single-stranded defective interfering particle RNA and L gene mRNA. The L gene ends at position 60 from the 5' terminus of the vesicular stomatitis genome. The data demonstrated that the first seven adenine residues in the polyadenylic acid tail of L gene mRNA may be coded for in the genome and suggested that the viral transcriptase itself may carry out polyadenylation, possibly by chattering at the uridine-rich sequence at the end of the L gene. Analysis of the 5'-terminal sequence of vesicular stomatitis virus genomic RNA revealed that it might fold into a complex secondary structure with possibly 62% of the bases paired.

Use of oligodeoxynucleotide primers to determine poly(adenylic acid) adjacent sequences in messenger ribonucleic acid. 3'-Terminal noncoding sequence of bovine growth hormone messenger ribonucleic acid

Twelve synthetic oligodeoxynucleotide primers of the general sequence d(pT8-N-N') were tested in a reverse transcriptase reaction for specific initiation of complementary deoxyribonucleic acid (cDNA) synthesis at the poly(adenylic acid) junction of a messenger ribonucleic acid (mRNA) template. Only the sequence d(pT8-G-C) functioned as a specific primer of cDNA synthesis with an enriched fraction of bovine growth hormone mRNA from the anterior pituitary gland and produced unique fragments in a dideoxy sequencing reaction. The nucleotide sequence obtained by this method extended into the protein coding region of bovine growth hormone mRNA and was confirmed by chemical sequencing of the cDNA initiated with [5'-32P]d(pT8-G-C). The 3'-untranslated region of bovine growth hormone mRNA is 104 nucleotides in length and contains regions of significant homology with both rat and human growth hormone mRNAs, including the region surrounding the common AAUAAA hexanucleotide. The method presented here for selection of the d(pT8-N-N') primer complementary to the poly(A) junction of mRNA is of general applicability for nucleotide sequence analysis of partially purified mRNAs.

Leader sequences of Strongylocentrotus purpuratus histone mRNAs start at a unique heptanucleotide common to all five histone genes

We have determined the sequence of the untranslated leader nucleotides of all five histone mRNAs from Strongylocentrotus purpuratus by the dideoxy chain termination method. Total polysomal RNA from sea urchin embryos was used as a substrate for cDNA synthesis primed by specific DNA restriction fragments. Each of the primers was derived from the 5'-terminal part of the coding region for a different histone protein. The five histone mRNA leader sequences are different in length and primary structure. The 5' termini of all five histone mRNAs coincide with the unique heptanucleotide Py-Py-A-T-T-C-Pu in genomic DNA. This sequence, which defines the start of the individual histone mRNAs, is preceded by the A+T-rich octanucleotide identified in front of all eukaryotic structural genes where sequences have been determined to date.

Oligonucleotide sequence analyses indicate that vesicular stomatitis virus large defective interfering virus particle RNA is made by internal deletion: evidence for similar transcription polyadenylation signals for the synthesis of all vesicular stomatitis virus mRNA species

RNase T(1) oligonucleotide fingerprint analyses of three vesicular stomatitis virus Indiana serotype small defective interfering (DI) particle RNA species indicate that they only have oligonucleotides derived from the 5' region of the viral genome. These studies also indicate that these three DI RNAs have partial L gene sequences as well as two 5' viral oligonucleotides (59 and 70) that are not transcribed into L (or other) mRNA species (J. P. Clewley and D. H. L. Bishop, J. Virol. 30:116-123, 1979). Analyses of the large DI RNA (LT DI) reveal a different origin. The LT DI RNA has oligonucleotides derived from both the 3' end of the genome (including all the large oligonucleotides identified for N, NS, M, and G genes), in addition to at least one of the 5'-proximal L gene oligonucleotides (47), as well as all seven oligonucleotides (3, 38, 42, 43, 44B, 59, and 70) that are not protected from nuclease digestion after the formation of mRNA-viral RNA duplexes (Clewley and Bishop). It appears therefore that the genesis of LT RNA involves a deletion of internal L gene sequences from the viral RNA. Oligonucleotide sequence analyses have been undertaken on several of the vesicular stomatitis viral RNA oligonucleotides, including all seven (3, 38, 42, 43, 44B, 59, and 70) that are not transcribed into mRNA. The analyses confirm that oligonucleotides 59 [3'...GAACACCAAAAAUAAAAAAUA(G)...5'] and 70 [3'...GACCAAAACACCA(G)...5'] are at the 5'-end region of the viral genome. Oligonucleotide 38 [3'...GAAAUUCAUACUUUUUU(U)(G)...5'] may represent the termination signal for L mRNA synthesis (R. A. Lazzarini, personal communication). Oligonucleotide 43 [3'...GUAUACUUUUUUU(G)...5'] corresponds to the sequence shown to be the N gene mRNA polyadenylation signal (D. J. McGeoch, Cell 17:673-681, 1979). The other three oligonucleotides share a common feature with oligonucleotides 43 and 38, viz., a stretch of 6 or 7 U residues preceded by an AUAC sequence. Thus the sequence of oligonucleotide 3 is 3'...GAAUUAAUAUAAAAUUAAAAAUUAAAAAUACUUUUUU(U)(G)...5', whereas that of oligonucleotide 42 is 3'...GAUACUUUUUUUCAU(U)(G)...5', and that of oligonucleotide 44B is 3'...G(U)AUACUUUUUU(G)...5'. These sequence analyses suggest a common polyadenylation signal for the synthesis of all vesicular stomatitis virus mRNA species, i.e., the sequence (3')...AUACUUUUUU(U)...(5').

Comparisons of nucleotide sequences in the genomes of the New Jersey and Indiana serotypes of vesicular stomatitis virus

Nucleotide sequences of around 200 residues were determined adjacent to the 3' terminus of the genome RNA of vesicular stomatitis virus, New Jersey serotype, and adjacent to the 3'-terminal polyadenylic acid tract of the N protein mRNA of the same virus. These sequences were compared with the corresponding sequences previously determined for the Indiana serotype of vesicular stomatitis virus. The sequences obtained for the two strains were readily aligned, showing 70.8% homology overall. Examination of the sequences allowed identification of the translation initiation and termination codons for the N mRNA of each serotype. The deduced N-terminal and C-terminal amino acid sequences of the two N polypeptides were each similar, and most of the differences between them consisted of substitution by a clearly homologous amino acid. It was proposed that these nucleotide sequences, within limits imposed by their functions, comprise reasonably representative measures of the extent of sequence homology between the genomes of the two serotypes, and that this is higher than previously estimated, but with little exact homology over extended regions.

An improved rapid enzymatic method of RNA sequencing using chemical modification

A version of rapid gel sequencing procedure based on the analysis of partial endonuclease hydrolizates of chemically modified 5'-32P-labelled RNA is suggested. Complete and selective modification of cytidilic residues by a methoxyamine-bisulfite mixture leads to the unfolding of the RNA secondary structure and, due to this effect, to the generation of a more uniform set of fragments after partial RNAase hydrolysis. The position of cytidines in an RNA sequence can be determined by restricting the hydrolysis of phosphodiester bonds between the modified CMP residues and their 3'-neighbours with T2 and A RNAases. The method was verified with tRNATrp (yeast) and 5S RNA (rat liver and yeast).

Complete nucleotide sequence of an influenza virus haemagglutinin gene from cloned DNA

A synthetic fowl plague virus (FPV) haemagglutinin gene has been cloned in bacteria and the complete sequence of the RNA gene deduced. It is 1,742 nucleotides long and the mRNA codes for 56.3 amino acids in an uninterrupted sequence. The nature of some of the important domains in the haemagglutinin has been established, and their structure is discussed in relation to their function. Extensive amino acid sequence homologies exist between FPV and human influenza haemagglutinins.

Nucleotide sequences from the 3'-ends of vesicular stomatitis virus mRNA's as determined from cloned DNA

Molecular clones of vesicular stomatitis virus mRNA's were used to determine the 3'-terminal sequences of mRNA's encoding the N and NS proteins. This new approach to VSV mRNA sequencing allowed the first comparison of 3'-terminal sequences. The sequences showed a tetranucleotide homology, UAUG, immediately preceding the polyadenylic acid. In addition, both mRNA's had an AU-rich region including the tetranucleotide AUAU at positions 16 to 19 nucleotides from the polyadenylic acid. A possible secondary structure between the 3' end of N mRNA and the 5' end of the adjacent NS mRNA is noted. These structural features may serve as signals for termination (or cleavage) and polyadenylation of vesicular stomatitis virus mRNA's. Neither mRNA had the polyadenylic acidproximal hexanucleotide, AAUAAA, found in eucaryotic cellular and viral mRNA's transcribed from nuclear DNA. The probable location of the translation termination codon for the NS protein is only six nucleotides from polyadenylic acid in NS mRNA.

Extensive sequence homology at the 3'-termini of the four RNAs of cucumber mosaic virus

The sequences of 270 residues from the 3'-termini of the four RNAs of cucumber mosaic virus have been determined by copying the in vitro polyadenylated RNAs with reverse transcriptase using d(pT8G) as primer and the 2',3'-dideoxynucleoside 5'-triphosphates as specific chain terminators. The terminal sequences of RNAs 3 and 4 were identical; this was expected since hybridization data has shown that the sequence of RNA 4 was present at the 3'-end of RNA 3 (Gould and Symons (1978) Eur. J. Biochem. 91, 269-278). The first 138 residues of RNAs 1 and 2 were identical to those of RNAs 3 and 4 except for one residue in RNA 1 and three residues in RNA 2. From residue 139 to 270 from the 3'-terminus, RNAs 1 and 2 showed, relative to RNAs 3 and 4, a non-homologous region of 33 residues, a homologous region of 40 residues, a partially homologous region of 14 residues which probably extended to about residue 300. There were 11 residues different between RNAs 1 and 2.

Sequence homology adjacent to the 3' terminal poly(A) of cowpea mosaic virus RNAs

We have determined the sequence of 80 nucleotides adjacent to 3' poly(A) of both (middle and bottom component) cowpea mosaic virus RNAs, using dideoxynucleotide termination of reverse transcription. Sequence conservation is indicated, there being about 80% homology between the first 65 bases of each RNA. Although both RNAs are polyadenylated, there is no AAUAAA sequence as associated with most known polyadenylated mRNAs of eukaryotes and viruses. However both RNAs are U and A-rich in this region.

Sequence of 200 nucleotides at the 3'-terminus of the genome RNA of vesicular stomatitis virus

The sequence of 200 nucleotides at the 3'-terminus of the genome RNA of vesicular stomatitis virus, Indiana serotype, was determined by adding a poly(A) tract to the 3'-terminus of genome RNA, then using the poly(A) as a binding site for a primer to initiate reverse transcription of the RNA, and analysing the complementary DNA sequence by the dideoxynucleoside triphosphate chain termination method. Proceeding 3' to 5', the genome RNA sequence consisted of a sequence complementary to the leader RNA, followed by the sequence AAA, followed by a sequence complementary to the 5'-extremity of N protein mRNA. These results are discussed in terms of leader RNA function, mechanism of transcript processing at the junction between leader RNA and N mRNA, and N mRNA structure.

Direct chemical method for sequencing RNA

Four different base-specific chemical reactions generate a means of directly sequencing RNA terminally labeled with 32P. After a partial, specific modification of each kind of RNA base, an amine-catalyzed strand scission generates labeled fragments whose lengths determine the position of each nucleotide in the sequence. Dimethyl sulfate modifies guanosine. Diethyl pyrocarbonate attacks primarily adenosine. Hydrazine attacks uridine and cytidine, but salt suppresses the reaction with uridine. In all cases, aniline induces a subsequent strand scission. The electrophoretic fractionation of the labeled fragments on a polyacrylamide gel, followed by autoradiography, determines the RNA sequence. RNA labeled at the 3' end yields clean cleavage patterns for each purine and pyrimidine and allows a determination of the entire RNA sequence out to 100-200 bases from the labeled terminus.

Rapid sequence determination of late simian virus 40 16S mRNA leader by using inhibitors of reverse transcriptase

A method for the determination of the primary structure of spliced mRNA junction and leader sequences is described. By analogy to the DNA sequencing procedure of Sanger et al. [Sanger, F., Nicklen, S. & Coulson, A. R. (1977) Proc. Natl. Acad. Sci USA 74, 5463--5467], we use 2",3'-dideoxynucleoside triphosphates as chain-terminating inhibitors of the reverse transcriptase (RNA-dependent DNA polymerase) reaction. By using specific DNA restriction fragments as primers in combination with this technique, we have determined the sequence of the spliced junction between the body and the leader sequence of the 16S late mRNA of simian virus 40. The method described should be of general utility in mapping spliced mRNA regions for which the corresponding protein sequence (if any) is unknown.