;instancetext:The double strand DNA molecule is 20 bps in length with an additional nucleotide at the 5'-end of each strand. The nucleotides of chains A and B are numbered 1-21 and 22-42, respectively. The unpaired nucleotides at the 5'-end of each chain are numbered 1 and 22. The complete sequence of this DNA is\
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5'-ACATGTAATTCATTTACACGC-3'\
3'- GTACATTAAGTAAATGTGCGT-5'\
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Suggested Activity: Choose "Auto Rotation" from the display menu. Enter rotation values of 0-3-0 degrees for x-y-z. Click "OK" and observe the overall molecule shape as it rotates. Can you distinguish the major and minor grooves? \
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Each successive view is designed to emphasize additional features of DNA structure. View each in turn, and perform the activity suggested.\
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Note: The DNA coordinates are from the Brookhaven pdb file "1apl", representing the operator DNA binding site for the mat2 alpha homeodomain protein.
;instancetext:The unpaired nucleotides at the 5'-end of each DNA strand are hilited in this view. Can you identify the A-nucleotide at the 5'-end of chain A, and the T-nucleotide at the 5'-end of chain B?
;instancetext:DNA normally occurs as two separate long polymers that wrap around each other in a helical spiral. The two individual strands have different colors in this view. \
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Suggested Activity: Choose "Auto Rotation" from the display menu. Enter rotation values of 0-3-0 degrees for x-y-z. Click "OK" amd observe how the 2 strands intertwine. Notice that there are no covalent bonds joining the two strands. They are held together by many weak interactions.
;instancetext:DNA (and RNA) are polymers made up of five-carbon sugars, organic nitrogen-containing bases, and phosphate groups. One of the 40 phosphate groups of our parent DNA structure is shown. The central phosphate atom is covalently bonded to four oxygen atoms. \
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Suggested Activity: Measure the 4 different O-P-O bond angles (click on the angle tool on the button bar, and then click on three atoms in a row. The angle appears in the comment line). Why are the angles not the same?
;instancetext:The location of the phosphate groups in the two DNA strands is emphasized in red and yellow color. Notice that the oxygen atoms, rich in negative charge, are located on the outermost surface of the DNA double helix. The phosphates form part of the backbone of the DNA molecule, alternating along the chain with the 5-carbon deoxyribose sugars.\
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Suggested Activity: Use the distance tool to measure the width of the major groove from phosphate to phosphate. Then measure the width of the minor groove.
;instancetext:DNA (and RNA) are polymers made up of five-carbon sugars, organic nitrogen-containing bases, and phosphate groups. One of the 42 deoxyribose sugars of our parent DNA structure is shown. \
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Suggested Activity: Use the information tool to identify different atoms. Look at the "aloc= " field of the comment line for the answers. The sugar structure has 5 carbon and 3 oxygen atoms. 4 carbons (C1'-C4') and one oxygen (O4') form a 5-membered, puckered ring. The remaining 2 oxygen atoms (O3' and O5') are linked to phosphate groups (not shown) in the repeating sugar-phosphate backbone of DNA. The sugar is a "deoxy" ribose due to the absence of a hydroxyl group (-OH) and the presence 2 hydrogen atoms on one of the ring carbon atoms (C2').
;instancetext:The (blue) nitrogen atom has been added to the previous view of deoxyribose. This nitrogen is from one of the organic nitrogen-containing bases of DNA. The bases are linked to the sugar-phosphate backbone through a bond with the C1' of the sugar ring.
;instancetext:The location of the deoxyribose sugars in the two DNA strands is emphasized in red (oxygen atoms) and green (carbon atoms). All other atoms are colored pale yellow.\
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Suggested Activity: Compare the location of the electronegative oxygen atoms of the sugar that are involved in phosphodiester bond formation to the location of the other two oxygen atoms of each phosphate group (see the "Phosphate group location" view). You may wish to zoom in for a closer look, and use the information tool to identify different types of oxygen atoms. Which oxygens are most exposed to the solvent? Why?
;instancetext:The A-chain and B-chain of the DNA helix are oriented in opposite direction along the DNA helix axis, much as cars move in opposite direction on a 2-way road. The orientation of the deoxyribose sugar is used to describe the direction (also called polarity) of the DNA chains. In this view, the 5 atoms that make up the sugar ring are shown, with the oxygen shown in red. Notice that when the oxygen points up on the yellow rings, it points down on the blue rings. DNA strands are said to be "antiparallel", meaning meaning parallel but moving in opposite direction.\
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In the next view, you will see how the DNA bases span the gap between the antiparallel sugar-phosphate backbone.
;instancetext:A view of the T9-A35 base pair from the major groove. The phoshpates (yellow/red) are on the outside, and the hydrophobic, nitrogen containing bases are on the inside. The edges of the basepair protrude into the major and minor grooves of the helix.\
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Can you identify the types of base pairs that stack above and below the T9-A35 base pair?\
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Note the antiparallel orientation of the sugar rings as described in the previous view.
;instancetext:Looking down on the T9-A35 base pair from the helix axis. Phosphates are on the outside, sugars intermediate, and the bases A and T are in the interior. Note the antiparallel orientation of the sugar rings as described in the previous two views. \
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Two hydrogen bonds are possible between the A and T bases. The first involves a hydrogen on the amino group of A to the oxygen 4 of T. The second is between ring nitrogen 1 of A and hydrogen 3 attached to ring nitrogen 3 of T. Measure the hydrogen bond distances. Do you get values of 1.77 and 1.53 angstroms?\
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In this view, the top edges of the base pair would protrude into the major groove of DNA, and the bottom edges would protrude into the minor groove.\
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To help identify the major and minor grooves, use the distance tool to measure the distance between the C1' atoms of the two sugars (C1' connects from the sugar to the ring nitrogen). Do you get a value of 10.33 angstroms? The measurement line passes along the edge toward the minor groove.
;instancetext:Looking down on the C11-G33 base pair from the helix axis. Phosphates are on the outside, sugars intermediate, and the bases A and T are in the interior. Three hydrogen bonds are possible. A good technique to visualize H-bonds is to switch to view in space filling mode, and note the overlap of the white atoms with the nearby electronegative oxygen (red) or nitrogen (blue) atoms. Measure the distance of the three hydrogen bonds. Do you get values between 1.60 and 1.68 angstroms?\
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Use the distance tool to measure the distance between the C1' atoms of the two sugars (C1' connects from the sugar to the ring nitrogen). The measurement line passes along the edge toward the minor groove. Do you get a value of 10.25 angstroms, very similar to the value for the previous view? Note that A-T and G-C base pairs occupy nearly the same amount of space in the DNA helix.\
;instancetext:What does a protein that binds to the major groove of a DNA double helix use to recognize a specific sequence of bases? In this view, the groups on the edges of base pairs that protrude into the major groove are color coded as follows:\
H-bond donors - blue\
H-bond acceptors - red\
Methyl group - yellow\
Hydrogen unable to H-bond - yellow\
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Compare the color coding of the major groove recognition elements in this view and the following 2 views for each of the four types of base pairs:\
TA pair: yellow-red-blue-red\
AT pair: red-blue-red-yellow\
GC pair: red-red-blue-yellow\
CG pair: yellow-blue-red-red\
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Can you use this color coding to read the DNA sequence for the view "Major groove recognition"? Does this help you understand how a DNA-binding protein might recognize a specific DNA sequence by binding in the major groove?
;instancetext:The hydrogen bond donor (blue), hydrogen bond acceptors (red), and methyl group (yellow) of the edge of the T9-A25 base pair that faces the major groove of the DNA helix are illustrated. \
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Compare the color coding of the major groove recognition elements in this view and the following view for each of the four types of base pairs:\
;instancetext:The hydrogen bond donor (blue), hydrogen bond acceptors (red), and hydrogen unable to form a hydrogen bond (yellow) of the edge of the C11-G33 base pair that faces the major groove of the DNA helix are illustrated. \
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Compare the color coding of the major groove recognition elements in the view and the previous view for each of the four types of base pairs:\
;instancetext:What does a protein that binds to the minr groove of a DNA double helix use to recognize a specific sequence of bases? In this view, the groups on the edges of base pairs that protrude into the minor groove are color coded as follows:\
H-bond donors - blue\
H-bond acceptors - red\
Hydrogen unable to H-bond - yellow\
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Suggested activity: Compare the ease of reading the DNA sequence from the color codes of the major groove and the minor groove. Click in the molecule window and then rotate the molecule as needed using the right and left arrow key on the keyboard.
;instancetext:The hydrogen bond acceptors (red), and hydrogen than does not hydrogen bond (yellow) of the edge of the T9-A25 base pair that faces the minor groove of the DNA helix are illustrated. \
;instancetext:In this view, the groups on the edges of base pairs that protrude into the minor groove are color coded as follows:\
H-bond donors - blue\
H-bond acceptors - red\
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Note that AT and GC pairs have different patterns in the minor groove, but that the distinction between a GC and a CG pair in terms on potential hydrogen bond interactions is minimal.\
