1.8.1 B DNA

Unit 1 structure. Their proposal, based on analysis of x-ray diffraction patterns coupled with careful model building, proved correct and paved the way for our modern understanding of how DNA functions as the genetic material.

Chargaff’s Rule:

Two Strands have complementary sequences 2 logical operations to obtain complementary strand 5' to 3' 1. Reverse: Rewrite the sequence, back to front 2. Complement: Swap A with T, C with G

1.8.1 B DNA

DNA consists of two associated polynucleotide strands that wind together to form a double helix. The two sugar phosphate backbones are on the outside of the double helix, and the bases project into the interior. The adjoining bases in each strand stack on top of one another in parallel planes. The orientation of the two strands is antiparallel; that is, their 5’ 3’ directions are opposite. The strands are held in precise register by formation of base pairs between the two strands: A is paired with T through two hydrogen bonds; G is paired with C through three hydrogen bonds. This base-pair complementarity is a consequence of the size, shape, and chemical composition of the bases. The presence of thousands of such hydrogen bonds in a DNA molecule contributes greatly to the stability of the double helix.

 Hydrophobic and van der Waals interactions between the stacked adjacent base pairs further stabilize the double-helical structure.  In natural DNA, A always hydrogen bonds with T and G with C, forming A·T and G·C base pairs as shown in figure.  These associations between a larger purine and smaller pyrimidine are often called Watson-Crick base pairs.  Two polynucleotide strands, or regions thereof, in which all the nucleotides form such base pairs are said to be complementary.  However, in theory and in synthetic DNAs other base pairs can form. For example, a guanine (a purine) could theoretically form hydrogen bonds with a thymine (a pyrimidine) causing only a minor distortion in the helix.  The space available in the helix also would allow pairing between the two pyrimidines cytosine and thymine. Although the nonstandard G·T and C·T base pairs are normally not found in DNA, G·U base pairs are quite common in double-helical regions that form within otherwise single-stranded RNA  The Most DNA in cells is a right-handed helix. The stacked bases are regularly spaced 0.36 nm apart along the helix axis. helix makes a complete turn every 3.6 nm; thus there are about 10.5 pairs per turn.  This is referred to as the B form of DNA, the normal form present in most DNA stretches in cells.  On the outside of B-form DNA, the spaces between the intertwined strands form two helical grooves of different widths described as the major groove and the minor groove  As a consequence, the atoms on the edges of each base within these grooves are accessible from outside the helix, forming two types of binding surfaces. DNA binding

Proteins can “read” the sequence of bases in duplex DNA by contacting atoms in either the major or the minor grooves.

Figure 1.8.2 Chargaff’s rule: Always A pairs with T / U and G pairs with C. Complementarity of strands in the DNA double helix. The complementary antiparallel strands of DNA follow the pairing rules proposed by Watson and Crick. The base-paired antiparallel strands differ in base composition: the left strand has the composition A3 T2 G1 C3; the right, A2 T3 G3 C1. They also differ in sequence when each chain is read in the 5 n 3 direction. Note the base equivalences: A T and G C in the duplex.