The aim of this work was to identify the PCNA cDNA sequence from the shrimp Litopenaeus vannamei, to build a theoretical structural model and to evaluate PCNA mRNA levels in different shrimp tissues, and to compare the mRNA levels of shrimp PCNA and WSSV-DNApol. Based in one L. vannamei PCNA learn more expressed sequence tag [31] and other shrimp PCNA sequences from Marsupenaeus japonicus (EU431336.1) and Fenneropenaeus chinensis (EF051247.1), three pairs of specific primers were designed and used for a DNA walking approach involving three PCR reactions (Seegene, USA) to obtain the complete 5′-UTR from the shrimp PCNA transcript. Muscle tissue was used for

RNA isolation and cDNA synthesis as described below in Section 2.3. For the first reaction, the pcnaRv1 primer (5′-TTGGGGGCCAAGAAGTAA-3′) was used while the second reaction was done with primer pcnaRv2 (5′-TGCAGATACGTGCGAACTCCC-3′); and for the third reaction the primer pcnaRv3 (5′-CCTGATGTACCCCTGGTCGTT-3′) was utilized. All the reactions were carried out as the manufacturer recommended. The PCR fragments were cloned into the pCR2.1 vector (Invitrogen, USA) according to manufacturer instructions. Plasmid DNA from recombinant

clones was isolated by the alkaline lysis method and digested with the restriction enzyme EcoRI [32]. Positive clones were sequenced at the UAGC laboratory at the University of Arizona (Tucson, AZ, USA). The resulting sequences were analyzed using BLAST (N, P and X) to identify them and to find homologies among sequences, ClustalW and BoxShade were http://www.selleckchem.com/products/Trichostatin-A.html used to make the alignments [33] and [34]. The homologous modeling of the LvPCNA was done by superimposing the deduced amino acid sequence into the known crystallographic structure of the human PCNA [35] (PDB:1AXC) using MOE 2010.10 (ChemComp, Montreal, Canada). We constructed 50 initial models under the 3-oxoacyl-(acyl-carrier-protein) reductase CHARMM27 force field starting from a multiple sequence alignment including the amino acid sequences of PDB 1VYJ, 2ZVV, 3GPN, 2IO4, 1RWZ, 2IJX, 1UD9, 1GE8, 3IFV and 3K4X. The coordinates of DNA template in complex

with the PCNA were taken from the crystallographic structure of Escherichia coli PCNA (PDB: 3BEP) [36] and Saccharomyces cerevisiae PCNA (PDB: 3K4X) [37] and included in the building of the shrimp PCNA model. The assignment of the LvPCNA domains and figures of the resulting structure were drawn also with either MOE or PyMOL 1.0 [38]. Total RNA was isolated from different tissues of healthy shrimp to evaluate PCNA differential expression. Also, total RNA was isolated using TRIzol (Invitrogen, USA), from the tail muscle of WSSV-infected organisms [31], and from non-infected shrimps to evaluate expression of the shrimp PCNA and WSSV-DNA polymerase following the manufacturer instructions. The RNA concentration and purity was assessed spectrophotometrically by measuring the absorbance at 260 and 280 nm in a Nanodrop spectrophotometer.