8.2 Structure of Nucleic Acids · Biochemistry 2027

DNA is a double helix that stores genetic information

The Watson-Crick duplex has two antiparallel strands with the backbone outside and the bases inside
The complement of 5-prime ATGCC 3-prime is 3-prime TACGG 5-prime, written 5-prime GGCAT 3-prime
That is the reverse complement, and confusing it with a simple complement causes errors in primer design and sequence analysis
A-T pairs have two hydrogen bonds and G-C pairs three, yet stacking, hydration, ions and neighbours also set stability
Equal GC content with a different order can still change melting temperature and local shape
B-DNA has a major and a minor groove of different width between the two backbones
The grooves expose hydrogen-bond donors and acceptors and non-polar groups in different arrangements
DNA-binding proteins read the chemical pattern together with local bending
Typical B-DNA values are a diameter of 2.0 nm, a rise of 0.34 nm per bp and 10.5 bp per turn, giving a pitch near 3.57 nm
Real DNA bends and twists with sequence, hydration, tension and protein binding
Example: 1,050 bp gives an axial length of 357 nm and 100 turns

A and B DNA are both right-handed, but A is shorter and wider with strongly tilted base pairs
A-DNA appears at reduced hydration and in DNA-RNA duplexes, and double-stranded RNA also adopts an A-like form
Z-DNA is a left-handed helix with a zigzag backbone, favoured by alternating purine-pyrimidine sequences
The pentose ring is not flat but puckered, with B-DNA tending to C2-prime-endo and A-DNA and A-RNA to C3-prime-endo
Sugar pucker constrains backbone geometry and base pair placement and so shapes the helix
Closed circular or rotationally fixed DNA is described by Lk = Tw + Wr
Tw is local twist and Wr is the spatial coiling of the duplex axis
Example: 2,100 bp with Lk0 near 200 and Lk 190 gives ΔLk of -10 and a superhelical density of -0.05, a negatively supercoiled state
A nick that allows free rotation means Lk cannot be treated as a topological invariant

Inverted repeats can form hairpins when strands separate and cruciforms in a closed duplex
Formation depends on supercoiling, salt and surrounding conditions as well as sequence
A G-quartet is a planar arrangement of four guanines held by Hoogsteen hydrogen bonds, and stacked quartets give a G-quadruplex
Monovalent cations such as K+ stabilise G4 in the central channel
Formation capacity can be shown in vitro, but cellular occupancy and function are separate questions
Cytosine-rich sequences can form i-motifs built on C-C+ base pairs
A triplex forms when a third strand binds the major groove of an existing duplex through Hoogsteen interactions
An R-loop forms when RNA pairs with one DNA strand and displaces the other
Capacity to form, observation in purified samples and a claim of cellular function require different levels of evidence

mRNA supplies codons and comprises a 5-prime cap, 5-prime UTR, ORF, 3-prime UTR and poly(A) tail
The ORF contains the start and stop codons, and the stop codon specifies no amino acid
Precursor mRNA matures through 5-prime capping, splicing, 3-prime cleavage and polyadenylation
The cap has an unusual 5-prime to 5-prime triphosphate linkage and the poly(A) tail supports stability, translation and transport
Alternative splice site choice yields several products from one gene
Eukaryotic mRNA is usually monocistronic and bacterial mRNA often polycistronic, though exceptions exist
Example: a 1,203 nucleotide ORF is 401 codons, giving 400 residues once the stop codon is excluded
A 5-prime UTR stem-loop changes initiation factor access, and 3-prime UTR structure couples to protein and regulatory RNA action
The iron response element of ferritin mRNA binds iron-regulatory proteins

Secondary structure is described with stems, hairpin loops, bulges, internal loops, multibranch loops and pseudoknots
Tertiary structure adds long-range contacts, the arrangement of bases, sugars and phosphates, and metal and protein binding
Besides A-U and G-C there are G-U wobble pairs and non-canonical interactions
tRNA has 70 to 90 nucleotides, drawn as a cloverleaf in two dimensions but folded into an L shape in three
Amino acids attach to the 3-prime CCA end and the anticodon pairs with the codon
In the ribosome, rRNA forms the scaffold, positions tRNA and mRNA, and provides the peptidyl transferase centre
Ribozymes catalyse reactions themselves, and the ribosome is the leading biological example
Secondary structure prediction uses nearest-neighbour free energies that count adjacent pairs and loop types
Example: ΔG° of -10.0 kJ/mol gives K near 56.5 and a folded fraction of about 98.3 percent
X-ray, cryo-EM, NMR, SHAPE, DMS, covariation analysis and prediction are complementary

References

**표 8.2-1**A, B and Z DNA compared
Feature	A-DNA	B-DNA	Z-DNA
Helix sense	Right-handed	Right-handed	Left-handed
Base pairs per turn	About 11	About 10.5	About 12
Rise per bp in nm	About 0.255	About 0.340	About 0.370
Diameter in nm	About 2.3	About 2.0	About 1.8
Character	Wide and short with strongly tilted pairs	The usual form in aqueous solution	Zigzag backbone favoured by alternating sequences

**표 8.2-2**Levels of evidence for non-canonical structures
Observation	What it supports	Further evidence needed
G-rich sequence	Possible G4 formation	Structure-specific assays and cellular detection
Change in CD spectrum	Possibly an average structural change	Independent structural analysis and controls
Signal from a specific antibody	The structure or antigen may be present	Specificity and cross-reactivity testing
X-ray, NMR or cryo-EM result	Three-dimensional constraints under those conditions	Cellular dynamics and physiological abundance