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Topic: Phosphodiester bond

Related Topics

Phosphodiesterase

DNA ligase

Cyclic adenosine monophosphate

Adenosine triphosphate

Hydrolysis

Ester

Cyclic guanosine monophosphate

Functional group

Ethyl acetate

Carbon

Ether

Organic compound

Crystallography

Organic chemistry

CAS registry number

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	Using Thiol-Modified Oligos
		Resuspend the lyophilized oligonucleotide in TE, pH 8.3 - 8.5 at a concentration of approximately 100 A260 units/milliliter.
		Reduce the disulfide bond by treatment with 0.1 M DTT (dithiothreitol) at room temperature for 30 minutes.
		Remove the excess DTT from the supernatant by gel filtration and proceed directly to the conjugation reaction.
	www.oligos.com /thiolModified.htm (347 words)

	Phosphodiester bonds - Definition, explanation
		In DNA and RNA, the phosphodiester bond is the linkage between the 3' Carbon atom and the 5' Carbon of the ribose sugar.
		In order for the phosphodiester bond to be formed and the nucleotides to be joined, the tri-phosphate or di-phosphate forms of the nucleotide building blocks are broken apart to give off energy required to drive the enzyme-catalyzed reaction.
		A phosphodiesterase is an enzyme that catalyzes the hydrolysis of phosphodiester bonds, for instance a bond in a molecule of cyclic AMP or cyclic GMP.
	www.calsky.com /lexikon/en/txt/p/ph/phosphodiester_bonds.php (340 words)

	Phosphodiester_bond - The Wordbook Encyclopedia (Site not responding. Last check: )
		In DNA and RNA, the phosphodiester bond is the linkage between the 3' carbon atom and the 5' Carbon of the ribose sugar.
		In order for the phosphodiester bond to be formed and the nucleotides to be joined, the tri-phosphate or di-phosphate forms of the nucleotide building blocks are broken apart to give off energy required to drive the enzyme-catalyzed reaction.
		A phosphodiesterase is an enzyme that catalyzes the hydrolysis of phosphodiester bonds, for instance a bond in a molecule of cyclic AMP or cyclic GMP.
	www.thewordbook.com /Phosphodiester_bond (369 words)

	Bambooweb: Phosphodiester bonds
		A phosphodiester bond is a group of strong covalent bonds between the phosphorous atom in a phosphate group and two other molecules over two ester bonds.
		Phosphodiester bonds are central to all life on Earth as they make up the backbone of the strands of DNA.
		Phosphodiester bonds can be catalyzed by the action of phosphodiesterases which play an important role in repairing DNA sequences.
	www.bambooweb.com /articles/p/h/Phosphodiester_bonds.html (259 words)

	A labile phosphodiester bond at the ligation junction in a circular intervening sequence RNA -- Zaug et al. 224 (4649): ...
		A labile phosphodiester bond at the ligation junction in a circular intervening sequence RNA -- Zaug et al.
		A labile phosphodiester bond at the ligation junction in a circular intervening sequence RNA
		The circular molecule undergoes slow reopening at a single phosphodiester bond, the one that was formed during cyclization.
	www.sciencemag.org /cgi/content/abstract/224/4649/574 (572 words)

	Analysis of Incision Sites Produced by Human Cell Extracts and Purified Proteins during Nucleotide Excision Repair of a ...
		A location of the major 3` incision 9 phosphodiester bonds from the cisplatin adduct was unexpected, because previous studies have shown that the human NER system incises pyrimidine dimer-containing DNA principally at the 5th phosphodiester bond on the 3` side of the lesion(1, 2).
		The position of the major 3` incision at the 9th phosphodiester bond from the lesion and the predominant formation of a 26-mer platinated oligonucleotide suggested that the major 5` incision was made 16 phosphodiester bonds 5` to the lesion.
		The main incisions produced by mammalian cell extracts and purified proteins are on the damaged DNA strand at the 16th phosphodiester bond 5` to the lesion and at the 9th phosphodiester bond 3` to the lesion, resulting in the release of a 26-mer oligonucleotide.
	www.jbc.org /cgi/content/full/271/12/7177 (8242 words)

	Highbeam Encyclopedia - Search Results for bond
		phosphodiester bond A bond between two molecules that is formed by phosphoric acid, which is esterified once to each molecule.
		Correlation between concrete-to-concrete bond strength and the roughness of the substrate surface.
		Bond package approval paves way for a wave of new schools.
	www.encyclopedia.com /SearchResults.aspx?Q=bond (523 words)

	NationMaster - Encyclopedia: Deoxyribonucleotide (Site not responding. Last check: )
		The nitrogenous base is always bonded to the 1' carbon of the deoxyribose, which is distinguished from ribose by the presence of a proton on the 2' carbon rather than an -OH group.
		When deoxyribonucleotides polymerize to form DNA, the phosphate group from one nucleotide will bond to the 3' carbon on another nucleotide, forming a phosphodiester bond via dehydration synthesis.
		Diagram of phosphodiester bonds between nucleotides A phosphodiester bond is a group of strong covalent bonds between the phosphorus atom in a phosphate group and two other molecules over two ester bonds.
	www.nationmaster.com /encyclopedia/Deoxyribonucleotide (479 words)

	Experimental Testing of Theories of an Early RNA World
		A plethora of models have proposed that the catalytic ability of primordial ribozymes may have extended well beyond simple phosphodiester bond transfers, and that ribozymes may have been involved in processes that ranged from self- replication to the biosynthesis of primary metabolites.
		The bounds of RNA catalysis have already expanded beyond phosphodiester bond rearrangements with the discovery of ribozyme esterase'2~ and peptidyl-transferase'2b activities, and in the next few years seminal enzymes such as kinases, oxidoreductases, and, most importantly, replicases should be added to this list.
		Essentially, an ester bond was foreed into the active site of a group I intron by tethering an amino acid (methionine) to an oligoribonucleotide sequence that would normally position a phosphodiester bond in the active site for cleavage.
	biotech.icmb.utexas.edu /pages/science/bkup_of_RNA.html (4746 words)

	ArchaeologyInfo.com Glossary
		peptide bond: A covalent bond in a polypeptide chain that joins the a-carboxyl group of one amino acid to the a-amino group of the adjacent amino acid.
		phosphodiester bond: A covalent bond in RNA and DNA between a sugar and a phosphate.
		Phosphodiester bonds form the repeating sugar-phosphate array of the backbone of DNA and RNA.
	www.archaeologyinfo.com /glossaryp.htm (4263 words)

	The Nucleic Acid Chain
		In a nucleic acid chain, two nucleotides are linked by a phosphodiester bond, which may be formed by the condensation reaction (Figure 3-A-5) similar to the formation of the peptide bond.
		However, the whole nucleic acid chain is usually synthesized by RNA polymerase or DNA polymerase.
		Formation of the phosphodiester bond through the condensation reaction.
	www.web-books.com /MoBio/Free/Ch3A5.htm (244 words)

	Kirjasto - Turun yliopisto
		RNA phosphodiester bonds are cleaved by an intramolecular transesterification reaction initiated by an attack of the neighbouring hydroxy group on the phosphorus atom.
		Toward this goal, the reactivity of phosphodiester bonds within linear single-stranded oligonucleotides of varying base sequence and within different secondary structures was examined experimentally, and the structures of these compounds were investigated theoretically.
		In summary, the cleavage of phosphodiester bonds within polymeric RNA molecules is a complicated phenomenon that is affected by several factors.
	kirjasto.utu.fi /julkaisupalvelut/ai/annaalit/AI314.html (431 words)

	PPT Slide (Site not responding. Last check: )
		Each of these reactions is a so-called transesterification reaction, that is, one phosphodiester bond is exchanged for another.
		Since the branch site adenosine is part of the RNA polynucleotide chain, its 3' hydroxyl is already involved in a covalent bond (the 3', 5' phosphodiester bond).
		Attack by this 2' hydroxyl breaks the bond at the 5' end of the intron by forming a bond between the 5' end of the intron and this branch site adenosine.
	www3.kumc.edu /jcalvet/bioc801f/sld005.htm (214 words)

	Merck & Company, Inc. - Phosphodiester bond hydrolysis in pneumococcal polys...
		Investigators have studied the base hydrolysis of phosphodiester bonds in pneumococcal polysaccharides.
		According to recent research published in the journal Biopolymers, "A comprehensive study of the base hydrolysis of all phosphodiester bond-containing capsular polysaccharides of the 23-valent pneumococcal vaccine is described here.
		Capsular polysaccharides from serotypes 6B, 10A, 17F, 19A, 19F, and 20 contain a phosphodiester bond that connects the repeating units in these polysaccharides (also referred to as backbone phosphodiester bonds), and polysaccharides from serotypes 11A, 15B, 18C, and 23F contain a phosphodiester bond that links a side chain to their...
	www.newsrx.com /newsletters/Biotech-Week/2004-11-10/11102004333553UW.html (177 words)

	[No title]
		Ligase can only synthesize a phosphodiester bond if it has a 5' phosphate and 3' OH.
		So it will synthesize phosphodiester bond between the 3' OH of the vector and 5' phosphate of the insert on one strand and the same kind of bond on the opposite strand..
		But when the 3' OH of the insert meets with the 5' end of the vector (where the phosphate used to be before dephosphorylation) there is no phosphate and hence no phosphodiester bond.
	www.protocol-online.org /forums/index.php?showtopic=16738&mode=linearplus (302 words)

	Nuclease Summary
		Enzymes that cleave the phosphodiester bonds of DNA are called deoxyribonucleases, and enzymes that cleave the phosphodiester bonds of RNA are called ribonucleases.
		The exonucleases are involved in trimming the ends of RNA and DNA polymers, cleaving the last phosphodiester bond in a chain.
		A nuclease is an enzyme capable of cleaving the phosphodiester bonds between the nucleotide subunits of nucleic acids.
	www.bookrags.com /Nuclease (2581 words)

	The C-terminal half of UvrC protein is sufficient to reconstitute (A)BC excinuclease.
		In vivo studies revealed that the C-terminal 314 amino acids of the 610-amino acid UvrC protein were sufficient to confer UV resistance to cells lacking the uvrC gene.
		The fusion protein, in combination with UvrA and UvrB subunits, reconstituted the excinuclease activity that incised the eighth phosphodiester bond 5' and the fourth phosphodiester bond 3' to a psoralen-thymine adduct.
		The portion of the uvrC gene encoding the C-terminal half of the protein was fused to the 3' end of the E. coli malE gene (which encodes maltose binding protein), and the fusion protein MBP-C314C was purified and characterized.
	www.ihop-net.org /UniPub/iHOP/gp/37763.html (210 words)

	Lecture 10_25_06
		Cleavage of phosphodiester bond between exon1 and the 5’end of intron.
		The attacking group is the 2’-OH group of an adenylate residue in the branch site, forming a 2’-5’ phosphodiester bond.
		Joining of exon1 and exon2 as the free 3’-OH group of exon1 attacks the phosphodiester bond between the intron and exon2.
	www.genome.ou.edu /3653/Lecture26-10_25_06.html (424 words)

	Dep't of Bioorganic Chemistry \| Research \| Ribozyme
		The cleavage at the 5'-junction in splicing is due to an intramolecular nucleophilic attack by a 2'-OH from within the intron.
		Subsequent cleavage at the 3'-junction results in the ligation of the exons and liberates the "free" intron in the form of a lariat.
		Studies on the specificity of the nucleobase requirement at the branch-accepting point have shown that the replacement of the central branch-accepting adenosine residue by any other nucleotide in mutants results in a considerable decrease in the efficiency of the splicing as compared to the wild type.
	www.boc.uu.se /boc14www/res_proj/Ribozymes.html (1613 words)

	DNA Replication
		In general, DNA is replicated by uncoiling of the helix, strand separation by breaking of the hydrogen bonds between the complementary strands, and synthesis of two new strands by complementary base pairing (def).
		As the strands continue to unwind and separate in both directions around the entire DNA molecule, new complementary strands are produced by the hydrogen bonding of free DNA nucleotides with those on each parent strand.
		As the phosphodiester bond forms between the 5' phosphate group of the new nucleotide and the 3' OH of the last nucleotide in the DNA strand, two of the phosphates are removed providing energy for bonding (see Fig.
	student.ccbcmd.edu /courses/bio141/lecguide/unit6/genetics/DNA/DNArep/dnarep.html (1986 words)

	Genetics Glossary P (Site not responding. Last check: )
		P53 levels are increased after DNA is damaged by UV and ionizing radiation and cells are arrested in cell division until either the damage is repaired or they die by apoptosis (programmed cell death).
		The enzymatic centre in the ribosome responsible for peptide bond formation during translation.
		A diester bond (between phosphoric acid and two sugar molecules) linking two nucleotides together to form the nucleotide polymers DNA and RNA.
	helios.bto.ed.ac.uk /bto/glossary/p.htm (2512 words)

	DNA Science
		The DNA polymerase is a proteinaceous enzyme that catalyzes the formation of phosphodiester bonds between the nucleotides of DNA.
		Transcription is accomplished by a proteinaceous enzyme called RNA polymerase that catalyzes the formation of phosphodiester bonds between the nucleotides to produce an RNA strand.
		A peptide bond catalyzed by an enzyme is formed between the two amino acids and separates the one in the P-site from its tRNA.
	homepages.ius.edu /GKIRCHNE/DNA.htm (3684 words)

	Dephosphorylation of the Linearized Vector (Site not responding. Last check: )
		During ligation, DNA ligase will catalyze the formation of a phosphodiester bond between adjacent nucleotides only if one nucleotide contains a 5'-phosphate group and the other a 3'-hydroxyl group.
		Recircularization of plasmid DNA can therefore be minimized by removing the 5' phosphates from both ends of the linear DNA with calf intestinal phosphatase [110, 111].
		As a result, neither strand of the duplex can form a phosphodiester bond .
	www.chemiestudium-graz.at /~binder/thesis/node49.html (190 words)

	exam 1 questions and review
		AMP removed and phosphodiester bond made between the 5'P and the 3'OH of the other nucleotide.
		It is a right-handed helix that is stabilized by hydrogen bonds between the C=O of one peptide linkage and the H-N of another peptide linkage located four linkages away.
		This activates the oxygen of the serine side chain which attacks the C=O of the peptide bond, causing the C to bond covalently to the serine, creating the first tetrahedral intermediate.
	www.udel.edu /biology/fschmieg/exam1qr.htm (2896 words)

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