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Topic: Wobble base pair

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	Wobble base pair - Biocrawler
		A wobble base pair is a G-U and I-U / I-A / I-C pair fundamental in RNA secondary structure.
		Wobble base pairs are critical for the proper translation of the genetic code.
		Another critical base pair is the G-U base pair which allows uracil to base pair with two bases: guanine and adenine.
	www.biocrawler.com /encyclopedia/Wobble_base_pair (127 words)

	Spartanburg SC \| GoUpstate.com \| Spartanburg Herald-Journal
		Another critical base pair is the G-U base pair, which allows uracil to pair with two bases: guanine and adenine.
		He postulated that the 5' base on the anti-codon was not as spatially confined as the other two bases, and could thus have non-standard base pairing.
		It is, therefore, possible for non-Watson-Crick base pairing to occur at the third codon position, i.e.
	www.goupstate.com /apps/pbcs.dll/section?category=NEWS&template=wiki&text=wobble_base_pair (241 words)

	Flambeau Outdoors Decoys - Foam Body Turkey Decoys
		The Wobble Gobble is the ultimate turkey hunting system.
		While most motion decoys sit on a stake and move with the wind, Flambeau's innovative Wobble Gobble perfectly simulates the motion a turkey makes walking through the woods or across a field.
		Imagine all the realistic hunting situations that can be created: pull the Wobble Gobble toward another decoy, by looping the string around a stake or another sapling pull the Wobble Gobble 90° to your hunting position, or pull a Jake Wobble Gobble behind a Hen Wobble Gobble.
	www.decoys.com /turkey/dcoy_turkey_foambody.html (717 words)

	Engineering a Ligand-Dependent RNA Transcriptional Activator.
		Based on structural models, we proposed that these two conserved bases, together with C19, form key C:G base pairs that stabilize a secondary structure required for activity (Figure 1A) [21].
		We hypothesize that the introduction of the G-U wobble pair destabilizes this pairing enough to significantly lower transcriptional activation potency, as evidenced by the lower activity of the selected clones in the absence of TMR compared with that of m26-11.
		In this mutant, a critical 3 base pair structural element was mutated from CCC (bases 27—29) to CCU.
	www.euchromatin.com /Buskirk02.htm (4310 words)

	Base pair Summary
		As DNA is usually double-stranded, the number of base pairs given for a particular DNA strand is the number of nucleotides in one of the strands.
		Paired DNA and RNA molecules are comparatively stable at room temperature but the two nucleotide strands will separate above a melting point that is determined by the length of the molecules, the extent of mispairing (if any), and the GC content.
		Base stacking interactions between the pi orbitals of the bases' aromatic rings also contribute to stability, and again GC stacking interactions with adjacent bases tend to be more favorable.
	www.bookrags.com /Base_pair (1262 words)

	Synthesis and crystal structure of an octamer RNA r(guguuuac)/r(guaggcac) with G{middle dot}G/U{middle dot}U tandem ...
		Schematic representations of base pairings of the three tandem G·U pairs: (a) motif I with the sequence r(guaugua)dC; (b) motif II with the sequence r(gugugua)dC; (c) motif III with the sequence r(guguuuac)/r(guaggcac).
		Base stacking of the wobble and flanking Watson–Crick base pairs in motifs I, II and III
		Base pair stacking in motifs I (a–c), II (d–f) and III (g–i).
	nar.oxfordjournals.org /cgi/content/full/28/21/4376 (2496 words)

	Nucleic Acid Standards - Standard Ref. Frame
		The y-axis runs along the long axis of the idealized base pair in the direction of the sequence strand, parallel to the C1'×××C1' vector, and displaced so as to pass through the intersection on the (pseudo-dyad) x-axis of the vector connecting the pyrimidine Y(C6) and purine R(C8) atoms.
		Notably, the hydrogen bonds closer to the minor groove edges of all base pairs are shorter than those nearer the major groove edges, as is observed in high resolution structures of Watson-Crick base-pair co-crystal complexes [6,7].
		For example, "wobble" G×T and A+×C base pairs are "sheared" ~2 Å relative to the Watson-Crick configuration, the displacement being positive for the Y×R pair and negative for the R×Y association.
	ndbserver.rutgers.edu /standards/standard_reference.html (3411 words)

	Protonation Studies and Multivariate Curve Resolution on Oligodeoxynucleotides Carrying the Mutagenic Base ...
		the P·C base pair and a Watson-Crick geometry for the P·T base
		for the wobble geometry for the P·C base pair.
		Base pairing and mutagenesis: observation of a protonated base pair between 2-aminopurine and cytosine in an oligonucleotide by proton NMR.
	www.biophysj.org /cgi/content/full/81/5/2886 (5111 words)

	Wobble (Site not responding. Last check: )
		Crick suggested that the base at the 5' end of the anticodon does not have as strict base-pairing requirements as the other two base pases, allowing it to form hydrogen bonds with several bases at the 3' end of the codon [Crick, 1966].
		Note that the first two bases of the codon and anticodon interact by standard Watson-Crick base pairing rules, but the third base of the anticodon can pair by the wobble rules.
		Based upon these rules a minimum of 32 tRNAs are needed to recognize all of the sense codons in mRNA.
	www.sci.sdsu.edu /~smaloy/MicrobialGenetics/topics/rev-sup/wobble.html (438 words)

	abstracts: section II
		Based on computer simulations and additionally visualized by video-tapes, the statics and dynamics of the structurally and functionally optimised short-peptide messengers involved are discussed in terms of native importance, possible artificial interferences with and modulations of native bioregulators.
		Superhelical parameters (N-the number of base pairs in one superhelical turn; H-the vertical displacement of residues along the superhelix axis; R-the radius of the superhelix) of double-helical DNA structures are investigated by modeling regular repeating sequences of the type XnY10-n.
		Pairing rules have been developed to control rationally the DNA sequence specificity of minor-groove-binding polyamides containing N-methylimidazole and N-methylpyrrole amino acids.1,2 An imidazole ring paired antiparallel with a pyrrole recognizes a G·C base pair, whereas a pyrrole-imidazole combination targets a C·G base pair.
	www.albany.edu /chemistry/sarma/abstracts1.html (13153 words)

	Translation by tRNA
		When a tRNA is brought to the ribosome by the pairing between its anticodon and the mRNA's codon, the amino acid attached at its 3' end will be added to the growing peptide.
		The reason why less than 61 tRNAs are required is because of the "wobble pairing" between anticodon and codon.
		The non-standard base pairing at the wobble position.
	www.web-books.com /MoBio/Free/Ch5C4.htm (390 words)

	The G[middot]U wobble base pair
		U pairs have now been found in virtually every class of functional RNA, and have been shown to play many essential roles that are based upon the unique chemical and structural properties of the wobble pair.
		U pair is most frequently found at the junction of the single-stranded V loop and the T helix where the polynucleotide chain makes a sharp turn (Clark and Klug, 1975).
		U pairs also possess unique conformational features dictated by the sequence context in which the wobble pair is found and by factors that bind to it.
	www.nature.com /cgi-taf/DynaPage.taf?file=/embor/journal/v1/n1/full/embor635.html (3280 words)

	J. Biochem. 130, pp. 9-12 (2001)[body text]
		Such a conformation and wobble pairing are not compatible with DNA polymerase binding because the enzyme only accepts Watson-Crick base pairs in a B-form duplex (9).
		The existence of the two types of base pairs is consistent with the results of a NMR study on a DNA heptamer (10).
		C:G pairs are introduced into the newly synthesized DNA when the template C is methoxylated (7) and the reactant dCTP is methoxylated (6).
	wwwsoc.nii.ac.jp /jbiochem/jb/130-1/1faaajtx.htm (1474 words)

	Correlation of deformability at a tRNA recognition site and aminoacylation specificity -- Chang et al. 96 (21): 11764 ...
		The broad base H5-H6 resonance of cytosine C3 is indicated by an arrow.
		Hydrogen bonding between base pairs is indicated by gray rectangles.
		Shown are the nucleotide pairings at position three and the backbones of positions 2-5.
	www.pnas.org /cgi/content/full/96/21/11764 (4181 words)

	The Scripps Research Institute - News and Views
		In most organisms the acceptor-stem base pair that is recognized by alanyl-tRNA synthetase is what is referred to in biology as a "wobble" base.
		This wobble base pair is located three base pairs from the acceptor end of the tRNA molecule.
		One might expect that they would be, since these molecules are very sensitive to the position of the base pair.
	www.scripps.edu /newsandviews/e_20040329/print-onpress2.html (977 words)

	Genetic code - Psychology Wiki - a Wikia wiki
		The purine bases adenine (A) and guanine (G) are larger and consist of two aromatic rings.
		Mutations that disrupt the reading frame by insertions or deletions of one or two nucleotide bases are known as frameshift mutations.
		These variable codes for amino acids are allowed because of modified bases in the first base of the anticodon of the tRNA, and the base-pair formed is called a wobble base pair.
	psychology.wikia.com /wiki/Genetic_code (2539 words)

	An Analysis of G-U Base Pair Occurrence in Eukaryotic 5S rRNAs -- Szyma et al. 17 (8): 1194 -- Molecular Biology and ...
		base pair causes irregularity of the helix by
		of the acceptor stem caused by the G-U pair is compensated by
		Stacking of Crick wobble pair and Watson-Crick pairs: stability rules of G-U pairs at ends of helical stems in tRNAs and the relation to codon-anticodon wobble interaction.
	mbe.oxfordjournals.org /cgi/content/full/17/8/1194 (2872 words)

	Small RNAs with Imperfect Match to Endogenous mRNA Repress Translation: IMPLICATIONS FOR OFF-TARGET ACTIVITY OF SMALL ...
		G·U wobble base pairing is tolerated in RNA-mediated silencing.
		GC base pairing in the center of RNA oligonucleotide-mRNA duplex is critical for RNA-mediated silencing.
		A, base pairing between the p21 mRNA and the center of antisense strand of p21 RNA duplexes is illustrated.
	www.jbc.org /cgi/content/full/278/45/44312 (5048 words)

	RNA Secondary Structure Prediction (Site not responding. Last check: )
		It is in the major groove that the chemical groups are sequence-specific and dependent on base identity, and therefore, this is where proteins tend to bind a DNA double helix.
		The triplet in the above example means that the bases "C C G", number 10, 11 and 12, base pair with the bases "C G G", bases number 17, 18 and 19.
		For this to happen, it would require that if a G mutated to an A, then the opposing C in the base pair would mutate to a U. These regions are found by aligning related RNA sequences, and applying an algorithm that looks for these sorts of paired mutations in predicted stem regions.
	cnx.org /content/m11065/latest (1405 words)

	tsukuba.text (Site not responding. Last check: )
		Base coordinates are derived from a survey of high resolution crystal structures of nucleic acid analogs stored in the Cambridge Structural Database
		Notably, the hydrogen bonds closer to the minor groove edges of all base pairs are shorter than those nearer the major groove edges, as is observed in high resolution structures of Watson-Crick base-pair co-crystal complexes
		T and A+ base pairs are "sheared" ~2 Å relative to the Watson-Crick configuration, the displacement being positive for the Y
	www.aist.go.jp /infobase/ndbserver/NDB/archives/report/tsukuba/index.html (3230 words)

	Specific cleavage of hyper-edited dsRNAs
		The sense strand was cleaved at one major position, 5' of a U residue, and within the sequence of alternating IU and UI base pairs.
		While the dsRNAs containing alternating IU and UI base pairs were cleaved (lanes 1−4), the dsRNAs that contained GU and UG base pairs were stable (lanes 5−8).
		An IU wobble base pair is isosteric with the GU base pair, but lacks the exocyclic amine group (circled) which projects into the minor groove.
	www.nature.com /emboj/journal/v20/n15/fig_tab/7593921f4.html (324 words)

	Conformational Deformability of RNA: A Harmonic Mode Analysis -- Zacharias and Sklenar 78 (5): 2528 -- Biophysical ...
		Each single mismatch or regular central base pair case (G:C, A:U, G:U, and G:A) involves a base pair step formed by the 5' base pair and central element (first bar) and one between the central element and the 3' base pair (second bar).
		with respect to the 5' flanking base pair are summarized.
		bulge base in the looped-out conformation the mobility of the
	www.biophysj.org /cgi/content/full/78/5/2528 (7685 words)

	Degenerate In Vitro Genetic Selection Reveals Mutations That Diminish Alfalfa Mosaic Virus RNA Replication without ...
		Covarying base pairs are shown in red, while the selected guanosine or uridine nucleotides that are involved in G-U pairs are underlined.
		Pink, positions where both covarying and wobble substitutions were observed; green, covariation at one site where wobble changes were not found; orange, two positions where wobble substitutions were seen but covariation was not observed.
		in the context of G=C and A-U pairs (Fig.
	jvi.asm.org /cgi/content/full/78/15/8036 (7609 words)

	The Individualist: Codon
		Because there are four bases, triplet codons are required to produce at least 22 different codes.
		These variable codes for amino acids are possible because of modified bases in the first base of the anticodon, and the basepair formed is called a wobble base pair.
		insertions or deletions of one or two nucleotide bases) severely impair the function of a protein and are thus exceedingly rare in in vivo protein-coding sequences, since they often lead to death before an organism is viable.
	www.dadamo.com /wiki/wiki.pl/Codon (1428 words)

	The Structure of a Mispaired RNA Double Helix at 1.6 Angstrom Resolution (Site not responding. Last check: )
		The G·U pair is a wobble base pair (A) analogous to the G·T pair found in DNA fragments.
		The C·U mismatch (B) involves one hydrogen-bonded contact between the bases and a bridging water molecule which ensures a good fit of the base pair in the RNA helix.
		U pair is held by two hydrogen bonds in an orientation which is compatible with duplex geometry.
	www.chemie.unibas.ch /~strazi/abstracts/5struct.htm (207 words)

	BioMed Central \| Full text \| RiboSubstrates: a web application addressing the cleavage specificities of ribozymes in ...
		This should permit the identification of all potential substrates, including both those that are perfectly matching as well those for which binding involves either Wobble base pairs or the presence of some mismatches.
		RiboSubstrates does not have a score cut off that indicates that a ribozyme should be re-designed because each RNA tool has its own specific requirements in order to be functional and the presence of both a Wobble base pair or a mismatch might affect different ribozymes differently.
		The sequence located between these two domains within the substrate is referred to as "the spacer", and its optimal length has been determined to be 1 to 6 nucleotides [16].
	www.biomedcentral.com /1471-2105/7/480 (3845 words)

	Algorithms for Molecular Biology \| Full text \| Partition function and base pairing probabilities of RNA heterodimers
		These base pairing patterns, usually referred to as secondary structures, not only comprise the dominating part of the energetics of structure formation, they also appear as intermediates in the formation of the tertiary structure of RNAs [25], and they are in many cases well conserved in evolution.
		Then we discuss the modifications that are necessary to treat intermolecular base pairs in the partition function setting and describe the computation of base pairing probabilities.
		In solution, the probability of an intermolecular base pair is proportional to the (concentration dependent) probability that a dimer is formed at all.
	www.almob.org /content/1/1/3 (5642 words)

	Refinement - Assemble (Site not responding. Last check: )
		In this section, you have to register all the base pairs and the sugar conformation for each residue in the structure
		To pair two residues, click on the label of the first one and drag it on the second one.
		The default conformation for a sugar ring is C3'-endo, corresponding to an empty checkbox beside the residue label.
	www.bioinformatics.org /assemble/wiki/index.php/Refinement (312 words)

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