• 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
  • The superposition of the 20 lowest-energy structures show that this G-A base pair is well defined by the NMR data, although two conformations with different propeller twists and buckles are observed in the ensemble of structure (Figure 4B). (nih.gov)
  • These two alternative conformations observed in the NMR structures may reflect insufficient NMR restraints and/or conformational dynamics for this base pair. (nih.gov)
  • 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)
  • backbone
  • Nucleic acids are chains of nucleotides, which are composed of three parts: a phosphate backbone, a pentose sugar, either ribose or deoxyribose, and one of four nucleobases. (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)
  • RNA may be too complex to be the first nucleic acid, so before the RNA world several simpler nucleic acids that differ in the backbone, such as TNA and GNA and PNA, have been offered as candidates for the first nucleic acids. (wikipedia.org)
  • This is partly because the extra oxygen in RNA increases the propensity for hydrogen bonding in the nucleic acid backbone. (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)
  • ribozyme
  • Similar to the hairpin ribozyme, the HDV ribozyme functions by acid-base catalysis. (wikipedia.org)
  • The Alt1 disrupts the stem P2 in the active conformation wherein P2 is proposed to have an activating role for both genomic and antigenomic ribozyme. (wikipedia.org)
  • 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)
  • base
  • In this review article we will introduce the study of nucleic acid base self-assembly by scanning tunneling microscopy (STM) at vacuum and ambient condition (the liquid/solid interface), respectively. (nih.gov)
  • 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
  • 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)
  • energy
  • 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)
  • design
  • Almost all nucleic acid design tasks are aided by computers, and a number of software packages are available for many of these tasks. (wikipedia.org)
  • length
  • Sequence symmetry minimization divides the nucleic acid sequence into overlapping subsequences of a fixed length, called the criterion length. (wikipedia.org)