scholarly journals Restriction enzymes use a 24 dimensional coding space to recognize 6 base long DNA sequences

2019 ◽  
Author(s):  
Thomas D. Schneider ◽  
Vishnu Jejjala
Keyword(s):  
Information Theory ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Sphere Packing ◽  
Restriction Enzymes ◽  
High Dimensional ◽  
Leech Lattice ◽  
Communications Systems ◽  
Single Protein ◽  
Specific Sequences

AbstractRestriction enzymes recognize and bind to specific sequences on invading bacteriophage DNA. Like a key in a lock, these proteins require many contacts to specify the correct DNA sequence. Using information theory we develop an equation that defines the number of independent contacts, which is the dimensionality of the binding. We show that EcoRI, which binds to the sequence GAATTC, functions in 24 dimensions. Information theory represents messages as spheres in high dimensional spaces. Better sphere packing leads to better communications systems. The densest known packing of hyperspheres occurs on the Leech lattice in 24 dimensions. We suggest that the single protein EcoRI molecule employs a Leech lattice in its operation. Optimizing density of sphere packing explains why 6 base restriction enzymes are so common.

Rapid genomic changes in newly synthesized amphiploids ofTriticumandAegilops. II. Changes in low-copy coding DNA sequences

Genome ◽  
1998 ◽  
Vol 41 (4) ◽  
pp. 535-542 ◽  
Author(s):  
B Liu ◽  
J M Vega ◽  
M Feldman
Keyword(s):  
Dna Methylation ◽  
Dna Sequences ◽  
Gene Dosage ◽  
Restriction Enzymes ◽  
Noncoding Dna ◽  
Ploidy Levels ◽  
Coding Sequences ◽  
Genomic Changes ◽  
Cdna Sequences ◽  
Specific Sequences

We recently reported that formation of allopolyploid wheat was accompanied by rapid nonrandom changes in low-copy noncoding DNA sequences. In this report we show that following allopolyploidization, changes also occurred in coding sequences. Genomic DNA of nine different newly synthesized amphiploids of different ploidy levels and their parental lines was digested with five restriction enzymes and probed with 43 coding sequences. The sequences, 19 genomic and 24 cDNA sequences, are group (homoeologous) specific and represent the proximal and distal regions of the short and long arms of the seven homoeologous groups of the Triticeae. We revealed three types of changes: disappearance of a parental hybridization fragment(s), appearance of a novel fragment(s), and simultaneous disappearance of a parental fragment(s) and appearance of a novel fragment(s). No elimination of sequences took place, since in every sequence studied the parental hybridization fragments were present in at least one of the enzyme digests. Variations in pattern among individual plants of the same amphiploid, as well as between several synthetic and natural amphiploids, indicated that at least some of the genomic changes occurred at random. Intergenomic recombination was not the cause of the observed changes. Evidence was obtained, however, that changes were also brought about by DNA methylation. Methylation may cause inactivation of genes or modify their expression levels in some of the newly synthesized amphiploid plants, leading to genetic diploidization and gene-dosage compensation and thus increasing variation among individuals.Key words: wheat, allopolyploidy, DNA methylation, genetic diploidization, genome evolution, group (homoeologous) specific sequences.

scholarly journals Information Theory and Multivariate Techniques for Analyzing DNA Sequence Data: An Example from Tomato Genes

1970 ◽  
Vol 1 (1) ◽  
pp. 1-8 ◽  
Author(s):  
Bal K Joshi ◽  
Dilip R Panthee
Keyword(s):  
Information Theory ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Sequence Data ◽  
Crop Improvement ◽  
Principal Component ◽  
Amino Acid Sequences ◽  
Multivariate Techniques ◽  
Sequence Complexity ◽  
Diversity Assessment

DNA and amino acid sequences are alphabetic symbols having no underlying metric. Use of information theory is one of the solutions for sequence metric problems. The reflection of DNA sequence complexity in phenotype stability might be useful for crop improvement. Shannon-Weaver index (Shannon Entropy, H') and mutual information (MI) index were estimated from DNA sequences of 22 genes, consisted of two gene families of tomato, namely disease resistance and fruit quality. Main objective was use of information theory and multivariate techniques to understand diversity among genes and relate the sequence complexity with phenotypes. The normalized H' value ranged from 0.429 to 0.461. The highest diversity was observed in the gene Crtr-B (beta carotene hydroxylase). Two principal components which accounted for 36.65% variation placed these genes into four groups. Groupings of these genes by both principal component and cluster analyses showed clearly the similarity at phenotypes levels within cluster. Sequences similarity among genes was observed within a family. Diversity assessment of genes applying information theory should link to understand the sequences complexity with respect to gene stability for example stability of resistance gene.Key words: Diversity analysis; DNA sequences; principal component analysis; tomato genesNepal Journal of Biotechnology, 2011, Vol. 1, No. 1 pp.1-9

DNA sequence mapping in interphase and metaphase chromosomes by fluorescence in situ hybridization

1992 ◽  
Vol 50 (1) ◽  
pp. 496-497
Author(s):  
Barbara Trask ◽  
Susan Allen ◽  
Anne Bergmann ◽  
Mari Christensen ◽  
Anne Fertitta ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Dual Band ◽  
Nick Translation ◽  
Metaphase Chromosomes ◽  
Band Pass ◽  
Texas Red ◽  
Fluorescent Spot

Using fluorescence in situ hybridization (FISH), the positions of DNA sequences can be discretely marked with a fluorescent spot. The efficiency of marking DNA sequences of the size cloned in cosmids is 90-95%, and the fluorescent spots produced after FISH are ≈0.3 μm in diameter. Sites of two sequences can be distinguished using two-color FISH. Different reporter molecules, such as biotin or digoxigenin, are incorporated into DNA sequence probes by nick translation. These reporter molecules are labeled after hybridization with different fluorochromes, e.g., FITC and Texas Red. The development of dual band pass filters (Chromatechnology) allows these fluorochromes to be photographed simultaneously without registration shift.

scholarly journals DNA thermodynamics shape chromosome organization and topology

2013 ◽  
Vol 41 (2) ◽  
pp. 548-553 ◽  
Author(s):  
Andrew A. Travers ◽  
Georgi Muskhelishvili
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
Chromosome Organization ◽  
Topological Properties ◽  
Genetic Organization ◽  
And Topology ◽  
Dna Translocases

How much information is encoded in the DNA sequence of an organism? We argue that the informational, mechanical and topological properties of DNA are interdependent and act together to specify the primary characteristics of genetic organization and chromatin structures. Superhelicity generated in vivo, in part by the action of DNA translocases, can be transmitted to topologically sensitive regions encoded by less stable DNA sequences.

scholarly journals An application of slow feature analysis to the genetic sequences of coronaviruses and influenza viruses

2021 ◽  
Vol 15 (1) ◽  
Author(s):  
Anastasios A. Tsonis ◽  
Geli Wang ◽  
Lvyi Zhang ◽  
Wenxu Lu ◽  
Aristotle Kayafas ◽  
...  
Keyword(s):  
Mathematical Method ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Transmission Rate ◽  
Complex Structure ◽  
Mortality Rates ◽  
Influenza Viruses ◽  
Feature Analysis ◽  
Slow Feature Analysis ◽  
Genetic Sequences

Abstract Background Mathematical approaches have been for decades used to probe the structure of DNA sequences. This has led to the development of Bioinformatics. In this exploratory work, a novel mathematical method is applied to probe the DNA structure of two related viral families: those of coronaviruses and those of influenza viruses. The coronaviruses are SARS-CoV-2, SARS-CoV-1, and MERS. The influenza viruses include H1N1-1918, H1N1-2009, H2N2-1957, and H3N2-1968. Methods The mathematical method used is the slow feature analysis (SFA), a rather new but promising method to delineate complex structure in DNA sequences. Results The analysis indicates that the DNA sequences exhibit an elaborate and convoluted structure akin to complex networks. We define a measure of complexity and show that each DNA sequence exhibits a certain degree of complexity within itself, while at the same time there exists complex inter-relationships between the sequences within a family and between the two families. From these relationships, we find evidence, especially for the coronavirus family, that increasing complexity in a sequence is associated with higher transmission rate but with lower mortality. Conclusions The complexity measure defined here may hold a promise and could become a useful tool in the prediction of transmission and mortality rates in future new viral strains.

Species-diagnostic and species-specific DNA sequences evenly distributed throughout pine and spruce chromosomes

Genome ◽  
2010 ◽  
Vol 53 (10) ◽  
pp. 769-777 ◽  
Author(s):  
Melanie Mehes-Smith ◽  
Paul Michael ◽  
Kabwe Nkongolo
Keyword(s):  
Dna Sequences ◽  
Random Amplified Polymorphic Dna ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Pinus Monticola ◽  
The Family ◽  
Species Specific ◽  
Rapd And Issr ◽  
Specific Sequences

Genome organization in the family Pinaceae is complex and largely unknown. The main purpose of the present study was to develop and physically map species-diagnostic and species-specific molecular markers in pine and spruce. Five RAPD (random amplified polymorphic DNA) and one ISSR (inter-simple sequence repeat) species-diagnostic or species-specific markers for Picea mariana , Picea rubens , Pinus strobus , or Pinus monticola were identified, cloned, and sequenced. In situ hybridization of these sequences to spruce and pine chromosomes showed the sequences to be present in high copy number and evenly distributed throughout the genome. The analysis of centromeric and telomeric regions revealed the absence of significant clustering of species-diagnostic and species-specific sequences in all the chromosomes of the four species studied. Both RAPD and ISSR markers showed similar patterns.

scholarly journals Information Theory for Data Communications and Processing

Entropy ◽  
2020 ◽  
Vol 22 (11) ◽  
pp. 1250
Author(s):  
Shlomo Shamai (Shitz) ◽  
Abdellatif Zaidi
Keyword(s):  
Information Theory ◽  
Data Communications ◽  
Special Issue ◽  
Communications Systems

This book, composed of the collection of papers that have appeared in the Special Issue of theEntropy journal dedicated to “Information Theory for Data Communications and Processing”,reflects, in its eleven chapters, novel contributions based on the firm basic grounds of informationtheory. The book chapters [1–11] address timely theoretical and practical aspects that carry bothinteresting and relevant theoretical contributions, as well as direct implications for modern currentand future communications systems. [...]

scholarly journals Structural defects of a Pax8 mutant that give rise to congenital hypothyroidism

1999 ◽  
Vol 341 (1) ◽  
pp. 89-93 ◽  
Author(s):  
Gianluca TELL ◽  
Lucia PELLIZZARI ◽  
Gennaro ESPOSITO ◽  
Carlo PUCILLO ◽  
Paolo Emidio MACCHIA ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Congenital Hypothyroidism ◽  
Dna Sequences ◽  
Dna Interaction ◽  
Structural Defects ◽  
Molecular Defect ◽  
Wild Type ◽  
Coding Region ◽  
Induced Fit ◽  
Helical Content

Pax proteins are transcriptional regulators that play important roles during embryogenesis. These proteins recognize specific DNA sequences via a conserved element: the paired domain (Prd domain). The low level of organized secondary structure, in the free state, is a general feature of Prd domains; however, these proteins undergo a dramatic gain in α-helical content upon interaction with DNA (‘induced fit’). Pax8 is expressed in the developing thyroid, kidney and several areas of the central nervous system. In humans, mutations of the Pax8 gene, which are mapped to the coding region of the Prd domain, give rise to congenital hypothyroidism. Here, we have investigated the molecular defects caused by a mutation in which leucine at position 62 is substituted for an arginine. Leu62 is conserved among Prd domains, and contributes towards the packing together of helices 1 and 3. The binding affinity of the Leu62Arg mutant for a specific DNA sequence (the C sequence of thyroglobulin promoter) is decreased 60-fold with respect to the wild-type Pax8 Prd domain. However, the affinities with which the wild-type and the mutant proteins bind to a non-specific DNA sequence are very similar. CD spectra demonstrate that, in the absence of DNA, both wild-type Pax8 and the Leu62Arg mutant possess a low α-helical content; however, in the Leu62Arg mutant, the gain in α-helical content upon interaction with DNA is greatly reduced with respect to the wild-type protein. Thus the molecular defect of the Leu62Arg mutant causes a reduced capability for induced fit upon DNA interaction.

Similar 150-kilobase DNA sequences are amplified in independently derived methotrexate-resistant Chinese hamster cells

1985 ◽  
Vol 5 (4) ◽  
pp. 619-627
Author(s):  
M Montoya-Zavala ◽  
J L Hamlin
Keyword(s):  
Dna Sequence ◽  
Cell Lines ◽  
Dihydrofolate Reductase ◽  
Dna Sequences ◽  
Consensus Sequence ◽  
Chinese Hamster ◽  
Ovary Cell ◽  
Chinese Hamster Cells ◽  
Reductase Gene ◽  
Reductase Domain

We have isolated overlapping recombinant cosmids that represent 150 kilobases of contiguous DNA sequence from the amplified dihydrofolate reductase domain of a methotrexate-resistant Chinese hamster ovary cell line (CHOC 400). This sequence includes the 25-kilobase dihydrofolate reductase gene and an origin of DNA synthesis. Eight cosmids that span this domain have been utilized as radioactive hybridization probes to analyze the similarities among the dihydrofolate reductase amplicons in four independently derived methotrexate-resistant Chinese hamster cell lines. We have observed no significant differences among the four cell lines within the 150-kilobase DNA sequence that we have examined, except for polymorphisms that result from the amplification of one or the other of two possible alleles of the dihydrofolate reductase domain. We also show that the restriction patterns of the amplicons in these four resistant cell lines are virtually identical to that of the corresponding, unamplified sequence in drug-susceptible parental cells. Furthermore, measurements of the relative copy numbers of fragments from widely separated regions of the amplicon suggest that all fragments in this 150-kilobase region may be amplified in unison. Our data show that in methotrexate-resistant Chinese hamster cells, the amplified unit is large relative to the dihydrofolate reductase gene itself. Furthermore, within the 150-kilobase amplified consensus sequence that we have examined, significant rearrangements do not seem to occur during the amplification process.

Sign in / Sign up

Export Citation Format

Share Document