• Next-generation sequencing (NGS) is a powerful technology for basic research and clinical applications because it can sequence hundreds of billions of DNA nucleotides in parallel in a single experiment. (justia.com)
  • Thus, 0.5 to 1% of all nucleotides are no real variants but incorrect sequence information which is generated during sample processing. (justia.com)
  • The article was also received and subsequently accepted and published by Nucleosides, Nucleotides this website and Nucleic Acids [3]. (peptide-solubility.com)
  • Apart from the long chain of nucleic acids, nucleotides also occur in cyclic forms. (biologyonline.com)
  • a]Nitrogen is found in amino acids, the monomers of proteins, and in the nitrogenous bases that make up nucleotides (the monomers of nucleic acids). (learn-biology.com)
  • It is a single stranded nucleic acid, composed of RNA nucleotides . (pediaa.com)
  • Moreover, as the word 'coding' refers to the relationship between nucleic acids and proteins, rather than the mere transcription of DNA into RNA, it is logical to call the strand with the mRNA sequence the coding strand, as in the first example. (genomicglossaries.com)
  • Isotype or positive controls by peptides, antibodies and deactivated samples.Aplha, transcription related growth factors and stimulating factors or repressing nuclear factors are complex subunits of proteins involved in cell differentiation. (homeodomains.com)
  • In addition to the well-established sense-antisense complementarity abundantly present in the nucleic acid world and serving as a basic principle of the specific double-helical structure of DNA, production of mRNA, and genetic code-based biosynthesis of proteins, sense-antisense complementarity is also present in proteins, where sense and antisense peptides were shown to interact with each other with increased probability. (usf.edu)
  • In proteins, the complementarity between sense and antisense peptides depends on a specific hydropathic pattern, where codons for hydrophilic and hydrophobic amino acids in a sense peptide are complemented by the codons for hydrophobic and hydrophilic amino acids in its antisense counterpart. (usf.edu)
  • Crucially, the sequence of bases in DNA contains the information for making proteins. (rainis.pics)
  • containing a basic amino group, an acidic carboxyl group, and a side chain attached to an alpha carbon atom, and that link together by peptide bonds to form proteins, or that function as chemical messengers and as intermediates in metabolism. (nih.gov)
  • Chymotrypsin -- A protease that catalyses the hydrolysis (the breakdown) of proteins into peptides or amino acids in the small intestine. (nih.gov)
  • Cysteine -- A sulfur-containing nonessential amino acid produced by the enzymatic or acid hydrolysis of proteins. (nih.gov)
  • Glutamic acid -- A nonessential amino acid occurring in proteins. (nih.gov)
  • After analysis of deduced amino acid sequences from cloned cDNAs of dipeptidyl peptidase IV (DPP IV) and aminopeptidase A (APA), it was noticed that DPP IV and APA are type II membrane proteins that have one transmembrane domain near the N-terminus. (nature.com)
  • Produced by a variety of cell types, extracellular vesicles (EVs) are able to transfer lipids, nucleic acids and proteins to recipient cells. (nature.com)
  • Protein location can be predicted either from the sequence of a protein alone by identification of targeting peptide sequences and motifs, or by homology to proteins of known location. (biomedcentral.com)
  • A third approach, which is complementary, exploits the differences in amino acid composition of proteins associated to different cellular locations, and can be useful if motif and homology information are missing. (biomedcentral.com)
  • For stage one, we trained multiple Support Vector Machines (SVMs) to score eukaryotic protein sequences for membership to each of three categories: nuclear, cytoplasmic and extracellular, plus extra category nucleocytoplasmic, accounting for the fact that a large number of proteins shuttles between those two locations. (biomedcentral.com)
  • Calibration of the method using predicted values of amino acid exposure allows classifying proteins without 3D-information with an accuracy of 62% and discerning proteins in different locations even if they shared high levels of identity. (biomedcentral.com)
  • Therefore computational prediction of protein features from their sequence is often used for designing strategies for experimental characterization of proteins and is also important for genome annotation and drug target identification [ 4 , 5 ]. (biomedcentral.com)
  • While DNA is responsible for storing genetic information, it is RNA that codes for the synthesis of amino acids and carries information between ribosomes and DNA, allowing ribosomes to make proteins. (databasefootball.com)
  • mRNA copies the genetic code from DNA and brings this information to the ribosomes, which are able to read the sequences of A, G, C and U. Thanks to this process the correct proteins will be synthesized by the ribosomes, and the mRNA will then typically break apart. (databasefootball.com)
  • In proteins, the secondary structure is determined by hydrogen bonds between the CO and NH groups of the peptide backbone. (zxc.wiki)
  • PNAs are able to bind with high affinity and sequence specificity to a complementary DNA sequence through Watson-Crick base pairing binding and are able to form triple helices through parallel orientation Hoogsteen bonds with the PNA facing the 5'-end of the DNA strand. (wikipedia.org)
  • The PNA-DNA triplex are stable because PNAs consist of a neutrally charged pseudopeptide backbone which binds to bind to the double stranded DNA (dsDNA) sequence. (wikipedia.org)
  • Similar to homopyrimidine in TFOs, homopyrimidine in PNAs are able to form a bond with the complementary homopurine in target sequence of the dsDNA. (wikipedia.org)
  • Peptide nucleic acids (PNAs) 1 are synthetic structural homologues of DNA and RNA in which the entire phosphate-sugar backbone of the polynucleotide has been replaced by a flexible polyamide backbone consisting of 2-aminoethyl glycine units. (archive.org)
  • Studies of homopyrimidine and homopurine PNAs show that this rapid and highly specific association with the complementary DNA strand is followed by the addition of a second PNA molecule to the PNA⅐DNA duplex to form a very stable (PNA) 2 -DNA triplex, while the noncomplementary DNA strand is left in the single-stranded state (8 -10). (archive.org)
  • We have tested the effects of PNAs complementary to the CAG triplet repeats that occur in many genes involved in transcriptional control. (archive.org)
  • We have now tested the effects of CAG-specific and c-mycspecific PNAs on AR, TBP, and c-myc transcription in human prostatic cancer cell lines, and we now show that each PNA can selectively target its complementary DNA sequence in the intact chromatin of permeabilized cells. (archive.org)
  • We analyzed certified reference materials containing different amounts of genetically modified DNA by using a detection method which combines the nanoparticle-enhanced surface plasmon resonance imaging (SPRI) biosensing to the peptide nucleic acids (PNAs) improved selectivity and sensitivity in targeting complementary DNA sequences. (cnr.it)
  • Bahal studied peptide nucleic acids (PNAs), a synthetic analogue of DNA or RNA, in the Department of Chemistry at Carnegie Mellon. (uconn.edu)
  • The objective of this work was to synthesize an antisense peptide nucleic acid (PNA) complementary to the first six codons of the bcl-2 open reading frame, conjugated to a membrane-permeating peptide for intracellular delivery, and modified with a bifunctional chelating agent for targeting imaging and therapeutic radiometals to tumors overexpressing bcl-2. (nih.gov)
  • Four peptide-PNA constructs were synthesized by a combination of manual and automated stepwise elongation techniques, including bcl-2 antisense conjugates and nonsense conjugates with no complementarity to any known mammalian gene or DNA sequence. (nih.gov)
  • Scanning confocal fluorescence microscopy of TMR-labeled ri-PTD-4-G-anti-bcl-2 PNA in Raji lymphoma cells demonstrated that the retro-inverso peptide was active in membrane permeation and mediated cellular internalization of the antisense PNA into the cytoplasm, where high concentrations of bcl-2 mRNA are expected to be present. (nih.gov)
  • Synthetic antisense DNAs are used to hybridize to complementary sequences in target RNAs or DNAs to effect the functioning of specific genes for investigative or therapeutic purposes. (genomicglossaries.com)
  • In nucleic acids, sense-antisense complementarity is achieved via the Watson-Crick complementarity of the base pairs or nucleotide pairing. (usf.edu)
  • We are showing here that in addition to this pattern of the complementary hydrophobicity, sense and antisense peptides are characterized by the complementary order-disorder patterns and show complementarity in sequence distribution of their disorder-based interaction sites. (usf.edu)
  • Synthesis of the DOTA-PNA conjugates was followed by automated elongation with a peptide sequence (PTD-4-glycine, PTD-4-G), known to mediate cellular internalization of impermeable effector molecules, or its retro-inverso analogue (ri-PTD-4-G). Preparation of the four conjugates required an innovative synthetic strategy, using mild acid conditions to generate hydrophobic, partially deprotected intermediates. (nih.gov)
  • Bahal's research interests are trifold: the development of synthetic nucleic acid molecules for correcting genes that cause disorders like sickle cell disease, selectively targeting cancer-causing genes, and establishing efficient delivery system for these molecules. (uconn.edu)
  • Nucleic acids, DNA and RNA, can be considered as the information molecules of the cell. (rainis.pics)
  • Aptamers (from the Latin aptus ("- fit") and Greek meros ("-part") that are oligonucleotides (since other aptamers can be peptide molecules) are created usually from a large random sequence pool and used mainly for research and clinical applications (e.g. as macromolecular drugs). (biologyonline.com)
  • Nucleic acids are the molecules of genetics and heredity, and includes DNA and RNA. (learn-biology.com)
  • Some RNA molecules are capable of folding into a three-dimensional structure known as hairpin loops via complementary base pairing. (pediaa.com)
  • Then, the translation of the genetic code in the mRNA molecule begins and tRNA molecules recognize the codon sequences in the mRNA. (pediaa.com)
  • In peptide nucleic acid (PNA), the sugar-phosphate backbone of DNA is replaced with a protein-like backbone. (wikipedia.org)
  • Phosphorus is found in the sugar-phosphate backbone of nucleic acids, in phospholipids, and in the energy transfer molecule ATP. (learn-biology.com)
  • These biological oligomers and polymers can be Solid-phase peptide synthesis (SPPS), or in continue produced for custom peptide synthesis projects. (homeodomains.com)
  • The High-efficiency solid phase peptide synthesis (HE-SPPS) is give very low production costs.The activation of transcription factor subunits is the first step of gene expression, in which a particular segment of DNA is copied into RNA (mRNA) by the enzyme RNA polymerases. (homeodomains.com)
  • The complementary structure immediately suggested to Watson and Crick how DNA could (and does) replicate, and further explains how information from DNA is transferred to RNA for protein synthesis. (rainis.pics)
  • During her M.S., she focused on the development of fluorescent amino acids and peptide synthesis. (rsc.org)
  • Oligomers are produced synthetically through solid-phase chemical synthesis for use in PCR (polymerase chain reaction, where the oligosaccharide used is referred to as the primer ), DNA sequencing, DNA microarrays, Southern blots, ASO analysis, FISH (florescent in situ hybridization), molecular probing, and library construction. (biologyonline.com)
  • Peptide nucleic acids are synthetic oligonucleotides that resist protease degradation and are used to induce repair at site specific triplex formation regions on DNA genomic sites. (wikipedia.org)
  • Dynamic and flexible nucleic acid models can provide current and future scientists with physical intuition for the structure of DNA and the ways that DNA and its synthetic mimics can be used to build self-assembling structures and advanced nanomachines. (allenpress.com)
  • till polypeptides that are long, continuous, and unbranched synthetic peptide chains. (homeodomains.com)
  • Later in his career while completing his doctorate at Carnegie Mellon University, Bahal's research moved toward the field of synthetic nucleic acids. (uconn.edu)
  • Synthetic nucleic acids are chemically modified analogues of DNA or RNA, the genetic material that directs all cellular functions. (uconn.edu)
  • Synthetic nucleic acids offer a promising approach for treatment of a variety of disorders. (uconn.edu)
  • Bahal's work on delivery systems for synthetic nucleic acid analogs like PNA is an essential piece of the treatment puzzle. (uconn.edu)
  • I have been intrigued by the activity of antimicrobial peptides for a long time, due to my interest in biological membranes. (rsc.org)
  • Antimicrobial peptides have long been hailed as a solution to the antibiotic resistance crisis, because they target the bacterial membrane and can cause quick bactericidal activity in bacterial cells. (rsc.org)
  • Most antimicrobial peptides are cationic amphiphilic compounds that function by binding to the negatively charged lipids of bacterial membranes, followed by membrane disruption. (rsc.org)
  • While binding to the lipid headgroup is detrimental for anion transport, I hypothesized that binding to the headgroup can provide membrane selectivity (e.g., bacterial membranes over human membranes) and can induce membrane perturbations similar to those observed for antimicrobial peptides. (rsc.org)
  • The phosphate groups and the sugar moieties form the backbone of a nucleic acid. (biologyonline.com)
  • With the exception of the beta loops and random coils , these areas are characterized by the fact that the only two possible angles of rotation ψ and φ of the peptide backbone are fixed in them and repeat themselves periodically over the length of the secondary structural element. (zxc.wiki)
  • The nucleotide sequence of a gene is transcribed into a messenger RNA molecule by the enzyme, RNA polymerase. (pediaa.com)
  • The opposing pairing of complementary base sequences is made possible in a special way by palindromic sequences in the nucleotide sequence of a nucleic acid strand. (zxc.wiki)
  • TFOs bind specifically to homopurine-homopyrimidine regions that are often common in promoter and intron sequences of genes, influencing cell signaling. (wikipedia.org)
  • The DNA sequence of the genes for the androgen receptor (AR) and TATA-binding protein (TBP), like many other genes encoding transcription factors, contains a series of tandem CAG repeats. (archive.org)
  • Conversely, a PNA complementary to a unique sequence of the c-myc gene did not inhibit transcription of the AR or TBP genes but did inhibit c-myc transcription. (archive.org)
  • NFKB 105 subunit for example is a polypetide gene enhancer of genes in B cells.Peptides short amino acid chains or epitopes or blocking antagonists. (homeodomains.com)
  • DNA, or deoxyribonucleic acid -- The primary genetic material of all cellular organisms and the DNA viruses. (nih.gov)
  • Deoxyribonucleic acid, or DNA, is often referred to as the building blocks for life. (databasefootball.com)
  • TFOs are short (≈15-25 nt) nucleic acid strands that bind in the major groove of double-stranded DNA to form intramolecular triplex DNA structures. (wikipedia.org)
  • Molecular biologists describing DNA sequences or referring to one of the two strands of double- stranded DNA frequently use complementary pairs of terms, such as coding/ non- coding, sense/ nonsense or transcribing/ non- transcribing. (genomicglossaries.com)
  • DNA is famous for its "double helix" structure, two intertwining strands with complementary bases. (databasefootball.com)
  • The absence of phosphate groups in the PNA molecule facilitates its invasion of negatively charged DNA duplexes containing the complementary base sequences (4 -6). (archive.org)
  • Yet DNA has a complementary molecule known as RNA. (databasefootball.com)
  • A specific amino acid is attached to the acceptor of the tRNA molecule. (pediaa.com)
  • The anticodon site of the tRNA molecule is capable of recognizing the complementary codon sequence in the mRNA molecule. (pediaa.com)
  • The specific amino acid carried by the tRNA molecule is attached to the growing polypeptide chain via a peptide bond. (pediaa.com)
  • The prerequisite for this is that the nucleic acid molecule is initially available as a single strand. (zxc.wiki)
  • All recognized mutations for AD are associated with increased deposition of amyloid-beta (Abeta), a peptide fragment comprising 39-43 amino acids that derive from the catabolism of the amyloid precursor protein (APP) molecule. (medscape.com)
  • Cistron -- A basic unit of hereditary material, it is the smallest genetic unit that must be intact to function as a transmitter of genetic information, i.e., to determine the sequence of amino acids of one polypeptide chain. (nih.gov)
  • Building on previous research, representative nucleic acid duplexes were split into logical monomer segments, and atomic coordinates were used to create solid models for 3D printing. (allenpress.com)
  • It is selective for peptide bonds with aromatic or large hydrophobic side chains on the carboxyl side of this bond. (nih.gov)
  • NA sequences downstream of the site of PNA⅐DNA hybridization, but not upstream of that site. (archive.org)
  • Each unit is linked to an appropriate purine or pyrimidine base to create the sequence required for hybridization to the targeted nucleic acid (1-3). (archive.org)
  • The method allowed us to obtain a 41 zM sensitivity in targeting genomic DNA even in the presence of a large excess of non-complementary DNA. (cnr.it)
  • Currently, most protein sequences in databases are the result of translation of hypothetical transcripts derived from genomic sequencing data [ 3 ]. (biomedcentral.com)
  • However, after genome sequencing it is critical to identify and demarcate the functional elements in the genome (structural annotation) and to link these genomic elements to biological function (functional annotation). (biomedcentral.com)
  • The formation of peptide bonds between incoming amino acid and the existing amino acid is governed by rRNA in the ribosome. (pediaa.com)
  • Depending on the distance remaining hydrogen bonds occur, give the the helices of α-helix , π-helix , 3 10 helix show the following hydrogen bonds: various helices (with different diameters or number of amino acids per turn). (zxc.wiki)
  • Complementary sections of the strand can then form hydrogen bonds, which leads to the formation of intramolecular base pairs with a double-stranded structure. (zxc.wiki)
  • The 2H relaxation data also provided information about the orientational order and internal motion of OD and ND bonds in side-chains and surface peptides. (lu.se)
  • When a PNA mol-ecule invades a targeted DNA sequence, one strand of the DNA is displaced (1, 5, 6, 9) , whereas the PNA binds quickly to its complementary DNA sequence by Watson-Crick base pairing (7). (archive.org)
  • We have shown previously that a biotinylated PNA targeted to CAG repeats will strand invade those DNA sequences in their transcriptionally active states in intact chromatin (21). (archive.org)
  • When DNA sequences are described by giving the sequence of only one strand, this is usually the strand with the same sequence as the RNA (messenger, ribosomal, transfer, etc.) and should therefore be called the coding strand. (genomicglossaries.com)
  • DNA that is complementary to the sense strand. (genomicglossaries.com)
  • The sense strand has the same sequence as the mRNA transcript. (genomicglossaries.com)
  • During transcription, a DNA sequence is read by an RNA polymerase, which produces a complementary, anti-parallel RNA strand called a primary transcript. (homeodomains.com)
  • TFOs can inhibit transcription by binding with high specificity to the DNA helix, thereby blocking the binding and function of transcription factors for particular sequences. (wikipedia.org)
  • One nucleic acid monomer, ATP, is also life's key energy currency. (learn-biology.com)
  • Germination of spores occurs in response Celecoxib to nutrients (or germinants) which are often single amino acids, sugars or purine nucleosides, and is initiated by binding of germinants to receptors located in the spore's inner membrane [69, 70]. (peptide-solubility.com)
  • PNA-LNA mediated LAMP reactions occurred under isothermal temperature conditions of with 4 primary primers set for the target regions on the KRAS gene, clamping PNA probe that was complimentary to the wild type sequence and LNA primers complementary to the mutated sequences. (nbrp.jp)
  • Competition of LNA clamping primers complementary to two different subtypes (G12D and G12V) of mutant KRAS gene indicated different amplification time depend on subtypes of mutant cDNA. (nbrp.jp)
  • As more research labs and classrooms dive into the field of structural nucleic acid nanotechnology, students and researchers need access to interactive, dynamic, handheld models. (allenpress.com)
  • In the structural modification of PNA, there are few types of base modification, mainly the introduction of monomers composed of pseudocytosine, in order to make the modified peptide nucleic acid and DNA form a triple helix without pH dependence. (creative-peptides.com)
  • Depending on the type of secondary structural element, certain amino acid side chains can have a destabilizing effect on its structure. (zxc.wiki)
  • The complete protein structure (i.e. the sequence or arrangement of the secondary structural elements) is called the tertiary structure. (zxc.wiki)
  • However, systems biology from functional genomics data is hindered in agricultural species because agricultural genome sequences have relatively poor structural and functional annotation and agricultural research communities are smaller with limited funding compared to many model organism communities. (biomedcentral.com)
  • A nucleotide is regarded as the basic building block of nucleic acid polymers (e.g. (biologyonline.com)
  • They can bind to the desired complementary sequence, thereby, can target specific RNAs. (biologyonline.com)
  • This allowed us to determine that the heparan sulfate pathway and the conserved oligomeric Golgi complex are key determinants allowing entry of both dsRNA and viral nucleic acid leading to cell death. (cnrs.fr)
  • 89, No. 21: 10537, 1992), a relatively non-toxic peptide that disrupts viral fusion thereby protecting CD4+ lymphocytes from de novo infection. (justia.com)
  • This pD dependence is due to labile protein deuterons in acidic side-chains and surface peptide groups, which exchange rapidly with water deuterons. (lu.se)
  • By studying nucleic acid chemistry, researchers can directly target the DNA at the core of several genetic disorders. (uconn.edu)
  • Accordingly, the technical problem underlying the present invention is the provision of means and methods to provide a reliable way of nucleic acid sequencing, in particular the identification of variations in the genome. (justia.com)
  • These intermediates were purified by semipreparative reversed-phase HPLC and completely deprotected to yield pure peptide-PNA conjugates in 6% to 9% overall yield. (nih.gov)
  • Recent studies have revealed an extensive superfamily of UDP-glucuronosyltransferases (UGTs), 2 previously termed glucuronyl transferases, which catalyze the conjugation of UDP-glucuronic acid with lipid-soluble substrates to form polar conjugates that are excreted in the urine and feces. (aspetjournals.org)
  • Technologies today available for the DNA detection rely on a combination of labeled probes hybridized to target sequences which are amplified by polymerase chain reaction (PCR). (cnr.it)
  • Upon the binding of receptors to germinants, release of cations and dipicolinic acid (DPA) occurs through hypothetical membrane channels. (peptide-solubility.com)
  • article{, title = {Comprehensive features of natural and in vitro selected GNRA tetraloop-binding receptors}, author = { C. Geary and S. Baudrey and L. Jaeger}, year = {2008}, date = {2008-01-01}, journal = {Nucleic Acids Res}, volume = {36}, number = {4}, pages = {1138-52}, abstract = {Specific recognitions of GNRA tetraloops by small helical receptors are among the most widespread long-range packing interactions in large ribozymes. (cnrs.fr)
  • The present invention relates to methods and systems for nucleic acid sequencing. (justia.com)
  • In particular, the present invention relates to methods and systems for reducing the number of false-positives in nucleic acid sequencing. (justia.com)
  • Such methods and systems of the invention can, e.g., be employed to identify (a) variation(s) in the nucleic acid sequence of a subject. (justia.com)
  • Custom Workflow for the Confident Identification of Sulfotyrosine-Containing Peptides and Their Discrimination from Phosphopeptides. (liverpool.ac.uk)
  • Plasma stability studies showed that (111)In-DOTA-labeled ri-PTD-4-G-anti-bcl-2 PNA was stable for 168 h at 37 degrees C, unlike the conjugate containing the parent peptide sequence. (nih.gov)
  • They have strong sequence stability when hybridizing PNA with DNA and RNA, can even form a stable triplex with DNA or RNA duplex. (creative-peptides.com)
  • With advances in genetic sequencing technology, scientists can identify the exact nucleic acid sequence of a gene as well as the disease-causing mutation. (uconn.edu)
  • Non-complementary sections remain single-stranded. (zxc.wiki)
  • An additional challenge for nucleic acids is that more than simply entering the cytoplasm of the cell, they need to enter the nucleus and bind to a specific part of the DNA which is tightly packed into chromosomes. (uconn.edu)
  • An effective nucleic acid therapy is of no use if it is unable to make its way into the cells where it interacts with the target DNA or RNA. (uconn.edu)