Properties of an equine herpesvirus 1 mutant devoid of the internal inverted repeat sequence of the genomic short region

Effects of secondary structures of DNA templates on the quantification of qPCR

In the current design of quantitative polymerase chain reaction (qPCR) systems, the sequences of primers are the primary concerns. The secondary structures of DNA templates have not been much considered, although they should be also critically important. In this paper, various hairpins with different stem lengths and loop sizes are placed near primer-binding sites, and their effects on the amplification efficiency of qPCR are systematically investigated. When a hairpin is formed either in the inside of the amplicon or in its outside, the amplification is notably suppressed. The magnitudes of suppression increase with the increase in stem length and the decrease in loop size, and are especially significant for the hairpins formed inside the amplicon. With very long stems (e.g., 20-bp), the effect is still more drastic, and no targeted amplification products are formed. On the basis of melting temperature (T_m) measurements, these suppression effects of hairpins have been mostly ascribed to competitive inhibition of primer binding to the template. It has been concluded that, in order to design precise and reliable qPCR systems, at least 60-bp sequences around primer-binding sites, both inside and outside the amplicons, must be analyzed to confirm that stable secondary structures are not formed in the vicinity of primer-binding sites. Communicated by Ramaswamy H. Sarma.

The early UL3 gene of equine herpesvirus-1 encodes a tegument protein not essential for replication or virulence in the mouse

The UL3 gene of equine herpesvirus-1 (EHV-1) is retained in the genome of defective interfering particles and encodes a ~33kDa myristylated protein. Further characterization showed that the UL3 gene is trans-activated only by the sole immediate early (IE) protein and encodes an early protein that is dispensable for EHV-1 replication and localizes in the tegument of purified virions. UL3-deleted EHV-1 (vL11ΔUL3) exhibits properties of host cell tropism, plaque size, and growth kinetics similar to those of the parental virus. Expression levels of EHV-1 proteins representative of all three gene classes in vL11ΔUL3-infected cells were identical to those in cells infected with parental virus. Mice intranasally infected with vL11ΔUL3 and parental virus showed no significant difference in mortality or virus lung titers. These findings suggest that the UL3 protein does not play a major role in the biology of EHV-1 in cell culture or virulence in the mouse.