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*  KH domain
The nucleic acid is bound in an extended conformation across one side of the domain. The binding occurs in a cleft formed ... An evolutionarily conserved sequence of around 70 amino acids, the KH domain is present in a wide variety of nucleic acid- ... Grishin NV (February 2001). "KH domain: one motif, two folds". Nucleic Acids Res. 29 (3): 638-43. doi:10.1093/nar/29.3.638. PMC ... Valverde and colleagues note that, "Nucleic acid base-to-protein aromatic side chain stacking interactions which are prevalent ...
*  Aspergillus nuclease S1
Wrede, Paul; Alexander Rich (1979). "Stability of the unique anticodon loop conformation of E.Col tRNAMetf". Nucleic Acids ...
*  List of MeSH codes (G06)
... nucleic acid conformation MeSH G06.184.603.790.486.100 --- base pairing MeSH G06.184.603.790.709 --- protein conformation MeSH ... amino acid MeSH G06.184.842.200.820 --- structural homology, protein MeSH G06.184.842.550 --- sequence homology, nucleic acid ... nucleic acid MeSH G06.184.603.080.689.330 --- enhancer elements (genetics) MeSH G06.184.603.080.689.330.240 --- e-box elements ... nucleic acid MeSH G06.184.603.080.708.330 --- interspersed repetitive sequences MeSH G06.184.603.080.708.330.200 --- dna ...
*  George B. Johnson
Abstract: Genetics 86: s33, (1977) Genetically controlled variation in conformation of enzymes, 1979, Prog. Nucleic Acid Res. ... 233-234 Purification and characterization of glutamic acid dehydrogenase from Escherichia coli strain K-12. Master's thesis, ...
*  Methylation
Nucleic Acids Research. 39 (8): e52-e52. doi:10.1093/nar/gkr035. PMC 3082908 . PMID 21297115. deltaMasses Detection of ... Wienken CJ, Baaske P, Duhr S, Braun D (2011). "Thermophoretic melting curves quantify the conformation and stability of RNA and ... a general method for the synthesis of pure 2-arylpropionic acids. 2-Phenylpropionic acid". Organic Syntheses. 76: 169. doi: ... Protein methylation typically takes place on arginine or lysine amino acid residues in the protein sequence. Arginine can be ...
*  Microscale thermophoresis
Nucleic Acids Res. 39 (8): e52. doi:10.1093/nar/gkr035. PMC 3082908 . PMID 21297115. Jerabek-Willemsen M, André T, Wanner A, ... Any change of the hydration shell of biomolecules due to changes in their structure/conformation results in a relative change ... dead link] Wienken CJ, Baaske P, Duhr S, Braun D (2011). "Thermophoretic melting curves quantify the conformation and stability ...
*  Oligonucleotide synthesis
... conformation and stability". Nucleic Acids Res. 18 (21): 6353-6359. doi:10.1093/nar/18.21.6353. PMC 332506 . PMID 2243780. ... Nucleic acids Nucleic acid analogues Peptide nucleic acid Bridged Nucleic Acids Beaucage, S. L.; Iyer, R. P. (1992). "Advances ... The DMT group is removed with a solution of an acid, such as 2% trichloroacetic acid (TCA) or 3% dichloroacetic acid (DCA), in ... Nucleic Acid Chem. 46 (16): 4.1.1-4.1.22. doi:10.1002/0471142700.nc0401s46. Pease A. C.; Solas D.; Sullivan E. J.; Cronin M. T ...
*  Wilma Olson
A second goal is to uncover structural details of nucleic acid structural transitions, such as those involving different DNA ... her research aims to understand the influence of chemical architecture on the conformation, properties, and interactions of ... Wilma Olson was involved in setting up the nucleic acid database, in collaboration with Helen M. Berman. Olson's studies DNA as ... nucleic acids. Olson received her bachelor's degree in Chemistry at the University of Delaware in 1967, with honors and ...
*  Hepatitis delta virus ribozyme
Nucleic Acids Res. 27: 795-802. doi:10.1093/nar/27.3.795. Mathews, D.; Sabina, J.; Zuker, M.; Turner, D. (1999). "Expanded ... The upstream inhibitory -24/-15 stretch from the aforementioned inhibitory conformation is now sequestered in a hairpin P(-1) ... 2010). "A 1.9 Å Crystal Structure of the HDV Ribozyme Precleavage Suggests both Lewis Acid and General Acid Mechanisms ... Nucleic Acids Res. 39 (18): 8065-8077. doi:10.1093/nar/gkr478. PMC 3185411 . PMID 21724615. Sánchez-Luque, FJ; López MC; Macias ...
*  Alireza Mashaghi
Circuit topology of Proteins and nucleic acids, Structure 22(9):1227-1237 (2014) Conformation Activity Relationships: Why Do ... proteins puzzle with amino acid chains Universal clamping protein stabilizes folded proteins: New insight into how the ...
*  Nucleic acid design
... acid design is the process of generating a set of nucleic acid base sequences that will associate into a desired conformation. ... Thus, in nucleic acids the sequence determines the pattern of binding and thus the overall structure. Nucleic acid design is ... Nucleic acid design encompasses all levels of nucleic acid structure: Primary structure-the raw sequence of nucleobases of each ... Nucleic acid design can be considered the inverse of nucleic acid structure prediction. In structure prediction, the structure ...
*  Crystallography
... particularly protein and nucleic acids such as DNA and RNA. In fact, the double-helical structure of DNA was deduced from ... X-ray crystallography is the primary method for determining the molecular conformations of biological macromolecules, ...
*  Nucleic acid secondary structure
Pseudoknots fold into knot-shaped three-dimensional conformations but are not true topological knots. The base pairing in ... Nucleic acid secondary structure is the basepairing interactions within a single nucleic acid polymer or between two polymers. ... In a non-biological context, secondary structure is a vital consideration in the nucleic acid design of nucleic acid structures ... "Paradigms for computational nucleic acid design". Nucleic Acids Research. 32 (4): 1392-1403. doi:10.1093/nar/gkh291. PMC 390280 ...
*  Influenza A segment 7 splice site
pseudoknot Non-coding RNA Nucleic acid secondary structure Moss WN, Priore SF, Turner DH (June 2011). "Identification of ... The hairpin conformation was predicted using RNAalifold, while the pseudoknot was predicted with DotKnot. Segment 7 encodes the ... Initial models of the secondary structure were based on computational methods for Nucleic acid structure prediction. ... Nucleic Acids Res. 38 (7): e103. doi:10.1093/nar/gkq021. PMC 2853144 . PMID 20123730. Moss WN, Dela-Moss LI, Kierzek E, Kierzek ...
*  Melting curve analysis
... the conformation and the modifications of DNA and RNA Nucleic acid thermodynamics Ansevin, A.T.; Vizard, D.L.; Brown, B.W.; ... Nucleic Acids Research, 39 (8): e52-e52, doi:10.1093/nar/gkr035, PMC 3082908 , PMID 21297115. Ririe, KM; Rasmussen, RP; Wittwer ... 1997 Dec;43(12):2262-7 Wienken CJ, Baaske P, Duhr S, Braun D (2011), "Thermophoretic melting curves quantify the conformation ...
*  Foldamer
... nucleic acids, and polysaccharides to fold into well-defined conformations, such as helices and β-sheets. The structure of a ... β-peptides are composed of amino acids containing an additional CH 2 unit between the amine and carboxylic acid. They are more ... Using a heteroligopeptide consisting of α-amino acids and cis-β-aminocyclopropanecarboxulic acids (cis-β-ACCs) they found the ... while nucleotidomimetic foldamers are based on the interactions in nucleic acids. Abiotic foldamers are stabilized by aromatic ...
*  Cre recombinase
Nucleic Acids Research. 31 (18): 5449-5460. doi:10.1093/nar/gkg732. PMC 203317 . PMID 12954782. Sternberg N, Hamilton D (Aug ... "Crystal structure of a wild-type Cre recombinase-loxP synapse reveals a novel spacer conformation suggesting an alternative ... The carboxy terminal domain of the enzyme consists of amino acids 132-341 and it harbours the active site of the enzyme. The ... Cre recombinase consists of 343 amino acids that form two distinct domains. The amino terminal domain encompasses residues 20- ...
*  Comparison of nucleic acid simulation software
Applications To Docking and Structure Prediction From The Distorted Native Conformation". J. Comp. Chem. 15: 488-506. doi: ... "Modeling unusual nucleic acid structures". Molecular Modeling of Nucleic Acids: 379-393. Petr Šulc; Flavio Romano; Thomas E. ... This is a list of computer programs that are used for nucleic acids simulations. Min - Optimization MD - Molecular dynamics MC ... Lavery, R., Zakrzewska, K. and Sklenar, H. (1995). "JUMNA: junction minimisation of nucleic acids". Comp. Phys. Commun. 91: 135 ...
*  Nucleic acid analogue
... tRNAs are heavily modified postranscriptionally in order to improve their conformation or base pairing, in particular in/near ... Artificial nucleic acids include peptide nucleic acid (PNA), Morpholino and locked nucleic acid (LNA), as well as glycol ... locked nucleic acid (LNA) or bridged nucleic acid (BNA), morpholino, and peptide nucleic acid (PNA). Although these ... RNA may be too complex to be the first nucleic acid, so before the RNA world several simpler nucleic acids that differ in the ...
*  Nucleic acid structure prediction
Some RNA sequences have more than one biologically active conformation (i.e., riboswitches) For this reason, the ability to ... Nucleic acid structure prediction is a computational method to determine secondary and tertiary nucleic acid structure from its ... Macke T, Case D (1998). Modeling unusual nucleic acid structures. In Molecular Modeling of Nucleic Acids. Edited by Leontes N, ... Zuker M (2003). "Mfold web server for nucleic acid folding and hybridization prediction". Nucleic Acids Research. 31 (13): 3406 ...
*  Nuclear magnetic resonance spectroscopy of nucleic acids
... and sugar pucker conformations. The presence or absence of imino proton resonances, or of coupling between 15N atoms across a ... Nucleic acid NMR uses techniques similar to those of protein NMR, but has several differences. Nucleic acids have a smaller ... Because nucleic acids have a relatively large number of protons which are solvent-exchangeable, nucleic acid NMR is generally ... deoxyadenosine are incorporated into the nucleic acid strand, as natural nucleic acids do not contain any fluorine atoms. 1H ...
*  Gel electrophoresis of nucleic acids
The conformation of the DNA molecule can significantly affect the movement of the DNA, for example, supercoiled DNA usually ... Once the nucleic acid is properly prepared, the samples of the nucleic acid solution are placed in the wells of the gel and a ... Voltage is, however, not the sole factor in determining electrophoresis of nucleic acids. The nucleic acid to be separated can ... Nucleic acid electrophoresis is an analytical technique used to separate DNA or RNA fragments by size and reactivity. Nucleic ...
*  Triple-resonance nuclear magnetic resonance spectroscopy
... nearly independent of conformation. Triple resonance experiments involving 31P may also be use for nucleic acid studies. ... 31P triple resonance experiments for sequential backbone correlations in nucleic acids". Journal of Biomolecular NMR. 5 (3): ... The resonances can then be assigned by comparing the sequence of peaks with the amino acid sequence of the protein. Ikura M; ... Stephan Grzesiek & Ad Bax (1993). "Amino acid type determination in the sequential assignment procedure of uniformly 13C/15N- ...
*  DNA nanotechnology
... nucleic acid strands are expected in most cases to bind to each other in the conformation that maximizes the number of ... Nucleic acid design is the process of assigning a specific nucleic acid base sequence to each of a structure's constituent ... Nucleic acid structures can be made to incorporate molecules other than nucleic acids, sometimes called heteroelements, ... In addition, there are nucleic acid metallization methods, in which the nucleic acid is replaced by a metal which assumes the ...
*  Fluorescence in the life sciences
... protein or nucleic acids come into contact or a doubly labelled single molecules is hydrolysed detect changed in conformation ... nucleic acids, lipids or small molecules can be "labelled" with an extrinsic fluorophore, a fluorescent dye which can be a ... Fluorescence has been used to study the structure and conformations of DNA and proteins with techniques such as Fluorescence ... DNA detection: the compound ethidium bromide, when free to change its conformation in solution, has very little fluorescence. ...
*  Sequence motif
Some of these are believed to affect the shape of nucleic acids (see for example RNA self-splicing), but this is only sometimes ... "An approach to detection of protein structural motifs using an encoding scheme of backbone conformations" (PDF). Proc. of 2nd ... "Noncoding" sequences are not translated into proteins, and nucleic acids with such motifs need not deviate from the typical ... Bailey TL, Williams N, Misleh C, Li WW (2006). "MEME: discovering and analyzing DNA and protein sequence motifs". Nucleic Acids ...