The transition temperatures corresponding to Δ F = 0 are obtained from simulations and Eq. ( 9). (g) The free energy difference Δ F = F D H 1 − F G * at k τ = 5. (f) The free energy landscape for the G * − D H 1 equilibrium at k θ = 7, k τ = 5, and T = 0.7. (e) The dependence of entropy loss, Δ S, for the G * − D H 1 transition on k θ and k τ at their respective transition temperatures. (d) The minimum parameter sets of k θ and k τ for the formation of D H 1. The linker in the polymer is marked in orange. (c) Representative structures in different phases: random coils ( R), random coils with flickering helical ordering ( R *), globules ( G), globules with local helical ordering ( G *), compact structures ( C 1), compact structures with local helical ordering ( C 2), two-helix bundles ( H 2), and double-helix structures ( D H 1). Colored regions stand for structural phases. The dotted lines represent the transition temperatures. (a) Varying the torsion stiffness k τ and the temperature T at a fixed bending stiffness k θ = 10. The term double helix refers to the shape of a double-stranded DNA molecule, a shape that is like a twisted ladder. Phew! You'd think something as elegant and beautiful as the famed double helix would be easier to explain but it's not.Phase diagrams for the self-folding of single semiflexible polymers of length N = 30 with reference angles θ 0 = 105 ° and τ 0 = 50 °. This extra twist at the end is the reason for the helical shape.įor the “steps” of the DNA “staircase” to fit together, they have to twist a little bit, making the final spiral shape of DNA. This turns our staircase into a spiral staircase. To avoid bumping into each other, the staircase has to twist a little bit. In this arrangement, neighboring atoms bump into each other. It turns out that although the skewed ladder closes the 'holes', it introduces a new problem. This double helix shape is often visualized as a spiral staircase. Its double helix consists of two spiral chains of DNA. We can think about this as turning a ladder into a staircase. Double helix is the biological term that describes the overall structure of DNA. One solution to get rid of the 'holes' is to skew the ladder to one side (see 3). This still doesn't take care of the holes between the bases. The double helix describes the appearance of double-stranded DNA, which is composed of two linear strands that run opposite to each other, or anti-parallel, and twist together. This is one of the reasons why DNA is double stranded. One obvious way to cover up this space is to bring in another chain to cover it up forming a straight ladder (see 2). The bases in DNA stay on the inside of the spiral, away from water, while the sugar and phosphate molecules stay on the outside.īut if the bases just stack themselves, this will still leave space between the bases through which water can sneak in (see 1). To avoid water, the bases have to stack themselves in the center, while the sugar and phosphates stay outside (see 1). They become water-soluble once they attach to a sugar and a phosphate to form a "nucleotide", the building block of DNA. How are these hydrophobic or water-insoluble bases going to exist in the cell? All the oil droplets will pool together and self-associate and not blend with the water.īut most of the space in the cells is filled by water. What happens to these molecules when you put them in water? Something similar to what happens when you mix oil and water. They are not water-soluble - they are hydrophobic. The bases, the famous A, G, T, and C's that you've probably heard about, hate water. Okay, the sugars and the phosphates are water-soluble and so are called hydrophilic molecules. To be used in these ways, phosphates need to be able to dissolve in water too. They are also used in baking mixes, fertilizer, and lots of other things. Phosphates aren't as well known as sugars but they are really important for our body. When something can dissolve in water, it is called "water-soluble" or hydrophilic. When James Watson and Francis Crick, with the help of critical data from Rosalind. To sweeten our coffee or lemonade, sugar has to dissolve in water. The DNA double helix is the most famous molecular structure in all of biology. The sugar molecule is like the sugar we use in our foods. Surprisingly, a big part of what makes DNA a spiral has to do with how well each part dissolves in water! Let's dig deeper, break open the DNA and figure out why it is put together in that shape.ĭNA has three parts - sugar, phosphate and bases that are linked together chemically in a particular way. But few people can tell us why.ĭNA is a spiral for a number of reasons that have to do with what it is made of. And that it forms a twisted ladder or a double helix. Almost everybody who talks about DNA can tell you it is double stranded.
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