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DNA Structure & Base Pairing
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DNA Structure & Base Pairing

DNA Structure
Overview
Here we will learn about about the structure of DNA.
Sugar-Phosphate Backbone
DNA has a fixed backbone that comprises units of:
  • Sugar (a deoxyribose)
  • Monophosphates
These give each DNA strand directionality: 5' to 3' vs 3' to 5'.
The Nitrogenous Bases
Denote the 4 nitrogen bases.
  • The purines: Adenine & Guanine
To remember the purines, think: Larger & think about ATP/GTP (adenine, guanine).
The pyrimidines: Thymine & Cytosine (Uracil is in RNA, only*).
To remember the pyrimidines, think: Smaller & think about the chemistry of UMP to dTMP (thymine) & CTP (cytosine).
Base Pairing
  • Adenine pairs with thymine (via two hydrogen bonds).
  • Guanine pairs with cytosine (via three hydrogen bonds).
Basic Organization
To begin, let's draw the basic organization of DNA in a railroad track layout:
Sugar-phosphate backbones
  • Show vertically-oriented sugar-phosphate backbones.
Nitrogenous bases
  • Then, show that the sugars link with nitrogenous bases, which link via hydrogen bonds.
uncoiled DNA
With that organization as a background, we're ready to tackle the sugar-phosphate backbones and what is meant by 5' to 3' orientation.
  • First, let's draw DNA in an UNCOILED state and then in its COILED state.
Sugar-Phosphate Backbone
5' to 3' Strand
  • Draw deoxyribose:
  • Draw a pentagon with an oxygen atom inserted at the top.
    • Label carbons 1' through 4', going clockwise from the oxygen atom.
    • Now add carbon 5' as an attachment to carbon 4'.
  • With the sugar in-place, next add a phosphate at the 5' end, which establishes the directionality of the strand of DNA – let's see how the rest, now, falls into place.
  • At the 3' carbon, add an oxygen.
  • Show that it forms a phosphate, which then connects to the next deoxyribose
    • This would continue along the strand.
  • We can cap the strand, though, at the 3' hydroxyl, because, we understand the pattern.
  • Draw the 5' (phosphate) to 3' (hydroxyl) orientation.
    • Note that we have not, yet, addressed the nitrogenous bases that attach to the 1' carbons on these sugars.
3' to 5' Strand
  • Now, let's skip to the opposite side, which presents in opposing (antiparallel) orientation.
  • Draw the deoxyribose (upside down in reference to the first one we drew).
  • Attach a phosphate to its 5' carbon.
  • At the 3' carbon, attach a phosphate.
  • Show that it attaches to another deoxyribose.
    • Again, cap the deoxyribose because we understand the pattern.
  • Draw the 5' to 3' directionality.
    • It's opposite (antiparallel) to the original.
Coiled DNA
With the sugar-phosphate backbone in-place, now we can introduce the nitrogenous base pairs and DNA coiling.
  • Draw two simplified strands of DNA in a double-helix structure.
    • Label the 5' and 3' ends of one strand.
    • Then, indicate that the second strand runs from 3' to 5', thus it is antiparallel to the first.
  • Indicate that the nitrogenous base pairs have hydrogen bonds that hold them and the double helix together.
  • Indicate that there are ten nitrogenous base pairs per full 360 degree helical turn.
    • Each base is rotated 36 degrees from the one above or below it.
    • Because there are 360 degrees per full turn, there are 10 (ten) bases per full 360 degree turn.
Nitrogenous Bases
Now, we're ready to add in the chemistry of the nitrogenous bases.
  • Indicate that there are two general categories of nitrogenous bases in nucleic acids: - Pyrimidines
    • Purines
For each category, we will first draw their general structures and then the bases that are part of this group.
Pyrimidines
Indicate that the pyrimidines are:
  • Thymine (T)
  • Cytosine (C).
    • To remember the pyrimidines, think: smaller & think about the chemistry of UMP to dTMP (Thymine) & CTP (Cytosine).
Purines
Indicate that the purines are:
  • Adenine (A)
  • Guanine (G)
    • To remember the pyrimidines, think: larger & think about ATP/GTP (adenine, guanine).
    • We leave out uracil (U) from this tutorial because it is an RNA nitrogenous base.
Pyrimidine Structure
Now, for reference, draw the general structure of a pyrimidine nitrogenous base.
  • For the general structure of a pyrimidine, draw a hexagon.
  • Label positions 1 through 6, going counterclockwise, beginning at the bottom of the hexagon.
  • Insert nitrogen atoms at positions 1 and 3.
  • Now add double bonds between N1 and C2, N3 and C4, and C5 and C6.
Purine Structure
For reference, draw the general structure of a purine nitrogenous base:
  • Draw a hexagon.
  • Label positions 1 through 6 going counterclockwise starting to the left of the top of the hexagon.
  • Insert nitrogens at positions 1 and 3.
  • Now add double bonds between N1 and C6, C2 and N3, C4 and C5.
  • Next, add a five-membered ring, shaped like a pentagon.
  • Now going clockwise from the top of the pentagon, label positions 7, 8, and 9.
  • Insert nitrogen atoms at positions 7 and 9.
  • Now add a double bond between N7 and C8.
  • Finally, add a hydrogen atom to N9.
Base Pairing
We're not quite ready to apply these bases to our DNA structure – first we need to see how they bond.
  • To do so, draw out the nitrogenous bases, so we can reference their hydrogen bonding sites.
Purines
Adenine
  • Redraw our general purine structure with its 4 double bonds but add an NH2 group at C6.
    • In the purine biosynthesis tutorial, we learn that adenylosuccinate synthetase catalyzes the addition of the amine group from via aspartate addition via GTP phosphorylation.
Guanine
  • Redraw our general purine structure with its 4 double bonds, here, add an NH2 group at N2 – the amine group is added via ammonia produced from glutamine hydrolysis in the process of inosinate (IMP) conversion to GMP.
  • Also, add an oxygen doubled-bonded to C6, since guanine derives from inosinate, which is oxygenated at C6.
    • Again we learn about inosinate and its conversion to guanine in our purine biosynthesis tutorial.
Pyrimidines
Thymine
  • Draw the standard pyrimidine ring.
  • Add a methyl at carbon 5 (which differentiates it from uracil (its RNA counterpart).
  • Then, include the oxygens that were found in orotate at carbons 2 and 4.
    • We learn about them in the pyrimidine biosynthesis tutorial.
Cytosine
  • Again, draw the pyrimidine ring.
  • Include the oxygen that was found in orotate at carbon 2 but at carbon 4, add an amino group, instead.
    • In the pyrimidine biosynthesis tutorial, we learn that that via glutamine hydrolysis, ammonia is added to convert UTP to CTP (via CTP synthetase).
BASE PAIRING
Adenine-Thymine
  • Show that adenine and thymine pair with each other via TWO hydrogen bonds as follows:
    • The hydrogen atom on N3 of THYMINE bonds with N1 of ADENINE.
    • An amino group hydrogen on C6 of ADENINE bonds with the carbonyl oxygen on C4 of THYMINE.
Cytosine-Guanine
  • Now write that cytosine and guanine pair with each other via hydrogen bonds
as follows:
    • An amino group hydrogen on C2 of GUANINE bonds with the carbonyl oxygen on C2 of CYTOSINE.
    • The hydrogen atom bound to N1 of GUANINE bonds with N3 of CYTOSINE.
    • An amino group hydrogen on C4 of CYTOSINE bonds with the carbonyl oxygen on C6 of GUANINE.
DNA Uncoiled (Conclusion)
Pyrimidines
  • Now, redraw a simplification of the pyrimidines on the left-hand side of the DNA (this is arbitrary: we show them on this side for simplicity).
  • Draw thymine
  • Draw cytosine
To remember the pyrimidines, think: Small & think about the chemistry of UMP to dTMP (Thymine) & CTP (Cytosine).
Purines
  • Now redraw a simplification of the purines on the right-hand side (again, this is arbitrary):
  • Draw adenine.
  • Draw guanine.
To remember the purines, think: Large & think about ATP/GTP (Adenine, Guanine).
Adenine & Thymine Pairing
TWO Hydrogen Bonds
  • The hydrogen atom on N3 of THYMINE bonds with N1 of ADENINE.
  • The carbonyl oxygen on C4 of THYMINE bonds with an amino group hydrogen on C6 of ADENINE.
Cytosine and Guanine Pairing
THREE Hydrogen Bonds
  • The carbonyl oxygen on C2 of CYTOSINE bonds with an amino group hydrogen on C2 of GUANINE.
  • N3 of CYTOSINE bonds with the hydrogen atom bound to N1 of GUANINE.
  • An amino group hydrogen on C4 of CYTOSINE bonds with the carbonyl oxygen on C6 of GUANINE.

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