DNA Sequencing & SNPlex/Molecular Genetics Core


The Molecular Genetics Core Facility (MGCF)  is now a part of Genome Sciences and is located in C2705.  We can provide custom DNA sequencing centered around an ABI 3130XL Capillary sequencer.

The Genome Sceinces Facility also provides genotyping, SNPlex analysis and fragment analysis. 


DNA Sequencing Order Sheet Instructions

DNA Sequencing order sheet is now an .xls spread sheet.   A copy of the Submission form may be found at the network pathway \\hersheymed.net\files\research\corefacility\Results\DNA-Sanger Sequencing.  

Please save completed Submission forms in the same network folder.  

Least preferred but acceptable submission is email to either rmb6@psu.edu or gvp103@psu.edu.

Template ID: use the laboratory P.I.'s initials and then number each DNA sample sequentially with every submission, e.g. JS10, JS11, JS12 etc. The template ID should also be used to label the tube of DNA submitted, on the top of each tube. If the same DNA is being tested with more than one primer, you may put the DNA in a single tube, but it must be labeled with more than one Template ID number, e.g. JS10-13

**Template concentration: SAMPLES MUST BE IN WATER. For PLASMID and BAC samples, the DNA concentration should be ~100ng/µl - please submit 800ng (=8 µl at 100ng/µl) of DNA per sequencing reaction. For PCR products, the DNA concentration should be ~10 ng/µl, and 5ng PCR product DNA/100bases length should be submitted. Please indicate SIZE of the PCR product in the Template size column above; also indicate in the Notes column that the template is PCR product.

Primer Name: Indicate here the name of the primer to be used for sequencing. Concentrations should be 5-10uM. The Core Facility provides at no charge common primers such as T7, T3, SP6, etc. - see full list of available primers.

If you are using your own primer(s), the Tm should be between 55 and 60°C; thus, the length should be approximately 18-25 nucleotides. The core uses the following equation to estimate Tm: Tm = 2°C X (A + T) + 4°C X (G + C).

Notes: should be used for three purposes: 1) you may write your own notes for reference here, 2) request any special reaction conditions required e.g. DMSO to minimize 2° structure in GC rich templates, 3) indicate if the DNA template is anything other than plasmid DNA, e.g. BAC, PCR product, etc.(for BAC or PAC samples provide either primer Tm or actual sequence for Tm determination).


DNA Sequencing - Standard Primers Available

BGH Reverse:  5' -d(TAG AAG GCA CAG TCG AGG C)
GL primer 2:  5' -d(TTT ATG TTT TTG GCG TCT TCC)
M13 forward (-21):  5' -d(TGT AAA ACG ACG GCC AG)
M13 reverse:  5' -d(CAG GAA ACA GCT ATG ACC)
SP6 promoter:  5' -d(ATT TAG GTG ACA CTA TA)
T3 promoter:  5' -d(AAT TAA CCC TCA CTA AAG GG)
T7 promoter:  5' -d(TAA TAC GAC TCA CTA TAG GG)
T7 terminator:  5' -d(GCT AGT TAT TGC TCA GCG G)

  • Recent Publications


Avella, D. M., Kimchi, E. T., Donahue, R. N., Tagaram, H. R., McLaughlin, P. J., Staveley-O'Carroll, K. F., and Zagon, I. S. (2009). The Opioid Growth Factor - Opioid Growth Factor Receptor Axis Regulates Cell Proliferation of Human Hepatocellular Cancer. Am J Physiol Regul Integr Comp Physiol. 19923357

Balliet, R. M., Chen, G., Dellinger, R. W., and Lazarus, P. (2009). UGT1A10: Activity against the tobacco-specific nitrosamine, NNAL, and a potential role for a novel UGT1A10 promoter deletion polymorphism in cancer susceptibility. Drug Metab Dispos. 20007297

Balliet, R. M., Chen, G., Gallagher, C. J., Dellinger, R. W., Sun, D., and Lazarus, P. (2009). Characterization of UGTs Active against SAHA and Association between SAHA Glucuronidation Activity Phenotype with UGT Genotype. Cancer Res 69, 2981-2989. 19318555

Baird, N. L., Starkey, J. L., Hughes, D. J., and Wills, J. W. (2009). Myristylation and palmitylation of HSV-1 UL11 are not essential for its function. Virology. 19944438

Blevins-Primeau, A. S., Sun, D., Chen, G., Sharma, A. K., Gallagher, C. J., Amin, S., and Lazarus, P. (2009). Functional Significance of UDP-Glucuronosyltransferase Variants in the Metabolism of Active Tamoxifen Metabolites. Cancer Res. 19244109

Cardone, G., Purdy, J. G., Cheng, N., Craven, R. C., and Steven, A. C. (2009). Visualization of a missing link in retrovirus capsid assembly. Nature 457, 694-698. 19194444

Cheng, F., McLaughlin, P. J., Banks, W. A., and Zagon, I. S. (2009). Passive diffusion of naltrexone into human and animal cells and upregulation of cell proliferation. Am J Physiol Regul Integr Comp Physiol 297, R844-852. 19605761

Cheng, F., McLaughlin, P. J., Verderame, M. F., and Zagon, I. S. (2009). Dependence on nuclear localization signals of the opioid growth factor receptor in the regulation of cell proliferation. Exp Biol Med (Maywood) 234, 532-541. 19244545

Conway, M. J., Alam, S., Christensen, N. D., and Meyers, C. (2009). Overlapping and independent structural roles for human papillomavirus type 16 L2 conserved cysteines. Virology. 19733888

Donahue, R. N., McLaughlin, P. J., and Zagon, I. S. (2009). Cell proliferation of human ovarian cancer is regulated by the opioid growth factor-opioid growth factor receptor axis. Am J Physiol Regul Integr Comp Physiol 296, R1716-1725. 19297547

Duncan, K. J., Eckert, K. A., and Clawson, G. A. (2009). Mechanisms of growth inhibition in human papillomavirus positive and negative cervical cancer cells by the chloromethyl ketone protease inhibitor, succinyl-alanine-alanine-proline-phenylalanine chloromethyl ketone. J Pharmacol Exp Ther 330, 359-366. 19401497

Grigoryev, S. A., Arya, G., Correll, S., Woodcock, C. L., and Schlick, T. (2009). Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions. Proc Natl Acad Sci U S A 106, 13317-13322. 19651606

Harper, A. L., Meckes, D. G., Jr., Marsh, J. A., Ward, M. D., Yeh, P. C., Baird, N. L., Wilson, C. B., Semmes, O. J., and Wills, J. W. (2009). Interaction Domains of the UL16 and UL21 Tegument Proteins of Herpes Simplex Virus. J Virol. 20042500

Heipertz, R. A., Jr., Starkey, J. L., Miller, T. G., Hu, J., and Isom, H. C. (2009). Trans-Complementation of HBV rtM204I mutant replication by HBV wild-type polymerase. Virology 388, 57-67. 19383566

Hengst, J. A., Guilford, J. M., Conroy, E. J., Wang, X., and Yun, J. K. (2009). Enhancement of sphingosine kinase 1 catalytic activity by deletion of 21 amino acids from the COOH-terminus. Arch Biochem Biophys. 19914200

Hengst, J. A., Guilford, J. M., Fox, T. E., Wang, X., Conroy, E. J., and Yun, J. K. (2009). Sphingosine kinase 1 localized to the plasma membrane lipid raft microdomain overcomes serum deprivation induced growth inhibition. Arch Biochem Biophys 492, 62-73. 19782042

Matters, G. L., Harms, J. F., McGovern, C. O., Jayakumar, C., Crepin, K., Smith, Z. P., Nelson, M. C., Stock, H., Fenn, C. W., Kaiser, J., Kester, M., and Smith, J. P. (2009). Growth of human pancreatic cancer is inhibited by down-regulation of gastrin gene expression. Pancreas 38, e151-161. 19465883

Mitchell, R. M., Lee, S. Y., Randazzo, W. T., Simmons, Z., and Connor, J. R. (2009). Influence of HFE variants and cellular iron on monocyte chemoattractant protein-1. J Neuroinflammation 6, 6. 19228389

Mitchell, R. M., Lee, S. Y., Simmons, Z., and Connor, J. R. (2009). HFE polymorphisms affect cellular glutamate regulation. Neurobiol Aging. 19560233

Nowak, M. G., Sudol, M., Lee, N. E., Konsavage, W. M., Jr., and Katzman, M. (2009). Identifying amino acid residues that contribute to the cellular-DNA binding site on retroviral integrase. Virology. 389, 141-148. 19447461

Olson, K. C., Dellinger, R. W., Zhong, Q., Sun, D., Amin, S., Spratt, T. E., and Lazarus, P. (2009). Functional characterization of low-prevalence missense polymorphisms in the UDP-glucuronosyltransferase 1A9 gene. Drug Metab Dispos 37, 1999-2007. 19589876

Pan, W., Xin, P., and Clawson, G. A. (2009). MicroRNAs align with accessible sites in target mRNAs. J Cell Biochem. 19998415

Popova, E. Y., Krauss, S. W., Short, S. A., Lee, G., Villalobos, J., Etzell, J., Koury, M. J., Ney, P. A., Chasis, J. A., and Grigoryev, S. A. (2009). Chromatin condensation in terminally differentiating mouse erythroblasts does not involve special architectural proteins but depends on histone deacetylation. Chromosome Res 17, 47-64. 19172406

Purdy, J. G., Flanagan, J. M., Ropson, I. J., and Craven, R. C. (2009). Retroviral Capsid Assembly: A Role for the CA Dimer in Initiation. J Mol Biol. 19361521

Rochman, M., Postnikov, Y., Correll, S., Malicet, C., Wincovitch, S., Karpova, T. S., McNally, J. G., Wu, X., Bubunenko, N. A., Grigoryev, S., and Bustin, M. (2009). The interaction of NSBP1/HMGN5 with nucleosomes in euchromatin counteracts linker histone-mediated chromatin compaction and modulates transcription. Mol Cell 35, 642-656. 19748358

Sharma, A., Sharma, A. K., Madhunapantula, S. V., Desai, D., Huh, S. J., Mosca, P., Amin, S., and Robertson, G. P. (2009). Targeting Akt3 Signaling in Malignant Melanoma Using Isoselenocyanates. Clin Cancer Res. 19208796

Starkey, J. L., Chiari, E. F., and Isom, H. C. (2009). Hepatitis B virus (HBV)-specific short hairpin RNA is capable of reducing the formation of HBV covalently closed circular (CCC) DNA but has no effect on established CCC DNA in vitro. J Gen Virol 90, 115-126. 19088280

Wang, S., Zhao, Y., Leiby, M. A., and Zhu, J. (2009). Studying human telomerase gene transcription by a chromatinized reporter generated by recombinase-mediated targeting of a bacterial artificial chromosome. Nucleic Acids Res. 19528078

Wang, S., Zhao, Y., Leiby, M., and Zhu, J. (2009). A New Positive/Negative Selection Scheme for Precise BAC Recombineering. Mol Biotechnol. 19160076

Wang, Y., Li, M., Stadler, S., Correll, S., Li, P., Wang, D., Hayama, R., Leonelli, L., Han, H., Grigoryev, S. A., et al. (2009). Histone hypercitrullination mediates chromatin decondensation and neutrophil extracellular trap formation. J Cell Biol 184, 205-213. 19153223

Zagon, I. S., Donahue, R. N., and McLaughlin, P. J. (2009). Opioid growth factor-opioid growth factor receptor axis is a physiological determinant of cell proliferation in diverse human cancers. Am J Physiol Regul Integr Comp Physiol 297, R1154-1161. 19675283

Zagon, I. S., Kreiner, S., Heslop, J. J., Conway, A. B., Morgan, C. R., and McLaughlin, P. J. (2008). Prevention and delay in progression of human pancreatic cancer by stable overexpression of the opioid growth factor receptor. Int J Oncol 33, 317-323.18636152

Zagon, I. S., Donahue, R. N., Rogosnitzky, M., and McLaughlin, P. J. (2008). Imiquimod upregulates the opioid growth factor receptor to inhibit cell proliferation independent of immune function. Exp Biol Med (Maywood) 233, 968-979.18480416

Yoshioka, M., Crum, M. M., and Sample, J. T. (2008). Autorepression of Epstein-Barr virus nuclear antigen 1 expression by inhibition of pre-mRNA processing. J Virol 82, 1679-1687. 18077719

Yeh, P. C., Meckes, D. G., Jr., and Wills, J. W. (2008). Analysis of the Interaction between the UL11 and UL16 Tegument Proteins of Herpes Simplex Virus. J Virol. 82, 10693-700. 18715918

Tatum, A. M., Mylin, L. M., Bender, S. J., Fischer, M. A., Vigliotti, B. A., Tevethia, M. J., Tevethia, S. S., and Schell, T. D. (2008). CD8+ T cells targeting a single immunodominant epitope are sufficient for elimination of established SV40 T antigen-induced brain tumors. J Immunol 181, 4406-4417. 18768900

Tagaram, H. R., Watson, A. M., Lemonnier, F. A., Staveley-O'Carroll, K., Tevethia, S. S., and Schell, T. D. (2008). An SV40 VP1-derived epitope recognized by CD8+ T cells is naturally processed and presented by HLA-A*0201 and cross-reactive with human polyomavirus determinants. Virology 376, 183-190. 18402997

Smith, T. M., Gilliland, K., Clawson, G. A., and Thiboutot, D. (2008). IGF-1 induces SREBP-1 expression and lipogenesis in SEB-1 sebocytes via activation of the phosphoinositide 3-kinase/Akt pathway. J Invest Dermatol 128, 1286-1293.17989724

Shan, W., Palkar, P. S., Murray, I. A., McDevitt, E. I., Kennett, M. J., Kang, B. H., Isom, H. C., Perdew, G. H., Gonzalez, F. J., and Peters, J. M. (2008). Ligand activation of peroxisome proliferator-activated receptor beta/delta (PPARbeta/delta) attenuates carbon tetrachloride hepatotoxicity by downregulating proinflammatory gene expression. Toxicol Sci 105, 418-428. 18622026

Purdy, J. G., Flanagan, J. M., Ropson, I. J., Rennoll-Bankert, K. E., and Craven, R. C. (2008). Critical role of conserved hydrophobic residues within the major homology region in mature retroviral capsid assembly. J Virol 82, 5951-5961. 18400856

Pan, W., Xin, P., and Clawson, G. A. (2008). Minimal primer and primer-free SELEX protocols for selection of aptamers from random DNA libraries. Biotechniques 44, 351-360.18361789

Nguyen, D. H., and Hu, J. (2008). Reverse transcriptase- and RNA packaging signal-dependent incorporation of APOBEC3G into hepatitis B virus nucleocapsids. J Virol 82, 6852-6861. 18480459

Mintz, A., Gibo, D. M., Madhankumar, A. B., Cladel, N. M., Christensen, N. D., and Debinski, W. (2008). Protein- and DNA-based active immunotherapy targeting interleukin-13 receptor alpha2. Cancer Biother Radiopharm 23, 581-589. 18976118

Meckes, D. G., Jr., and Wills, J. W. (2008). Structural Rearrangement within an Enveloped Virus upon Binding to the Host Cell. J Virol. 82, 10429-10435. 18715922

McLaughlin, P. J., Kreiner, S., Morgan, C. R., and Zagon, I. S. (2008). Prevention and delay in progression of human squamous cell carcinoma of the head and neck in nude mice by stable overexpression of the opioid growth factor receptor. Int J Oncol 33, 751-757.18813788

Madhunapantula, S. V., Desai, D., Sharma, A., Huh, S. J., Amin, S., and Robertson, G. P. (2008). PBISe, a novel selenium-containing drug for the treatment of malignant melanoma. Mol Cancer Ther 7, 1297-1308.18483317

Lokhandwala, P. M., Nguyen, T. L., Bowzard, J. B., and Craven, R. C. (2008). Cooperative role of the MHR and the CA dimerization helix in the maturation of the functional retrovirus capsid. Virology. 18433823

Lin, L., Wan, F., and Hu, J. (2008). Functional and Structural dynamics of Hepadnavirus Reverse Transcriptase During Protein-Primed Initiation of Reverse Transcription: Effects of Metal Ions. J Virol. 82, 5703-14. 18400846

Lin, L., and Hu, J. (2008). Inhibition of hepadnavirus reverse transcriptase-epsilon RNA interaction by porphyrin compounds. J Virol 82, 2305-2312. 18094191

Konsavage, W. M., Jr., Sudol, M., and Katzman, M. (2008). Effects of varying the spacing within the D,D-35-E motif in the catalytic region of retroviral integrase. Virology 379, 223-233. 18687451

Kinder, M., Chislock, E., Bussard, K. M., Shuman, L., and Mastro, A. M. (2008). Metastatic breast cancer induces an osteoblast inflammatory response. Exp Cell Res 314, 173-183. 17976581

Hu, J., Cladel, N., Peng, X., Balogh, K., and Christensen, N. D. (2008). Protective immunity with an E1 multivalent epitope DNA vaccine against cottontail rabbit papillomavirus (CRPV) infection in an HLA-A2.1 transgenic rabbit model. Vaccine 26, 809-816. 18187239 

de Witte, M. A., Bendle, G. M., van den Boom, M. D., Coccoris, M., Schell, T. D., Tevethia, S. S., van Tinteren, H., Mesman, E. M., Song, J. Y., and Schumacher, T. N. (2008). TCR gene therapy of spontaneous prostate carcinoma requires in vivo T cell activation. J Immunol 181, 2563-2571. 18684947

Cladel, N. M., Hu, J., Balogh, K. K., and Christensen, N. D. (2008). CRPV genomes with synonymous codon optimizations in the CRPV E7 gene show phenotypic differences in growth and altered immunity upon E7 vaccination. PLoS ONE 3, e2947. 18698362

Cladel, N. M., Hu, J., Balogh, K., Mejia, A., and Christensen, N. D. (2008). Wounding prior to challenge substantially improves infectivity of cottontail rabbit papillomavirus and allows for standardization of infection. J Virol Methods 148, 34-39. 18061687

Cheung, M., Sharma, A., Madhunapantula, S. V., and Robertson, G. P. (2008). Akt3 and mutant V600E B-Raf cooperate to promote early melanoma development. Cancer Res 68, 3429-3439. 18451171

Cheng, F., McLaughlin, P. J., Verderame, M. F., and Zagon, I. S. (2008). The OGF-OGFr Axis Utilizes the p16INK4a and p21WAF1/CIP1 Pathways to Restrict Normal Cell Proliferation. Mol Biol Cell 20, 319-327. 18923142

Cheng, F., McLaughlin, P. J., Verderame, M. F., and Zagon, I. S. (2008). The OGF-OGFr axis utilizes the p21 pathway to restrict progression of human pancreatic cancer. Mol Cancer 7, 5-17. 18190706

Chen, G., Dellinger, R. W., Gallagher, C. J., Sun, D., and Lazarus, P. (2008). Identification of a prevalent functional missense polymorphism in the UGT2B10 gene and its association with UGT2B10 inactivation against tobacco-specific nitrosamines. Pharmacogenet Genomics 18, 181-191. 18300939 

Chen, G., Dellinger, R. W., Sun, D., Spratt, T. E., and Lazarus, P. (2008). Glucuronidation of tobacco-specific nitrosamines by UGT2B10. Drug Metab Dispos 36, 824-830.18238858

Baird, N. L., Yeh, P. C., Courtney, R. J., and Wills, J. W. (2008). Sequences in the UL11 tegument protein of herpes simplex virus that control association with detergent-resistant membranes. Virology 374, 315-321. 18261757

Bae, D. S., Blazanin, N., Licata, M., Lee, J., and Glick, A. B. (2008). Tumor suppressor and oncogene actions of TGFbeta1 occur early in skin carcinogenesis and are mediated by Smad3. Mol Carcinog.18942075