DNA

DNA is composed of purine (adenine and guanine) and pyrimidine (cytosine and thymine) bases, each connected through a ribose sugar to a phosphate backbone. Many variations are possible in the chemical structure of the bases and the sugar, and in the structural relationship of the base to the sugar that result in differences in helical shape and form. The most common DNA helix, B-DNA, is a double helix of two DNA strands with about 10.5 base pairs per helical turn.

Bases and Base Pairs.

The four bases found in DNA are shown in Figures 1 and 2. The purines and pyrimidines are the informational molecules of the genetic blueprint for the cell. The two sides of the helix are held together by hydrogen bonds between base pairs. Hydrogen bonds are weak attractions between a hydrogen atom on one side and an oxygen or nitrogen atom on the other. Hydrogen atoms of amino groups serve as the hydrogen bond donor while the carbonyl oxygens and ring nitrogens serve as hydrogen bond acceptors. The specific location of hydrogen bond donor and acceptor groups gives the bases their specificity for hydrogen bonding in unique pairs. Thymine (T) pairs with adenine (A) through two hydrogen bonds, and cytosine (C) pairs with guanine (G) through three hydrogen bonds (Figure 2). T does not normally pair with G, nor does C normally pair with A.

Figure 1. DNA nucleotides include a base, a deoxyribose sugar, and a phosphate. The carbons on the sugar are numbered 1′ ("one prime") to 5′. The phosphate group links the 3′ end of one nucleotide to the 5′ end of the next. The phosphates are negatively charged, promoting their attraction to positively charged histone proteins (not shown).

Deoxyribose Sugar.

In DNA the bases are connected to a β-D-2-deoxyribose sugar with a hydrogen atom at the 2′ ("two prime") position. The sugar is a very dynamic part of the DNA molecule. Unlike the nucleotide bases, which are planar and rigid, the sugar ring is easily bent and twisted into various conformations (which exist in different structural forms of DNA). In canonical B-DNA, the accepted and most common form of DNA, the sugar configuration is known as C2′ endo.

Nucleosides and Nucleotides.

The term "nucleoside" refers to a base and sugar. "Nucleotide," on the other hand, refers to the base, sugar, and phosphate group (Figure 1). A bond, called the glycosidic bond, holds the base to the sugar and the 3′-5′ ("three prime-five prime") phosphodiester bond holds the individual nucleotides together. Nucleotides are joined from the 3′ carbon of the sugar in one nucleotide to the 5′ carbon of the sugar of the adjacent nucleotide. The 3′ and the 5′ ends are chemically very distinct and have different reactive properties. During DNA replication, new nucleotides are added only to the 3′ OH end of a DNA strand. This fact has important implications for replication.

As mentioned above, the two individual strands are held together by hydrogen bonds between individual T·A and C·G base pairs. In DNA, the Figure 2. Hydrogen bonding between the bases. Note that the sets of distances between the base pairs are almost identical for the two base pairs, so that the distance across the double helix is unchanged. Hoogsteen hydrogen bonding can link a double helix to a third strand, to make a triple helix. distance between the atoms involved is 2.8 to 2.95 angstroms (10⁻¹⁰ meters). While individually weak, the large number of hydrogen bonds along a DNA chain provides sufficient stability to hold the two strands together.

The stabilization of duplex (double-stranded) DNA is also dependent on base stacking. The planar, rigid bases stack on top of one another, much like a stack of coins. Since the two purine.pyrimidine pairs (A.T and C.G) have the same width, the bases stack in a rather uniform fashion. Stacking near the center of the helix affords protection from chemical and environmental attack. Both hydrophobic interactions and van der Waal's forces hold bases together in stacking interactions. About half the stability of the DNA helix comes from hydrogen bonding, while base stacking provides much of the rest.

Double-stranded DNA in its canonical B-form is a right-handed helix formed by two individual DNA strands aligned in an antiparallel fashion (a right-handed helix, when viewed on end, twists clockwise going away from the viewer). Antiparallel DNA has the two strands organized in the opposite polarity, with one strand oriented in the 5′-3′ direction and the other oriented in the 3′-5′ direction.

In the right-handed B-DNA double helix, the stacked base pairs are separated by about 3.24 angstroms with 10.5 base pairs forming one helical turn (360°), which is 35.7 angstroms in length. Two successive base pairs, therefore, are rotated about 34.3° with respect to each other. The width of the helix is 20 angstroms. An idealized model of the double helix is shown in Figure 3. As can be seen, the organization of the bases creates a major groove and a minor groove.

Adenine and thymine are said to be complementary, as are cytosine and guanine. Complementary means "matching opposite." The shapes and charges of adeninne and thymine complement each other, so that they attract one another and link up (as do cytosine and guanine). Indeed, one entire strand of duplex DNA is complementary to the opposing strand. During replication, the two strands unwind, and each serves as a template Figure 3. Canonical BDNA double helix. for formation of new complementary strand, so that replication ends with two exact double-stranded copies.

While the vast majority of the DNA exists in the canonical B-DNA form, DNA can adopt an amazing array of alternative structures. This is the result of certain particular sequence arrangements of DNA and, in many cases, energy in the DNA double helix from DNA supercoiling, the property of DNA in which the double helix, in a high-energy state, becomes twisted around itself. Some alternative DNA conformations identified are shown in Figure 4.

Unwound DNA.

Since A·T base pairs contain two hydrogen bonds and C·G base pairs contain three, A+T-rich tracts are less thermally stable that C+G-rich tracts in DNA. Under denaturing conditions (heat or alkali), the DNA begins to "melt" (separate), and unwound regions of DNA will form, and it is the A+T-rich sequences that melt first. In addition, in the presence of superhelical energy (a high-energy state of DNA resulting from its supercoiling, which is the natural form of DNA in the chromosomes of most organisms), A+T-rich regions can unwind and remain unwound under conditions normally found in the cell. Such sites often provide places for DNA replication proteins to enter DNA to begin the process of chromosome duplication.

Cruciform Structures.

DNA sequences are said to be palindromic when they contain inverted repeat symmetry, as in the sequence GGAATTAATTCC, reading from the 5′ to the 3′ end. Palindromic sequences can form intramolecular bonds (within a single strand), rather than the normal intermolecular (between the two complementary strands), hydrogen bonds. To form cruciforms ("cross-shaped"), the DNA must form a small unwound structure, and then base pairs must begin to form within each individual strand, thus forming the four-stranded cruciform structure.

Slipped-Strand DNA.

Slipped-strand DNA structures can form within direct repeat DNA sequences, such as (CTG)_n·(CAG)_n and (CGG)_n·(CCG)_n (where "n" denotes a variable number of repetitions). They form following denaturation, after the strands become unwound, and during renaturation, when the strands come back together. To form slipped-strand DNA, the opposite strands come together in an out-of-alignment fashion, during renaturation. Expansion of such triplet repeats are features of certain neurological diseases.

Intermolecular Triplex DNA.

Three-stranded, or triplex DNA, can form within tracts of polypurine.polypyrimidine sequence, such as (GAA)_n·(TTC)_n. Purines, with their two-ring structures, have the potential to form hydrogen bonds with a second base, even while base paired in the canonical A·T and G·C configurations. This second type of base pair is called a Hoogsteen base pair, and it can form in the major groove (the top of the base pair representations in Figure 2). Pyrimidines can only pair with a single other base, and thus a long Pu·Py tract must be present for triplex DNA formation. The important factor for triplex DNA formation is the presence of an extended purine tract in a single DNA strand. The third-strand base-pairing code is as follows: A can pair with A or T; G can pair with a protonated C (C⁺) or G.

Figure 4. DNA can exist in a variety of conformations. "Canonical" DNA is the most common, but each of the other forms have particular functions or are found in certain conditions.

Intramolecular Triplex DNA.

When a Pu·Py tract exists that has mirror repeat symmetry (5′ GAAGAG-GAGAAG 3′), an intramolecular triplex can form, in which half of the Pu.Py tract unwinds and one strand wraps into the major groove, forming a triplex. The structure in Figure 4 shows the pyrimidine strand (CTT) pairing with the purine strand (GAA) of a canonical DNA duplex. In an intramolecular triplex, one strand of the unwound region remains unpaired, as shown.

Quadruplex DNA.

DNA sequences containing runs of G·C base pairs can form quadruplex, or four-stranded DNA, in which the four DNA strands are held together by Hoogsteen hydrogen bonds between all four guanines. The four guanines are aligned in a plane, and the successive rings of guanines are stacked one upon another.

Left-handed Z-DNA.

Alternating runs of (CG)_n·(CG)_n or (TG)_n·(CA)_n dinucleotides in DNA, under superhelical tension or high salt (more than 3 M NaCl) (M, moles per liter) can adopt a left-handed helix called Z-DNA. In this form, the two DNA strands become wrapped in a left-handed helix, which is the opposite sense to that of canonical B-DNA. This can occur within a small region of a larger right-handed B-DNA molecule, creating two junctions at the B-Z transition region.

Curved DNA.

DNA containing tracts of (A)_3-4·(T)_3-4 (that is, runs of three or four bases of A in one strand and a similar run of T in the other) spaced at 10-base pair intervals can adopt a curved helix structure.

In summary, DNA can exist in a very stable, right-handed double helix, in which the genetic information is very stable. Certain DNA sequences can also adopt alternative conformations, some of which are important regulatory signals involved in the genetic expression or replication of the DNA.