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Proceedings of the National Academy of... Jul 2005We have performed restriction mapping of DNA molecules using restriction endonucleases in nanochannels with diameters of 100-200 nm. The location of the restriction...
We have performed restriction mapping of DNA molecules using restriction endonucleases in nanochannels with diameters of 100-200 nm. The location of the restriction reaction within the device is controlled by electrophoresis and diffusion of Mg2+ and EDTA. We have successfully used the restriction enzymes SmaI, SacI, and PacI, and have been able to measure the positions of restriction sites with a precision of approximately 1.5 kbp in 1 min using single DNA molecules.
Topics: DNA; DNA Restriction Enzymes; Magnesium; Microscopy; Nanostructures; Nanotechnology; Restriction Mapping
PubMed: 16000405
DOI: 10.1073/pnas.0503809102 -
Biochemistry and Molecular Biology... 2011
Topics: Adenosine Triphosphate; DNA; DNA Cleavage; Deoxyribonuclease EcoRI; Electrophoresis, Polyacrylamide Gel; Nucleotides; Phosphates; Phosphorylation; Polynucleotide 5'-Hydroxyl-Kinase; Problem-Based Learning; Restriction Mapping; Sequence Analysis, DNA
PubMed: 21948513
DOI: 10.1002/bmb.20547 -
Restriction mapping of genes by capillary electrophoresis with laser-induced fluorescence detection.Analytical Chemistry Apr 1997Restriction mapping is one of the essential steps in gene analysis and molecular biology studies. Slab gel electrophoresis is the traditional way to separate DNA...
Restriction mapping is one of the essential steps in gene analysis and molecular biology studies. Slab gel electrophoresis is the traditional way to separate DNA fragments for restriction mapping. However, slab gel electrophoresis does not provide sufficient resolution as required in many mapping applications, and the use of radioisotopes in traditional mapping methods creates health hazards. In the present study, capillary electrophoresis coupled with laser-induced fluorescence detection and a modified partial digestion mapping procedure was developed to map DNA fragments. By using capillary electrophoresis, a restriction map of genomic lambda phage clone of human interleukin 5 receptor alpha chain (IL5R alpha) gene was constructed. The IL5R alpha gene was analyzed to have five XbaI enzyme cutting sites at locations 1370, 2290, 2950, 5430, and 9330. The system was further characterized by using pBluescript SK(+) phagemid DNA as a model. Using a sequence-derived map as a reference, the pBluescript SK(+) restriction map constructed by capillary electrophoresis had an accuracy greater than 90%.
Topics: DNA; Electrophoresis, Capillary; Humans; Lasers; Receptors, Interleukin; Receptors, Interleukin-5; Restriction Mapping; Spectrometry, Fluorescence
PubMed: 9105179
DOI: 10.1021/ac9609586 -
Anticancer Research 2008Many different single nucleotide polymorphisms (SNPs) genotyping methods have been developed recently. However, most of them are expensive. Using restriction enzymes for... (Review)
Review
Many different single nucleotide polymorphisms (SNPs) genotyping methods have been developed recently. However, most of them are expensive. Using restriction enzymes for SNP genotyping is a cost-effective method. However, restriction enzyme mining for SNPs in a genome sequence is still challenging for researchers who do not have a background in genomics and bioinformatics. In this review, the basic bioinformatics tools used for restriction enzyme mining for SNP genotyping are summarized and described. The objectives of this paper include: i) the introduction of SNPs, genotyping and PCR-restriction fragment length polymorphism (RFLP); ii) a review of components for genotyping software, including tools for primer design only or restriction enzyme mining only; iii) a review of software providing the flanking sequence for primer design; iv) recent advances in PCR-RFLP tools and natural and mutagenic PCR-RFLP; v) highlighting the strategy for restriction enzyme mining for SNP genotyping; vi) a discussion of potential problems for multiple PCR-RFLP. The different implications for restriction enzymes on sense and antisense strands are also discussed. Our PCR-RFLP freeware, SNP-RFLPing, is included in this review to illustrate many characteristics of PCR-RFLP software design. Future developments will include further sophistication of PCR-RFLP software in order to provide better visualization and a more interactive environment for SNP genotyping and to integrate the software with other tools used in association studies.
Topics: Animals; DNA Restriction Enzymes; Genome; Genotype; Humans; Polymerase Chain Reaction; Polymorphism, Restriction Fragment Length; Polymorphism, Single Nucleotide; Restriction Mapping
PubMed: 18649739
DOI: No ID Found -
Computer Applications in the... Jul 1990Restriction site mapping requires a generator to put forward possible maps and a constraint checker to reject false maps. Ideally these combine to give an algorithm...
Restriction site mapping requires a generator to put forward possible maps and a constraint checker to reject false maps. Ideally these combine to give an algorithm which calculates a sound and complete solution set. Three algorithms for generation are presented and compared. Two decompose a multi-enzyme problem (greater than or equal to 3) into subproblems. The constraint checker is based on separation theory. Some insights into the extent of constraint checking involved in and feasibility of more checking for three or more enzymes are discussed. The trade-off between computation time and the soundness of the solution set is examined.
Topics: Algorithms; DNA Restriction Enzymes; Mathematical Computing; Methods; Restriction Mapping
PubMed: 2169968
DOI: 10.1093/bioinformatics/6.3.195 -
GigaScience 2015Optical mapping is a technology that gathers long-range information on genome sequences similar to ordered restriction digest maps. Because it is not subject to cloning,... (Review)
Review
Optical mapping is a technology that gathers long-range information on genome sequences similar to ordered restriction digest maps. Because it is not subject to cloning, amplification, hybridisation or sequencing bias, it is ideally suited to the improvement of fragmented genome assemblies that can no longer be improved by classical methods. In addition, its low cost and rapid turnaround make it equally useful during the scaffolding process of de novo assembly from high throughput sequencing reads. We describe how optical mapping has been used in practice to produce high quality vertebrate genome assemblies. In particular, we detail the efforts undertaken by the Genome Reference Consortium (GRC), which maintains the reference genomes for human, mouse, zebrafish and chicken, and uses different optical mapping platforms for genome curation.
Topics: Animals; Genome; Genomics; Restriction Mapping; Sequence Analysis; Vertebrates
PubMed: 25789164
DOI: 10.1186/s13742-015-0052-y -
Methods in Molecular Biology (Clifton,... 2022Optical mapping plays an important role in plant genomics, particularly in plant genome assembly and large-scale structural variation detection. While DNA sequencing...
Optical mapping plays an important role in plant genomics, particularly in plant genome assembly and large-scale structural variation detection. While DNA sequencing provides base-by-base nucleotide information, optical mapping shows the physical locations of selected enzyme restriction sites in a genome. The long single-molecule maps produced by optical mapping make it a useful auxiliary technique to DNA sequencing, which generally cannot span large and complex genomic regions. Although optical mapping, therefore, offers unique advantages to researchers, there are few dedicated tools to assist in optical mapping analyses. In this chapter, we present runBNG2, a successor of runBNG to help optical-mapping data analysis for diverse datasets.
Topics: Genome, Plant; Genomics; Plants; Restriction Mapping; Sequence Analysis, DNA
PubMed: 35037210
DOI: 10.1007/978-1-0716-2067-0_13 -
BioTechniques May 1994A protocol for the non-isotopic restriction mapping of cosmid DNA was developed. After digestion with lambda terminase and partial digestion with restriction enzymes,...
A protocol for the non-isotopic restriction mapping of cosmid DNA was developed. After digestion with lambda terminase and partial digestion with restriction enzymes, DNA fragments containing right or left cohesive cos termini were selectively captured by hybridization with biotinylated oligonucleotides, bound to magnetic beads coated with streptavidin and recovered by heating. Recovered DNA fragments containing cos ends were resolved by agarose gel electrophoresis, and fluorescence from the DNA fragments in the ethidium bromide-stained gel was detected with the fluorescent image analyzer, FMBIO. Restriction maps were directly determined from the ladder of the partial digestion products. Two micrograms of cosmid DNA for each partial digestion were sufficient for mapping the restriction enzyme sites. This procedure provides a prototype for other cos sequence-mediated or other specific sequence-mediated DNA isolation technologies and a convenient method for non-isotopic DNA analysis. The rapid physical analysis of cosmid DNA that we present here will contribute to large DNA structural analyses like the human genome project.
Topics: Base Sequence; Cosmids; DNA; Molecular Sequence Data; Restriction Mapping
PubMed: 8068347
DOI: No ID Found -
BioTechniques Mar 2000
Topics: DNA; Genetic Vectors; Plasmids; Restriction Mapping; Retroviridae
PubMed: 10723571
DOI: 10.2144/00283cr01 -
Genetics Jul 2017Assembly of complex genomes using short reads remains a major challenge, which usually yields highly fragmented assemblies. Generation of ultradense linkage maps is...
Assembly of complex genomes using short reads remains a major challenge, which usually yields highly fragmented assemblies. Generation of ultradense linkage maps is promising for anchoring such assemblies, but traditional linkage mapping methods are hindered by the infrequency and unevenness of meiotic recombination that limit attainable map resolution. Here we develop a sequencing-based "" linkage mapping approach (called RadMap), where chromosome breakage and segregation are realized by generating hundreds of "subhaploid" fosmid/bacterial-artificial-chromosome clone pools, and by restriction site-associated DNA sequencing of these clone pools to produce an ultradense whole-genome restriction map to facilitate genome scaffolding. A bootstrap-based minimum spanning tree algorithm is developed for grouping and ordering of genome-wide markers and is implemented in a user-friendly, integrated software package (AMMO). We perform extensive analyses to validate the power and accuracy of our approach in the model plant and human. We also demonstrate the utility of RadMap for enhancing the contiguity of a variety of whole-genome shotgun assemblies generated using either short Illumina reads (300 bp) or long PacBio reads (6-14 kb), with up to 15-fold improvement of N50 (∼816 kb-3.7 Mb) and high scaffolding accuracy (98.1-98.5%). RadMap outperforms BioNano and Hi-C when input assembly is highly fragmented (contig N50 = 54 kb). RadMap can capture wide-range contiguity information and provide an efficient and flexible tool for high-resolution physical mapping and scaffolding of highly fragmented assemblies.
Topics: Arabidopsis; Genetic Linkage; Genome, Plant; Restriction Mapping; Software
PubMed: 28468906
DOI: 10.1534/genetics.117.200303