Guide to Drawing Base Pairs Correctly with ChemDraw
Learn how to draw Watson-Crick base pairs accurately using ChemDraw software. Follow step-by-step instructions and visual aids to create base pairs and understand nucleotide structures effectively.
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How to draw a base pair (with ChemDraw) (correctly)
Draw two parallel lines that are spaced vertically about the size you intend to draw the Watson-Crick base pair.
Draw a third line parallel to, and equidistant between, the first two lines.
Draw a two more lines parallel to the three lines so that you now have five equally spaced lines.
A T Decide which base pair you will draw, and on which side you will have the purine base and on which side you will have the pyrimidine base.
A T Draw the first base hexagon oriented as shown above.
N N A T Add two nitrogen atoms at the positions above
N N A T Draw a template hexagon, as above.
N N A T And a second template hexagon, as above.
N N N N A T Draw the second base hexagon, include two nitrogen atoms.
N N N N A T Delete the two template hexagons.
N N N N O A T T has two keto oxygens. Draw the first.
O N N N N O A T T has two keto oxygens. Draw the second.
O N H N N N O A T Add the hydrogen to the WC nitrogen of the T
O N H N N N O A T Add the methyl group to the T
O N H N N N O R A T Add the glycosidic bond, and the deoxyribose.
O N H N N N O R A T Add the double bond.
O N H N N N O R A T Draw lower WC hydrogen bond.
H O N H N H N N N O R A T Add amino group to the A. Draw the hydrogen atoms at 120 degrees. Do not use -NH2
H O N H N N N H N N N O R A T Add the 5-membered ring to the purine (A). Indicate both nitrogen atoms.
H O N H N N N H N R N N O R A T Add the glycosidic bond and the deoxyribose.
H O N H N N N H N R N N O R A T Add all the double bonds.
H O N H N N N H N R N N O R A T Now the next base pair.
H O N H N N N H N R N N O R A T G C
H O N H N N N H N R N N O R A T N N G C
H O N H N N N H N R N N O R A T N N G C
H O N H N N N H N R N N O R A T N N N N G C
H O N H N N N H N R N N O R A T N N N N O G C C has one keto group.
H O N H N N N H N R N N O R A T H H N N N N N O G C And an amino group
H O N H N N N H N R N N O R A T H H N N N N N O R G C Draw two parallel lines that are spaced vertically about the size you intend to draw the Watson-Crick base pair.
H O N H N N N H N R N N O R A T H H N N N N N O R G C Add the double bonds to the C.
H O N H N N N H N R N N O R A T H H N N N H N N O R G C Draw two parallel lines that are spaced vertically about the size you intend to draw the Watson-Crick base pair.
H O N H N N N H N R N N O R A T H O H N N N H N N O R G C G has one keto group
H O N H N N N H N R N N O R A T H O H N N N H N N O R N H H G C G has one amino group
H O N H N N N H N R N N O R A T H O H N N N N N H N N O R N H H G C
H O N H N N N H N R N N O R A T H O H N N N N N H R N N O R N H H G C
H O N H N N N H N R N N O R A T H O H N N N N N H R N N O R N H H G C
H O N H N N N H N R N N O R A T H O H N N N N N H R N N O R N H H G C Remove the template lines
H O N H N 4 5 N N H N 3 6 R 2 1 N N O R A T H O H N N 4 5 N N N H 3 6 R 2 1 N N O R N H H G C Number the atoms.
H O N H N 5 6 4 5 N N H N 3 6 4 1 3 2 R 2 1 N N O R A T H O H N N 4 5 5 6 N N N H 3 6 4 1 3 2 R 2 1 N N O R N H H G C Notice the difference in the numbering of the 6-membered rings.
H O N H N 87 5 6 4 5 9 N N H N 3 6 4 1 3 2 R 2 1 N N O R A T H O H N N 87 4 5 5 6 9 N N N H 3 6 4 1 3 2 R 2 1 N N O R N H H G C The glycosidic bond is at the N1 of the pyrimidines. The glycoside bond is at the N9 of the purines
The N7, O6/N6 and O4/N4 are in the major groove. Major Groove H O N H N 87 5 6 4 5 9 N N H N 3 6 4 1 3 2 R 2 1 N N Minor Groove O R A T H Major Groove O H N N 87 4 5 5 6 9 N N N H 3 6 4 1 3 2 R 2 1 N N O R N H Minor Groove H G C The N3 and O2 are in the minor groove - and so is the N2 if it is a GC base pair.
