Literature (Product Manuals, Specifications, MSDS)

G's: The Unresolved Dilemma

Catalog No.	Product	PDF Guide
R26-6400-XXG	G's: The Unresolved Dilemma

Gs and GC Content Effect on Yield
Yield will gradually decrease as length of oligo increases. Palindromes, hairpins and high GC content oligos and oligos containing stretches of 3 or more G's induces strong secondary structure and base stacking thus decreasing purity and yield.

G's ; The Unresolved Dilemma
Ever wonder why we have not yet discovered a polymerase that can breeze through a stretch of G's? A stretch of three or more G's in an oligo sequence induces strong secondary structure. A string of G's and C's can exhibit internal Hoogsteen base pairing, non- Watson-Crick triple base pairing and should be avoided. Although this anomalous behavior is difficult to predict, in general, avoid runs of more than three consecutive G's in primers. Also, examine potential primers for self-complementary and hairpin structures

Base Composition
Higher GC content stabilizes hybridization, but a string of G's and C's can exhibit internal Hoogsteen base pairing, non-Watson-Crick base pairing and should be avoided. Although this anomalous behavior is difficult to predict, these structures can disrupt stable primer binding. In general, avoid runs of more than three consecutive G's in primers. Also, examine potential primers for self-complementary and hairpin structures. Nuclear Magnetic Resonance (NMR) studies have shown that a stable hairpin can form with just four G-C basepairs in the stem and just three bases in the loop.