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hairpin genetics

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	From The Cover: Hairpin-bisulfite PCR: Assessing epigenetic methylation patterns on complementary strands of ...
		Hairpin sequences are folded into their original complementary patterns to illustrate the methylation states of CpG dyads.
		Other highlighting shows: hairpin linker, gray; unconverted CpG dyads, red; converted CpG dyads, blue; unconverted non-CpG cytosines, magenta; CpG dyads that are uninformative because of PCR or sequencing errors, as well as ambiguous sequence polymorphisms, yellow; PCR errors, green.
		Because the presence/absence of complementarity within hairpin sequences can be used to distinguish between evolutionary mutations and PCR errors, the non-CpG cytosine in sequence NM848158A was counted as a PCR error rather than as a nonconversion.
	www.pnas.org /cgi/content/full/101/1/204 (4446 words)

	Category:Genetics - Wikipedia, the free encyclopedia
		Genetics is the science of genes, heredity, and the variation of organisms, as well as the medical practice of diagnosing, treating, and counseling patients with genetic disorders.
		Humans began applying knowledge of genetics in prehistory with the domestication and breeding of plants and animals.
		Within organisms, genetic information generally is carried in chromosomes, where it is represented in the chemical structure of particular DNA molecules.
	en.wikipedia.org /wiki/Category:Genetics (149 words)

	Hairpin (genetics) - Wikipedia, the free encyclopedia
		In genetics, a hairpin, or hairpin loop, is a sequence of nucleotides part of single-stranded DNA or RNA, usually a palindromic sequence, where two segments can base-pair with each other, but a segment within that sequence cannot base pair, causing hairpin-like structure.
		Hairpin loops are important in prokaryotic transcription termination.
		The hairpin loop forms during transcription and the structure causes the RNA polymerase to become dissociated from the DNA template strand.
	en.wikipedia.org /wiki/Hairpin_(genetics) (149 words)

	Hairpin
		A hairpin is a blunt needle in the form of a narrow U to fixate hair into position.
		A road in the mountains often has hairpin turns, almost 180 degrees turns (with a shape like a hairpin) for zigzagging up and down slopes, to reduce the steepness.
		In genetics, a hairpin is a part of single-stranded DNA, usually a palindromic sequence, that aligns with itself to form a needle-like structure.
	www.ebroadcast.com.au /lookup/encyclopedia/ha/Hairpin.html (141 words)

	Bridal Hairpins -- Recommendations and Resources (Site not responding. Last check: 2007-11-06)
		Highways with hairpin turns allow easier, safer ascents and descents of mountainous terrain than a direct, steep climb and descent, at the price of greater distances of travel.
		A hairpin loop in RNA is a sequence of nucleotides where a long segment of RNA can base-pair with each other, but a segment within that sequence can not base pair, causing a hairpin loop.
		In the opera, the chorus is sung after the ceremony by the women of the wedding party, as they accompany the heroine Elsa to the bridal chamber.
	www.becomingapediatrician.com /health/22/bridal-hairpins.html (543 words)

	CSHL - Press release - Apr. 14th 2002
		The study also established that such short hairpin activated gene silencing (which the researchers playfully termed "SHAGging") operates in a variety of normal and cancer cell lines, and in mouse cells as well as in human cells.
		In one approach, he is using small hairpin RNAs to silence known cancer-causing genes ("oncogenes") and thereby control the growth of cancer cells.
		He predicts that small hairpin RNAs could be incorporated into novel therapeutic approaches within a few years, although additional time would be required for such treatments make their way to the clinic.
	www.cshl.edu /public/releases/press041402.html (982 words)

	syngenta cuts (Site not responding. Last check: 2007-11-06)
		Hairpin gene silencing, also known as RNA interference (RNAi), is a simple, quick, but exquisitely precise way of exploring gene function in higher organisms - it can be applied to switching off genes in plants, animals, insects, or any other higher organism.
		When viruses infect living cells, they produce a double-stranded RNA (dsRNA) copy of their genetic blueprints as a prelude to mass-replicating new virus particles.
		The gene sequence, and the complementary DNA code from the non-gene strand, are joined end-to-end, separated by a small sequence that forms a hinge.
	www.checkbiotech.org /blocks/dsp_document.cfm?doc_id=4816 (1074 words)

	CSHL - Harbor Transcript - Summer/Fall 2002
		They were inspired to try these short hairpin RNAs (shRNAs) by their finding, in collaboration with Dutch worm researcher Ronald Plasterk, that some genes naturally regulate other genes, through RNAi, by coding for just such short hairpin-shaped RNA molecules.
		In one approach, he is using short hairpin RNAs to silence known cancer-causing genes (“oncogenes”) and thereby control the growth of cancer cells.
		He predicts that short hairpin RNAs could be incorporated into novel therapeutic approaches within a few years, although additional time would be required for such treatments make their way to the clinic.
	www.cshl.edu /public/HT/sf02_petunias.html (1007 words)

	Modifications and deletions of helices within the hairpin ribozyme-substrate complex: An active ribozyme lacking helix ...
		The hairpin ribozyme catalyzes a reversible RNA cleavage reaction
		Donahue, C.P., Yadava, R.S., Nesbitt, S.M., and Fedor, M.J. The kinetic mechanism of the hairpin ribozyme in vivo: Influence of RNA helix stability on intracellular cleavage kinetics.
		Walter, N.G. and Burke, J.M. The hairpin ribozyme: Structure, assembly and catalysis.
	www.rnajournal.org /cgi/content/full/10/3/395 (3392 words)

	MMG Faculty Research: J. M. Burke
		The hammerhead and hairpin ribozymes both catalyze RNA cleavage reactions through a phosphoester transfer pathway that does not involve metal ions in the reaction mechanism.
		We showed that the hairpin ribozyme undergoes a dramatic conformational change during formation of an active complex in which the active site is buried in a solvent-inaccessible zone within the three-dimensional structure.
		Current work focuses on (i) optimizing ribozyme inhibition, (ii) using genetics to prove the site and mechanism of antiviral activity, and (iii) extending this technology to develop therapeutic strategies for significant infectious and genetic diseases, and to the area of functional genomics.
	www.uvm.edu /~mmg1/research_burke.htm (466 words)

	Rfam 7.0 : Hairpin (Site not responding. Last check: 2007-11-06)
		The hairpin ribozyme, like the hammerhead (RFAM:RF00008 and RFAM:RF00163), is found in RNA satellites of plant viruses.
		It was first identified in the minus strand of the tobacco ringspot virus (TRSV) satellite RNA where it catalyses a self-cleavage reaction to process the products of rolling circle virus replication to unit-length satellite RNA.
		The hairpin ribozyme: from crystal structure to function.
	rfam.wustl.edu /cgi-bin/getdesc?name=Hairpin (147 words)

	Mouse Genetics Appendix
		Genetic drift is fueled by spontaneous neutral mutations that disappear or become fixed in a population at random.
		The formal genetic definition is an allele that exerts a deleterious effect on phenotype.
		The term has been co-opted for use in transmission genetics to describe any locus at which at least two alleles are available for use in breeding studies, irrespective of their actual frequencies in natural populations.
	www.princeton.edu /~lsilver/book/MGapp.html (10660 words)

	[No title] (Site not responding. Last check: 2007-11-06)
		The hairpin ribozyme catalytic RNA motif was originally isolated from the negative strand of the tobacco ringspot virus satellite RNA, (-)sTRSV.
		The hairpin ribozyme is composed of two independent folding domains that must dock together in order to carry out the cleavage reaction.
		Although the modeling of the hairpin ribozyme was done using constraints generated in two sets of experimental conditions, either with Mg2+ or with cobalt hexamine.
	www.uvm.edu /~swgordon/231-02/finprojects/dominic/web_page.html (3155 words)

	About VCC : Members : John M. Burke (Site not responding. Last check: 2007-11-06)
		Burke showed that the hairpin ribozyme undergoes a dramatic conformational change during formation of an active complex in which the active site is buried in a solvent-inaccessible zone within the three-dimensional structure.
		The genetic architecture necessary for transgressive segregation is common in both natural and domesticated populations.
		A conformational change in the "loop E-like" motif of the hairpin ribozyme is coincidental with domain docking and is essential for catalysis.
	www.vermontcancer.org /getpage.php?pid=173 (1061 words)

	Development and Neurobiology: Genetics of Childhood Disorders: Fragile X Syndrome
		Karyotyping of cells grown in folate-depleted cell culture media revealed that many patients had a ³fragile² site on one of their X chromosomes that appeared as a constriction on the distal long arm.
		This genetic syndrome is of particular interest to clinicians and scientists who want to understand brain development and function in children.
		The hairpin structure is also known to be a signal that leads to an increase in methylation that eventually blocks FMR-1 transcription.
	info.med.yale.edu /chldstdy/plomdevelop/genetics/00febgen.htm (1470 words)

	Current Research - Chromosome Stability - The Laboratory of Molecular Genetics - NIEHS
		The Chromosomal Stability Section pursues the mechanisms and genetic controls of genome stability, the consequences of chromosomal changes, and the roles of environmental factors.
		Because of similarities in genome organization, enzymatic processes, and genetic controls between yeast and humans, our approaches are often directly applicable to human disease.
		Through genetic and enzymatic analyses, we are also characterizing the switching of nascent strands between the polymerization and the exonuclease sites of DNA polymerase d.
	dir.niehs.nih.gov /dirlmg/cs/research.htm (1089 words)

	Program in Genetics and Development: Peter Tattersall
		We are using a genetic approach to determine which amino acid residues in the coat protein gene of the murine parvovirus MVM are important for viral host range switching between fibrotropic and T-cell tropic variants.
		A collaboration with Dr. Michael Rossmann's lab at Purdue has recently resulted in determination of the atomic structure of the T-cell-tropic MVM virion by X-ray crystallography, and we are currently reconciling both genetic and physical maps of the viral coat.
		We are also pursuing genetic and biochemical analyses of the 83kd major non-structural protein NS1.
	info.med.yale.edu /genetics/gendev/faculty/tattersall.html (553 words)

	Dr. Martin Gellert
		It is shown here that the hairpins are formed by a chemical mechanism of direct trans-esterification, very similar to the early steps of transpositional recombination and retroviral integration.
		The hairpin is made as a direct consequence of the cleavage mechanism.
		Both nicking and hairpin formation are remarkably tolerant of variations in DNA structure.
	ben-may.bsd.uchicago.edu /symposium/1996/gellert.html (759 words)

	Targeted Gene Silencing in the Model Mushroom Coprinopsis cinerea (Coprinus cinereus) by Expression of Homologous ...
		an intron in the hairpin loop (31, 57).
		Genetic interference in Trypanosoma brucei by heritable and inducible double-stranded RNA.
		Heritable and inducible genetic interference by double-stranded RNA encoded by transgenes.
	ec.asm.org /cgi/content/full/5/4/732 (7276 words)

	Combinatorial Screening and Intracellular Antiviral Activity of Hairpin Ribozymes Directed against Hepatitis B Virus -- ...
		are the substrate-binding region of the hairpin ribozyme, and
		A hairpin ribozyme library was generated by in vitro transcription of synthetic DNA templates.
		The catalytic RNA folds into a two-dimensional structure that resembles a hairpin consisting of helices 3 and 4 and internal loop B. In addition, helices 1 and 2 and internal loop A form between the ribozyme and its substrate.
	jvi.asm.org /cgi/content/full/73/7/5381 (5153 words)

	Reverse Genetic System for the Analysis of Parvovirus Telomeres Reveals Interactions between Transcription Factor ...
		The left-hand hairpin of MVM is shown in diagrammatic form.
		Synthetic oligonucleotides that regenerate the terminal hairpin were ligated to the linearized plasmid.
		The sequences of the central regions of mutant hairpin oligonucleotides used in this study are shown below the wild-type hairpin.
	jvi.asm.org /cgi/content/full/77/16/8650 (7555 words)

	In vitro resolution of adeno-associated virus DNA hairpin termini by wild-type Rep protein is inhibited by a ...
		In vitro resolution of adeno-associated virus DNA hairpin termini by wild-type Rep protein is inhibited by a dominant-negative mutant of rep.
		We analyzed nuclear extracts from both expression systems for the ability to complement uninfected HeLa cell cytoplasmic extracts in an in vitro terminal resolution assay in which a covalently closed AAV terminal hairpin structure is converted to an extended linear duplex.
		We propose that the dominant-negative replication phenotype of AAV genomes carrying the K340H mutation is mediated by mutant Rep proteins binding to the terminal repeat hairpin.
	www.aegis.com /aidsline/1992/apr/M9240081.html (456 words)

	Bacterial chromosome structure
		There are examples of linear DNA molecules in bacteria that are protected by both types of telomeres: palindromic hairpin loops are protected by the lack of free double-stranded ends, and invertron telomeres are protected by proteins that bind to the 5'-ends.
		The important take-home point is that we are just beginning to appreciate the similarity of many processes once thought to be completely different between bacteria and eukaryotes, partly because we now have better tools for studying these processes and partly because most of the earlier studies focused on relatively few types of bacteria.
		The circular genomes of mitochondrial and chloroplast are a notable exception to the rule that eukaryotic chromosomes are linear.
	www.sci.sdsu.edu /~smaloy/MicrobialGenetics/topics/chroms-genes-prots/chromosomes.html (1201 words)

	trans activation of human immunodeficiency virus type 1 is sequence specific for both the single-stranded bulge and ...
		trans activation of human immunodeficiency virus type 1 is sequence specific for both the single-stranded bulge and loop of the trans-acting-responsive hairpin: a quantitative analysis.
		We have used site-directed mutagenesis to delineate sequence specific domains within the human immunodeficiency virus type 1 (HIV-1) trans-acting-responsive (TAR) RNA element that are required for trans activation by the viral Tat protein.
		A second sequence, important for trans activation, was found in the 3-base bulge loop (+22 to +24) of the TAR hairpin.
	www.aegis.com /aidsline/1990/mar/M9030080.html (429 words)

	Human :: Mammal : RSS Feeds : Gourt
		Genetic studies show that one of the identified families with the R345W mutation has a novel haplotype.
		Genetic Health - Background on genetics, genetic aspects of specific conditions and diseases, counseling and testing, and clinical trials.
		Human Genetics Programme - World Health Organization program which develops genetic approaches to the control of the most common hereditary diseases and those with a genetic predisposition.
	science.gourt.com /Biology/Genetics/Eukaryotic/Animal/Mammal/Human.html (1851 words)

	Sequence and DNA structural determinants of N4 virion RNA polymerase-promoter recognition -- Dai and Rothman-Denes 12 ...
		hairpin, whereas the nontemplate strand hairpin is destabilized;
		Specific sequences and a hairpin structure in the template strand are required for N4 virion RNA polymerase promoter recognition.
		Hairpin formation within the enhancer region of the human enkephalin gene.
	www.genesdev.org /cgi/content/full/12/17/2782 (4296 words)

	Distance Learning Genetics Course(s)
		Principles of Genetics is copyright protected, is the sole property of the author, Dr Jamie Love (© 2002 - 2005) and is sold exclusively by Merlin Science.
		By studying Cytogenetics you will learn the foundations of Genetics and be prepared to study the more advanced courses.
		This newsletter comprises the news or happenings in the field of genetics, research articles, upcoming events and a term of the week.
	www.synapses.co.uk /genetics (515 words)

	hairpin - OneLook Dictionary Search
		hairpin : The American Heritage® Dictionary of the English Language [home, info]
		Hairpin : Drug Discovery and Development [home, info]
		Phrases that include hairpin: hairpin crochet, hairpin curve, hairpin turn, hairpin vessels, short hairpin rna
	www.onelook.com /?w=hairpin&ls=a (210 words)

	Robert Landick
		We are tackling the problem by first analyzing the interaction of RNA polymerase with RNA and DNA sequences and structures that direct pausing, arrest, and termination during chain elongation.
		Using methods for regulated overproduction of the b and b’ subunits of RNA polymerase, we have isolated and studied amino acid substitutions that alter transcriptional termination or that compromise cell growth.
		Preferential interaction of the his pause RNA hairpin with RNA polymerase β subunit residues 904-950 correlates with strong transcriptional pausing, Proc.
	www.genetics.wisc.edu /faculty/profile.php?id=132 (293 words)

	New RNA libraries can selectively inactivate human genes
		To construct a library of mammalian genes for short hairpin RNA molecules, Hannon and his colleagues first had to settle on an optimal design for a short-hairpin-RNA molecule.
		Once an optimized basic design of the short hairpin RNA molecule was finished, the researchers then produced a library of genes for short hairpin RNAs that could target 9,610 human genes and 5,563 mouse genes.
		By determining the sequence of a given bar code for a short hairpin RNA, researchers using the library to screen for genes affecting a specific cellular process can identify which RNA molecule among the thousands in the library is switching off the activity of a particular gene.
	www.eurekalert.org /pub_releases/2004-03/hhmi-nrl032404.php (917 words)

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