1. The annealing temperature may need to be optimized. The NEB Tm Calculator is recommended for calculation of an appropriate annealing temperature. 2. The DNA template is too long (>5 kb). 3. The DNA template is GC rich and contains secondary structure. Use a polymerase better suited for high GC content, such as OneTaq® DNA Polymerase (NEB# M0480) or Q5® High-Fidelity DNA Polymerase (NEB# M0491). Alternatively, DMSO may be added to the reaction to lower the melting temperature of GC rich nucleic acids (1). 4. Primer concentration may be too low. We typically recommend 0.2 μM of each primer, but the range may be from 0.05-1 μM of each. 5. Try fresh nucleotides. References: 1. Sun, Y., Hegamyer, G. and Colburn, N. (1993). Biotechniques. 15, 372-374.