![]() A., Bonomi, M., Branduardi, D., Camilloni, C. & Laure, E.) 3–27 (Lecture Notes in Computer Science 8759, Springer, 2015). in Solving Software Challenges for Exascale (eds Markidis, S. ![]() EMRinger: side chain-directed model and map validation for 3D cryo-electron microscopy. Quantifying the local resolution of cryo-EM density maps. Resmap: automated representation of macromolecular interfaces as two-dimensional networks. Sampling the conformational space of the catalytic subunit of human γ-secretase. RELION: implementation of a Bayesian approach to cryo-EM structure determination. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. A pipeline approach to single-particle processing in RELION. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Automated molecular microscopy: the new Leginon system. Initial stages of V(D)J recombination: the organization of RAG1/2 and RSS DNA in the postcleavage complex. Modernizing the nonhomologous end-joining repertoire: alternative and classical NHEJ share the stage. The catalytic domain of all eukaryotic cut-and-paste transposase superfamilies. Retroviral integrase superfamily: the structural perspective. Chromosomal loop domains direct the recombination of antigen receptor genes. V(D)J recombination: a functional definition of the joining signals. Distinct DNA sequence and structure requirements for the two steps of V(D)J recombination signal cleavage. Structural insights into the mechanism of double strand break formation by Hermes, a hAT family eukaryotic DNA transposase. Structural gymnastics of RAG-mediated DNA cleavage in V(D)J recombination. Transposase–DNA complex structures reveal mechanisms for conjugative transposition of antibiotic resistance. Optimization of the CHARMM additive force field for DNA: improved treatment of the BI/BII conformational equilibrium. nucleic acids force field based on reference quantum chemical calculations of glycosidic torsion profiles. Base-stacking and base-pairing contributions into thermal stability of the DNA double helix. Requirements for DNA hairpin formation by RAG1/2. Autoinhibition of DNA cleavage mediated by RAG1 and RAG2 is overcome by an epigenetic signal in V(D)J recombination. Crystal structures of RNase H bound to an RNA/DNA hybrid: substrate specificity and metal-dependent catalysis. Cryo-EM structures and atomic model of the HIV-1 strand transfer complex intasome. Structural basis of hAT transposon end recognition by Hermes, an octameric DNA transposase from Musca domestica. The Mu transpososome structure sheds light on DDE recombinase evolution. Retroviral intasome assembly and inhibition of DNA strand transfer. Molecular architecture of the Mos1 paired-end complex: the structural basis of DNA transposition in a eukaryote. Three-dimensional structure of the Tn5 synaptic complex transposition intermediate. DNA melting initiates the RAG catalytic pathway. Cracking the DNA code for V(D)J recombination. Molecular mechanism of V(D)J recombination from synaptic RAG1–RAG2 complex structures. Assembly pathway and characterization of the RAG1/2–DNA paired and signal-end complexes. The mechanism of V(D)J joining: lessons from molecular, immunological, and comparative analyses. Sequences at the somatic recombination sites of immunoglobulin light-chain genes. Crystal structure of the V(D)J recombinase RAG1–RAG2. V(D)J recombination: mechanisms of initiation. V(D)J recombination: RAG proteins, repair factors, and regulation. Transpositional recombination: mechanistic insights from studies of Mu and other elements. The two complementary strands with hydrogen bonds between each nucleotide form a secondary structure, the double helix (Figure 2).Mizuuchi, K. Adenine forms hydrogen bonds with thymine, and cytosine forms hydrogen bonds with guanine, so the complementary sequence for ACTG is TGAC. ![]() Because of the orientation of the nucleotides, a phosphate on one side and a nitrogenous base on the other, there is a 5’ end and a 3’ end of the nucleotide and therefore the strand (Figure 1).įor each strand, the cell contains a complementary strand, which provides a Watson-Crick pair for each nucleotide base. The nucleotides create a long string by forming bonds between the phosphate group of one nucleotide and a carbon in the sugar of another nucleotide. Each of the nucleotides is composed of a sugar (deoxyribose) attached to a phosphate group and a nitrogenous base. DNA carries the genetic code for all cells and is made up of four nucleotide bases: adenine (A), cytosine (C), guanine (G), and thymine (T). ![]()
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