Nucleic Acid Heteroduplexes
Heteroduplex Analysis
Peptide Nucleic Acids
Nucleic Acid Denaturation
Base Sequence
Nucleic Acid Hybridization
Nucleic Acid Conformation
Base Pair Mismatch
MutS DNA Mismatch-Binding Protein
DNA
Nucleic Acid Renaturation
Oligonucleotides
DNA Repair
Nucleic Acid Probes
Polymerase Chain Reaction
Molecular Sequence Data
RNA
Escherichia coli
Nucleic Acid Amplification Techniques
DNA Restriction Enzymes
Carbodiimides
Ribonuclease H
Mutation
Recombination, Genetic
DNA, Single-Stranded
Electrophoresis, Capillary
Methylation
Endodeoxyribonucleases
Osteogenesis Imperfecta
Bacteriophage lambda
Cloning, Molecular
Oligodeoxyribonucleotides
Crossing Over, Genetic
Microscopy, Electron
DNA Repair Enzymes
Plasmids
Gene Conversion
Genes
Artifacts
Deletion mutation analysis of the mutS gene in Escherichia coli. (1/975)
The MutS protein is part of the dam-directed MutHLS mismatch repair pathway in Escherichia coli. We have constructed deletion derivatives in the mutS gene, which retain the P-loop coding region for ATP binding. The mutant proteins were assayed for ATP hydrolysis, heteroduplex DNA binding, heterodimer MutS formation, and the ability to interact with MutL. Dimerization was assayed by expressing His6-tagged wild-type and non-tagged deletion mutant proteins in the same cell and isolating the His6-tagged protein followed by MutS immunoblotting after SDS-polyacrylamide gel electrophoresis. MutS-MutL interaction was measured using the same technique except that the MutL protein carried the His6 tag. Our results indicate that DNA binding ability resides in the N-terminal end of MutS, and dimerization and MutL interactions are located in the C-terminal end. Given the extensive amino acid homology in the MutS family our results with E. coli should be applicable to MutS homologues in other prokaryotes and eukaryotes. (+info)The role of the mismatch repair machinery in regulating mitotic and meiotic recombination between diverged sequences in yeast. (2/975)
Nonidentical recombination substrates recombine less efficiently than do identical substrates in yeast, and much of this inhibition can be attributed to action of the mismatch repair (MMR) machinery. In this study an intron-based inverted repeat assay system has been used to directly compare the rates of mitotic and meiotic recombination between pairs of 350-bp substrates varying from 82% to 100% in sequence identity. The recombination rate data indicate that sequence divergence impacts mitotic and meiotic recombination similarly, although subtle differences are evident. In addition to assessing recombination rates as a function of sequence divergence, the endpoints of mitotic and meiotic recombination events involving 94%-identical substrates were determined by DNA sequencing. The endpoint analysis indicates that the extent of meiotic heteroduplex DNA formed in a MMR-defective strain is 65% longer than that formed in a wild-type strain. These data are consistent with a model in which the MMR machinery interferes with the formation and/or extension of heteroduplex intermediates during recombination. (+info)Suppression of intrachromosomal gene conversion in mammalian cells by small degrees of sequence divergence. (3/975)
Pairs of closely linked defective herpes simplex virus (HSV) thymidine kinase (tk) gene sequences exhibiting various nucleotide heterologies were introduced into the genome of mouse Ltk- cells. Recombination events were recovered by selecting for the correction of a 16-bp insertion mutation in one of the tk sequences. We had previously shown that when two tk sequences shared a region of 232 bp of homology, interruption of the homology by two single nucleotide heterologies placed 19 bp apart reduced recombination nearly 20-fold. We now report that either one of the nucleotide heterologies alone reduces recombination only about 2.5-fold, indicating that the original pair of single nucleotide heterologies acted synergistically to inhibit recombination. We tested a variety of pairs of single nucleotide heterologies and determined that they reduced recombination from 7- to 175-fold. Substrates potentially leading to G-G or C-C mispairs in presumptive heteroduplex DNA (hDNA) intermediates displayed a particularly low rate of recombination. Additional experiments suggested that increased sequence divergence causes a shortening of gene conversion tracts. Collectively, our results suggest that suppression of recombination between diverged sequences is mediated via processing of a mispaired hDNA intermediate. (+info)Damage increases the flexibility of duplex DNA. (4/975)
It is proposed that much of the recognition of specific types of damaged DNAs is based on accessible structural features, while much of the recognition of damaged DNAs, as a class, is based on flexibility. The more flexible a DNA the faster its diffusion rate. The diffusion rates of each member of a series of damaged duplex DNAs has been found to be significantly faster than that of the corresponding undamaged duplex DNA. The damaged sites studied include apurinic and apyrimidinic a basic sites, thymine glycol and urea. The presence of mismatched sites also increases the diffusion. Thus, damaged DNAs appear to have sufficient flexibility for recognition and the flexibility may allow damaged sites to act as a universal joint or hinge that allows distant sites on the DNA to come together. (+info)Molecular basis of AmpC hyperproduction in clinical isolates of Escherichia coli. (5/975)
DNA sequencing data showed that five clinical isolates of Escherichia coli with reduced susceptibility to ceftazidime, ceftriaxone, and cefotaxime contain an ampC gene that is preceded by a strong promoter. Transcription from the strong promoter was 8- to 18-fold higher than that from the promoter from a susceptible isolate. RNA studies showed that mRNA stability does not play a role in the control of AmpC synthesis. (+info)DNA aptamers selected against the HIV-1 trans-activation-responsive RNA element form RNA-DNA kissing complexes. (6/975)
In vitro selection was performed in a DNA library, made of oligonucleotides with a 30-nucleotide random sequence, to identify ligands of the human immunodeficiency virus type-1 trans-activation-responsive (TAR) RNA element. Aptamers, extracted after 15 rounds of selection-amplification, either from a classical library of sequences or from virtual combinatorial libraries, displayed an imperfect stem-loop structure and presented a consensus motif 5'ACTCCCAT in the apical loop. The six central bases of the consensus were complementary to the TAR apical region, giving rise to the formation of RNA-DNA kissing complexes, without disrupting the secondary structure of TAR. The RNA-DNA kissing complex was a poor substrate for Escherichia coli RNase H, likely due to steric and conformational constraints of the DNA/RNA heteroduplex. 2'-O-Methyl derivatives of a selected aptamer were binders of lower efficiency than the parent aptamer in contrast to regular sense/antisense hybrids, indicating that the RNA/DNA loop-loop region adopted a non-canonical heteroduplex structure. These results, which allowed the identification of a new type of complex, DNA-RNA kissing complex, demonstrate the interest of in vitro selection for identifying non-antisense oligonucleotide ligands of RNA structures that are of potential value for artificially modulating gene expression. (+info)Inhibition of gene expression by anti-sense C-5 propyne oligonucleotides detected by a reporter enzyme. (7/975)
Using a reporter plasmid containing the luciferase gene under the control of the insulin-like growth factor 1 (IGF-1) promoter region [including its 5' untranslated region (UTR)], we demonstrate that a 17-mer oligophosphorothioate containing C-5 propyne pyrimidines is able to inhibit luciferase gene expression in the nanomolar concentration range when the anti-sense oligonucleotide is targeted either to a coding sequence in the luciferase gene or to the 5' UTR of the gene for IGF-1. Inhibition was obtained independently of whether the plasmid and the anti-sense oligonucleotide were co-transfected or transfected separately into hepatocarcinoma cells. However, the efficiency of inhibition by the anti-sense oligonucleotides was 10-fold greater in the first case. The unmodified oligophosphorothioate targeted to the 5' UTR of IGF-1 did not inhibit luciferase gene expression at a 100-fold higher concentration unless its length was increased from 17 to 21 nt, in which case an inhibition of gene expression was obtained and an IC50 of 200 nM was observed. (+info)Structural properties of DNA:RNA duplexes containing 2'-O-methyl and 2'-S-methyl substitutions: a molecular dynamics investigation. (8/975)
The physical properties of a DNA:RNA hybrid sequence d(CCAACGTTGG)*(CCAACGUUGG) with modifications at the C2'-positions of the DNA strand by 2'-O-methyl (OMe) and 2'-S-methyl (SMe) groups are studied using computational techniques. Molecular dynamics simu-lations of SMe_DNA:RNA, OMe_DNA:RNA and standard DNA:RNA hybrids in explicit water indicate that the nature of the C2'-substituent has a significant influence on the macromolecular conformation. While the RNA strand in all duplexes maintains a strong preference for C3'-endo sugar puckering, the DNA strand shows considerable variation in this parameter depending on the nature of the C2'-substituent. In general, the preference for C3'-endo puckering follows the following trend: OMe_DNA>DNA>SMe_DNA. These results are further corroborated using ab initio methods. Both gas phase and implicit solvation calculations show the C2'-OMe group stabilizes the C3'-endo conformation while the less electronegative SMe group stabilizes the C2'-endo conformation when compared to the standard nucleoside. The macromolecular conformation of these nucleic acids also follows an analogous trend with the degree of A-form character decreasing as OMe_DNA:RNA>DNA:RNA>SMe_DNA:RNA. A structural analysis of these complexes is performed and compared with experimental melting point temper-atures to explain the structural basis to improved binding affinity across this series. Finally, a possible correlation between RNase H activity and conformational changes within the minor groove of these complexes is hypothesized. (+info)A nucleic acid heteroduplex is a double-stranded structure formed by the pairing of two complementary single strands of nucleic acids (DNA or RNA) that are derived from different sources. The term "hetero" refers to the fact that the two strands are not identical and come from different parents, genes, or organisms.
Heteroduplexes can form spontaneously during processes like genetic recombination, where DNA repair mechanisms may mistakenly pair complementary regions between two different double-stranded DNA molecules. They can also be generated intentionally in laboratory settings for various purposes, such as analyzing the similarity of DNA sequences or detecting mutations.
Heteroduplexes are often used in molecular biology techniques like polymerase chain reaction (PCR) and DNA sequencing, where they can help identify mismatches, insertions, deletions, or other sequence variations between the two parental strands. These variations can provide valuable information about genetic diversity, evolutionary relationships, and disease-causing mutations.
Heteroduplex analysis is a laboratory technique used in molecular biology to detect genetic variations or mutations between two DNA sequences. It involves denaturing (separating) the double-stranded DNA molecules of two different samples, allowing the single strands to reanneal or hybridize with each other. If there are any sequence differences between the two samples, this will result in the formation of heteroduplexes - mismatched double-stranded regions where the base pairing does not follow the usual A-T and G-C rules.
These heteroduplexes can be detected by various methods such as denaturing gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE), or mismatch cleavage using enzymes like T7 endonuclease I or CEL I. The presence and mobility shift of heteroduplex bands in the analysis can indicate the location and type of genetic variation, making it a valuable tool for mutation screening, genotyping, and DNA fingerprinting.
Peptide Nucleic Acids (PNAs) are synthetic, artificially produced molecules that have a structure similar to both peptides (short chains of amino acids) and nucleic acids (DNA and RNA). They consist of repeating units called "monomers" made up of a pseudopeptide backbone with nucleobases attached. The backbone is composed of N-(2-aminoethyl)glycine units, which replace the sugar-phosphate backbone found in natural nucleic acids.
PNAs are known for their high binding affinity and sequence-specific recognition of DNA and RNA molecules. They can form stable complexes with complementary DNA or RNA strands through Watson-Crick base pairing, even under conditions where normal nucleic acid hybridization is poor. This property makes them valuable tools in molecular biology for various applications such as:
1. Gene regulation and silencing
2. Antisense and antigen technologies
3. Diagnostics and biosensors
4. Study of protein-DNA interactions
5. DNA repair and mutation analysis
However, it is important to note that Peptide Nucleic Acids are not naturally occurring molecules; they are entirely synthetic and must be produced in a laboratory setting.
Nucleic acid denaturation is the process of separating the two strands of a double-stranded DNA molecule, or unwinding the helical structure of an RNA molecule, by disrupting the hydrogen bonds that hold the strands together. This process is typically caused by exposure to high temperatures, changes in pH, or the presence of chemicals called denaturants.
Denaturation can also cause changes in the shape and function of nucleic acids. For example, it can disrupt the secondary and tertiary structures of RNA molecules, which can affect their ability to bind to other molecules and carry out their functions within the cell.
In molecular biology, nucleic acid denaturation is often used as a tool for studying the structure and function of nucleic acids. For example, it can be used to separate the two strands of a DNA molecule for sequencing or amplification, or to study the interactions between nucleic acids and other molecules.
It's important to note that denaturation is a reversible process, and under the right conditions, the double-stranded structure of DNA can be restored through a process called renaturation or annealing.
A base sequence in the context of molecular biology refers to the specific order of nucleotides in a DNA or RNA molecule. In DNA, these nucleotides are adenine (A), guanine (G), cytosine (C), and thymine (T). In RNA, uracil (U) takes the place of thymine. The base sequence contains genetic information that is transcribed into RNA and ultimately translated into proteins. It is the exact order of these bases that determines the genetic code and thus the function of the DNA or RNA molecule.
Nucleic acid hybridization is a process in molecular biology where two single-stranded nucleic acids (DNA, RNA) with complementary sequences pair together to form a double-stranded molecule through hydrogen bonding. The strands can be from the same type of nucleic acid or different types (i.e., DNA-RNA or DNA-cDNA). This process is commonly used in various laboratory techniques, such as Southern blotting, Northern blotting, polymerase chain reaction (PCR), and microarray analysis, to detect, isolate, and analyze specific nucleic acid sequences. The hybridization temperature and conditions are critical to ensure the specificity of the interaction between the two strands.
Nucleic acid conformation refers to the three-dimensional structure that nucleic acids (DNA and RNA) adopt as a result of the bonding patterns between the atoms within the molecule. The primary structure of nucleic acids is determined by the sequence of nucleotides, while the conformation is influenced by factors such as the sugar-phosphate backbone, base stacking, and hydrogen bonding.
Two common conformations of DNA are the B-form and the A-form. The B-form is a right-handed helix with a diameter of about 20 Å and a pitch of 34 Å, while the A-form has a smaller diameter (about 18 Å) and a shorter pitch (about 25 Å). RNA typically adopts an A-form conformation.
The conformation of nucleic acids can have significant implications for their function, as it can affect their ability to interact with other molecules such as proteins or drugs. Understanding the conformational properties of nucleic acids is therefore an important area of research in molecular biology and medicine.
A base pair mismatch is a type of mutation that occurs during the replication or repair of DNA, where two incompatible nucleotides pair up instead of the usual complementary bases (adenine-thymine or cytosine-guanine). This can result in the substitution of one base pair for another and may lead to changes in the genetic code, potentially causing errors in protein synthesis and possibly contributing to genetic disorders or diseases, including cancer.
The MutS DNA mismatch-binding protein is a key component of the bacterial DNA mismatch repair system, which plays a crucial role in maintaining genomic stability by correcting errors that occur during DNA replication. This protein is responsible for recognizing and binding to mismatched base pairs or small insertion/deletion loops (known as heteroduplexes) that escape the proofreading activity of polymerase enzymes.
Once bound to a mismatch, MutS undergoes a conformational change and recruits other proteins to form a complex that initiates the repair process. The complex uses the intact strand as a template to remove the incorrect segment, followed by resynthesis of the corrected sequence. This enzyme is highly conserved across various species, including humans, where it is involved in similar DNA repair processes and has been implicated in several hereditary cancer syndromes.
Deoxyribonucleic acid (DNA) is the genetic material present in the cells of organisms where it is responsible for the storage and transmission of hereditary information. DNA is a long molecule that consists of two strands coiled together to form a double helix. Each strand is made up of a series of four nucleotide bases - adenine (A), guanine (G), cytosine (C), and thymine (T) - that are linked together by phosphate and sugar groups. The sequence of these bases along the length of the molecule encodes genetic information, with A always pairing with T and C always pairing with G. This base-pairing allows for the replication and transcription of DNA, which are essential processes in the functioning and reproduction of all living organisms.
Nucleic acid renaturation, also known as nucleic acid reassociation or hybridization, is the process of rejoining two complementary single-stranded nucleic acids (DNA or RNA) to form a double-stranded structure. This process occurs naturally in cells during transcription and DNA replication, but it can also be performed in vitro as a laboratory technique.
Renaturation typically involves denaturing the double-stranded nucleic acids into single strands by heat or chemical methods, followed by controlled cooling or modification of conditions to allow the complementary strands to find each other and reanneal. The rate and specificity of renaturation can be used to study the relatedness and concentration of nucleic acid sequences in a sample.
In molecular biology research, nucleic acid renaturation is often used in techniques such as Southern blotting, Northern blotting, and polymerase chain reaction (PCR) to detect and analyze specific DNA or RNA sequences.
Oligonucleotides are short sequences of nucleotides, the building blocks of DNA and RNA. They typically contain fewer than 100 nucleotides, and can be synthesized chemically to have specific sequences. Oligonucleotides are used in a variety of applications in molecular biology, including as probes for detecting specific DNA or RNA sequences, as inhibitors of gene expression, and as components of diagnostic tests and therapies. They can also be used in the study of protein-nucleic acid interactions and in the development of new drugs.
DNA repair is the process by which cells identify and correct damage to the DNA molecules that encode their genome. DNA can be damaged by a variety of internal and external factors, such as radiation, chemicals, and metabolic byproducts. If left unrepaired, this damage can lead to mutations, which may in turn lead to cancer and other diseases.
There are several different mechanisms for repairing DNA damage, including:
1. Base excision repair (BER): This process repairs damage to a single base in the DNA molecule. An enzyme called a glycosylase removes the damaged base, leaving a gap that is then filled in by other enzymes.
2. Nucleotide excision repair (NER): This process repairs more severe damage, such as bulky adducts or crosslinks between the two strands of the DNA molecule. An enzyme cuts out a section of the damaged DNA, and the gap is then filled in by other enzymes.
3. Mismatch repair (MMR): This process repairs errors that occur during DNA replication, such as mismatched bases or small insertions or deletions. Specialized enzymes recognize the error and remove a section of the newly synthesized strand, which is then replaced by new nucleotides.
4. Double-strand break repair (DSBR): This process repairs breaks in both strands of the DNA molecule. There are two main pathways for DSBR: non-homologous end joining (NHEJ) and homologous recombination (HR). NHEJ directly rejoins the broken ends, while HR uses a template from a sister chromatid to repair the break.
Overall, DNA repair is a crucial process that helps maintain genome stability and prevent the development of diseases caused by genetic mutations.
Nucleic acid probes are specialized single-stranded DNA or RNA molecules that are used in molecular biology to identify and detect specific nucleic acid sequences, such as genes or fragments of DNA or RNA. These probes are typically labeled with a marker, such as a radioactive isotope or a fluorescent dye, which allows them to be detected and visualized.
Nucleic acid probes work by binding or "hybridizing" to their complementary target sequence through base-pairing interactions between the nucleotides that make up the probe and the target. This specificity of hybridization allows for the detection and identification of specific sequences within a complex mixture of nucleic acids, such as those found in a sample of DNA or RNA from a biological specimen.
Nucleic acid probes are used in a variety of applications, including gene expression analysis, genetic mapping, diagnosis of genetic disorders, and detection of pathogens, among others. They are an essential tool in modern molecular biology research and have contributed significantly to our understanding of genetics and disease.
Bacterial DNA refers to the genetic material found in bacteria. It is composed of a double-stranded helix containing four nucleotide bases - adenine (A), thymine (T), guanine (G), and cytosine (C) - that are linked together by phosphodiester bonds. The sequence of these bases in the DNA molecule carries the genetic information necessary for the growth, development, and reproduction of bacteria.
Bacterial DNA is circular in most bacterial species, although some have linear chromosomes. In addition to the main chromosome, many bacteria also contain small circular pieces of DNA called plasmids that can carry additional genes and provide resistance to antibiotics or other environmental stressors.
Unlike eukaryotic cells, which have their DNA enclosed within a nucleus, bacterial DNA is present in the cytoplasm of the cell, where it is in direct contact with the cell's metabolic machinery. This allows for rapid gene expression and regulation in response to changing environmental conditions.
Viral DNA refers to the genetic material present in viruses that consist of DNA as their core component. Deoxyribonucleic acid (DNA) is one of the two types of nucleic acids that are responsible for storing and transmitting genetic information in living organisms. Viruses are infectious agents much smaller than bacteria that can only replicate inside the cells of other organisms, called hosts.
Viral DNA can be double-stranded (dsDNA) or single-stranded (ssDNA), depending on the type of virus. Double-stranded DNA viruses have a genome made up of two complementary strands of DNA, while single-stranded DNA viruses contain only one strand of DNA.
Examples of dsDNA viruses include Adenoviruses, Herpesviruses, and Poxviruses, while ssDNA viruses include Parvoviruses and Circoviruses. Viral DNA plays a crucial role in the replication cycle of the virus, encoding for various proteins necessary for its multiplication and survival within the host cell.
Polymerase Chain Reaction (PCR) is a laboratory technique used to amplify specific regions of DNA. It enables the production of thousands to millions of copies of a particular DNA sequence in a rapid and efficient manner, making it an essential tool in various fields such as molecular biology, medical diagnostics, forensic science, and research.
The PCR process involves repeated cycles of heating and cooling to separate the DNA strands, allow primers (short sequences of single-stranded DNA) to attach to the target regions, and extend these primers using an enzyme called Taq polymerase, resulting in the exponential amplification of the desired DNA segment.
In a medical context, PCR is often used for detecting and quantifying specific pathogens (viruses, bacteria, fungi, or parasites) in clinical samples, identifying genetic mutations or polymorphisms associated with diseases, monitoring disease progression, and evaluating treatment effectiveness.
Molecular sequence data refers to the specific arrangement of molecules, most commonly nucleotides in DNA or RNA, or amino acids in proteins, that make up a biological macromolecule. This data is generated through laboratory techniques such as sequencing, and provides information about the exact order of the constituent molecules. This data is crucial in various fields of biology, including genetics, evolution, and molecular biology, allowing for comparisons between different organisms, identification of genetic variations, and studies of gene function and regulation.
RNA (Ribonucleic Acid) is a single-stranded, linear polymer of ribonucleotides. It is a nucleic acid present in the cells of all living organisms and some viruses. RNAs play crucial roles in various biological processes such as protein synthesis, gene regulation, and cellular signaling. There are several types of RNA including messenger RNA (mRNA), ribosomal RNA (rRNA), transfer RNA (tRNA), small nuclear RNA (snRNA), microRNA (miRNA), and long non-coding RNA (lncRNA). These RNAs differ in their structure, function, and location within the cell.
'Escherichia coli' (E. coli) is a type of gram-negative, facultatively anaerobic, rod-shaped bacterium that commonly inhabits the intestinal tract of humans and warm-blooded animals. It is a member of the family Enterobacteriaceae and one of the most well-studied prokaryotic model organisms in molecular biology.
While most E. coli strains are harmless and even beneficial to their hosts, some serotypes can cause various forms of gastrointestinal and extraintestinal illnesses in humans and animals. These pathogenic strains possess virulence factors that enable them to colonize and damage host tissues, leading to diseases such as diarrhea, urinary tract infections, pneumonia, and sepsis.
E. coli is a versatile organism with remarkable genetic diversity, which allows it to adapt to various environmental niches. It can be found in water, soil, food, and various man-made environments, making it an essential indicator of fecal contamination and a common cause of foodborne illnesses. The study of E. coli has contributed significantly to our understanding of fundamental biological processes, including DNA replication, gene regulation, and protein synthesis.
Nucleic acid amplification techniques (NAATs) are medical laboratory methods used to increase the number of copies of a specific DNA or RNA sequence. These techniques are widely used in molecular biology and diagnostics, including the detection and diagnosis of infectious diseases, genetic disorders, and cancer.
The most commonly used NAAT is the polymerase chain reaction (PCR), which involves repeated cycles of heating and cooling to separate and replicate DNA strands. Other NAATs include loop-mediated isothermal amplification (LAMP), nucleic acid sequence-based amplification (NASBA), and transcription-mediated amplification (TMA).
NAATs offer several advantages over traditional culture methods for detecting pathogens, including faster turnaround times, increased sensitivity and specificity, and the ability to detect viable but non-culturable organisms. However, they also require specialized equipment and trained personnel, and there is a risk of contamination and false positive results if proper precautions are not taken.
DNA restriction enzymes, also known as restriction endonucleases, are a type of enzyme that cut double-stranded DNA at specific recognition sites. These enzymes are produced by bacteria and archaea as a defense mechanism against foreign DNA, such as that found in bacteriophages (viruses that infect bacteria).
Restriction enzymes recognize specific sequences of nucleotides (the building blocks of DNA) and cleave the phosphodiester bonds between them. The recognition sites for these enzymes are usually palindromic, meaning that the sequence reads the same in both directions when facing the opposite strands of DNA.
Restriction enzymes are widely used in molecular biology research for various applications such as genetic engineering, genome mapping, and DNA fingerprinting. They allow scientists to cut DNA at specific sites, creating precise fragments that can be manipulated and analyzed. The use of restriction enzymes has been instrumental in the development of recombinant DNA technology and the Human Genome Project.
Coliphages are viruses that infect and replicate within certain species of bacteria that belong to the coliform group, particularly Escherichia coli (E. coli). These viruses are commonly found in water and soil environments and are frequently used as indicators of fecal contamination in water quality testing. Coliphages are not harmful to humans or animals, but their presence in water can suggest the potential presence of pathogenic bacteria or other microorganisms that may pose a health risk. There are two main types of coliphages: F-specific RNA coliphages and somatic (or non-F specific) DNA coliphages.
Carbodiimides are a class of chemical compounds with the general formula R-N=C=N-R, where R can be an organic group. They are widely used in the synthesis of various chemical and biological products due to their ability to act as dehydrating agents, promoting the formation of amide bonds between carboxylic acids and amines.
In the context of medical research and biochemistry, carbodiimides are often used to modify proteins, peptides, and other biological molecules for various purposes, such as labeling, cross-linking, or functionalizing. For example, the carbodiimide cross-linker EDC (1-ethyl-3-(3-dimethylaminopropyl)carbodiimide) is commonly used to create stable amide bonds between proteins and other molecules in a process known as "EDC coupling."
It's important to note that carbodiimides can be potentially toxic and should be handled with care. They can cause irritation to the skin, eyes, and respiratory tract, and prolonged exposure can lead to more serious health effects. Therefore, appropriate safety precautions should be taken when working with these compounds in a laboratory setting.
Ribonuclease H (RNase H) is an enzyme that specifically degrades the RNA portion of an RNA-DNA hybrid. It cleaves the phosphodiester bond between the ribose sugar and the phosphate group in the RNA strand, leaving the DNA strand intact. This enzyme plays a crucial role in several cellular processes, including DNA replication, repair, and transcription.
There are two main types of RNase H: type 1 and type 2. Type 1 RNase H is found in both prokaryotic and eukaryotic cells, while type 2 RNase H is primarily found in eukaryotes. The primary function of RNase H is to remove RNA primers that are synthesized during DNA replication. These RNA primers are replaced with DNA nucleotides by another enzyme called polymerase δ, leaving behind a gap in the DNA strand. RNase H then cleaves the RNA-DNA hybrid, allowing for the repair of the gap and the completion of DNA replication.
RNase H has also been implicated in the regulation of gene expression, as it can degrade RNA-DNA hybrids formed during transcription. This process, known as transcription-coupled RNA decay, helps to prevent the accumulation of aberrant RNA molecules and ensures proper gene expression.
In addition to its cellular functions, RNase H has been studied for its potential therapeutic applications. For example, inhibitors of RNase H have been shown to have antiviral activity against HIV-1, as they prevent the degradation of viral RNA during reverse transcription. On the other hand, activators of RNase H have been explored as a means to enhance the efficiency of RNA interference (RNAi) therapies by promoting the degradation of target RNA molecules.
Base composition in genetics refers to the relative proportion of the four nucleotide bases (adenine, thymine, guanine, and cytosine) in a DNA or RNA molecule. In DNA, adenine pairs with thymine, and guanine pairs with cytosine, so the base composition is often expressed in terms of the ratio of adenine + thymine (A-T) to guanine + cytosine (G-C). This ratio can vary between species and even between different regions of the same genome. The base composition can provide important clues about the function, evolution, and structure of genetic material.
A mutation is a permanent change in the DNA sequence of an organism's genome. Mutations can occur spontaneously or be caused by environmental factors such as exposure to radiation, chemicals, or viruses. They may have various effects on the organism, ranging from benign to harmful, depending on where they occur and whether they alter the function of essential proteins. In some cases, mutations can increase an individual's susceptibility to certain diseases or disorders, while in others, they may confer a survival advantage. Mutations are the driving force behind evolution, as they introduce new genetic variability into populations, which can then be acted upon by natural selection.
Genetic recombination is the process by which genetic material is exchanged between two similar or identical molecules of DNA during meiosis, resulting in new combinations of genes on each chromosome. This exchange occurs during crossover, where segments of DNA are swapped between non-sister homologous chromatids, creating genetic diversity among the offspring. It is a crucial mechanism for generating genetic variability and facilitating evolutionary change within populations. Additionally, recombination also plays an essential role in DNA repair processes through mechanisms such as homologous recombinational repair (HRR) and non-homologous end joining (NHEJ).
Single-stranded DNA (ssDNA) is a form of DNA that consists of a single polynucleotide chain. In contrast, double-stranded DNA (dsDNA) consists of two complementary polynucleotide chains that are held together by hydrogen bonds.
In the double-helix structure of dsDNA, each nucleotide base on one strand pairs with a specific base on the other strand through hydrogen bonding: adenine (A) with thymine (T), and guanine (G) with cytosine (C). This base pairing provides stability to the double-stranded structure.
Single-stranded DNA, on the other hand, lacks this complementary base pairing and is therefore less stable than dsDNA. However, ssDNA can still form secondary structures through intrastrand base pairing, such as hairpin loops or cruciform structures.
Single-stranded DNA is found in various biological contexts, including viral genomes, transcription bubbles during gene expression, and in certain types of genetic recombination. It also plays a critical role in some laboratory techniques, such as polymerase chain reaction (PCR) and DNA sequencing.
Capillary electrophoresis (CE) is a laboratory technique used to separate and analyze charged particles such as proteins, nucleic acids, and other molecules based on their size and charge. In CE, the sample is introduced into a narrow capillary tube filled with a buffer solution, and an electric field is applied. The charged particles in the sample migrate through the capillary towards the electrode with the opposite charge, and the different particles become separated as they migrate based on their size and charge.
The separation process in CE is monitored by detecting the changes in the optical properties of the particles as they pass through a detector, typically located at the end of the capillary. The resulting data can be used to identify and quantify the individual components in the sample. Capillary electrophoresis has many applications in research and clinical settings, including the analysis of DNA fragments, protein identification and characterization, and the detection of genetic variations.
Methylation, in the context of genetics and epigenetics, refers to the addition of a methyl group (CH3) to a molecule, usually to the nitrogenous base of DNA or to the side chain of amino acids in proteins. In DNA methylation, this process typically occurs at the 5-carbon position of cytosine residues that precede guanine residues (CpG sites) and is catalyzed by enzymes called DNA methyltransferases (DNMTs).
DNA methylation plays a crucial role in regulating gene expression, genomic imprinting, X-chromosome inactivation, and suppression of repetitive elements. Hypermethylation or hypomethylation of specific genes can lead to altered gene expression patterns, which have been associated with various human diseases, including cancer.
In summary, methylation is a fundamental epigenetic modification that influences genomic stability, gene regulation, and cellular function by introducing methyl groups to DNA or proteins.
Endodeoxyribonucleases are a type of enzyme that cleave, or cut, phosphodiester bonds within the backbone of DNA molecules. These enzymes are also known as restriction endonucleases or simply restriction enzymes. They are called "restriction" enzymes because they were first discovered in bacteria, where they function to protect the organism from foreign DNA by cleaving and destroying invading viral DNA.
Endodeoxyribonucleases recognize specific sequences of nucleotides within the DNA molecule, known as recognition sites or restriction sites, and cut the phosphodiester bonds at specific locations within these sites. The cuts made by endodeoxyribonucleases can be either "sticky" or "blunt," depending on whether the enzyme leaves single-stranded overhangs or creates blunt ends at the site of cleavage, respectively.
Endodeoxyribonucleases are widely used in molecular biology research for various applications, including DNA cloning, genome mapping, and genetic engineering. They allow researchers to cut DNA molecules at specific sites, creating defined fragments that can be manipulated and recombined in a variety of ways.
Osteogenesis Imperfecta (OI), also known as brittle bone disease, is a group of genetic disorders that mainly affect the bones. It is characterized by bones that break easily, often from little or no apparent cause. This happens because the body produces an insufficient amount of collagen or poor quality collagen, which are crucial for the formation of healthy bones.
The severity of OI can vary greatly, even within the same family. Some people with OI have only a few fractures in their lifetime while others may have hundreds. Other symptoms can include blue or gray sclera (the white part of the eye), hearing loss, short stature, curved or bowed bones, loose joints, and a triangular face shape.
There are several types of OI, each caused by different genetic mutations. Most types of OI are inherited in an autosomal dominant pattern, meaning only one copy of the altered gene is needed to cause the condition. However, some types are inherited in an autosomal recessive pattern, which means that two copies of the altered gene must be present for the condition to occur.
There is no cure for OI, but treatment can help manage symptoms and prevent complications. Treatment may include medication to strengthen bones, physical therapy, bracing, and surgery.
Bacteriophage lambda, often simply referred to as phage lambda, is a type of virus that infects the bacterium Escherichia coli (E. coli). It is a double-stranded DNA virus that integrates its genetic material into the bacterial chromosome as a prophage when it infects the host cell. This allows the phage to replicate along with the bacterium until certain conditions trigger the lytic cycle, during which new virions are produced and released by lysing, or breaking open, the host cell.
Phage lambda is widely studied in molecular biology due to its well-characterized life cycle and genetic structure. It has been instrumental in understanding various fundamental biological processes such as gene regulation, DNA recombination, and lysis-lysogeny decision.
Molecular cloning is a laboratory technique used to create multiple copies of a specific DNA sequence. This process involves several steps:
1. Isolation: The first step in molecular cloning is to isolate the DNA sequence of interest from the rest of the genomic DNA. This can be done using various methods such as PCR (polymerase chain reaction), restriction enzymes, or hybridization.
2. Vector construction: Once the DNA sequence of interest has been isolated, it must be inserted into a vector, which is a small circular DNA molecule that can replicate independently in a host cell. Common vectors used in molecular cloning include plasmids and phages.
3. Transformation: The constructed vector is then introduced into a host cell, usually a bacterial or yeast cell, through a process called transformation. This can be done using various methods such as electroporation or chemical transformation.
4. Selection: After transformation, the host cells are grown in selective media that allow only those cells containing the vector to grow. This ensures that the DNA sequence of interest has been successfully cloned into the vector.
5. Amplification: Once the host cells have been selected, they can be grown in large quantities to amplify the number of copies of the cloned DNA sequence.
Molecular cloning is a powerful tool in molecular biology and has numerous applications, including the production of recombinant proteins, gene therapy, functional analysis of genes, and genetic engineering.
Oligodeoxyribonucleotides (ODNs) are relatively short, synthetic single-stranded DNA molecules. They typically contain 15 to 30 nucleotides, but can range from 2 to several hundred nucleotides in length. ODNs are often used as tools in molecular biology research for various applications such as:
1. Nucleic acid detection and quantification (e.g., real-time PCR)
2. Gene regulation (antisense, RNA interference)
3. Gene editing (CRISPR-Cas systems)
4. Vaccine development
5. Diagnostic purposes
Due to their specificity and affinity towards complementary DNA or RNA sequences, ODNs can be designed to target a particular gene or sequence of interest. This makes them valuable tools in understanding gene function, regulation, and interaction with other molecules within the cell.
Crossing over, genetic is a process that occurs during meiosis, where homologous chromosomes exchange genetic material with each other. It is a crucial mechanism for generating genetic diversity in sexually reproducing organisms.
Here's a more detailed explanation:
During meiosis, homologous chromosomes pair up and align closely with each other. At this point, sections of the chromosomes can break off and reattach to the corresponding section on the homologous chromosome. This exchange of genetic material is called crossing over or genetic recombination.
The result of crossing over is that the two resulting chromosomes are no longer identical to each other or to the original chromosomes. Instead, they contain a unique combination of genetic material from both parents. Crossing over can lead to new combinations of alleles (different forms of the same gene) and can increase genetic diversity in the population.
Crossing over is a random process, so the location and frequency of crossover events vary between individuals and between chromosomes. The number and position of crossovers can affect the likelihood that certain genes will be inherited together or separated, which is an important consideration in genetic mapping and breeding studies.
Electron microscopy (EM) is a type of microscopy that uses a beam of electrons to create an image of the sample being examined, resulting in much higher magnification and resolution than light microscopy. There are several types of electron microscopy, including transmission electron microscopy (TEM), scanning electron microscopy (SEM), and reflection electron microscopy (REM).
In TEM, a beam of electrons is transmitted through a thin slice of the sample, and the electrons that pass through the sample are focused to form an image. This technique can provide detailed information about the internal structure of cells, viruses, and other biological specimens, as well as the composition and structure of materials at the atomic level.
In SEM, a beam of electrons is scanned across the surface of the sample, and the electrons that are scattered back from the surface are detected to create an image. This technique can provide information about the topography and composition of surfaces, as well as the structure of materials at the microscopic level.
REM is a variation of SEM in which the beam of electrons is reflected off the surface of the sample, rather than scattered back from it. This technique can provide information about the surface chemistry and composition of materials.
Electron microscopy has a wide range of applications in biology, medicine, and materials science, including the study of cellular structure and function, disease diagnosis, and the development of new materials and technologies.
DNA repair enzymes are a group of enzymes that are responsible for identifying and correcting damage to the DNA molecule. These enzymes play a critical role in maintaining the integrity of an organism's genetic material, as they help to ensure that the information stored in DNA is accurately transmitted during cell division and reproduction.
There are several different types of DNA repair enzymes, each responsible for correcting specific types of damage. For example, base excision repair enzymes remove and replace damaged or incorrect bases, while nucleotide excision repair enzymes remove larger sections of damaged DNA and replace them with new nucleotides. Other types of DNA repair enzymes include mismatch repair enzymes, which correct errors that occur during DNA replication, and double-strand break repair enzymes, which are responsible for fixing breaks in both strands of the DNA molecule.
Defects in DNA repair enzymes have been linked to a variety of diseases, including cancer, neurological disorders, and premature aging. For example, individuals with xeroderma pigmentosum, a rare genetic disorder characterized by an increased risk of skin cancer, have mutations in genes that encode nucleotide excision repair enzymes. Similarly, defects in mismatch repair enzymes have been linked to hereditary nonpolyposis colorectal cancer, a type of colon cancer that is inherited and tends to occur at a younger age than sporadic colon cancer.
Overall, DNA repair enzymes play a critical role in maintaining the stability and integrity of an organism's genetic material, and defects in these enzymes can have serious consequences for human health.
A plasmid is a small, circular, double-stranded DNA molecule that is separate from the chromosomal DNA of a bacterium or other organism. Plasmids are typically not essential for the survival of the organism, but they can confer beneficial traits such as antibiotic resistance or the ability to degrade certain types of pollutants.
Plasmids are capable of replicating independently of the chromosomal DNA and can be transferred between bacteria through a process called conjugation. They often contain genes that provide resistance to antibiotics, heavy metals, and other environmental stressors. Plasmids have also been engineered for use in molecular biology as cloning vectors, allowing scientists to replicate and manipulate specific DNA sequences.
Plasmids are important tools in genetic engineering and biotechnology because they can be easily manipulated and transferred between organisms. They have been used to produce vaccines, diagnostic tests, and genetically modified organisms (GMOs) for various applications, including agriculture, medicine, and industry.
DNA Mutational Analysis is a laboratory test used to identify genetic variations or changes (mutations) in the DNA sequence of a gene. This type of analysis can be used to diagnose genetic disorders, predict the risk of developing certain diseases, determine the most effective treatment for cancer, or assess the likelihood of passing on an inherited condition to offspring.
The test involves extracting DNA from a patient's sample (such as blood, saliva, or tissue), amplifying specific regions of interest using polymerase chain reaction (PCR), and then sequencing those regions to determine the precise order of nucleotide bases in the DNA molecule. The resulting sequence is then compared to reference sequences to identify any variations or mutations that may be present.
DNA Mutational Analysis can detect a wide range of genetic changes, including single-nucleotide polymorphisms (SNPs), insertions, deletions, duplications, and rearrangements. The test is often used in conjunction with other diagnostic tests and clinical evaluations to provide a comprehensive assessment of a patient's genetic profile.
It is important to note that not all mutations are pathogenic or associated with disease, and the interpretation of DNA Mutational Analysis results requires careful consideration of the patient's medical history, family history, and other relevant factors.
Gene conversion is a process in genetics that involves the non-reciprocal transfer of genetic information from one region of a chromosome to a corresponding region on its homologous chromosome. This process results in a segment of DNA on one chromosome being replaced with a corresponding segment from the other chromosome, leading to a change in the genetic sequence and potentially the phenotype.
Gene conversion can occur during meiosis, as a result of homologous recombination between two similar or identical sequences. It is a natural process that helps maintain genetic diversity within populations and can also play a role in the evolution of genes and genomes. However, gene conversion can also lead to genetic disorders if it occurs in an important gene and results in a deleterious mutation.
A gene is a specific sequence of nucleotides in DNA that carries genetic information. Genes are the fundamental units of heredity and are responsible for the development and function of all living organisms. They code for proteins or RNA molecules, which carry out various functions within cells and are essential for the structure, function, and regulation of the body's tissues and organs.
Each gene has a specific location on a chromosome, and each person inherits two copies of every gene, one from each parent. Variations in the sequence of nucleotides in a gene can lead to differences in traits between individuals, including physical characteristics, susceptibility to disease, and responses to environmental factors.
Medical genetics is the study of genes and their role in health and disease. It involves understanding how genes contribute to the development and progression of various medical conditions, as well as identifying genetic risk factors and developing strategies for prevention, diagnosis, and treatment.
An artifact, in the context of medical terminology, refers to something that is created or introduced during a scientific procedure or examination that does not naturally occur in the patient or specimen being studied. Artifacts can take many forms and can be caused by various factors, including contamination, damage, degradation, or interference from equipment or external sources.
In medical imaging, for example, an artifact might appear as a distortion or anomaly on an X-ray, MRI, or CT scan that is not actually present in the patient's body. This can be caused by factors such as patient movement during the scan, metal implants or other foreign objects in the body, or issues with the imaging equipment itself.
Similarly, in laboratory testing, an artifact might refer to a substance or characteristic that is introduced into a sample during collection, storage, or analysis that can interfere with accurate results. This could include things like contamination from other samples, degradation of the sample over time, or interference from chemicals used in the testing process.
In general, artifacts are considered to be sources of error or uncertainty in medical research and diagnosis, and it is important to identify and account for them in order to ensure accurate and reliable results.
Temperature, in a medical context, is a measure of the degree of hotness or coldness of a body or environment. It is usually measured using a thermometer and reported in degrees Celsius (°C), degrees Fahrenheit (°F), or kelvin (K). In the human body, normal core temperature ranges from about 36.5-37.5°C (97.7-99.5°F) when measured rectally, and can vary slightly depending on factors such as time of day, physical activity, and menstrual cycle. Elevated body temperature is a common sign of infection or inflammation, while abnormally low body temperature can indicate hypothermia or other medical conditions.
Nucleic Acid Heteroduplexes | Profiles RNS
Characterization of protein-nucleic acid interactions that are required for transcription processivity
Some regions of nucleic acid targets aren't accessible to heteroduplex formation - DNA Topoisomerase - Synthesis and Structure...
Heteroduplex - Wikipedia
Homeowners caught up in Oak Bay's duplex complexities - Greater Victoria News
Chromosomal instability. Medical search
The solution structure of a DNA*RNA duplex containing 5-propynyl U and C; comparison with 5-Me modifications. - Department of...
oligonucleotide synthesis - WikiChoeclaiste
Enhancement of trans-cleavage activity of Cas12a with engineered crRNA enables amplified nucleic acid detection | bioRxiv
Nucleic Acids Metabolism
Chromosomal Basis of Inheritance: Summary - Botany
Nose2Brain: Better therapy for multiple sclerosis | ScienceDaily
Cardiac Resynchronization Therapy Outcomes in Type 2 Diabetic Patients: Role of MicroRNA Changes
Viruses | Free Full-Text | Effective Reduction of SARS-CoV-2 RNA Levels Using a Tailor-Made Oligonucleotide-Based RNA Inhibitor
HBV Nucleic Acid Analyses - ICE-HBV
The poor homology stringency in the heteroduplex allows strand exchange to incorporate desirable mismatches without sacrificing...
The role of the molecular footprint of EGFR in tailoring treatment decisions in NSCLC | Journal of Clinical Pathology
DNA annealing by Redβ is insufficient for homologous recombination and the additional requirements involve intra- and inter...
Appendix 1 | Rapid Molecular Testing | Laboratory Info | TB | CDC
JBPC Publications: 2000 - 2010 | Marine Biological Laboratory
molecular biology - What makes/breaks the hydrogen bonds between DNA and RNA during transcription? - Biology Stack Exchange
TargetSpy: a supervised machine learning approach for microRNA target prediction | BMC Bioinformatics | Full Text
1hxw - Proteopedia, life in 3D
I2CT - IBMC
3cyx - Proteopedia, life in 3D
I2CT - IBMC
Pesquisa | Prevenção e Controle de Câncer
Walking the interactome to identify human miRNA-disease associations through the functional link between miRNA targets and...
Molecular biology - Karlan
Mutational Analysis | Bio-Rad
PEPTIDE NUCLE1
- Locked or peptide nucleic acids improve OGT nuclease resistance but not specificity. (thno.org)
Hybridization3
- One such example is the heteroduplex DNA strand formed in hybridization processes, usually for biochemistry-based phylogenetic analyses. (wikipedia.org)
- in vitro, they are formed by nucleic acid hybridization. (nih.gov)
- THERESA N. H. LEE, WILLIAM W. BROCKMAN anp DANIEL NATHANS Department of Microbiology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 Accepted February 11, 1975 Two cloned evolutionary variants of simian virus 40 (SV40) containing substitutions of cellular DNA have been characterized by restriction endonuclease analysis, electron microscopic heteroduplex mapping, and DNA-DNA hybridization. (nih.gov)
Homology1
- Electron microscopic analysis of the resulting heteroduplexes facilitates the mapping of regions of base sequence homology of nucleic acids. (nih.gov)
Proteins3
- Saccharomyces cerevisiae Rad51, Rad54, and replication protein A (RPA) proteins work in concert to make heteroduplex DNA joints during homologous recombination. (nih.gov)
- To adhere, mussels secrete adhesive proteins rich in the catecholic amino acid 3,4-dihydroxyphenylalanine (Dopa) and positively charged lysine. (bvsalud.org)
- 1. The proteins encoded by these genes are classified as alpha or beta forms on the basis of the predicted amino acid sequences and have homologs in man. (everypatent.com)
Molecules4
- Double-stranded nucleic acid molecules (DNA-DNA or DNA-RNA) which contain regions of nucleotide mismatches (non-complementary). (nih.gov)
- Remedy of capsid-derived nucleic acids through the DMSO control cells with exogenous RNAseH led to partial conversion of the double-stranded molecules to single-stranded kinds. (mtor-inhibitors.com)
- The use of a lower denaturation temperature in COLD-PCR results in selective denaturation of amplicons with mutation-containing molecules within wild-type mutant heteroduplexes or with a lower melting temperature. (medscape.com)
- The MGH CCIB DNA Core presently can only accept samples for sequencing that are exempt from regulation under the current NIH Guidelines for Research Involving Recombinant or Synthetic DNA Molecules under Section III-F-2, covering nucleic acids that are not in organisms, cells, or viruses and that have not been modified or manipulated (e.g., encapsulated into synthetic or natural vehicles) to render them capable of penetrating cellular membranes. (harvard.edu)
Mismatch2
- Current approaches make use of the mismatch that occurs between complimentary strands of DNA when there is a genetic mutation, the electrophoretic mobility differences caused by small sequence changes, and chemicals or enzymes that can cleave heteroduplex sites. (nih.gov)
- In this system, the transposition of Mu-end DNA at a site is used to indicate the presence of a nucleic acid mismatch or mutation at that site. (nih.gov)
Recombination5
- A heteroduplex is a double-stranded (duplex) molecule of nucleic acid originated through the genetic recombination of single complementary strands derived from different sources, such as from different homologous chromosomes or even from different organisms. (wikipedia.org)
- At various steps of these recombination processes, heteroduplex DNA (double-stranded DNA consisting of single strands from each of the two homologous chromosomes which may or may not be perfectly complementary) is formed. (wikipedia.org)
- During homologous recombination, RecA forms a helical filament on a single stranded (ss) DNA that searches for a homologous double stranded (ds) DNA and catalyzes the exchange of complementary base pairs to form a new heteroduplex. (elifesciences.org)
- Yin Y , Dominska M, Yim E, Petes T. High-resolution mapping of heteroduplex DNA formed during UV-induced and spontaneous mitotic recombination events in yeast. (recombination.dev)
- Mispairs generated by the spontaneous deamination of 5-methylcytosine and heteroduplexes formed following genetic recombination are also corrected via MMR. (diff.org)
Viral4
- Huh7 cells were transfected with genomic expression vectors for HBV genotype A or D isolates, the cells were taken care of with 10 or 50 mM compounds, and viral nucleic acids had been isolated from intracellular HBV capsids just after four days. (mtor-inhibitors.com)
- b) HIV- specific IgM, IgA (IgA1 and IgA2) and IgG, including nonspecific immune factors including SLPI, mucins, lactoferrin, lysozyme and lactoperoxidase, as well as HIV-1 viral load as measured by culture and nucleic acid detection HIV (RNA PCR). (nih.gov)
- The outer protein protective shell of a virus, which protects the viral nucleic acid. (lookformedical.com)
- Sensitivity of Escherichia coli to viral nucleic acid. (wikidata.org)
Polymerase2
- A polymerase chain reaction (PCR) heteroduplex assay (HDA) was developed to identify avian derived mosquito blood meals to the species level. (nih.gov)
- Our results suggest that the distance between the RNase H and polymerase active sites corresponds to the length of a 14-nucleotide RNA-DNA heteroduplex. (cnrs.fr)
Vivo1
- The dominant mutations in the P-loop consensus caused severely reduced repair of heteroduplex DNA in vivo in a mutS mutant host strain. (umassmed.edu)
Genetic4
- As an alternative to extensive DNA sequence analysis, genetic relateness between pairs of HIV quasispecies was estimated using the reduced electrophoretic mobilities of HIV-1 envelope DNA heteroduplexes through polyacrylamide gels. (nih.gov)
- The ability to easily detect small mutations in nucleic acids, such as single base substitutions, can provide a powerful tool for use in cancer detection, perinatal screens for inherited diseases, and analysis of genetic polymorphisms such as genetic mapping or for identification purposes. (nih.gov)
- Deoxyribonucleic acid that makes up the genetic material of viruses. (lookformedical.com)
- Genetic studies with heteroduplex DNA of bacteriophage fl. (wikidata.org)
Chemistry1
- Further improvements in this area such as, introduction of high throughput synthesizers, better coupling reagents, improved polymer supports, newer sets of protecting groups for exocyclic amino groups of nucleic bases and introduction of universal polymer supports have completely revolutionized the entire field of nucleic acids chemistry. (researchgate.net)
Double-stranded2
- The signature of RNAseH inhibition is accumulation of RNA:DNA heteroduplexes that migrate as double-stranded species without exogenous RNAseH remedy but as faster-migrating singlestranded DNAs following RNAseH treatment. (mtor-inhibitors.com)
- The mobility of HBV DNAs from cells replicating HBV genotype A handled with DMSO was unaffected by RNAseH digestion , but treatment method of cells with compound #12 at ten mM blocked production with the slowestmigrating double-stranded forms and led to accumulation of RNA:DNA heteroduplexes whose mobility greater on removal of RNA. (mtor-inhibitors.com)
Molecular1
- 1996. Molecular modelling study of the netropsin complexation with a nucleic acid triple helix . (ibpc.fr)
Bases2
- Also consider adding modified bases, such as 2′- O -methyl (2′-OMe) or Affinity Plus™ locked nucleic acid bases, in chimeric antisense designs to increase nuclease stability and affinity (T m ) of the antisense oligo to the target mRNA [ 1 ]. (idtdna.com)
- By showing that a DNA-protein complex can slide along another DNA molecule to search for a target, these results could lead to new insights into other systems in which it is necessary for protein-nucleic acid complexes to locate a particular sequence of bases. (elifesciences.org)
Mismatches1
- When mismatches occur in heteroduplex DNA, the sequence of one strand can be repaired to bind the other strand with perfect complementarity. (wikipedia.org)
Assay2
- and (e) Replication kinetics and heteroduplex mobility assay (HMA). (nih.gov)
- This assay utilizes a DNA endonuclease with single-strand cleavage activity specific to heteroduplex structures (Figure 1). (stemcell.com)
Rad543
- Functional cross-talk among Rad51, Rad54, and replication protein A in heteroduplex DNA joint formation. (nih.gov)
- 2. Rad54 protein stimulates heteroduplex DNA formation in the synaptic phase of DNA strand exchange via specific interactions with the presynaptic Rad51 nucleoprotein filament. (nih.gov)
- In the resulting pairing intermediate, the Rad54 motor protein displaces Rad51, while threading out a heteroduplex DNA (hDNA) and a displaced strand, to create a stable intermediate called the displacement loop (or D-loop) ( Wright and Heyer, 2014 ). (elifesciences.org)
19971
- 1997 Nucleic acids Res. (lbl.gov)
Mutation1
- The surprising discovery that the Mu transposase displays a strong preference for inserting Mu-end DNA into mismatched sites, the very sites which occur when DNA is mutated and paired with its complimentary strand that does not have the corresponding mutation, makes it a powerful tool for detecting variations in nucleic acid sequences. (nih.gov)
DNAs2
- Replicate nucleic acid aliquots had been mock taken care of or taken care of with DNAse-free E. coli RNAseH to destroy RNA:DNA heteroduplexes, after which HBV DNAs had been detected by Southern blotting. (mtor-inhibitors.com)
- All four possible dI-containing heteroduplex DNAs, including A-I, C-I, G-I, and T-I were introduced to repair reactions containing extracts from human cells. (biomedcentral.com)
Detection1
- Microarray technology has become an important tool for detection and analysis of nucleic acid targets. (researchgate.net)
Antisense2
- these heteroduplexes result from performing antisense techniques using single-stranded peptide nucleic acid, 2'-O-methyl phosphorothioate or Morpholino oligos to bind with RNA. (wikipedia.org)
- the synthetic oligonucleotide is introduced into the cell and hybridizing on the target mRNA leads to the cleavage of the mRNA by the RNAse H. The antisense oligonucleotides with a portion of DNA modified or not with phosphotiorate, can form heteroduplexes with the target RNA, degrading it and preventing the translation of the protein of interest. (biofabresearch.com)
Mutations2
- Nine of these mutations altered the P-loop motif of the ATP-binding site, resulting in four amino acid substitutions. (umassmed.edu)
- With one exception, the remaining sequenced mutations all caused substitution of amino acids conserved during evolution. (umassmed.edu)
Structures1
- In the presence of an NNRTI, the RNA/DNA structure differs from all prior nucleic acid-RT structures including the RNA/DNA hybrid. (nih.gov)
Analysis1
- The methods of the invention relate generally to amplification of nucleic acid on a solid support and analysis of the amplified nucleic acid. (justia.com)
Isolation1
- Since the isolation of nucleic acids to the mapping of human genome, chemical synthesis of nucleic acids has undergone tremendous advancements. (researchgate.net)
Viruses1
- Viruses whose nucleic acid is DNA. (lookformedical.com)
Residues1
- Catalytic activity of the recombinant protein was detected only when amino acid residues encoded by the integrase gene were added to the N-terminus of the reverse transcriptase-RNase H domain. (cnrs.fr)
Base1
- Upon combining these two solutions, the researcher adds ammonium persulfate to form a crystal clear 6% 19:1 electrophoresis matrix containing 1X TBE (89 mM tris base, 89 mM boric acid, 2 mM EDTA, pH 8.3) and 6M urea. (nationaldiagnostics.com)
Accumulation1
- mRNA accumulation is modulated by abscisic acid. (or.jp)
Rapid1
- The simple and rapid technique of DNA heteroduplex tracking can therefore assist epidemiological investigations of HIV transmission and potentially of other genetically variable infectious agents. (nih.gov)
Research2
- Nucleic acids research. (rochester.edu)
- 6-TET is widely used in nucleic acid sequencing and related research. (aatbio.com)
Investigations1
- These same assays have also been leveraged for highly parallel quantitative investigations of the structure-function relationships of nucleic acid interactomes. (nature.com)
Structure1
- Crosslinker with a 1,2-diol structure that may be oxidatively cleaved by periodic acid. (nationaldiagnostics.com)
Wild-type1
- DNA from edited cells may reanneal with DNA from non-edited (wild-type) cells to create a heteroduplex. (stemcell.com)