Determination of a nucleotide sequence in bacteriophage f1 DNA by primed synthesis with DNA polymerase

A Review of the Rumen Microbiota and the Different Molecular Techniques Used to Identify Microorganisms Found in the Rumen Fluid of Ruminants

Variations in environments, including climate, diet, and agricultural practices, significantly impact the composition and microbial activity. A profound understanding of these adaptations allows for the improvement of nutrition and ruminant production. Therefore, this review aims to compile data from the literature on the rumen microbiota and molecular techniques for identifying the different types of microorganisms from the rumen fluid of ruminants. Analyzing the literature on rumen microbiology in different ruminants is complex due to microbial interactions, influenced by the environment and nutrition of these animals. In addition, it is worth noting that the genera of protozoa and fungi most evident in the studies used in this review on the microbiology of rumen fluid were Entodinium spp. and Aspergillus spp., respectively, and Fibrobacter spp. for bacteria. About the techniques used, it can be seen that DNA extraction, amplification, and sequencing were the most cited in the studies evaluated. Therefore, this review describes what is present in the literature and provides an overview of the main microbial agents in the rumen and the molecular techniques used.

Application of Next Generation Sequencing in Laboratory Medicine

The rapid development of next-generation sequencing (NGS) technology, including advances in sequencing chemistry, sequencing technologies, bioinformatics, and data interpretation, has facilitated its wide clinical application in precision medicine. This review describes current sequencing technologies, including short- and long-read sequencing technologies, and highlights the clinical application of NGS in inherited diseases, oncology, and infectious diseases. We review NGS approaches and clinical diagnosis for constitutional disorders; summarize the application of U.S. Food and Drug Administration-approved NGS panels, cancer biomarkers, minimal residual disease, and liquid biopsy in clinical oncology; and consider epidemiological surveillance, identification of pathogens, and the importance of host microbiome in infectious diseases. Finally, we discuss the challenges and future perspectives of clinical NGS tests.

DNA sequencing, genomes and genetic markers of microbes on fruits and vegetables

The development of DNA sequencing technology has provided an effective method for studying foodborne and phytopathogenic microorganisms on fruits and vegetables (F & V). DNA sequencing has successfully proceeded through three generations, including the tens of operating platforms. These advances have significantly promoted microbial whole‐genome sequencing (WGS) and DNA polymorphism research. Based on genomic and regional polymorphisms, genetic markers have been widely obtained. These molecular markers are used as targets for PCR or chip analyses to detect microbes at the genetic level. Furthermore, metagenomic analyses conducted by sequencing the hypervariable regions of ribosomal DNA (rDNA) have revealed comprehensive microbial communities in various studies on F & V. This review highlights the basic principles of three generations of DNA sequencing, and summarizes the WGS studies of and available DNA markers for major bacterial foodborne pathogens and phytopathogenic fungi found on F & V. In addition, rDNA sequencing‐based bacterial and fungal metagenomics are summarized under three topics. These findings deepen the understanding of DNA sequencing and its application in studies of foodborne and phytopathogenic microbes and shed light on strategies for the monitoring of F & V microbes and quality control.

Polymerase chain reaction and deoxyribonucleic acid-sequencing based study on distribution of human papillomavirus 16/18 among histopathological types of cervical intra-epithelial neoplasia and primary invasive cervical carcinoma: A scenario in North Bengal, India

Introduction:

Human papillomavirus (HPV) types 16/18 are reportedly most common in cervical cancer (CaCx) with geographical variation of genotypes. HPV16 predominates both in squamous cell carcinoma (SCC) and adenocarcinoma in India, contrary to reported global predominance of HPV18 in the latter. Our study was aimed to determine the occurrence of HPV16/18 among histopathological types of cervical intra-epithelial neoplasia (CIN) and invasive CaCx from North Bengal, India and to identify any major deviation from the known Indian scenario of distribution of HPV16/18 genotypes in cases of SCC and adenocarcinoma.

Materials and Methods:

This was a retrospective, cross-sectional, case-only type of study, in which 40 cases were histopathologically diagnosed as CIN/CaCx, on which polymerase chain reaction (PCR), deoxyribonucleic acid (DNA)-sequencing and bioinformatics by basic search local alignment tool were performed for HPV-genotyping.

Statistical Analysis:

The distribution of HPV genotypes among cases of SCC and adenocarcinoma was compared by Fisher's exact-test.

Results:

HPV was detected in 97.5% (39/40) cases. HPV16-infected cases (32/39; 82.05%) predominated over HPV18-infected ones (7/39; 17.95%). However, HPV18-only infection was significantly (P = 0.0045, one-sided Fisher's exact test) more among adenocarcinoma (3/4; 75%) than SCC (2/26; 7.69%) contrary to HPV16-only infection (SCC = 24/26, 92.31%; adenocarcinoma = 1/4; 25%) whereas both CIN3 cases were HPV16-positive.

Conclusion:

Predominance of HPV18 over HPV16 in cases of adenocarcinoma in this region was contrasting to that of earlier Indian studies suggesting research on HPV18 related cervical carcinogenesis. PCR and DNA-sequencing could prove to be highly effective tools in HPV detection and genotyping. The study reported HPV16/18 infection in almost 98% of the cases, the knowledge about which might prove useful in future population based studies on HPV genotyping and designing of appropriate HPV-vaccines for this region.

Next-generation sequencing platforms

Automated DNA sequencing instruments embody an elegant interplay among chemistry, engineering, software, and molecular biology and have built upon Sanger's founding discovery of dideoxynucleotide sequencing to perform once-unfathomable tasks. Combined with innovative physical mapping approaches that helped to establish long-range relationships between cloned stretches of genomic DNA, fluorescent DNA sequencers produced reference genome sequences for model organisms and for the reference human genome. New types of sequencing instruments that permit amazing acceleration of data-collection rates for DNA sequencing have been developed. The ability to generate genome-scale data sets is now transforming the nature of biological inquiry. Here, I provide an historical perspective of the field, focusing on the fundamental developments that predated the advent of next-generation sequencing instruments and providing information about how these instruments work, their application to biological research, and the newest types of sequencers that can extract data from single DNA molecules.

Expression of melatonin (MT1, MT2) and melatonin-related receptors in the adult rat testes and during development

It is well known that melatonin provokes reproductive alterations in response to changes in hours of daylight in seasonally breeding mammals, exerting a regulatory role at different levels of the hypothalamic–pituitary–gonadal axis. Although it has also been demonstrated that melatonin may affect testicular activity in vertebrates, until now, very few data support the hypothesis of a local action of melatonin in the male gonads. The aim of this study was to investigate whether MT1, MT2 melatonin receptors and the H9 melatonin-related receptor, are expressed in the adult rat testes and during development. A semi-quantitative RT-PCR method was used to analyse the expression of MT1, MT2 and H9 receptors mRNAs in several rat tissues, mainly focusing on testes during development and adult life. Our results provide molecular evidences of the presence of both MT1 and, for the first time, MT2 melatonin receptors as well as of the H9 melatonin-related receptor in the examined tissues, including adult testes. During development MT1 and MT2 transcripts are expressed at lower levels in testes of rats from 1 day to 1 week of age, lightly increased at 2 weeks of age and remained permanently expressed throughout development until 6 months. These data strongly support the hypothesis that melatonin acts directly in male vertebrate gonads suggesting that rat testes may be a suitable model to verify the role of indolamine in vertebrate testicular activity.

Essentiality of the early transcript in the replication origin of the lactococcal prolate phage c2

The genome of the prolate-headed lytic lactococcal bacteriophage c2 is organized into two divergently oriented blocks consisting of the early genes and the late genes. These blocks are separated by the noncoding origin of DNA replication. We examined the functional role of transcription of the origin in a plasmid model system. Deletion of the early promoter P(E)1 abolished origin function. Introduction of mutations into P(E)1 which did not eliminate promoter activity or replacement of P(E)1 with an unrelated but functional promoter did not abolish replication. The A-T-rich region upstream of P(E)1, which is conserved in prolate phages, was not required for plasmid replication. Replacement of the P(E)1 transcript template sequence with an unrelated sequence with a similar G+C content abolished replication, showing that the sequence encoding the transcript is essential for origin function. Truncated transcript and internal deletion constructs did not support replication except when the deletion was at the very 3' end of the DNA sequence coding for the transcript. The P(E)1 transcript could be detected for all replication-proficient constructs. Recloning in a plasmid vector allowed detection of P(E)1 transcripts from some fragments that did not support replication, indicating that stability of the transcript alone was not sufficient for replication. The data suggest that production of a transcript of a specific length and with a specific sequence or structure is essential for the function of the phage c2 origin in this model system.

Detection of specific alleles by using allele-specific primer extension followed by capture on solid support

This article describes a method for determining whether a particular nucleic acid sequence is present in a sample and for discriminating between any two nucleic acid sequences if such sequences differ only by a single nucleotide. The method entails extension of a novel two-component primer on templates that may or may not include a target nucleic acid sequence. The 3' portion of the primer is complementary to a portion of the template adjacent to the target sequence (for example, the polymorphic nucleotide). The 5' portion of the primer is complementary to a different preselected nucleic acid sequence. Extension of the 3' portion of the primer with a labeled deoxynucleoside triphosphate yields a labeled extension product, but only if the template includes the target sequence. The presence of such a labeled primer-extension product is detected by hybridization of the 5' portion to the preselected sequence. The preselected sequence is immobilized on a solid support. The method has been applied to genotyping individuals for the two-allele polymorphism of the human tyrosinase gene.

Efficient repression by a heterodimeric repressor in Escherichia coli

Previous studies with purified variants of the 434 repressor having different operator-binding specificities have demonstrated the interactions of a heterodimeric repressor with a hybrid operator site. The present study investigates the interactions between the 434 repressor and its operator site. The optimum 434 operator half-site is used with a P22 operator half-site to create a hybrid 434/P22 operator. We show that this hybrid operator can be efficiently bound by a heterodimeric repressor, consisting of one wild-type 434 repressor monomer and one 434 repressor monomer with the binding specificity of the P22 repressor, to bring about repression in Escherichia coli.

Single-step elongation of oligodeoxynucleotides using terminal deoxynucleotidyl transferase

Procedures for the stepwise addition of one or more deoxyribonucleotide residues to the 3' end of an oligodeoxyribonucleoside phosphate acceptor using commercially available terminal deoxynucleotidyl transferase is described. 2-80 nmol of acceptors with a chain length of four, five or nine monomer units were elongated with a single 2'-deoxyribonucleoside 5'-triphosphate in yields of 20-30%. The monomers carried no protecting groups and were used both radioactively labelled and unlabelled. The elongated oligodeoxynucleoside phosphates were isolated by reverse-phase (Nucleosil C18) high-performance liquid chromatography or paper chromatography. The isolated products were sequenced by the fingerprint method. Advantages and disadvantages of this new methodology for the enzymatic synthesis of defined oligodeoxynucleotides are discussed.

Gene expression: chemical synthesis of E. coli ribosome binding sites and their use in directing the expression of mammalian proteins in bacteria

Mammalian genes, when inserted into bacterial plasmid or phage DNAs, will not be expressed into the corresponding specific proteins in E. coli unless proper initiations signals required for recognition by E. coli ribosomes are provided. We have studied these signals and chemically synthesized two DNA duplexes each containing different initiation signals. These have been inserted in front of the Simian virus 40 (SV40) small tumor antigen gene (SV40 t gene) at varying distances from the ATG initiation codon prior to its cloning into pBR322 plasmid DNA. Plasmid containing clones carrying either of these two synthetic ribosome binding sites (RBS) at varying distances from the SV40 t gene all produced a 17K protein identical to authentic t antigen by immunologic, electrophoretic and proteolytic digestion analyses. This provides a novel method to ensure the specific expression of any contiguous mammalian gene to be cloned to bacteria, and also a unique in vivo method for studying the structure-function (efficiency) relationship of RBS with specific base changes.

Nucleotide sequence of bacteriophage f1 DNA

The nucleotide sequence of the DNA of the filamentous coliphage f1 has been determined. In agreement with earlier conclusions, the genome was found to comprise 6,407 nucleotides, 1 less than that of the related phage fd. Phage f1 DNA differs from that of phage M13 by 52 nucleotide changes, which lead to 5 amino acid substitutions in the corresponding proteins of the two phages, and from phage fd DNA by 186 nucleotide changes (including the single-nucleotide deletion), which lead to 12 amino acid differences between the proteins of phages f1 and fd. More than one-half of the nucleotide changes in each case are found in the sequence of 1,786 nucleotides comprising gene IV and the major intergenic region between gene IV and gene II. The sequence of this intergenic region (nucleotides 5501 to 6005) of phage f1 differs from the sequence reported by others through the inclusion of additional single nucleotides in eight positions and of a run of 13 nucleotides between positions 5885 and 5897, a point of uncertainty in the earlier published sequence. The differences between the sequence of bacteriophage f1 DNA now presented and a complete sequence for the DNA previously published by others are discussed, and the f1 DNA sequence is compared with those of bacteriophages M13 and fd.

A large database DNA sequence handling program with generalized searching specifications

The program described allows for the creation and manipulation of files of DNA sequence data up to very great lengths. The program uses its own paging system to load segments of the sequence into a small internal buffer so that the program does not have excessive memory requirements. The program offers a menu of functions to the user, and has been written to be forgiving of user errors. A code for the generalised specification of bases as a series of groups (i.e. A or T, Purine, etc.) has been devised and can be used in search specifications or in sequence files. Versions of the program have been developed to run with special efficiency under DIGITAL's RT11 operating system or to run under systems with a suitable implementation of FORTRAN VI.

Nucleotide sequence and genome organisation of filamentous bacteriophages fl and fd

The DNA sequence of the filamentous phage F1, consisting of 6407 nucleotides, has been determined. When compared with the DNA sequence of the related filamentous phage fd (Beck et al., 1978), the f1 sequence is one nucleotide shorter and differs in 180 positions from the fd DNA. Only ten of these base exchanges cause amino acid exchanges in the known gene products. Most of the exchanges in f1 are the same as in M13 (Van Wezenbeek et al., 1980), showing a near identity of these two phage (there are only 59 nucleotide differences). Regulatory units for replication, transcription, and translation are in their essential parts identical in all three phage.

Predicting coding function from nucleotide sequence or survival of "fitness" of tRNA

The sequence of a nucleotide region of f1 bacteriophage was determined on a bonded ultrathin acrylamide gel with a discontinuous buffer system by using the dideoxy-DNA sequencing method. This sequence and one other were analyzed for maximal base pairing with tRNAs. The results allow a prediction of the direction and phase of possible coding functions. The implication of sequence constraints on mRNA codon frequency, tRNA structure, the origin of protein synthesis, and triplet reading are discussed in terms of neutral, Darwinian, and genotypic selectionist perspectives of evolution. The model of F. H. C. Crick, S. Brenner, A. Klug, and G. Pieczenik [(1976) Origins of Life 7, 389-397] for the origin of the genetic code is used to interpet contemporary adaptive and functional nucleic acid sequences.

Nucleotide sequences in bacteriophage f1 DNA: nucleotide sequence of genes V, VII, and VIII

The sequence of nucleotides comprising genes V, VII, and VIII of bacteriophage f1 was determined. The sequence was found to differ from that of the corresponding region of the related fd genome by eight base substitutions in gene V and one in gene VIII. The structure of gene VII was completely conserved between these two viruses and was identical to that of bacteriophage M13. Both transitions and transversions were found in cases where bases were substituted, but all substitutions were in the third codon position and had no effect on the structure of the corresponding protein product. The gene V protein product could thus be deduced to be identical to that of the corresponding proteins from bacteriophages fd and M13. A potential EcoRII cleavage site was formed by nucleotides 172 to 176 of gene V. Replicative form DNA form DNA from bacteriophage f1 is normally resistant to this enzyme, and evidence is presented to suggest that the sequence was modified through methylation of cytosine 173. The probable locations of other modified nucleotides in the sequence are discussed.

Nucleotide sequence of the recognition site of the B-specific restriction modification system in E. coli

Two sB mutations in the genome of bacteriophage fd were located by sequence analysis in the fd sequence at positions 971 and 6341. Base changes at or close to these positions in phage M13 and in phage fl am 124 also correlate with a loss of sensitivity to B restriction. From the sequence homology between the sequences at the two sB sites the recognition signal for the E. coli B restriction/modification enzzyme is predicted to be: 5' TGA---8N---TGCT 3' 3' ACT---8N---ACGA 5'.

High-pressure liquid chromatography in polynucleotide synthesis

Reverse phase high-pressure liquid chromatography (HPLC) using columns containing microparticulate materials with bonded octadecyl groups has been developed as a rapid and efficient method for the separation of nucleosides, nucleotides, and, in particular, of protected oligonucleotides which are standard intermediates in the stepwise synthesis of deoxyribopolynucleotides. Reported are extensive studies of the influence of the different purine and pyrimidine bases, of protecting groups, of the phosphate groups, and of the chain lengths of oligonucleotides on their retention on such columns. Further, the application of HPLC in the stepwise synthesis of an oligonucleotide, d(G-G-A-A-G-C-T-T-A-A-C), has been described. The methods, which are herein described, lend themselves to separations on a preparative scale and effect a marked reduction (up to 50%) in the time required for the synthesis of oligonucleotides.

Use of the lipophilic tert-butyldiphenylsilyl protecting group in synthesis and rapid separation of polynucleotides

Butyldiphenylchlorosilanes react with deoxy- and N-protected deoxymononucleotides to give, in each case, the 3'-O-butyldiphenylsilyl ether in high yield. A comparative study of n-, sec-, and tert-butyldiphenylchlorosilanes showed, as expected, a wide variation in the rate of formation and in the stability of the 3'-O-silyl ethers, the tert-butylphenylsilyl group being the one of choice in polynucleotide synthesis. The silyl group can be readily removed on treatment with fluoride ion in buffered pyridine at room temperature. This property markedly increases flexibility of the current methodology for polynucleotide synthesis. Secondly, because of its high lipophilicity, the silyl group allows rapid solvent extraction of synthetic intermediates, and thirdly, it greatly facilitates the isolation of the required product in synthetic reactions because of the selective and strong retention of the condensation product during reverse-phase high-pressure liquid chromatography. Several examples of synthetic procedures, including a stepwise synthesis of an undecanucleotide, are given which demonstrate overall simplification of polynucleotide synthesis.

Nucleotide clusters in deoxyribonucleic acids: sequence analysis of DNA using pyrimidine oligonucleotides as primers in the DNA polymerase I repair reaction

Pyrimidine oligonucleotides have been shown to prime the E. coli DNA polymerase I repair reaction, specifically and reproducibly. DNA molecules up to 30 nucleotides long have been obtained from the extension of oligopyrimidine primers, 9 to 11 nucleotides long isolated from the complementary (minus) strand of bacteriophage S13 RFDNA using S13 viral DNA as the template molecule. The sequences of the extended primers were determined from mobility shift following separation of partially extended primers by ionophoresis and homochromatography, and by a modification of the "plus" system of Sanger and Coulson (1975). The 3' leads to 5' exonuclease activity of E. coli DNA polymerase was utilized for the "plus" system in the presence of single dNTPs and also with two dNTPs in the reaction, to give a nearest neighbor type of analysis for sequence confirmation. The ready availability of oligopyrimidine primers from any DNA and the simplification of the "plus" method broaden the range of applicability of the primed DNA polymerase I repair reaction for DNA sequence analysis.

Complete nucleotide sequence of the 5' noncoding region of human alpha-and beta-globin mRNA

The 5' noncoding regions of human alpha-and beta-globin mRNAs, 37 and 50 nucleotides in length, have been sequenced. A variation of the "plus and minus" gel technique described by Brownlee and Cartwright (1977) was used, and the results were cross-checked by the Maxam and Gilbert (1977) procedure. These studies completed the knowledge of all the noncoding region sequences of both mRNAs, and it was then possible to calculate their exact size. Human alpha-and beta-globin mRNAs are 575 and 626 nucleotides in length, excluding the poly(A). Furthermore, because the coding and 3' noncoding regions of the latter were known from previous studies (Marotta et al., 1977; Proudfoot, 1977), the primary structure of human beta-globin mRNA is now complete except for six ambiguities in the coding region. The human and rabbit 5' noncoding region sequences are about 80% homologous. This suggests that they are under a moderate selective pressure.

Sequence analysis of the nicks and termini of bacteriophage T5 DNA

Bacteriophage T5 DNA, when isolated from mature phage particles, contains several nicks in one of the two strands. The 5'-terminal nucleotides at the nicks were labeled with polynucleotide kinase and [gamma-32P]ATP, and the 3'-terminal nucleotides were labeled with Escherichia coli DNA polymerase I and [alpha-32P]dGTP. The sequences around the nicks were analyzed by partial nuclease digestion followed by homochromatography fractionation of the resulting oligonucleotides. The nicks had at least the sequence -PuOH pGpCpGpC- in common. In addition, the two 5' external termini had the first seven nucleotides in common.

Selective breakage of DNA alongside 5-bromodeoxyuridine nucleotide residues by high temperature hydrolysis

The substitution of thymine mucleotides (pT) in oligodeoxynucleotides by bromouracil nucleotides (pBU) changes the properties of the oligonucleotides in two ways: (1) It alters their mobility during DEAE-Cellulose homochromatography1. (2) It substantially enhances their sensitivity to high temperature hydrolysis under mildly alkaline conditions (pH 8.9). The resultant breaks occur adjacent to pBU residues and leave terminal phosphates on the breakage products. With more extreme conditions some loss of terminal phosphates can occur. Heating at 100 degrees for 16 hr at pH 8.9 produces cleavage at about half of the pBU residues with minimal loss of terminal phosphates. The properties described here may explain the thermal sensitivity of bacteria grown in 5BU2 and may have a use in DNA sequencing technology.

Complete nucleotide sequence of the 5' noncoding region of rabbit beta-globin mRNA

The 5' noncoding region sequence of rabbit beta-globin mRNA has been determined. This region is 53 nucleotides long, not including the A-U-G initiator sequence or m7Gppp "cap" structure. 32P-labeled DNA complementary to the 5' noncoding region was synthesized using reverse transcriptase with the synthetic deoxyoctanucleotide d(G-C-A-C-C-A-T-T) as a "primer". The cDNA produced was then sequenced using a modification of the gel-sequencing technique previously developed for DNA sequencing (G.G. Brownlee and E.M. Cartwright, manuscript in preparation). The sequence obtained was checked by depurination and nearest-neighbor analysis. The known sequence at the 3' end of rabbit 18S ribosomal RNA cannot base-pair extensively with the 5' noncoding region of beta-globin mRNA; however, it does form 6 base pairs around the initiation codon.

3' non-coding region sequences in eukaryotic messenger RNA

The sequence A-A-U-A-A-A is present in six different purified messenger RNA molecules (specifically the alpha-and beta-globulin mRNAs of rabbit and human, the immunoglobulin light chain mRNA of mouse (MOPC 21) and the ovalbumin mRNA of chicken) about 20 residues away from the 3'-terminal poly (A) sequence. In addition, a large selection of the 3' non-coding regions of rabbit and human globulin mRNAs (both the alpha and beta globin mRNAs) are 85% homologous, demonstrating that this region is significantly conserved in evolution.

Nucleotide clusters in deoxyribonucleic acids. XIII. Sequence analysis of the longer unique pyrimidine oligonucleotides of bacteriophage S13 DNA by a method using unlabeled atarting oligonucleotides

A method has been designed for sequence analysis of unlabeled oligodeoxynucleotides of chain length up to 20 nucleotides with no restriction on base composition. The unlabeled oligonucleotide preparation, is partially degraded with spleen exonuclease to give a series of products each differing in size by one nucleotide. The oligonucleotides in the digest are 5'-32 P terminally labeled with [psi-32] P ATP and T4 polynucleotide kinase, the excess ATP removed by chromatography on Sephadex G-25 then the oligonucleotides fractionated according to change length on DEAE-Sephadex. Each isostich fraction is analyzed for base composition and the nucleotide at the 5' terminus determined by its 32P label, resulting in direct read off of the sequence up to the penultimate 3'- terminal nucleotide. The 3'-terminal dinucleotide is analyzed by DEAE-cellulose chromatography of the Sephadex G-25 dinucleotide fraction. The method has been demonstrated by sequence analysis of the unique longer pyrimidine oligonucleotides C5T6, C2T8, C6T4 and C6T3 from S13 DNA. The sequences have extensive internal sequence homology.

Determination of nucleotide sequences beyond the sites of transcriptional termination

A procedure is described by which a discrete high-molecular-weight RNA transcription product can be used as a primer by DNA polymerase (DNA nucleotidyltransferase; EC 2.7.7.7; deoxynucleoside triphosphate: DNA deoxynucleotidyltransferase) for determining nucleic acid sequence in the template DNA beyond the 3'-terminus of the transcript. This procedure is applied to two lambda phage transcripts, the 4S "oop" RNA [Short l-strand RNA transcript from the region of origin of replication (ori) and the 6S RNA. Sequences of 35 and 19 nucleotides, respectively, following the sites at which these two transcripts terminate, are determined. Little structural homology is apparent in the template DNA beyond the 3'-ends of these two transcripts. The lack of homology suggests that this region might not be important to the termination process.

The use of primed synthesis by DNA polymerase I to study an intercistronic sequence of phiX-174 DNA

A decadeoxynucleotide complementary to ten nucleotides in the major ribosome-protected fragment of phiX-174 plus-strand DNA has been chemically synthesized and used as a primer for DNA polymerase I on phiX-174 plus-strand DNA as template. The sequence of the first 40 nucleotides incorporated onto the decadeoxynucleotide has been determined. This sequence extends further the sequence of the intercistronic region preceding gene G and shows the presence of another termination codon. The sequence was determined by using manganese as the activating cation for DNA polymerase I which allows ribonucleotides to be incorporated as well as deoxyribonucleotides. The ribo-substituted product was then cleaved specifically at the ribonucleotide residues to generate a series of overlapping ribo-terminated fragments whose sequences were sufficient to determine the complete sequence of the first 40 nucleotides. No evidence for misincorporation by DNA polymerase I in the presence of manganese was detected.