Mutation detection with MutH, MutL, and MutS mismatch repair proteins

Genomic Insights into the Radiation-Resistant Capability of Sphingomonas qomolangmaensis S5-59T and Sphingomonas glaciei S8-45T, Two Novel Bacteria from the North Slope of Mount Everest

Mount Everest provides natural advantages to finding radiation-resistant extremophiles that are functionally mechanistic and possess commercial significance. (1) Background: Two bacterial strains, designated S5-59T and S8-45T, were isolated from moraine samples collected from the north slope of Mount Everest at altitudes of 5700m and 5100m above sea level. (2) Methods: The present study investigated the polyphasic features and genomic characteristics of S5-59^T and S8-45^T. (3) Results: The major fatty acids and the predominant respiratory menaquinone of S5-59^T and S8-45^T were summed as feature 3 (comprising C16:1 ω6c and/or C16:1 ω7c) and ubiquinone-10 (Q-10). Phylogenetic analyses based on 16S rRNA sequences and average nucleotide identity values among these two strains and their reference type strains were below the species demarcation thresholds of 98.65% and 95%. Strains S5-59^T and S8-45^T harbored great radiation resistance. The genomic analyses showed that DNA damage repair genes, such as mutL, mutS, radA, radC, recF, recN, etc., were present in the S5-59^T and S8-45^T strains. Additionally, strain S5-59^T possessed more genes related to DNA protection proteins. The pan-genome analysis and horizontal gene transfers revealed that strains of Sphingomonas had a consistently homologous genetic evolutionary radiation resistance. Moreover, enzymatic antioxidative proteins also served critical roles in converting ROS into harmless molecules that resulted in resistance to radiation. Further, pigments and carotenoids such as zeaxanthin and alkylresorcinols of the non-enzymatic antioxidative system were also predicted to protect them from radiation. (4) Conclusions: Type strains S5-59^T (=JCM 35564T =GDMCC 1.3193T) and S8-45^T (=JCM 34749T =GDMCC 1.2715T) represent two novel species of the genus Sphingomonas with the proposed name Sphingomonas qomolangmaensis sp. nov. and Sphingomonas glaciei sp. nov. The type strains, S5-59^T and S8-45^T, were assessed in a deeply genomic study of their radiation-resistant mechanisms and this thus resulted in a further understanding of their greater potential application for the development of anti-radiation protective drugs.

Complex Evolution of the Mismatch Repair System in Eukaryotes is Illuminated by Novel Archaeal Genomes

Repairing DNA damage is one of the most important functions of the ‘housekeeping’ proteins, as DNA molecules are constantly subject to different kinds of damage. An important mechanism of DNA repair is the mismatch repair system (MMR). In eukaryotes, it is more complex than it is in bacteria or Archaea due to an inflated number of paralogues produced as a result of an extensive process of gene duplication and further specialization upon the evolution of the first eukaryotes, including an important part of the meiotic machinery. Recently, the discovery and sequencing of Asgard Archaea allowed us to revisit the MMR system evolution with the addition of new data from a group that is closely related to the eukaryotic ancestor. This new analysis provided evidence for a complex evolutionary history of eukaryotic MMR: an archaeal origin for the nuclear MMR system in eukaryotes, with subsequent acquisitions of other MMR systems from organelles.

Enrichment of error-free synthetic DNA sequences by CEL I nuclease

As the availability of DNA sequence information has grown, so has the need to replicate DNA sequences synthetically. Synthetically produced DNA sequences allow the researcher to exert greater control over model systems and allow for the combinatorial design and construction of novel metabolic and regulatory pathways, as well as optimized protein-coding sequences for biotechnological applications. This utility has made synthetically produced DNA a hallmark of the molecular biosciences and a mainstay of synthetic biology. However, synthetically produced DNA has a significant shortcoming in that it typically has an error rate that is orders of magnitude higher when compared to DNA sequences derived directly from a biological source. This relatively high error rate adds to the cost and labor necessary to obtain sequence-verified clones from synthetically produced DNA sequences. This unit describes a protocol to enrich error-free sequences from a population of error-rich DNA via treatment with CEL I (Surveyor) endonuclease. This method is a straightforward and quick way of reducing the error content of synthetic DNA pools and reliably reduces the error rates by >6-fold per round of treatment.

Gene synthesis: methods and applications

DNA synthesis techniques and technologies are quickly becoming a cornerstone of modern molecular biology and play a pivotal role in the field of synthetic biology. The ability to synthesize whole genes, novel genetic pathways, and even entire genomes is no longer the dream it was 30 years ago. Using little more than a thermocycler, commercially synthesized oligonucleotides, and DNA polymerases, a standard molecular biology laboratory can synthesize several kilobase pairs of synthetic DNA in a week using existing techniques. Herein, we review the techniques used in the generation of synthetic DNA, from the chemical synthesis of oligonucleotides to their assembly into long, custom sequences. Software and websites to facilitate the execution of these approaches are explored, and applications of DNA synthesis techniques to gene expression and synthetic biology are discussed. Finally, an example of automated gene synthesis from our own laboratory is provided.

Maintaining a sense of direction during long-range communication on DNA

Many biological processes rely on the interaction of proteins with multiple DNA sites separated by thousands of base pairs. These long-range communication events can be driven by both the thermal motions of proteins and DNA, and directional protein motions that are rectified by ATP hydrolysis. The present review describes conflicting experiments that have sought to explain how the ATP-dependent Type III restriction-modification enzymes can cut DNA with two sites in an inverted repeat, but not DNA with two sites in direct repeat. We suggest that an ATPase activity may not automatically indicate a DNA translocase, but can alternatively indicate a molecular switch that triggers communication by thermally driven DNA sliding. The generality of this mechanism to other ATP-dependent communication processes such as mismatch repair is also discussed.

Robust physical methods that enrich genomic regions identical by descent for linkage studies: confirmation of a locus for osteogenesis imperfecta

BACKGROUND

The monogenic disease osteogenesis imperfecta (OI) is due to single mutations in either of the collagen genes ColA1 or ColA2, but within the same family a given mutation is accompanied by a wide range of disease severity. Although this phenotypic variability implies the existence of modifier gene variants, genome wide scanning of DNA from OI patients has not been reported. Promising genome wide marker-independent physical methods for identifying disease-related loci have lacked robustness for widespread applicability. Therefore we sought to improve these methods and demonstrate their performance to identify known and novel loci relevant to OI.

RESULTS

We have improved methods for enriching regions of identity-by-descent (IBD) shared between related, afflicted individuals. The extent of enrichment exceeds 10- to 50-fold for some loci. The efficiency of the new process is shown by confirmation of the identification of the Col1A2 locus in osteogenesis imperfecta patients from Amish families. Moreover the analysis revealed additional candidate linkage loci that may harbour modifier genes for OI; a locus on chromosome 1q includes COX-2, a gene implicated in osteogenesis.

CONCLUSION

Technology for physical enrichment of IBD loci is now robust and applicable for finding genes for monogenic diseases and genes for complex diseases. The data support the further investigation of genetic loci other than collagen gene loci to identify genes affecting the clinical expression of osteogenesis imperfecta. The discrimination of IBD mapping will be enhanced when the IBD enrichment procedure is coupled with deep resequencing.

A method for HLA genotyping using the specific cleavage of DNA-rN1-DNA/DNA with RNase HII from Chlamydia pneumoniae

Single nucleotide polymorphisms (SNPs) provide a great opportunity for the study of human disease and bacterial drug resistance. However, many SNP typing techniques require dedicated instruments and high cost. Here, we develop a novel method for SNP genotyping based on specific cleavage properties of RNase HII from Chlamydia pneumoniae (CpRNase HII), termed the "CpRNase HII-based method." CpRNase HII cleaves the DNA-rN(1)-DNA/DNA duplex at the 5'-side of the ribonucleotide (rN(1) = one ribonucleotide). Moreover, the cleavage efficiencies of the perfectly matched DNA-rN(1)-DNA/DNA duplexes are higher than those carrying a mismatched ribonucleotide. DNA-rN(1)-DNA fragments are modified with a fluorophore at the 5'-end and a quencher at the 3'-end to generate molecular beacons (MBs), which hybridize with single-stranded DNA (analyte) to be cleaved by CpRNase HII. As perfectly matched duplexes can be cleaved efficiently and mismatched duplexes cannot, CpRNase HII-catalyzed reactions can differentiate between one-nucleotide variations on the DNA-rN(1)-DNA/DNA duplexes. We have validated this method with nine SNPs of the HLA gene, which were successfully determined by endpoint measurements of fluorescence intensity. The new method is simple and effective, because the design of MBs is easy, and all steps of the genotyping consist of simple additions of solutions and incubation. This method will be suitable for large-scale genotyping.

A simple fluorescent method for detecting mismatched DNAs using a MutS-fluorophore conjugate

A fluorescent method was developed for the detection of unpaired and mismatched DNAs using a MutS-fluorophore conjugate. The fluorophore, 2-(4'-(iodoacetoamido)anilino) naphthalene-6-sulfonic acid (IAANS), was site-specifically attached to the 469 position of Thermus aquaticus (Taq.) MutS mutant (C42A/T469C). The fluorophore labeled residue located at the dimer interface of the protein undergoes a drastic conformational change upon binding with mismatched DNA. The close proximity of the two identical fluorescent molecules presumably causes the self-quenching of the fluorophore, since fluorescence emission of the biosensor decreases with increasing concentrations of mismatched DNA. The order of binding affinity for each unpaired and mismatched DNA obtained by this method was DeltaT (Kd=52 nM)>GT (62 nM)>DeltaC (130 nM)>CT (160 nM)>DeltaG (170 nM)>DeltaA (250 nM)>CC (720 nM)>AT (950 nM). This order is comparable to the previous results of the gel mobility shift assay. Thus, this method can be a simple, useful tool for elucidating the mechanism of DNA mismatch repair as well as a novel probe for detecting of genetic mutation.

Electrochemical detection of mismatched DNA using a MutS probe

A direct and label-free electrochemical biosensor for the detection of the protein–mismatched DNA interaction was designed using immobilized N-terminal histidine tagged Escherichia coli. MutS on a Ni-NTA coated Au electrode. General electrochemical methods, cyclic voltammetry (CV), electrochemical quartz crystal microbalance (EQCM) and impedance spectroscopy, were used to ascertain the binding affinity of mismatched DNAs to the MutS probe. The direct results of CV and impedance clearly reveal that the interaction of MutS with the CC heteroduplex was much stronger than that with AT homoduplex, which was not differentiated in previous results (GT > CT > CC ≈ AT) of a gel mobility shift assay. The EQCM technique was also able to quantitatively analyze MutS affinity to heteroduplexes.

Detection of 100% of mutations in 124 individuals using a standard UV/Vis microplate reader: a novel concept for mutation scanning

We report the development of a simple and inexpensive assay for the detection of DNA polymorphisms and mutations that is based on the modification of mismatched bases by potassium permanganate. Unlike the chemical cleavage of mismatch assay, which also exploits the reactivity of potassium permanganate to detect genomic variants, the assay we describe here does not require a cleavage manipulation and therefore does not require expensive or toxic chemicals or a separation step, as mismatches are detected using direct optical methods in a microplate format. Studies with individual deoxynucleotides demonstrated that the reactivity with potassium permanganate resulted in a specific colour change. Furthermore, studies with synthetic oligonucleotide heteroduplexes demonstrated that this colour change phenomenon could be applied to detect mismatched bases spectrophotometrically. A collection of plasmids carrying single point mutations in the mouse beta-globin promoter region was used as a model system to develop a functional mutation detection assay. Finally, the assay was validated as 100% effective in detecting mismatches in a blinded manner using DNA from patients previously screened for mutations using established techniques, such as sequencing, SSCP and denaturing high-performance liquid chromatography (DHPLC) analysis in DNA fragments up to 300 bp in length.

Novel approach to mapping of resistance mutations in whole genomes by using restriction enzyme modulation of transformation efficiency

Restriction enzyme modulation of transformation efficiencies (REMOTE) is a method that makes use of genome restriction maps and experimentally observed differences in transformation efficiencies of genomic DNA restriction digests to discover the location of mutations in genomes. The frequency with which digested genomic DNA from a resistant strain transforms a susceptible strain to resistance is primarily determined by the size of the fragment containing the resistance mutation and the distance of the mutation to the end of the fragment. The positions of restriction enzyme cleavage sites immediately flanking the resistance mutation define these parameters. The mapping procedure involves a process of elimination in which digests that transform with high frequency indicate that the restriction enzyme cleavage sites are relatively far away from the mutation, while digests that transform with low frequency indicate that the sites are close to the mutation. The transformation data are compared computationally to the genome restriction map to identify the regions that best fit the data. Transformations with PCR amplicons encompassing candidate regions identify the resistance locus and enable identification of the mutation. REMOTE was developed using Haemophilus influenzae strains with mutations in gyrA, gyrB, and rpsE that confer resistance to ciprofloxacin, novobiocin, and spectinomycin, respectively. We applied REMOTE to identify mutations that confer resistance to two novel antibacterial compounds. The resistance mutations were found in genes that can decrease the intracellular concentration of compounds: acrB, which encodes a subunit of the AcrAB-TolC efflux pump; and fadL, which encodes a long-chain fatty acid transporter.

Construction and characterization of different MutS fusion proteins as recognition elements of DNA chip for detection of DNA mutations

Three MutS fusion systems were designed as the mutation recognition and signal elements of DNA chips for detection of DNA mutations. The expression vectors containing the encoding sequences of three recombinant proteins, Trx-His6-GFP-(Ser-Gly)6-MutS (THGLM), Trx-His6-(Ser-Gly)6-Strep tagII-(Ser-Gly)6-MutS (THLSLM) and Trx-His6-(Ser-Gly)6-MutS (THLM), were constructed by gene slicing in vitro. THGLM, THLSLM and THLM were then expressed in Escherichia coli AD494(DE3), respectively. SDS-PAGE analysis revealed that each of the expected proteins was approximately 30% of the total bacterial proteins. The recombinant proteins were purified to the purity over 90% by immobilized metal (Co2+) chelation affinity chromatography. Bioactivity assay indicated that three fusion proteins retained the mismatch-binding activity and the functions of other fusion partners. DNA chips arrayed both mismatched and unpaired DNA oligonucleotides as well as rpoB gene from Mycobacterium tuberculosis were prepared. THGLM, THLSLM and THLM that was labeled with Fluorolinktrade mark Cy3 reactive dye, were then used as both mutation recognition and labeling elements of DNA chips. The resulting DNA chips were used to detect the mismatched and unpaired mutations in the synthesized oligonucleotides and single base mutation in rpoB gene of M. tuberculosis that is resistant to rifamycin.

High sensitivity EndoV mutation scanning through real-time ligase proofreading

The ability to associate mutations in cancer genes with the disease and its subtypes is critical for understanding oncogenesis and identifying biomarkers for clinical diagnosis. A two-step mutation scanning method that sequentially used endonuclease V (EndoV) to nick at mismatches and DNA ligase to reseal incorrectly or nonspecifically nicked sites was previously developed in our laboratory. Herein we report an optimized single-step assay that enables ligase to proofread EndoV cleavage in real-time under a compromise between buffer conditions. Real-time proofreading results in a dramatic reduction of background cleavage. A universal PCR strategy that employs both unlabeled gene-specific primers and labeled universal primers, allows for multiplexed gene amplification and precludes amplification of primer dimers. Internally labeled PCR primers eliminate EndoV cleavage at the 5' terminus, enabling high-throughput capillary electrophoresis readout. Furthermore, signal intensity is increased and artifacts are reduced by generating heteroduplexes containing only one of the two possible mismatches (e.g. either A/C or G/T). The single-step assay improves sensitivity to 1:50 and 1:100 (mutant:wild type) for unknown mutations in the p53 and K-ras genes, respectively, opening prospects as an early detection tool.

The binding of guanine–guanine mismatched DNA to naphthyridine dimer immobilized sensor surfaces: kinetic aspects

Naphthyridine dimer composed of two naphthyridine chromophores and a linker connecting them strongly, and selectively, binds to the guanine-guanine mismatch in duplex DNA. The kinetics for the binding of the G-G mismatch to the naphthyridine dimer was investigated by surface plasmon resonance assay. The sensor surface was prepared by immobilizing naphthyridine dimer through a long poly(ethylene oxide) linker with the ligand density of 9.1 x 10(-12) fmolnm(-2). The kinetic analyses revealed that the binding of the G-G mismatch was sequence dependent on the flanking base pairs, and the G-G mismatches flanking at least one G-C base pair bound to the surface via a two-step process with a 1:1 DNA-ligand stoichiometry. The first association rate constant for the binding of the G-G mismatch in the 5'-CGG-3'/3'-GGC-5' sequence to the naphthyridine dimer-immobilized sensor surface was 3.2 x 10(3)M(-1)s(-1) and the first dissociation rate constant was 1.4 x 10(-2)s(-1). The association and dissociation rate constants for the second step were insensitive to the flanking sequences, and were almost of the same order of magnitude as the first dissociation rate constant. This indicates that the second step had only a small energetic contribution to the binding. The association constant calculated from kinetic parameters was 2.7 x 10(5)M(-1), which is significantly smaller than the apparent association constants obtained from experiments in solution. Electrospray ionization time-of-flight (ESI-TOF) mass spectrometry on the complex produced from the G-G mismatch and naphthyridine dimer showed the formation of the 1:1 complex and a 1:2 DNA-ligand complex in solution. The latter complex became the dominant complex when a six-fold excess of naphthyridine dimer was added to DNA.

Mutation-replication statistics of polymerase chain reactions

The variability of the products of polymerase chain reactions, due to mutations and to incomplete replications, can have important clinical consequences. Sun (1995) and Weiss and von Haeseler (1995) modeled these errors by a branching process and introduced estimators of the mutation rate and of the efficiency of the reaction based, for example, on the empirical distribution of the mutations of a random sequence. This distribution involves a noncanonical branching Markov chain which, although easy to describe, is not analytically tractable except in the infinite-population limit. These authors for the infinite-target limit, and Wang et al. (2000) for finite targets, solved the infinite-population limit. In this paper, we provide bounds of the difference between the finite-target finite-population case and its finite-target infinite-population approximation. The bounds are explicit functions of the efficiency of the reaction, the mutation rate per site and per cycle, the size of the target, the number of cycles, and the size of the initial population. They concern every moment and, what might be more surprising, the histogram itself of the distributions. The bounds for the moments exhibit a phase transition at the value 1 - 1/N = 3/4 of the mutation rate per site and per cycle, where N = 4 is the number of letters in the encoding alphabet of DNA and RNA. Of course, in biological contexts, the mutation rates are much smaller than 3/4.

Detection of guanine-adenine mismatches by surface plasmon resonance sensor carrying naphthyridine-azaquinolone hybrid on the surface

We have discovered a new molecule naphthyridine-azaquinolone hybrid (Npt-Azq) that strongly stabilized the guanine-adenine (G-A) mismatch in duplex DNA. In the presence of Npt-Azq, the melting temperature (T(m)) of 5'-d(CTA ACG GAA TG)-3'/3'-d(GAT TGA CTT AC)-5' containing a single G-A mismatch increased by 15.4 degrees C, whereas fully matched duplex increased its T(m) only by 2.2 degrees C. Npt-Azq was immobilized on the sensor surface for the surface plasmon resonance (SPR) assay to examine SPR detection of duplexes containing a G-A mismatch. Distinct SPR signals were observed when 27mer DNA containing a G-A mismatch was analyzed by the Npt-Azq immobilized sensor surfaces, whereas the signal of the fully matched duplex was approximately 6-fold weaker in intensity. The SPR signals for the G-A mismatch were proportional to the concentration of DNA in a range up to 1 microM, confirming that the SPR signal is in fact due to the binding of the G-A mismatch to Npt-Azq immobilized on the surface. Examination of all 16 G-A mismatches regarding the flanking sequence revealed that the sensor surface reported here is applicable to eight flanking sequences, covering 50% of all possible G-A mismatches.

Ligation of high-melting-temperature 'clamp' sequence extends the scanning range of rare point-mutational analysis by constant denaturant capillary electrophoresis (CDCE) to most of the human genome

Mutations cause or influence the prevalence of many diseases. In human tissues, somatic point mutations have been observed at fractions at or below 4/10,000 and 5/100,000 in mitochondrial and nuclear DNA, respectively. In human populations, fractions for the multiple alleles that code for recessive deleterious syndromes are not expected to exceed 5 x 10(-4). Both nuclear and mitochondrial point mutations have been measured in human cells and tissues at fractions approaching 10(-6) using constant denaturant capillary electrophoresis (CDCE) coupled with high-fidelity PCR (hifiPCR). However, this approach is only applicable to those target sequences (approximately 100 bp) juxtaposed with a 'clamp', a higher-melting-temperature sequence, in genomic DNA; such naturally clamped targets represent approximately 9% of the human genome. To open up most of the human genome to rare point-mutational analysis, a high-efficiency DNA ligation procedure was recently developed so that a clamp could be attached to any target of interest. We coupled this ligation procedure with prior CDCE/hifiPCR and achieved a sensitivity of 2 x 10(-5) in human cells for the first time using an externally attached clamp. At this sensitivity, somatic mutations, each representing an anatomically distinct cluster of cells (turnover unit) derived from a mutant stem cell, may be detected in a series of tissue samples, each containing as many as 5 x 10(4) turnover units. Additionally, rare inherited mutations may be scanned in pooled DNA samples, each derived from as many as 10(5) persons.

Single nucleotide polymorphism seeking long term association with complex disease

Successful investigation of common diseases requires advances in our understanding of the organization of the genome. Linkage disequilibrium provides a theoretical basis for performing candidate gene or whole-genome association studies to analyze complex disease. However, to constructively interrogate SNPs for these studies, technologies with sufficient throughput and sensitivity are required. A plethora of suitable and reliable methods have been developed, each of which has its own unique advantage. The characteristics of the most promising genotyping and polymorphism scanning technologies are presented. These technologies are examined both in the context of complex disease investigation and in their capacity to face the unique physical and molecular challenges (allele amplification, loss of heterozygosity and stromal contamination) of solid tumor research.

Sequence variation in genes and genomic DNA: methods for large-scale analysis

The large-scale typing of sequence variation in genes and genomic DNA presents new challenges for which it is not clear that current technologies are sufficiently sensitive, robust, or scalable. This review surveys the current platform technologies: separation-based approaches, which include mass spectrometry; homogeneous assays; and solid-phase/array-based assays. We assess techniques for discovering and typing variation on a large scale, especially that of single-nucleotide polymorphisms. The in-depth focus is the DNA chip/array platform, and some of the published large-scale studies are closely examined. The problem of large-scale amplification is addressed, and emerging technologies for present and future needs are indicated.

A commented dictionary of techniques for genotyping

Several tools, differing in their technical and practical parameters, are available for the detection of point mutations as well as small deletions and insertions. In this article, a dictionary featuring over fifty methods for detection of mutation is presented. The distinguishing principle for each method is briefly explained. Sorting of and discussion on the methods give the reader a brief introduction to the field of genotyping.

Dynamic localization of bacterial and plasmid chromosomes

Plasmid-encoded partition genes determine the dynamic localization of plasmid molecules from the mid-cell position to the 1/4 and 3/4 positions. Similarly, bacterial homologs of the plasmid genes participate in controlling the bidirectional migration of the replication origin (oriC) regions during sporulation and vegetative growth in Bacillus subtilis, but not in Escherichia coli. In E. coli, but not B. subtilis, the chromosomal DNA is fully methylated by DNA adenine methyltransferase. The E. coli SeqA protein, which binds preferentially to hemimethylated nascent DNA strands, exists as discrete foci in vivo. A single SeqA focus, which is a SeqA-hemimethylated DNA cluster, splits into two foci that then abruptly migrate bidirectionally to the 1/4 and 3/4 positions during replication. Replicated oriC copies are linked to each other for a substantial period of generation time, before separating from each other and migrating in opposite directions. The MukFEB complex of E. coli and Smc of B. subtilis appear to participate in the reorganization of bacterial sister chromosomes.

PCR candidate region mismatch scanning: adaptation to quantitative, high-throughput genotyping

Linkage and association analyses were performed to identify loci affecting disease susceptibility by scoring previously characterized sequence variations such as microsatellites and single nucleotide polymorphisms. Lack of markers in regions of interest, as well as difficulty in adapting various methods to high-throughput settings, often limits the effectiveness of the analyses. We have adapted the Escherichia coli mismatch detection system, employing the factors MutS, MutL and MutH, for use in PCR-based, automated, high-throughput genotyping and mutation detection of genomic DNA. Optimal sensitivity and signal-to-noise ratios were obtained in a straightforward fashion because the detection reaction proved to be principally dependent upon monovalent cation concentration and MutL concentration. Quantitative relationships of the optimal values of these parameters with length of the DNA test fragment were demonstrated, in support of the translocation model for the mechanism of action of these enzymes, rather than the molecular switch model. Thus, rapid, sequence-independent optimization was possible for each new genomic target region. Other factors potentially limiting the flexibility of mismatch scanning, such as positioning of dam recognition sites within the target fragment, have also been investigated. We developed several strategies, which can be easily adapted to automation, for limiting the analysis to intersample heteroduplexes. Thus, the principal barriers to the use of this methodology, which we have designated PCR candidate region mismatch scanning, in cost-effective, high-throughput settings have been removed.

Bidirectional migration of SeqA-bound hemimethylated DNA clusters and pairing of oriC copies in Escherichia coli

BACKGROUND

We previously found that SeqA protein, which binds preferentially to newly replicated hemimethylated DNA, is localized as discrete fluorescent foci in Escherichia coli cells. A single SeqA focus, localized at midcell, separates into two foci and these foci migrate abruptly in opposite directions.

RESULTS

The present study shows that (i) appearance of SeqA foci depends on continuous DNA replication, suggesting that the SeqA foci represent clusters consisting of SeqA and newly replicated hemimethylated DNA, (ii) in a synchronous round of replication, a single SeqA focus at midcell separates into two foci and these foci abruptly migrate in opposite directions midway through replication from oriC to the terminus, and (iii) oriC is replicated at midcell but replicated oriC copies remain linked with each other at midcell for 40 min after replication at 30 degrees C. Subsequently, the linked oriC copies separate and migrate gradually towards both borders of the nucleoid before cell division.

CONCLUSIONS

A single cluster of SeqA-bound hemimethylated DNA segment separates into two clusters and these clusters migrate abruptly in a bipolar fashion during progress of replication and prior to separation of linked sister oriC copies.

Genome-wide detection of unknown subtle mutations in bacteria by combination of MutS and RDA

We propose a procedure for detecting unknown, subtle DNA changes throughout the entire bacterial genome by a combination of MutS and RDA. Current techniques detect subtle mutations after PCR amplification of the target regions, so the mutation detection is done between amplified PCR fragments. In this paper, genome-wide subtle mutation scanning in bacteria was performed by combining the MutS and RDA techniques. Our strategy for cloning a small mutation region is composed of two steps: an enrichment of fragments containing subtle mutations using MutS, followed by an RDA subtraction procedure for further enrichment. We successfully identified small mutations such as a four-base insertion, a two-base insertion, and transition mutations in bacteria.

Mining for SNPs: putting the common variants--common disease hypothesis to the test

Classical molecular genetic strategies have succeeded in identifying mutations responsible for numerous rare diseases with Mendelian patterns of inheritance, but have been largely unsuccessful in unravelling the (genetic basis of complex medical conditions like cardiovascular disease' diabetes and mental illness. These common disorders are shaped by multiple genes that exert weak allelic effects in the setting of confounding environmental variables. Association study designs provide statistical povwer to reveal the modest contributions of weak alleles, and evidence is mounting that common genetic polymorphisms play a role in complex diseases. Cataloguing genetic variation in human populations is a prerequisite for further validation of the 'common variants-common disease' hypothesis, and polymorphism discovery has begun in earnest in the academic and private sector. We will review several strategies for high-throughput polymorphism discovery and discuss the implications of early results from polymorphism screens for future genetic studies.

Enzymatic and chemical cleavage methods

Cleavage-based methods of mutation detection offer a simple and intuitive means to detect and in most cases locate mutations within DNA fragment sizes ranging from 500 to 1500 bases. Their main advantages as a presequencing screening technology when scanning for unknown mutations is the potential to increase throughput by multiplexing. Combined with lower reagent costs per sample, mutation scanning methods offer significant advantages over currently available sequencing techniques and are likely to be of increasing importance as genomic sequence data becomes more readily available. Although enzymatic methods offer the advantages of simpler and less hazardous protocols, at present the most robust cleavage methods are based around chemical methods.

Mutation detection using fluorescent enzyme mismatch cleavage with T4 endonuclease VII

Mutation detection techniques are often limited by sensitivity, ease of use and short fragment lengths. Enzyme mismatch cleavage (EMC) is a technique capable of rapidly scanning 1 kbp fragments of DNA for mutations. It relies on the ability of a bacteriophage resolvase enzyme, T4 endonuclease VII, to cleave DNA at single base pair mismatches and small heteroduplex loops. Originally the process was performed using radioactively labeled DNA and the results analysed after denaturing polyacrylamide gel electrophoresis and autoradiography. However, access to systems capable of detecting fluorescent species migrating through a gel and the widespread availability of fluorescently tagged primers have greatly improved upon the original technique. A number of mutations were detected using fluorescent EMC and the results compared to performing the technique using radiolabeled DNA. Fluorescent EMC detected the presence, position and number of mutations in DNA fragments as large as 1 kbp. The fluorescent method was found to have advantages over the original method in its ease of use, increase in signal-to-noise ratio and the ability to multiplex samples by labeling DNA fragments with different fluorophores. This improvement on an already established method provides a sensitive, robust technique for mutation detection.

Automated mutation analysis

Automated mutation analysis brings with it a vastly increased capacity in the number of test samples that can be processed at a time, as well as much improved test reproducibility. Until now, the introduction of automation into this field had been restricted to the use of semiautomated sequencing systems to make the most of the sequence information extractable from a single lane in an electrophoretic gel or in a polymer-filled glass capillary. Much effort is now being directed into harnessing the potential of DNA microarrays (DNA chips) and there is increasing interest in the potential of matrix-assisted mass spectrometry for determining the detail of large nucleic acid molecules. Meanwhile, there are other important recent developments already available, including robotic workstations, the further development of the allele-specific oligonucleotide assay into microtitre formats, and its use with fluorescence for real-time quantitative PCR analysis. Implementation of these developments in appropriate settings can further streamline the routine of molecular diagnostic laboratories, allowing them to take greater advantage of the recent surge of gene discoveries and their associated disease-causing mutations.

Enzymatic methods for mutation scanning

Enzymatic methods for mutation scanning still lack the sensitivity and specificity of the chemical cleavage of mismatch method. However developments in our understanding of the mismatch recognition process should lead to improvements. Several promising candidates exist with potential for more specific and sensitive mutation detection.

Chemical mismatch cleavage combined with capillary electrophoresis: detection of mutations in exon 8 of the cystathionine β-synthase gene

Mutation detection by chemical mismatch cleavage (CMC) is based on the chemical modification and cleavage at the site of mismatched C or T in heteroduplexes, using hydroxylamine or osmium tetroxide (OsO4) as chemical probes. In the present study, we evaluated CMC in combination with capillary electrophoresis (CE) by determining the common T833C and G919A mutations in exon 8 of the cystathionine β-synthase gene in heterozygous and homozygous samples. A 186-bp fragment encompassing exon 8 was amplified by PCR with both primers labeled with 5′-fluorescein. Labeled single strands of 40 and 61 nucleotides (nt) were formed from the coding strand of the T833C sample and non-coding strand from the G919A sample, respectively. These single-stranded DNA (ssDNA) products were analyzed under denaturing conditions by CE with short-chain linear polyacrylamide as the sieving matrix and were detected by laser-induced fluorescence (LIF), using a sensitive, one-channel sheath-flow detector. The CE-LIF format afforded relatively high resolution of ssDNA (down to 1 nt), precise size assessment of CMC products, sensitive detection with small sample requirements, and fast analysis. Thus, CMC combined with CE-LIF is suitable for screening of known mutations, giving expected CMC products, but will also detect unknown mutations, the locations of which are indicated by the fragment sizes.

Role of MutS ATPase activity in MutS,L-dependent block of in vitro strand transfer

In addition to mismatch recognition, Escherichia coli MutS has an associated ATPase activity that is fundamental to repair. Hence, we have characterized two MutS mutant gene products to define the role of ATP hydrolysis in homeologous recombination. These mutants, denoted MutS501 and MutS506, have single point mutations within the Walker A motif, and rate constants for ATP hydrolysis are down 60-100-fold as compared with wild type. Both MutS501 and MutS506 retain mismatch binding and, unlike wild type, fail to relinquish this specificity in the presence of ATP, adenosine 5'-O-(thiotriphosphate), and adenosine 5'-(beta, gamma-imino)triphosphate. Both MutS501 and MutS506 blocked the level of strand transfer between M13 and fd DNAs. The level of inhibition varied between the mutants and corresponded with the relative affinities to a G/T mispair. Neither MutS501 nor MutS506, however, would afford complete block of full-length heteroduplex in the presence of MutL. DNase I footprinting data are consistent with these results, as the region of protection by MutS501 and MutS506 was unchanged in the presence of ATP and MutL. Taken together, these studies suggest that 1) MutS impedes RecA-mediated homeologous exchange as a distinct mismatch-provoked event and 2) the role of MutL is coupled to MutS-dependent ATP hydrolysis. These observations are in good agreement with the present model for E. coli methyl-directed mismatch repair.

Rapid detection of genetic mutations using the chemiluminescent hybridization protection assay (HPA): overview and comparison with other methods

The detection of genetic mutations is of paramount importance for the study, diagnosis, and treatment of human genetic disease. Methods of detection generally fall into one of two categories: those to scan for unknown mutations and those to detect known mutations. This review focuses on methods for the detection of known mutations. The hybridization protection assay (HPA) is described in detail. The HPA method utilizes short oligonucleotide probes covalently labeled with a highly chemiluminescent acridinium ester (AE). The assay format is completely homogeneous, requiring no physical separation steps, and can rapidly and sensitively detect all single-base mismatches as well as multiple mismatches, insertions, deletions, and genetic translocations. When very low copy number targets are assayed, HPA is coupled with transcription-mediated amplification (TMA), an isothermal method that amplifies DNA or RNA targets. Other methods that are described for the detection of known mutations include hybridization with sequence-specific oligonucleotides, hybridization to oligonucleotide arrays, allele-specific amplification, ligase-mediated detection, primer extension, and restriction fragment analysis. The advantages and limitations of each of these methods are discussed. Methods to scan for unknown mutations are briefly described.

Linkage-disequilibrium mapping without genotyping

Genomic mismatch scanning (GMS) is a technique that enriches for regions of identity by descent (IBD) between two individuals without the need for genotyping or sequencing. Regions of IBD selected by GMS are mapped by hybridization to a microarray containing ordered clones of genomic DNA from chromosomes of interest. Here we demonstrate the feasibility and efficacy of this form of linkage-mapping, using congenital hyperinsulinism (HI), an autosomal recessive disease, whose relatively high frequency in Ashkenazi Jews suggests a founder effect. The gene responsible (SUR1) encodes the sulfonylurea receptor, which maps to chromosome 11p15.1. We show that the combination of GMS and hybridization of IBD products to a chromosome-11 microarray correctly maps the HI gene to a 2-Mb region, thereby demonstrating linkage-disequilibrium mapping without genotyping.

The polymerase chain reaction: from functional genomics to high-school practical classes

After a decade of intensive use as an in vitro alternative to cloning DNA, PCR is now well established as the default method for DNA and RNA analysis. Recent developments have consolidated this position by the introduction of more robust formats, improvements in thermal cyclers and labelling and detection methods. The trend is towards increasing automation, although comparatively few diagnostic kits based on PCR are in wide use. At the same time the applications of PCR are being extended with modifications such as long, accurate PCR and arrayed oligonucleotides or expressed sequences.

Genomic mismatch scanning identifies human genomic DNA shared identical by descent

Genomic mismatch scanning (GMS) is a high-throughput, high-resolution identity by descent mapping technique that enriches for genomic DNA fragments that are shared between related individuals. In GMS, DNA heteroduplexes are formed from restriction-digested genomic DNA fragments from two relatives. Mismatch-free DNA heteroduplexes, likely representing DNA shared identical by descent between the two individuals, are relatively purified by depleting the mismatch-containing heteroduplexes using the Escherichia coli mismatch repair proteins and exonuclease. Here, we demonstrate using quantitative microsatellite genotyping that, despite the complexity of the human genome, GMS can enrich the majority of restriction fragments that are identical by descent between two related humans. As the entire genome is selected in GMS, an extraordinarily dense set of markers (up to 200,000 markers) may be screened in parallel. The demonstration of the molecular enrichment of identical DNA fragments in the context of the whole human genome establishes conditions for the application of GMS to human genetics. This forms a frame-work for the further development of GMS as a hybridization-based mapping technique that utilizes DNA microarray technology to map the selected identical by descent DNA fragments.

DNA variation and the future of human genetics

The use of DNA variants in the mapping of the human genome and in the positional cloning of monogenic disease genes is well established. Determining the genetic bases of the more common "multifactorial" diseases, however, presents a major challenge. The genetics of these diseases are complicated by the interplay between many genes and the environment. These investigations will require large numbers of DNA markers and the technology to screen large populations with these markers. The systematic identification of the common DNA polymorphisms in the human genome coupled with the development of high throughput screening methods should allow ultimately the elucidation of the genetic component of most clinical and nonclinical phenotypes.

Will genetics really revolutionize the drug discovery process?

Genetics has played only a modest role in drug discovery, but new technologies will radically change this. Whole genome sequencing will identify new drug discovery targets, and emerging methods for the determination of gene function will increase the ability to select robust targets. Detection of single nucleotide polymorphisms and common polymorphisms will enhance the investigation of polygenic diseases and the use of genetics in drug development. Oligonucleotide arraying technologies will allow analysis of gene expression patterns in novel ways.

Genotypic selection methods for the direct analysis of point mutations

Genotypic selection enriches a particular DNA sequence relative to another closely-related DNA sequence based only on a change of one or a few bases. This review is a survey of the genotypic selection methods that have the sensitivity to detect rare point mutations. These methods are primarily being used to study mutations caused by environmental mutagens; however, the ability to detect and measure very minor DNA sequence populations is likely to further research efforts in many fields. The approaches for allele-selection have intrinsic strengths and weaknesses, and vary greatly in sensitivity. The most sensitive method is Restriction Fragment Length Polymorphism/Polymerase Chain Reaction (RFLP/PCR) by which mutant fractions as low as 1 mutant allele in 10(8) wild-type alleles can be detected. The RFLP/PCR approach is presented as a prototype genotypic selection method. Genotypic selection methods are categorized in terms of those that (1) selectively destroy the abundant or wild-type allele, (2) selectively amplify the rare or mutant allele, or (3) spatially separate the alleles. Issues relevant to the further development of genotypic selection methods include initial DNA pool size, strategies to eliminate the bulk of extraneous DNA, the use of an internal copy number standard in quantitative PCR, the fidelity of thermostable DNA polymerases, and the effective use of PCR in linking two or more genotypic selection techniques. We conclude that proficient genotypic selection requires more than one allele-enrichment technique with at least one of these preceding a high-fidelity PCR amplification step.

Search for DNA sequence variations using a MutS-based technology

The search for DNA sequence variations (DSV) is emphasized with genetic studies of a large number of multifactorial diseases. Saturation of regions of interest with diallelic polymorphisms will be an essential step to pinpoint, through association studies, predisposing genes. We have developed a solid-phase method based on the ability of mismatch binding protein MutS to recognize single nucleotide mismatches. This approach was applied to the study of 83 sequence-tagged sites (STSs) extracted from an eight centimorgans (cM) chromosome 21 region. One-third of tested STSs were found to be polymorphic leading to a frequency of one DSV every 822 base pairs (bp). Sequencing of analyzed STSs showed the high reliability of the MutS-based technology for mismatches up to 2 bp in DNA fragments ranging in size from 200 bp to 1 kilobase (kb). The entire assay which is performed in a solid-phase format without the need of electrophoresis or sequencing, will provide an efficient tool for new polymorphism detection.

Removal of polymerase-produced mutant sequences from PCR products

Heteroduplex DNA lacking d(GATC) methylation is subject to mismatch-provoked double-strand cleavage at d(GATC) sites in a reaction dependent on MutH, MutL, MutS, and ATP. We have exploited this reaction to develop a method for removal of polymerase-produced mutant sequences that arise during sequence amplification by PCR. After denaturation and reannealing, the PCR product pool is subjected to MutH, MutL, and MutS mismatch repair proteins under double-strand cleavage conditions, followed by isolation of uncleaved product by size selection. Use of an Escherichia coli lac forward mutation assay has shown that this procedure reduces the incidence of polymerase-induced mutant sequences by an order of magnitude. Twenty mutants that originated from three independent PCR amplification reactions and survived MutHLS treatment all were found to contain an infrequently occurring A.T --> T.A transversion mutation at a unique position within the product. By contrast, the majority of mutations in untreated PCR products were transitions occurring throughout the amplified region, although frameshifts and transversions also were observed. The MutHLS method thus can be used to effectively remove the majority of mutant sequences produced by polymerase errors during PCR amplification.

Analysis of the mismatch and insertion/deletion binding properties of Thermus thermophilus, HB8, MutS

The methyl-directed long patch repair pathway in Escherichia coli is involved in increasing the fidelity of replication specific repair of DNA polymerase incorporation errors. This pathway is mediated by three gene products, MutS, MutL, and MutH, which are conserved in higher eukaryotes. Mutations in human homologues of these proteins have been shown to be implicated in hereditary non-polyposis colorectal cancer (HNPCC). A MutS homologue has recently been identified in the extremely thermophilic bacterium, Thermus thermophilus. Here we describe analysis of the binding properties of this protein, which has indicated it can identify all specific base mismatches as well as one, two and three base pair insertion/deletion mutations. We therefore believe this protein may be generally useful for applications involving mismatch detection.