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

3 Chapter 3 Figure 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(G 4TTG 4TGT ...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[TAG 3(T 2AGFigure 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 entry site ...Figure 7.13 Secondary and tertiary structures of H-type pseudoknot derived f...Figure 7.14 Ribosomal frameshift during translation elongation. (a) Change o...Figure 7.15 Effect of translation elongation process affected by RNA G-quadr...Figure 7.16 Rescue of stalled ribosome mediated by no-go mRNA decay (NGD). C...Figure 7.17 Rescue system of aberrant translation mediated by trans-translat...

8 Chapter 8Figure 8.1 Schematic illustration of the cell cycle. G 1= Gap 1, G 2= Gap 2,...Figure 8.2 The initiation steps of replication in human cells. First, ORC bi...Figure 8.3 Potential mechanisms involving the action of G4 structures in ori...Figure 8.4 The mechanism of delay of replication firing mediated by Rif1 bin...Figure 8.5 G4-inducing genetic variations that are inherited after mitosis. ...Figure 8.6 (a) Replication-accompanying histone binding to newly synthesized...Figure 8.7 Expansion and contraction of repeat sequence. A repeat sequence c...Figure 8.8 Topology-dependent replication. (a) The plot shows the correlatio...Figure 8.9 Schematic illustration of the recovery of a mutated G4 by intermo...

9 Chapter 9Figure 9.1 Scheme of control of biological reaction by helicases. In replica...Figure 9.2 Representations of DNA helicases from different superfamilies. Sc...Figure 9.3 Crystal structures of SF1 helicase UvrD with the substrate DNA (P...Figure 9.4 Scheme of unwinding of DNA containing a G4 structure by G4 helica...Figure 9.5 Proposed schemes of G4 unwinding by BLM helicase with cooperative...Figure 9.6 Overall structure of the DHX36–G4 DNA complex. (a) Crystal struct...Figure 9.7 The mechanism of G4 unwinding by FANCJ helicase with assistance o...Figure 9.8 Scheme of telomere shortening through replication of the G-rich l...

10 Chapter 10Figure 10.1 Illustration of cell cycle. Cells replicate genome DNA and proli...Figure 10.2 Comparison of reaction rates in central dogma between eukaryote ...Figure 10.3 Structure features of nucleic acids fluctuation and structure al...Figure 10.4 Chemical modification of DNA involved in epigenetic gene regulat...Figure 10.5 Co-transcriptional RNA folding. Nascent RNAs sequentially form t...Figure 10.6 Conformational dynamics of RNA affecting the function itself. Co...Figure 10.7 Modulation of gene expression through transcription attenuation ...Figure 10.8 Functional mechanisms of riboswitches acting on (a) transcriptio...

11 Chapter 11Figure 11.1 Malignant tumor formation at colorectal mucosa.Figure 11.2 (a) Multistage carcinogenesis caused by genetic damage. (b) Gene...Figure 11.3 Image of the proportion for gene promoters that contain at least...Figure 11.4 Example of DNA G-quadruplexes in the promoter region.Figure 11.5 G-quadruplex in a mild cancer cell and an aggressive cancer cell...Figure 11.6 Typical example of transcription regulation responsive to chemic...

12 Chapter 12Figure 12.1 Aggregation mechanism of abnormally elongated polyQ.Figure 12.2 Structures formed by repeat DNA sequences for (a) hairpin, (b) t...Figure 12.3 Extension of CTG repeats by hairpin structure during replication...Figure 12.4 Typical human protein coding RNA including the untranslated regi...Figure 12.5 Structures formed by repeat RNA sequences for (a) single strand,...