Chemistry and Biology of Non-canonical Nucleic Acids. Naoki Sugimoto

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      1 Chapter 1Figure 1.1 The diffraction pattern of the canonical DNA duplex and its chemi...Figure 1.2 Chemical structures of base pairs via Watson–Crick or Hoogsteen t...

      2 Chapter 2Figure 2.1 Watson–Crick and Hoogsteen base pairs in double helix. Chemical s...Figure 2.2 Wobble base pairs in duplexes. Chemical structures of G-T (a), G-...Figure 2.3 Mismatched G-A and G-G base pairs observed in nucleic acid struct...Figure 2.4 Mismatched T-T, C-T, and C-C base pairs observed in nucleic acid ...Figure 2.5 Structures of A-type (PDB ID: 3V9D) (a) and Z-type (PDB ID: 4OCB)...Figure 2.6 Structure of four-way junction to form cruciform and Holliday jun...Figure 2.7 Typical structures of multi-stranded DNA helices. (a) Canonical d...Figure 2.8 Hairpin structure. (a) General secondary structure of hairpin. (b...Figure 2.9 Bulge structure. (a) General secondary structure of bulge. (b) Se...Figure 2.10 Internal loop structure. (a) General secondary structure of inte...Figure 2.11 Distribution of RNA tertiary motifs except coaxial stacking of h...Figure 2.12 A-minor interactions. Examples of hydrogen bonding patterns of c...Figure 2.13 Ribose zipper interactions in tertiary structure of group I intr...Figure 2.14 T-loop motifs. (a) General secondary structure of T-loop motif c...Figure 2.15 Kissing-loop interaction. (a) General secondary structure of kis...Figure 2.16 Tetraloop receptor interaction. (a) General secondary structure ...Figure 2.17 Pseudoknot structure. (a) Base pairing patterns on the primary s...

      3 Chapter 3Figure 3.1 Potential hydrogen bonding sites in bases of the nucleosides. Hyd...Figure 3.2 (a) Hydrogen bond formation in base pairs in a DNA duplex. The hy...Figure 3.3 Torsion angles in a polyribonucleotide chain.Figure 3.4 UV melting curves of the self-complementary duplex (5′-ATGCGCAT-3...Figure 3.5 (a) Hydrogen bond formation in base triads in a DNA triplex. The ...Figure 3.6 (a) Sequence for the intermolecular triplex (iT). Typical images ...Figure 3.7 Probable structures adopted by the poly(dG)-poly(dC) sequence in ...Figure 3.8 (a) Hydrogen bond formation in base pairs in a DNA G-quadruplex. ...Figure 3.9 Images of the melting temperature of 8-bromoguanosine gels as a f...Figure 3.10 (a) Hydrogen bond formation in base pairs in a DNA i-motif. The ...Figure 3.11 (a) The unfolding process for the intermolecular tetraplex. (b) ...Figure 3.12 (a–c) Typical examples for intermolecular and intramolecular tet...

      4 Chapter 4Figure 4.1 UV spectroscopic property of nucleic acids structure. (a) Transit...Figure 4.2 A schematic illustration of the stacking arrangement of the G-qua...Figure 4.3 Typical CD spectra of (a) antiparallel topology from d(G₄TTG₄TGT ...Figure 4.4 NMR analysis for nucleic acid structures. (a) NMR chemical shifts...Figure 4.5 X-ray spectroscopy for structural analysis of non-canonical nucle...Figure 4.6 Image of ribozyme structure by cryo-TEM.Figure 4.7 Possible hydrated regions on DNA structures of duplex and G4.Figure 4.8 The binding modes of cation to phosphate in (a) inner sphere type...Figure 4.9 The structure of coordination of a monovalent cation within G-qua...Figure 4.10 Chemical structures of cytosine (5-methylcytosine and 5-hydroxym...Figure 4.11 Categorization of ligand types based on target nucleic acid stru...Figure 4.12 Binding modes of ligands to G4 DNA.Figure 4.13 Emission manners of fluorescence of ligand upon binding to the n...Figure 4.14 Illustration of the cellular crowding effects on target biomolec...Figure 4.15 Schematic representation of intracellular crowding within organe...Figure 4.16 The roles of non-canonical structures regulated by the local env...

      5 Chapter 5Figure 5.1 The location of telomere on the chromosome and the generation mec...Figure 5.2 Schematic view of the shelterin complex showing T- and D-loops, v...Figure 5.3 (a) The sequence forming human telomeric G4s and the four major e...Figure 5.4 The tertiary structure of human telomeric G4 from (a) d[TAG₃(T₂AGFigure 5.5 Two hypothetical models for the assembly of the telomeric single-...Figure 5.6 The modeled structure of G4 units based on the parallel topology ...Figure 5.7 Human telomerase and the substrate DNA. (a) The tertiary structur...Figure 5.8 Schematic view of the effects of G4 formation in the 3′ overhang ...Figure 5.9 Schematic view of TRAP assay. A single-stranded DNA having TTAGGG...Figure 5.10 The scheme of the alternative lengthening of telomeres (ALT) (le...Figure 5.11 The tertiary structure of i-motif from human telomeric sequence....Figure 5.12 Proposed functions of TERRA at functional and dysfunctional telo...Figure 5.13 Representation of (a) the crystal structure (PDB: 3MIJ) and (b) ...

      6 Chapter 6Figure 6.1 Transcription takes place in three steps: (a) initiation, (b) elo...Figure 6.2 Schematic model of the transcription bubble. RNA polymerase melts...Figure 6.3 Structure of RNA polymerase II during transcription. RNA polymera...Figure 6.4 Schematic model of the elongation complex. Core RNA polymerase (i...Figure 6.5 (a) Rho-independent termination: the RNA polymerase traverses the...Figure 6.6 Effects on RNA polymerase elongation by sequences in template DNA...Figure 6.7 DNA structural polymorphism of (a) B-form, (b) Z-form, (c) hairpi...Figure 6.8 Possible mechanisms for sequence-specific transcription mutation....Figure 6.9 Scheme of intramolecular T.A.T triplex in supercoiled DNA and bin...

      7 Chapter 7Figure 7.1 Differences in compositions between eukaryotic and prokaryotic mR...Figure 7.2 Typical codon tables in chart (a) and circle (b).Figure 7.3 Conserved secondary and tertiary structures of tRNA. (a) Secondar...Figure 7.4 Structure and composition of ribosome. Ribosome consists of large...Figure 7.5 Interactions between mRNA and ribosome and translation initiation...Figure 7.6 Translation elongation reaction. (a) Three tRNA binding sites, A-...Figure 7.7 Reaction flow of translation termination. Stop codon appears on A...Figure 7.8 Efficiency of translation initiation depending on interaction str...Figure 7.9 Effect of biomolecular interaction at or around RBS of prokaryoti...Figure 7.10 Tertiary structure interactions and motifs observed in aptamers ...Figure 7.11 Modulation of translation in response to iron in cells. Iron-reg...Figure 7.12 Translation initiation mediated by internal ribosome СКАЧАТЬ