Base Sequence Changes Research Articles

ITGB5 mutation discovered in a Chinese family with blepharophimosis-ptosis-epicanthus inversus syndrome.

Blepharophimosis-ptosis-epicanthus inversus syndrome (BPES) is a rare autosomal-dominant genetic disorder, and mutations in the forkhead box L2 (FOXL2) gene are one of the major genetic causes. As this study shows, there are many patients with BPES who do not have FOXL2 mutations, as the screening results in all family members were negative. Using whole-exome sequence analysis, we discovered another possible mutational cause of BPES in integrin subunit beta 5 (ITGB5). The ITGB5 mutation (c.608T>C, p.Ile203Thr) appears in the base sequence of all BPES+ patients in this family, and it appears to be a three-generation-inherited mutation. It can cause changes in base sequence and protein function, and there may be cosegregation of disease phenotypes. ITGB5 is located on the long arm of chromosome three (3q21.2) and is close to the known pathogenic gene FOXL2 (3q23). This study is the first to report ITGB5 mutations in BPES, and we speculate that it may be directly involved in the pathogenesis of BPES or indirectly through the regulation of FOXL2.

Sequence variation of latent membrane protein 2A (LMP2A)gene from Epstein-Barr virus epitope cytotoxic T-lymphocyte (CTL)related to human leucocyte antigen-A24 (HLA-A24)in peripheral blood sample and cytobrushof nasopharyngeal cancer patients

Epstein-Barr virus (EBV) infects lymphocyte B and triggers latent phase in the host so that it causes nasopharyngeal carcinoma (NPC). Latent membraneprotein 2A (LMP2A) epitope CTL-HLA-A24 is a target for recognition by cytotoxic T lymphocyte(CTL). The change in the epitope could influence the latency of particular EBV in the host due toits ability to evade immune surveillance mediated by CTL. The study aimed to determine thesequence variation of LMP2A epitope CTL-HLA-A24 gene from the peripheral blood samples and cytobrush of the NPC patients. Case-series study was conducted with total 16 cytobrush samples from NPC patients. DNA isolation, polymerasechain reaction (PCR) and gene sequencing were performed in this study. From cytobrush samples of NPC patients, it was found the changes of base sequence variation of LMP2A gene from GGC>GGA, CCA>CCC, TGC>TCC, GGT>GGC and TCT>ACT. CCA>CCC and TGC>TCC variations were found in epitope associated with HLA-A2 where there was a change of epitope sequence from TYGPVFMCL to TYGPVFMSL caused by missense mutation. The change of base sequence caused amino acid alteration from cysteine to serine. Whereas the variation of CCA>CCC did not change the sequence of amino acid proline so that the epitopewas unaffected. In epitope associated HLA-A2 (CLGGLLTMV), there was a change in base sequence from GGT to GGC, but there was no changes in amino acid and still as glycine. There were some new variations: in the upstream sequence of LMP2A from GGC>GGA which is silent mutation and the other variation is in downstream sequence of LMP2A from TCT>ACT which is missense mutation. Thesequence variations of LMP2A gene found in this research were GGC>GGA, CCA>CCC, TGC>TCC, GGT>GGC and TCT>ACT. In our research, we found another variation compared the previous research. The variation was in the upstream sequence of LMP2A from GGC>GGA which is silent mutation and the other variation is in the downstream sequence of LMP2A from TCT>ACT which is missense mutation.

Analysis of de novo germline genome mutations

Gene mutations are permanent alterations in sections of DNA sequences called genes. This causes a significant and distinguishable change in the base sequence of the affected DNA. They are changes to the base sequence that can occur spontaneously or in response to cellular damage and can vary greatly in size and position, ranging from a single base pair mutation, to changes that span segments of chromosomes, across several genes. Mutations in somatic (non-reproductive) cells are not passed on to the next generation, however germline mutations can occur in germ line cells that can produce egg and sperm, thus causing changes to the basic genome to become fixed in the DNA for future generations to come. This article focuses on germline mutations that are of particular interest to Ohno and her team. Many of these mutations - so called de novo mutations - are genetic alterations present for the first time in one family member as a result of a variation or mutation in a germ cell in either an egg or sperm of one of the parents. DNA repair systems allow for many of the mutations to be prevented and, in reality, only a low level of them become carried forward in the genome. Ohno and her team recognise the causes of germline mutation and are seeking to understand the implications of mutation, with a view to establishing how they may evolve and the possibilities for our future selves. The current human genome is a result of amassed mutations that have accumulated in our genome and driven it along certain pathways to yield what we are now. Ohno is currently working with gene-modified mice but the work is transferable to any mammalian genome, including humans to determine a possible future pathway.

Development, Epigenetics and Metabolic Programming.

It is now widely recognized that the environment in early life can have important effects on human growth and development, including the 'programming' of far-reaching effects on the risk of developing common metabolic and other noncommunicable diseases in later life. We have shown that greater childhood adiposity is associated with higher maternal adiposity, low maternal vitamin D status, excessive gestational weight gain and short duration of breast-feeding; maternal dietary patterns in pregnancy and vitamin D status have been linked with childhood bone mineral content and muscle function. Human studies have identified fetal liver blood flow adaptations and epigenetic changes as potential mechanisms that could link maternal influences with offspring body composition. In experimental studies, there is now substantial evidence that the environment during early life induces altered phenotypes through epigenetic mechanisms. Epigenetic processes, such as DNA methylation, covalent modifications of histones and non-coding RNAs, can induce changes in gene expression without a change in DNA base sequence. Such processes are involved in cell differentiation and genomic imprinting, as well as the phenomenon of developmental plasticity in response to environmental influences. Elucidation of such epigenetic processes may enable early intervention strategies to improve early development and growth.

SRAP analysis of DNA base sequence changes in lotus mutants induced by Fe+ implantation

Ion implantation, a new biophysically mutagenic technique, has shown great potential for crop breeding. To reveal the mutation effect of low-energy ion implantation on Baiyangdian red lotus, sequence-related amplified polymorphism markers were used to amplify and detect the DNA sequence differences in mutants induced by Fe(+) ion implantation. A total of 121 primer combinations were tested in 6 mutants and a control. Seven primer combinations (me1 + em3, me1 + em14, me9 + em3, me8 + em2, me6 + em1, me11 + em5, and me6 + em5) generated clear bands with high polymorphism and good repeatability. The results showed that among 15,317 bases cloned, 146 bases in 6 mutants were different from those of the wild type, showing a variation frequency of 0.95%. The types of base changes included deletion, insertion, transversion, and transition. Adenine was more sensitive to the irradiation than were the other bases. The results suggested that mutational "hotspots" probably exists in lotus and are induced by low-energy ion implantation.

SNP-PHAGE – High throughput SNP discovery pipeline

BackgroundSingle nucleotide polymorphisms (SNPs) as defined here are single base sequence changes or short insertion/deletions between or within individuals of a given species. As a result of their abundance and the availability of high throughput analysis technologies SNP markers have begun to replace other traditional markers such as restriction fragment length polymorphisms (RFLPs), amplified fragment length polymorphisms (AFLPs) and simple sequence repeats (SSRs or microsatellite) markers for fine mapping and association studies in several species. For SNP discovery from chromatogram data, several bioinformatics programs have to be combined to generate an analysis pipeline. Results have to be stored in a relational database to facilitate interrogation through queries or to generate data for further analyses such as determination of linkage disequilibrium and identification of common haplotypes. Although these tasks are routinely performed by several groups, an integrated open source SNP discovery pipeline that can be easily adapted by new groups interested in SNP marker development is currently unavailable.ResultsWe developed SNP-PHAGE (SNP discovery Pipeline with additional features for identification of common haplotypes within a sequence tagged site (Haplotype Analysis) and GenBank (-dbSNP) submissions. This tool was applied for analyzing sequence traces from diverse soybean genotypes to discover over 10,000 SNPs. This package was developed on UNIX/Linux platform, written in Perl and uses a MySQL database. Scripts to generate a user-friendly web interface are also provided with common queries for preliminary data analysis. A machine learning tool developed by this group for increasing the efficiency of SNP discovery is integrated as a part of this package as an optional feature. The SNP-PHAGE package is being made available open source at .ConclusionSNP-PHAGE provides a bioinformatics solution for high throughput SNP discovery, identification of common haplotypes within an amplicon, and GenBank (dbSNP) submissions. SNP selection and visualization are aided through a user-friendly web interface. This tool is useful for analyzing sequence tagged sites (STSs) of genomic sequences, and this software can serve as a starting point for groups interested in developing SNP markers.

Detection of base sequence changes in the CEBPD gene in human breast cancer cell lines and primary breast cancer isolates

Single strand conformation polymorphism (SSCP) analysis was performed on genomic DNA from 97 human breast cancer samples and 10 breast cell lines to screen for mutations in the single exon C/EBPD gene. Three C→T transitions resulting in silent mutations were detected in three individual breast cancer samples. One breast cancer sample also contained a G→T transversion (Q253H). The SUM-52PE cell line contained an A→T transversion (ĀAG→T̄AG) resulting in a nonsense mutation (K180Stop). All mutations identified in genomic DNA isolates were in highly conserved regions of the C/EBPD gene. This study indicates that mutational alterations in the coding region of the C/EBPD gene are relatively uncommon in human breast cancer.

Mutations induced by (-)-anti-11R,12S-dihydrodiol 13S,14R-epoxide of dibenzo[a,l]pyrene in the coding region of the hypoxanthine phosphoribosyltransferase (Hprt) gene in Chinese hamster V79 cells.

The polycyclic aromatic hydrocarbon dibenzo[a,l]pyrene (DB[a,l]P) is an exceptionally potent carcinogen. Its direct DNA-reactive metabolite, the fjord region (-)-anti-11R,12S-dihydrodiol 13S,14R-epoxide [(-)-anti-DB[a,l]PDE], was used to investigate induction of mutations in the coding region of the hypoxanthine phosphoribosyltransferase (Hprt) gene in Chinese hamster V79 cells. Cells exposed to 1-10 nM (-)-anti-DB[a,l]PDE exhibited a close dose-responsive increase in the frequency of mutant clones resistant to 6-thioguanine. RNA was isolated from mutant clones and cDNAs were prepared by reverse transcription. The coding region of the cDNA of the Hprt gene was amplified by polymerase chain reaction and sequenced. Analysis of the DNA base sequence changes induced by (-)-anti-DB[a,l]PDE indicated that base substitutions were the most prevalent mutations, followed by exon deletions. Among the groups of V79 cells treated with low concentrations of (-)-anti-DB[a,l]PDE, most displayed high selectivity for both A:T-->T:A transversions and A:T-->G:C transitions, while cells exposed to a higher dose (10 nM) formed predominantly G:C-->T:A transversions. Also, the number of base substitutions per mutant clone increased with dose. In general, the mutation profiles induced by (-)-anti-DB[a,l]PDE exhibited a wide spectrum; in addition to base substitutions, deletions, insertions, frameshift mutations, as well as tandem mutations were detected. Analysis of the DNA adduct levels induced by (-)-anti-DB[a,l]PDE revealed that a concentration-dependent increase in the level of adduct formation preceded the concentration-dependent increase in mutational events in these cells and that an increasing proportion of DNA adducts at deoxyadenosine were formed with dose. The results of this study demonstrate a correspondence between the concentration and types of DNA adducts and the frequency and types of mutations induced by (-)-anti-DB[a,l]PDE in V79 cells.

Importance of specific nucleotides in the folding of the natural form of the hairpin ribozyme.

The hairpin ribozyme in its natural context consists of two loops in RNA duplexes that are connected as arms of a four-way helical junction. Magnesium ions induce folding into the active conformation in which the two loops are in proximity. In this study, we have investigated nucleotides that are important to this folding process. We have analyzed the folding in terms of the cooperativity and apparent affinity for magnesium ions as a function of changes in base sequence and functional groups, using fluorescence resonance energy transfer. Our results suggest that the interaction between the loops is the sum of a number of component interactions. Some sequence variants such as A10U, G+1A, and C25U exhibit loss of cooperativity and reduced affinity of apparent magnesium ion binding. These variants are also very impaired in ribozyme cleavage activity. Nucleotides A10, G+1, and C25 thus appear to be essential in creating the conformational environment necessary for ion binding. The double variant G+1A/C25U exhibits a marked recovery of both folding and catalytic activity compared to either individual variant, consistent with the proposal of a triple-base interaction among A9, G+1, and C25 [Pinard, R., Lambert, D., Walter, N. G., Heckman, J. E., Major, F., and Burke, J. M. (1999) Biochemistry 38, 16035-16039]. However, substitution of A9 leads to relatively small changes in folding properties and cleavage activity, and the double variant G+1DAP/C25U (DAP is 2,6-diaminopurine), which could form an isosteric triple-base interaction, exhibits folding and cleavage activities that are both very impaired compared to those of the natural sequence. Our results indicate an important role for a Watson--Crick base pair between G+1 and C25; this may be buttressed by an interaction with A9, but the loss of this has less significant consequences for folding. 2'-Deoxyribose substitution leads to folding with reduced magnesium ion affinity in the following order: unmodified RNA > dA9 > dA10 > dC25 approximately dA10 plus dC25. The results are interpreted in terms of an interaction between the ribose ring of C25 and the ribose and base of A10, in agreement with the proposal of Ryder and Strobel [Ryder, S. P., and Strobel, S. A. (1999) J. Mol. Biol. 291, 295-311]. In general, there is a correlation between the ability to undergo ion-induced folding and the rate of ribozyme cleavage. An exception to this is provided by G8, for which substitution with uridine leads to severe impairment of cleavage but folding characteristics that are virtually unaltered from those of the natural species. This is consistent with a direct role for the nucleobase of G8 in the chemistry of cleavage.

Influence of nucleotide excision repair and of dose on the types of vermilion mutations induced by diethyl sulfate in postmeiotic male germ cells of Drosophila

The role of a defect for nucleotide excision repair (NER) in oocytes on the repair of DNA ethyl adducts induced by diethyl sulfate (DES) in male germ cells of Drosophila was analysed. Frequencies of mutations at multiple loci (recessive lethal mutations) and at the vermilion gene induced in NER + conditions (cross NER +× NER +) were compared with those fixed in a NER − background ( NER −× NER +). The M NER − /M NER + mutability ratios for two DES concentrations, 10 mM and 15 mM, were 2.21 and 1.49, respectively, indicating that NER repairs part of the DES-induced damage. The majority of 28 fertile vermilion mutations produced by DES in NER − are transitions, both GC–AT (46.4%) and AT–GC (21.4%) transitions are found, the consequences of O 6-ethylguanine and O 4-ethylthymine, respectively. Transversions (21.5%), one +1 frameshift mutation (3.6%) and two deletions (7.1%) are most likely the result of N-alkylation damage. Furthermore, the DES-induced mutation spectra show interesting differences in relation to the exposure dose. All 10 mutants isolated in this and a previous [L.M. Sierra, A. Pastink, M.J.M. Nivard, E.W. Vogel, DNA base sequence changes induced by DES in postmeiotic male germ cells of Drosophila melanogaster, Mol. Gen. Genet. 237 (1993) 370–374] study from experiments with low DES-effectiveness are exclusively transitions, independent whether the females were of the NER + or NER − genotype. This indicates that at lower DES effectiveness only O-alkylation damage is relevant, and that N-alkylation damage is repaired. In experiments revealing high DES-effectiveness, vermilion mutations representing N-alkylation damage reached 43% (9/21) with NER − and 26% (7/27) with NER + females, suggesting (i) that NER becomes involved at high adduct levels because then the base excision repair (BER) may be saturated, and (ii) that this involvement of NER causes the relative decrease from 43% to 26% N-alkylation mediated sequence changes.

Very frequent p53 mutations in metastatic prostate carcinoma and in matched primary tumors

The frequency of mutant p53 in bone marrow metastases of patients with carcinoma of the prostate (CaP) and in matched sets of metastatic and primary lesions from the same patients was investigated. The data were examined in relation to prior treatment with androgen ablation (AA) therapy and were compared with the frequency of mutant p53 reported for primary CaP. Seventeen patients with M1b (bone metastasis: TNM Stage IV) CaP had either unilateral or bilateral bone marrow biopsies taken for these studies. Specimens were divided and the outer one-third examined histologically to confirm the presence of CaP cells. Immunohistochemical (IHC) staining for accumulated p53 protein was performed by an antibody cocktail technique. RNA was extracted from the remaining portion of the biopsy, and p53 transcripts were amplified by reverse transcriptase-polymerase chain reaction (RT-PCR) and screened for base sequence changes in the exon 4-11 region using nonisotopic single-strand conformation polymorphism (SSCP) analysis and direct DNA sequencing. Ten of 17 metastases (59%) demonstrated accumulation of p53. Six of 7 (86%) of the p53 IHC positive bone marrow samples contained RT-PCR-SSCP abnormalities, as did 2 of 3 IHC negative samples. Overall, 12 of 17 metastases (71%) contained mutant p53. Four of 7 biopsies (57%) retrieved prior to AA contained mutant p53, whereas 8 of 10 post-AA biopsies (80%) contained mutant p53. One patient showed identical SSCP abnormalities in right and left iliac crest metastases after therapy, and in this patient DNA sequencing demonstrated a missense mutation at codon 126 (TAC --> GGC, Tyr --> Gly). Archival primary cancers from seven patients were retrieved. All seven were IHC positive for p53 accumulation. p53 mutations are associated with increased metastatic potential of CaP. Abnormalities are found at approximately twice the frequency in metastases than in unselected samples of primary CaP, whereas in matched specimens there is a high rate of consonance. Mutant p53 may contribute to systemic therapy resistance, due to increased association with post-AA CaP specimens.

A mutation spectra database for bacterial and mammalian genes: 1998.

This database consists of over 24 000 mutations in 18 viral, bacterial, yeast or mammalian genes. The data are grouped as sets of DNA base sequence changes or spectra caused by a particular mutagen under defined conditions. The spectra are available on the World Wide Web at http://info.med.yale.edu/mutbase/ in two formats; in text format that can be browsed on-line or downloaded for use with a text editor and in dBASEIII format for use, after downloading, by relational database programs or by spreadsheets. Researchers are encouraged to submit DNA sequence changes to a suitable mutation database such as ours. A data entry program, MUTSIN, can be retrieved from this site. MUTSIN diagrams each mutation on the computer screen and alerts the user to any discrepancies.

Mutagenic Specificity ofN-Methyl-N′-nitro-N-nitrosoguanidine in thetonBGene on the Chromosome ofEscherichia coli recA+andrecA−Cells

DNA base sequence changes induced byN-methyl-N′-nitro-N-nitrosoguanidine (MNNG) mutagenesis has been determined for the endogenoustonBgene ofEscherichia coli recA+strain and its isogenicrecA56strain. In therecA+strain, base substitutions accounted for 48 mutations among 54 MNNG-induced independent mutations analyzed and consisted of 45 G:C to A:T transitions, two A:T to G:C transitions and one A:T to C:G transversion. In therecA56strain, 67% (34/51) were base substitutions among which G:C to A:T transition (28/51) predominated, followed by three A:T to T:A transversions, two G:C to T:A transversions, and one A:T to G:C transition. These mutagenic specificities were consistent with the mispairing predicted by the methylation of the O6position of guanine. In both strains the G:C to A:T mutations were found at guanine residues preceded by either guanine or thymine on the non-transcribed strand of the target gene.

The notion of the Cambrian pananimalia genome.

The toil by photosynthesizing cyanobacteria and blue-green algae of nearly three billion years appeared to have finally resulted in the sufficient accumulation of molecular oxygen. So, the stage was set for the emergence, at the ocean bottom, of diverse animals that were consumers of molecular oxygen. It now appears that this Cambrian explosion, during which nearly all the extant animal phyla have emerged, was of an astonishingly short duration, lasting only 6-10 million years. Inasmuch as only a 1% DNA base sequence change is expected in 10 million years under the standard spontaneous mutation rate, I propose that all those diverse animals of the early Cambrian period, some 550 million years ago, were endowed with nearly identical genomes, with differential usage of the same set of genes accounting for the extreme diversities of body forms. Some of the more pertinent genes that are thought to be included in the Cambrian pananimalia genome are as follows. (i) A gene for lysyloxidase that, in the presence of molecular oxygen, crosslinked collagen triple helices to produce ligaments and tendons, thus contributing to the stout bodies of the Cambrian animals. (ii) Genes for hemoglobin; these internal transporters of molecular oxygen are today seen sporadically in members of diverse animal phyla. (iii) The Pax-6 gene for eye formation; the eyes of a ribbon worm to a human are organized by this gene. In animals without eyes, the same gene organizes other sensory systems and organs. (iv) A series of Hox genes for the anterior-posterior (cranio-caudal) body plans: these genes are also present in all phyla of the kingdom Animalia.

Spectrum of mutations induced by methyl and ethyl methanesulfonate at the hprt locus of normal and tag expressing Chinese hamster fibroblasts.

This work describes the isolation and characterization of methyl methanesulfonate (MMS) and ethyl methanesulfonate (EMS) induced 6-thioguanine-resistant mutants in normal and Escherichia coli tag gene expressing Chinese hamster fibroblast, RJKO, cells. It was previously shown that increased removal of 3-alkylated adenine, effected by 3-methyladenine DNA glycosylase I (Tag), reduces the frequencies of hprt mutations induced by alkylating agents which produce mostly N-alkylation (MMS and EMS) to half the normal rate. In order to identify which type of mutation is suppressed by increased 3-alkyladenine repair we have determined the DNA base sequence changes of the hprt cDNA in 61 independent MMS- and EMS-induced mutant clones. For both cell types and irrespective of the agent used, the majority of mutations were GC to AT transitions originating in the non-transcribed strand. Only 6/55 base substitutions occurred at AT base pairs: five AT to GC transitions and one AT to CG transversion. Six mutations were found to be deletions. These results indicate that 3-alkylated adenines in DNA are not directly premutagenic. The fact that the mutation frequency is reduced by increased 3-alkyladenine removal might be explained by postulating the existence in mammalian cells of an SOS-like response turned on by cytotoxic lesions like 3-alkyladenine, or, alternatively, that increased removal of 3-alkyladenine increases the number of single-strand breaks in DNA, which stalls DNA replication and allows a prolonged time for DNA repair by the alkyltransferase.

The application of the restriction site mutation assay to the study of the induction of mutations in the tissues of rodents.

The restriction site mutation (RSM) assay has been developed as a methodology for the study of base changes induced in restriction enzyme recognition sequences. In principle, the RSM methodology may be used to the study mutation induction in any organ, of any species, for which DNA sequence information is available. This paper describes the analysis of the induction of base sequence changes in restriction enzyme recognition sites present in the p53 and alpha-haemoglobin genes of male mice exposed to 1-ethyl-1-nitrosourea. Our results demonstrate the induction of G-->A transitions and G-->T transversions in a number of restriction enzyme recognition sites (BamH1, Pst1, Ban1, Msp1, Alu1) in DNA extracted from a number of different tissues from animals harvested 2-7 days after exposure. The data presented indicates that the RSM methodology has considerable potential for development for the study of induced base changes in the endogenous genes of a variety of species.

DNA base sequence changes induced by diethyl sulfate in postmeiotic male germ cells of Drosophila melanogaster.

The DNA base sequence changes induced by diethyl sulfate (DES) were analyzed in postmeiotic male germ cells of Drosophila melanogaster. 31 transmissible vermilion mutants were recovered in F1 and F2 generations, with a frequency of 2.6 x 10(-4) for the F1, and of 1.8-13 x 10(-4) for the F2. The results show that DES induces both base pair substitutions (93%) and deletions (7%). In accord with its relatively high ability to alkylate oxygens in DNA, the most frequent type of sequence alteration among the basepair changes are GC-AT transitions, accounting for 73% of mutations, followed by transversions AT-TA (10%). DES also induced AT-GC transitions and AT-CG transversions. Both induced deletions were intralocus deletions, not occurring between basepair repeats. No influence of neighboring bases on the mutation position was found.

DNA base sequence changes in spontaneous and ethyl methanesulfonate-induced mutations of a chromosomally-integrated gene in Chinese hamster ovary cells

A series of spontaneous and ethyl methanesulfonate-induced 6-thioguanine-resistant mutants were isolated in the CHO-10T5 cell line. This cell line was constructed by the introduction of a shuttle vector containing the Escherichia coli gpt gene into a hypoxanthine-guanine phosphoribosyltransferase deficient derivative of the Chinese hamster cell line CHO-K1. Shuttle vector sequences were recovered from many of the mutant cell lines by the COS cell fusion technique and the DNA base sequence of the gpt genes was determined whenever possible. The base sequences were determined for gpt genes recovered from 29 spontaneous mutants. Of these 29 mutants, 9 have single base substitutions, 1 has a small duplication, 17 have simple deletions, 1 has a deletion with additional bases inserted at the deletion site, and 1 has no change in the gpt coding sequence. Many of the deletions were less than 20 basepairs in length and several occurred in a region previously observed to be a hotspot for spontaneous deletions. The generation of the deletion/insertion mutation may have involved a quasi-palindromic intermediate. A total of 59 ethyl methansesulfonate-induced mutants were isolated and vector sequences were recovered from 50 mutants. All 50 mutants sequenced had single base substitutions and most (45) were G:C to A:T transitions. While there were no strong hotspots in this collection of mutations, the site distribution was obviously nonrandom. Many of the G:C to A:T transitions either produced a nonsense codon or occurred at glycine codons.

Dideoxy fingerprinting (ddF): A rapid and efficient screen for the presence of mutations

We describe dideoxy fingerprinting (ddF), a hybrid between dideoxy sequencing and SSCP that can detect the presence of single base and other sequence changes in PCR-amplified segments. As implemented herein, ddF involves a Sanger sequencing reaction with one dideoxynucleotide followed by nondenaturing gel electrophoresis. When ddF was used to examine segments of the human factor IX gene, 84 of 84 different mutations were detected with a very low rate of false positive signals. The approximate locations of the sequence changes could be determined from the ddF pattern and samples with different sequence changes had different fingerprints. In addition, large segments could be amplified and rapidly screened by ddF in multiple smaller subsegments. The patterns observed with ddF are instructive in that they suggest an inherent limitation in the detection of certain mutations by SSCP.

Dose-dependent differences in the profile of mutations induced by an ultimate carcinogen from benzo[a]pyrene.

Mutations in the coding region of the hypoxanthine (guanine) phosphoribosyltransferase (HPRT) gene of Chinese hamster V-79 cells were examined after exposure of the cells to a high cytotoxic dose (0.48 microM; 35% survival) and a low noncytotoxic dose (0.04 microM; 100% survival) of the ultimate carcinogen (+)-7R,8S-dihydroxy-9S,10R-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene [(+)-BPDE]. Independent 8-azaguanine-resistant colonies were isolated and cDNAs were prepared by reverse transcription. The coding region of the cDNA of the HPRT gene was amplified by the polymerase chain reaction and sequenced. An examination of the DNA base sequence changes induced by different doses of (+)-BPDE demonstrated that the high dose of (+)-BPDE caused base substitution mutations almost exclusively at G.C base pairs whereas the low dose of (+)-BPDE caused mutations at both G.C and A.T base pairs. Thus, use of a low dose of (+)-BPDE allowed the detection of mutations (at A.T base pairs) that were not readily observed with a high dose of (+)-BPDE. The data also suggest that the low dose of (+)-BPDE may have caused a different profile of base substitutions at G.C base pairs and exon deletions than the high dose. The results indicate dose-dependent differences in the profile of mutations for an ultimate carcinogen.