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Figure 2.6 Structure of four-way junction to form cruciform and Holliday junction. (a) S-type and C-type pathways to form cruciform structure from long duplex. (b) Structure of Holliday junction formed by DNA strand with 5′-TCGGTACCGA-3′ sequence (PDB ID: 1M6G). Top view of four TA consecutive nucleobases at the region of interstrand exchange are shown above the structure.

2.5 Multi-stranded DNA Helices

Base paring through hydrogen bonds and stacking interactions between the assembled nucleobases are the main factors that maintain the organized structure of nucleic acids. Multi-stranded structures are formed when nucleobases present in different strands more than three interact with each other to form the assembled structure and stably stack over. Figure 2.7 shows canonical duplex and other typical multi-stranded helices of nucleic acids, in which structures are resisted in protein data bank, including those consisting of unnatural nucleobases.

      Among the multi-stranded nucleic acid structures, triplexes and tetraplexes composed of three and four strands, respectively, have been confirmed in not only aqueous solutions but also intracellular conditions and have attracted attention as non-canonical structures that contribute to gene regulations. Various studies have been conducted on the molecular mechanisms of their influence on the gene expressions from viewpoints of their thermodynamic stabilities and conformational dynamics. The structural characteristics and factors that contribute to the thermodynamic stabilities of triplex and representative tetraplexes, G-quadruplex and i-motif, are described in Chapter 3. The effects of these multi-stranded structures on gene expressions are explained in Chapters 5–8, focusing on DNA replication including telomeric regions, RNA transcription, and protein translation.

2.6 Structures in RNA

      RNA is transcribed from DNA as a single strand, whereas the natural DNA basically exists as a set of complementary strands. The information transformed into functional proteins as a sequence of amino acids is encoded on the primary sequence of RNA. On the other hand, information to modulate the gene expressions exists in their higher-order structures, which are dependent on the secondary and tertiary interactions.

      2.6.1 Basic Structure Distinctions of RNA

As described in Chapter 1, by comparing natural RNA to DNA, there are two difference in their chemical structures. One is the ribose sugar, which bears a 2′-hydroxyl group, and the other is uracil nucleobase, which lacks the 5-methyl group of thymidine in DNA. Regarding structure formation, 2′-hydroxyl group of ribose is the most important factor that confers unique conformational features compared to the DNA. The basic feature that RNA forms an A-type duplex is based on the fact that RNA ribose adopts C3′-endo-type conformation in its sugar pucker due to the presence of 2′-hydroxyl group. The constitutive characteristic that RNA is basically single-stranded is also an important element for RNA to form various secondary and tertiary structures.