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DNA structures - Coggle Diagram

- - - - Function
        
        DNA-protein interaction can be inhibited if a hairpin overlaps a protein recognition site.
        
        DNA hairpins can act as a recognition site for proteins as proteins can directly recognize and bind to them
        
        In replication, hairpins allow for a lesion bypass. For example, when there is a mutation or a mistake where the repair mechanism is not fast enough to fix it, hairpins can form at the lesion and allow for the DNA polymerase to continue function and replicate DNA.
        
        In bacteria such as E.coli, hairpins can affect transcription termination.
        
        Usually hairpins do not form as Single strand binding proteins will prevent it from happening. However, there is another type of protein that is able to stabilize hairpins. Whether a hairpin is formed or not, depends on the competition between the two proteins.
        
        Its location
        
        Hairpins can be found in several situations involving single stranded DNA and RNA. In RNA, thymine bases are repalced with Uracil.
        
        On the template for lagging-strand synthesis during DNA replication,
        
        How a hairpin loop is formed
        
        Hairpin loops are formed by a fold in a single strand of DNA, causing several bases to remain unpaired before the strand loops back upon itself.
        
        A hairpin loop is only possible if the strand of DNA contains the complimentary bases in correct sequence to those that appear earlier in the strand also known as palindromes.
        
        For example if a DNA strand contained ATCGCA followed by several bases including TAGCGT, this DNA strand can form a hairpin loop.
        
        A hairpin loop cannot exist in the length of three bases as the steric hindrance makes it too unstable
  - - - How is cruciform formed
        
        Cruciform form in double-stranded DNA and similarly to DNA hairpins, the formation of cruciform requires the presence of palindromes called inverted repeats.
        
        What inverted repeats means is that a sequence of DNA in one strand is repeated in the opposite direction on the other strand.
        
        To form a cruciform, it requires at least a 6 nucleotide seqeuce of inverted repeats.
        
        Cruciform are stabilized by negative DNA supercoiling.
        
        Function
        
        Cruciform affect the proteins that can interact with the area around it.
        
        Cruciform can also act as a recognition site for proteins that can directly recognize it and bind to it.
        
        An example of protein that can bind to a cruciform is Crp1p which is found in yeast Saccharomyces cerevisiae
- - - - Forms when two double-stranded DNA molecules become separated into four strands
        
        The two double stranded DNA strands that are involved in forming Holliday junction must be highly homologous.
        
        These two homologous DNA will move very close to one another. Until one strand from each double stranded DNA invades one another. This is known as a formation of a D-loop.
        
        After the formation of a D-loop, there will be cleavage in both strands from both double stranded DNA followed by ligation.
        
        Isomerization then takes place where of the DNA strands flips to form a Holliday junction.
    - - For exchange of segment of genetic information
        
        During a double stranded break where genetic information is lost, A Holliday junction can form where another highly homologous DNA comes close to it. Overhangs caused by the break at the 3' of each strand can invade the sister chromatid where it can be used as a template. Genetic information lost might not be the same as the template but it will be very similar.
    - - Holliday junction is held together by hydrogen bonds
    - - Resolvase can cleave the Holliday junction in two axis
        
        Horizontal axis
        
        Cutting this way produces duplexes where parental segments remain covalently linked and are not being exchanged. However, there is a small hetero duplex region found in these products.
        
        Called non-recombination products
        
        Vertical axis
        
        Cutting this way results in duplexes in which parental duplexes have been exchanged. Franklin segments are covalently linked. Which means A is linked to b while a is linked to B
        
        Called recombinant products.
- - - - Guanin rich regions can form four stranded quadruplex structures. All four strands are parallel with the three linking trinucleotide loops positioned on the exterior of the quadruplex core in a propeller like arrangement.
        
        Interactions like stacking interactions, electrostatic interactions, hydrophobic interactions and hydrogen bonds stabilizes the G-quad structure.
        
        A G-quad is made up of a few G-quartet. Within the hydrogen bonding among the guanine bases stabilizes the structure. It is also stabilized by some form of electrostatic interaction. in the center of the g-quartet there will be a monovalent ion can be na+ or lithium. Lone pair of electrons from oxygen can form an interaction with this ion to form co-ordinate bond. On top of this, between two layers of g-quartet, the guanine bases will make hydrophobic interactions between the different layers this is called stacking interaction.
      - No watson-crick pairing
        
        Watson-crick uses atom 6 and 1 for binding while hoogsteen uses atom 6 and 7 for binding.
    - - End of telomores
      - Promoter
      - 5' UTR
    - - At the end of the chromosome is a single stranded 3' DNA. This ssDNA is usually arranged in a form of multiple G-quadruplex structures. The purpose of these structures are to prevent nucleases from damaging the DNA. The nucleases has to break the G-quad first before getting to the genetic information.
        
        It might also have a role to play in the regulation of gene transcription. If it is found at the promoter region, RNA or DNA polymerase cannot bind to the promoter. This adds another layer of complication to better regulate things.