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  • genetics
  • Wild type and mutant stocks of Aspergillus nidulans, (with R.W. Barratt and W.N. Ogata), 1965, Genetics 52: 233-234 Purification and characterization of glutamic acid dehydrogenase from Escherichia coli strain K-12. (wikipedia.org)
  • structures
  • Nucleic acid design has similar goals to protein design: in both, the sequence of monomers is rationally designed to favor the desired folded or associated structure and to disfavor alternate structures. (wikipedia.org)
  • One of the greatest concerns in nucleic acid design is ensuring that the target structure has the lowest free energy (i.e. is the most thermodynamically favorable) whereas misformed structures have higher values of free energy and are thus unfavored. (wikipedia.org)
  • Sequence symmetry minimization is the oldest approach to nucleic acid design and was first used to design immobile versions of branched DNA structures. (wikipedia.org)
  • amino acid
  • A genetically encoded photocaged amino acid. (biomedsearch.com)
  • This structured region was first discovered in a bioinformatics survey of influenza A based on thermodynamic folding free energy and amino acid codon suppression. (wikipedia.org)
  • Although these oligonucleotides have a different backbone sugar or, in the case of PNA, an amino acid residue in place of the ribose phosphate, they still bind to RNA or DNA according to Watson and Crick pairing, but are immune to nuclease activity. (wikipedia.org)
  • bases
  • Most often, H-phosphonate building blocks are protected at the 5'-hydroxy group and at the amino group of nucleic bases A, C, and G in the same manner as phosphoramidite building blocks (see below). (wikipedia.org)
  • structural
  • However, due to the shifted pKa values that causes the acid-base catalysis, there is a likelihood that it may be caused form the structural environment within the nucleoside. (wikipedia.org)
  • Each conformation places important splicing regulatory sites in different structural environments, which has implications for the modulation of splicing of the segment 7 transcript. (wikipedia.org)
  • The amino acids of these peptides only differ by one (β), two (γ) or three (δ) methylene carbons, yet the structural changes were profound. (wikipedia.org)
  • Investigation of the structural features of nucleic acids. (wikipedia.org)
  • ribosomes
  • Further studies revealed that ZαADAR1 could bind to ribosomes and inhibit translation in both E. coli and mammalian systems in a Z-conformation dependent manner. (ntu.edu.sg)
  • bind
  • Here, a protein probe that could specifically bind to Z-conformation was used to map the Z-DNA distribution in the human genome. (ntu.edu.sg)
  • cytosine
  • With support data, the current model of cytosine acting as a general acid within the reaction to donate a proton to the 5'-bridging oxygen. (wikipedia.org)
  • methods
  • However, nucleic acid design has the advantage of being a much computationally simpler problem, since the simplicity of Watson-Crick base pairing rules leads to simple heuristic methods which yield experimentally robust designs. (wikipedia.org)
  • hairpin
  • Similar to the hairpin ribozyme, the HDV ribozyme functions by acid-base catalysis. (wikipedia.org)
  • The hairpin conformation was predicted using RNAalifold, while the pseudoknot was predicted with DotKnot. (wikipedia.org)
  • For example, the splice site, polypyrimidine tract, branch point, and ASF/SF2 exonic enhancer binding sites are expected to be more accessible in the hairpin conformation and less accessible in the pseudoknot (Figure 1). (wikipedia.org)
  • volume
  • Volume II begins with Chapter 10 as continuation of Volume I and discusses the infrared and Raman spectroscopy of nucleic acids and polynucleotides. (elsevier.com)
  • motif
  • An example is the N-glycosylation site motif: Asn, followed by anything but Pro, followed by either Ser or Thr, followed by anything but Pro where the three-letter abbreviations are the conventional designations for amino acids (see genetic code). (wikipedia.org)
  • complex
  • Systematic assessment of RNA and DNA constructs, as well as 4 aptamers of different lengths and secondary structures, revealed that increasing length and double-stranded segments of nucleic acids augment complex formation with PF4, while single nucleotides or single-stranded polyA or polyC constructs do not. (bloodjournal.org)
  • single
  • Various techniques including DGGE (Denaturing Gradient Gel Electrophoresis), DHPLC (Denaturing High Performance Liquid Chromatography), and SSCA (Single Strand Conformation Analysis) effectively identify SNPs and small insertions and deletions. (wikipedia.org)
  • structures
  • A pseudoknot is a nucleic acid secondary structure containing at least two stem-loop structures in which half of one stem is intercalated between the two halves of another stem. (wikipedia.org)
  • form
  • More specifically, we identified the PF4 binding site on gram-negative bacteria as the phosphate groups of lipid A. 7 Based on this observation, we hypothesized that nucleic acids might also form multimolecular complexes with PF4 because they also expose multiple negatively charged phosphate groups. (bloodjournal.org)
  • shape
  • Some of these are believed to affect the shape of nucleic acids (see for example RNA self-splicing), but this is only sometimes the case. (wikipedia.org)