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DNA Structure

On This Page
DNA Structure
Bases - purines, pyrimidines
Nucleosides, Nucleotides
5' -> 3' directionality
Catalysis
Double helix - A=T, C=G, antiparallel strands, major and minor grooves
Semiconservative Replication
Higher orders of DNA structure
Major and Minor Grooves
Supercoiling
Open regions - AT rich sequences
Secondary structure - palindrome/inverted repeat/dyad symmetry
Cruciform - hairpin loop/stem loop
Alternative helices - B vs. A, C and Z forms

Study Questions from Textbook Reading
Of what is a nucleotide composed?
What distinguishes purines from pyrimidines?
What distinguishes the different purines (pyrimidines) from one another?
What is the difference between ribose and deoxyribose?
To which position is each component of a nucleotide attached to the sugar?
What abbreviations are used to refer to various nucleotides?
How are nucleotides linked into single strands of nucleic acid?
What distinguishes RNA from DNA?
How are double-stranded nucleic acids linked?
What impact on this linkage does the nucleotide sequence (sequence of bases) have?
What is the general mechanism of replication of DNA?
Describe some alternative structures of DNA.

After reading the text and web page, you may choose to test your knowledge of DNA structure by taking the on-line test at this site.

DNA Structure
Deoxyribonucleic acid (DNA) is a macromolecule composed of individual subunits known as nucleotides. A nucleotide is a composed of a nitrogenous base, a sugar, and one or more phosphate groups. (DNA is one of two types of nucleic acid; RNA is the other. Although this lecture is primarily about DNA, structural features of RNA are also noted. RNA will be discussed more fully in the future.)

Bases
The nitrogenous bases of nucleotides are ring structures of nitrogen and carbon with other organic side chains attached at specific locations.

Bases classified as purines have a double structure and, depending on the organic side chains attached, may be either adenine or guanine. Bases classified as pyrimidines have a single ring structure and may be cytosine, uracil, or thymine. (Note that uracil is not normally found in DNA but replaces thymine in RNA.) The numbering shown around the generalized structures in these figures are used for orientation.

Sugars
The sugar found in the nucleotides of DNA is deoxyribose. Ribose is found in RNA. Deoxyribose and ribose are pentose sugars (containing 5 carbon atoms). Their ring forms as found in nucleotides are shown here. The carbon atoms are numbered for orientation and "primes" are used to distinguish the atoms of the sugars from the atoms of the nitrogenous bases in nucleotides. Note that the 5' ("five prime") carbon atom is not a part of the ring. The fifth atom of the ring is an oxygen.

The only difference between deoxyribose and ribose is that deoxyribose lacks a hydroxyl group at the 2' position. Thus, the deoxyribose found in nucleic acids is more properly known as 2'-deoxyribose.

 

 

Nucleotides and Nucleosides
Deoxyribose (or ribose) forms the central component of a nucleotide with the base attached to the 1' carbon and one or more phosphate groups attached to the 5' carbon atom. (A phosphate group is a phosphorus atom surrounded by oxygen atoms. Phosphates carry negative charges at cellular pH and give the nucleotides their acidic character.)

The technical nomenclature is as follows.

The following table summarizes the nomenclature. In everyday verbal communication, one often simpifies and uses the names of the bases regardless of whether one is speaking of a base, a nucleotide, or a nucleoside.

Base Nucleoside Nucleotide Abbreviation in
RNA / DNA
adenine adenosine adenylic acid AMP / dAMP
guanine guanosine guanylic acid GMP / dGMP
cytosine cytidine cytidylic acid CMP / dCMP
thymine tymidine thymidylic acid ------ / dTMP
uracil uridine uridylic acid UMP / ------

Single strands
Nucleotides are combinded end-to-end to form a single strand of nucleic acid. In a single strand, nucleotides are linked by a phosphodiester bond, a covalent bond, between the alpha phosphate of one nucleotide to the 3' carbon of the adjacent nucleotide.

At one end of the stand, a free (unattached) 5' phosphate group from the terminal nucleotide is found. This end is referred to as the 5' end of the nucleic acid strand. At the opposite end is a free 3' hydroxyl group marking the 3' end of the strand. Thus, each nucleic acid strand has a 5'->3' directionality as indicated by the arrow in the figure.

Catalysis
Energy for catalysis of the reaction joining nucleotides is provided by the nucleotide triphosphates themselves. The energy carrying molecule, ATP, that you learned about when studying glycolysis and the Kreb's cycle is actually the nucleotide ATP. The energy released when the bond between the alpha and beta phospate groups is broken is used to catalyze the linkage of the alpha phosphate to the free 3' hydroxyl group of the growing strand.

Thus, as indicated in the figure, nucleotide triphosphates are required for synthesis of nucleic acids and, in normal synthesis, new nucleotides are always added to the 3' end of the strand. Again, we see the 5'-> 3' directionality of the strand reflected in the direction of synthesis.

Base pairing
DNA typically exists as a double standed molecule. The two strands are held together by hydrogen bonding between bases, forming a base pair. Only bases which are complementary to one another may pair appropriately.

Thymine (and uracil) is complementary to adenine, and cytosine is complementary to guanine.

Thymine and adenine pair via two hydrogen bonds, and cytosine and guanine pair via three hydrogen bonds.

 

Hydrogen bonds (conventionally depicted with dashed lines) form between one electronegative atom and a hydrogen attached to another electronegative atom. An electronegative atom is one which tends to draw electrons toward it giving it a partial negative charge and leaving an adjacent atom with a partial positive charge. (Partial charges are depicted in the figure with the Greek letter delta.)

As relatively weak interactions, hydrogen bonds are susceptible to heat denaturation.

When James Watson and Francis Crick elucidated the strucuture of DNA, it immediately suggested a mechanism by which DNA could replicate accurately. How might DNA replicate based on the structure?

Double stranded helix
This figure represents complementary base paired, double stranded DNA. Notice that each base pair is composed of one purine paired with one pyrimidine so that the width of the chain is roughly equivalent.

The strands are antiparallel to one another with each strand oriented 5'->3' in opposite directions.


In three dimensions, the two strands twist into a double helix, similar to a spiral staircase, with the base pairs perpendicular to the axis like the steps of the staircase.

 

This animation depicts a space filling model of the DNA double helix.

Notice the wide, major groove wrapping around the helix and the narrower minor groove.

pdb image of DNA bound by Cro protein

Semiconservative Replication

Matthew Meselson - Franklin Stahl

This experiment confirmed the hypothesis based on Watson and Crick's structure that DNA replicated semiconservatively. Prior to Meselson and Stahl's experiments, there were three models that could explain replication of DNA. For a graphical description of the possibilities, go here.

In their experiment, Meselson and Stahl grew DNA in a medium containing a heavy isotope of nitrogen (15N) so both strands were fully labeled; they then changed to a medium containing 14N for one round of replication. They expected some heavy molecules and some light molecules if conservative or all intermediate molecules if semiconservative. Can you diagram the expected results through two generations for each possibility? The actual results supported the conservative model.

Higher Orders of DNA Structure

Even though we know that DNA differs in its nucleotide sequence from one location on the double helix to another, a quick glance at the rotating helix above indicates that local differences are not immediately obvious from the structural appearance. But is it really so symmetrical? We must assume that there are detectible differences since different portions of DNA have different functions. For example, a gene located at one spot on a DNA strand may be actively involved in RNA and protein production in one cell and inactive in another. Since proteins regulate this activity, they must be able to recognize signals contained within the local DNA structure and initiate or inhibit molecular events there. Thus the theme of the following discussion is how DNA can be recognized by proteins if, at first glance, it is a relatively non-descript fibrous molecule.

1) A certain sequence of nucleotides in DNA means that a unique pattern of organic side chains of the bases will result. Such patterns are represented in the arrangement of atoms of the side chains in the major and minor grooves of the double helix. Most DNA-binding proteins studied to date recognize and bind specific sequences of DNA in this manner.

2) Supercoiling - The double helix is by its very nature a coiled molecule. However, if the coiling is increased or decreased, supercoiling results. Increased supercoiling is known as positive supercoiling; decreased supercoiling is known as negative supercoiling. To understand supercoiling, think of a telephone cord. (The spiral cord is a helix.) As the receiver is picked up and replaced repeatedly in normal use, it is often replaced after twisting the cord once or twice. After awhile, a number of twists are introduced and the cord wraps around itself. This is supercoiling. The only way to relieve the supercoiling is to let the cord unwind some.

In cells, DNA is either in circular form (e.g. in bacterial chromosomes, in plasmids, and in many viruses) or it is bound at ends or points along the strand such that it acts as if it is circular (e.g. in animal chromosomes). Furthermore, DNA tends to exist is a somewhat negatively supercoiled state. As indicated in the figure, negative supercoiling can be converted into localized unwinding and strand separation at regions where weaker hydrogen bonding occurs (as determined by the nucleotide sequence). Proteins may then recognize the general region of unwinding or a specific sequence of exposed nucleotides, and initiate functions.

Figure 5.10, Lewin's Genes VI



3) Certain nucleotide sequences of DNA may be capable of folding back on themselves and forming hydrogen bonds within strands rather than between strands. Intrastrand hydrogen bonding is known as secondary structure. (RNA certainly forms secondary structure, although it is unlikely that DNA does in vivo). In order to support secondary structure, the nucleotides must be repeated in an inverted fashion. Inverted repeats in DNA are palindromes. (In language, a palindrome is a series of letters spelled the same way forwards and backwards, e.g. rotor -- see end of lecture notes for other palindromes.)

In DNA, the theoretical structure formed by double stem-loops is a cruciform. In single stranded RNA, a hairpin loop forms. If the loop at the end contains many unpaired bases, the structure is a stem-loop.


Figure 5.6, Lewin's Genes VI

4) Depending on nucleotide sequences and environmental conditions, certain small DNA (or double stranded RNA) molecules may adopt a helical arrangement different than that determined by Watson and Crick. The native Watson and Crick helix is known as the B form. However, A, C, and Z form helices have been identified. The figure below shows three of these forms.

Notice that A and B forms differ in pitch (# of bases per turn), in the way sugars are bent to form the backbone, and in the tilt of base pairs from the fiber axis. Furthermore, while A, B and C forms are right hand helices (looking down the axis, the helix rotates to the right, clockwise), Z-DNA is a left hand helix.

Thus, there are clearly several ways in which specific nucleotides can contribute to structural variation in the double helix. Any or all of these must be considered when studying physical interactions between DNA sequences and regulatory proteins.



Other Palindromes

rotor, racecar

A Toyota

MalayalaM. (It is the language spoken in Kerala (God's own Country, as the department of Tourism calls it!). Kerala is a small, reportedly beautiful state in the southern tip of India.

A man, a plan, a canal, Panama

Napoleon's Lament : "Able was I ere I saw Elba"

A wart remedy : "Straw? No, too stupid a fad; I put soot on warts.

Greek : NIP·ON ANOMHMATA ME MONAN OP·IN.
- Which means: Wash your sins away not only your face.

Barney Fife may have once said: "Sit on a potato pan, Otis".

Perhaps the first spoken palindrome: "Madam, I'm Adam."

In the small city of Yreka, California there is the "Yreka bakery".

Was it a bar or a bat I saw?

If you know of interesting palindromes you'd like to see included here, please email them to me.


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Copyright©2011, Gary J. Lindquester. All rights reserved.