Center for Protein and Nucleic Acid Research

La Jolla, California Campus

The Center for Protein and Nucleic Acid Research, housed in Science Park 3040 Room 290, is a full-service facility focusing on Edman protein sequencing, peptide array and library synthesis, specialty nucleic acid synthesis and aptamer selection (SELEX). The facility also works collaboratively with the Next Generation Sequencing Core and the Microarray Core to develop and implement novel sequencing and array applications.

DNA sequencing: Sanger sequencing service is no longer offered. For Next Generation Sequencing (NGS), please see the NGS Core website.

Protein sequencing: We are equipped with an ABI Procise 494 protein sequencer.

Nucleic acid synthesis: We are equipped with an ABI 8909 Synthesizer. 

Peptide array and library synthesis: We utilize an IntavisAG SPOT peptide synthesizer to make our peptides for arrays and libraries. Peptides are synthesized on membrane, up to 1,536 different peptides per synthesis and cleaved to produce approx. 35 ug of peptide. These can be arrayed onto standard microscope slides up to 6,000 spots per slide for peptide binding or activity assays. 

Aptamer selection (SELEX): The Center has extensive experience in the techniques employed for in vitro selection (SELEX) experiments. 

Please call or email to discuss potential projects.

Affiliated Cores
NGS Core Website
Microarray Core Website 


ResearchGate-Phillip Ordoukhanian

Krishnaswami SR, Kumar S, Ordoukhanian P, Yu BD (2014) Fate and Plasticity of the Epidermis in Response to Congenital Activation of BRAF. J Invest Dermatol. 2014 Sep 9. doi: 10.1038/jid.2014.388. [Epub ahead of print] PMID: 25202828

Dhami K, Malyshev DA, Ordoukhanian P, Kubelka T, Hocek M, Romesberg FE (2014) Systematic exploration of a class of hydrophobic unnatural base pairs yields multiple new candidates for the expansion of the genetic alphabet. Nucleic Acids Res. 2014 42(16):10235-44. doi: 10.1093/nar/gku715

Helsmoortel C, Vandeweyer G, Ordoukhanian P, Van Nieuwerburgh F, Van der Aa N, Kooy RF. Challenges and opportunities in the investigation of unexplained intellectual disability using family based whole exome sequencing. Clin Genet. (2014) doi: 10.1111/cge.12470. PMID: 25081361 

Head SR, Komori HK, Lamere SA, Whisenant T, Van Nieuwerburgh F, Salomon DR, Ordoukhanian P (2014). Library construction for next-generation sequencing: Overviews and challenges. Biotechniques. Feb 1;56(2):61-77. PMID: 24502796

Ruwona TB, McBride R, Chappel R, Head SR, Ordoukhanian P, Burton DR, Law M (2014). Optimization of peptide arrays for studying antibodies to hepatitis C virus continuous epitopes.  J Immunol Methods. Jan 15;402(1-2):35-42. PMID: 24269751

Bhargava V, Head SR, Ordoukhanian P, Mercola M, Subramaniam S (2014). Technical Variations in Low-Input RNA-seq Methodologies. Sci Rep. Jan 14;4:3678. PMC3890974

Li L, Degardin M, Lavergne T, Malyshev DA, Dhami K, Ordoukhanian P, Romesberg FE (2014) Natural-like replication of an unnatural base pair for the expansion of the genetic alphabet and biotechnology applications. J Am Chem Soc. 136(3):826-9. doi: 10.1021/ja408814g. Epub 2013 Oct 23.

Li Z, Lavergne T, Malyshev DA, Zimmermann J, Adhikary R, Dhami K, Ordoukhanian P, Sun Z, Xiang J, Romesberg FE (2013). Site-specifically arraying small molecules or proteins on DNA using an expanded genetic alphabet. Chemistry. 19(42):14205-9. doi: 10.1002/chem.201302496. Epub 2013 Sep

Head SR, Mondala T, Gelbart T, Ordoukhanian P, Chappel R, Hernandez G, Salomon DR. (2013) RNA purification and expression analysis using microarrays and RNA deep sequencing. Methods Mol Biol. 1034:385-403. doi: 10.1007/978-1-62703-493-7_25. PMID: 23775753

Lavergne T, Degardin M, Malyshev DA, Quach HT, Dhami K, Ordoukhanian P, Romesberg FE (2013). Expanding the scope of replicable unnatural DNA: stepwise optimization of a predominantly hydrophobic base pair. J Am Chem Soc. 135(14): 5408-19. PMID:23547847

Routh A, Ordoukhanian P, Johnson JE (2012). Nucleotide-resolution profiling of RNA recombination in the encapsidated genome of a eukaryotic RNA virus by next-generation sequencing. J Mol Biol 424, 257-69. PMC 3502730

Malyshev DA, Dhami K, Quach HT, Lavergne T, Ordoukhanian P, Torkamani A, Romesberg FE (2012). Efficient and sequence-independent replication of DNA containing a third base pair establishes a functional six-letter genetic alphabet. Proc Natl Acad Sci U S A 109, 12005-10. PMC 3409741

Betz K, Malyshev DA, Lavergne T, Welte W, Diederichs K, Dwyer TJ, Ordoukhanian P, Romesberg FE, Marx A (2012). KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry. Nat Chem Biol 8, 612-4. PMID: 22660438

Van Nieuwerburgh F, Thompson RC, Ledesma J, Deforce D, Gaasterland T, Ordoukhanian P, Head SR. (2012) Illumina mate-paired DNA sequencing-library preparation using Cre-Lox recombination. Nucleic Acids Res. 40(3):e24. doi: 10.1093/nar/gkr1000. Epub 2011 Nov 29. PMID: 22127871

Van Nieuwerburgh F, Soetaert S, Podshivalova K, Ay-Lin Wang E, Schaffer L, Deforce D, Salomon DR, Head SR, Ordoukhanian P (2011). Quantitative bias in Illumina TruSeq and a novel post amplification barcoding strategy for multiplexed DNA and small RNA deep sequencing. PLoS One 6, e26969

Seo YJ, Malyshev DA, Lavergne T, Ordoukhanian P, Romesberg FE (2011) Site-specific labeling of DNA and RNA using an efficiently replicated and transcribed class of unnatural base pairs. J Am Chem Soc. Dec 14;133(49):19878-88. doi: 10.1021/ja207907d. Epub 2011 Nov 18. PMID: 21981600

Lau JL, Baksh MM, Fiedler JD, Brown SD, Kussrow A, Bornhop DJ, Ordoukhanian P, Finn MG. (2011) Evolution and protein packaging of small-molecule RNA aptamers. ACS Nano. 5(10):7722-9. doi: 10.1021/nn2006927. Epub 2011 Sep 7. PMID: 21899290

Komori HK, Lamere SA, Torkamani A, Hart GT, Kotsopoulos S, Warner J, Samuels ML, Olson J, Head SR, Ordoukhanian P, Lee PL, Link DR, Salomon DR (2011). Application of microdroplet PCR for large-scale targeted bisulfite sequencing. Genome Res 21, 1738-45. PMC 3202290

Head SR, Komori HK, Hart GT, Shimashita J, Schaffer L, Salomon DR, Ordoukhanian PT (2011). Method for improved Illumina sequencing library preparation using NuGEN Ovation RNA-Seq System. Biotechniques. 50(3):177-80. doi: 10.2144/000113613. PMID: 21486238

Malyshev DA, Seo YJ, Ordoukhanian P, Romesberg FE (2009). PCR with an expanded genetic alphabet. J Am Chem Soc 131(41):14620-1. doi: 10.1021/ja906186f. PMID: 19788296

Seo YJ, Hwang GT, Ordoukhanian P, Romesberg FE (2009). Optimization of an unnatural base pair toward natural-like replication. J Am Chem Soc. 131(9):3246-52. doi: 10.1021/ja807853m. PMID: 19256568

Reader JS, Ordoukhanian PT, Kim JG, de Crécy-Lagard V, Hwang I, Farrand S, Schimmel P (2005). Major biocontrol of plant tumors targets tRNA synthetase. Science 309, 1533.

Ordoukhanian P, Joyce GF (2002). RNA-cleaving DNA enzymes with altered regio- or enantioselectivity. J Am Chem Soc. 124(42):12499-506. PMID: 12381192

Sheppard TL, Ordoukhanian P, Joyce GF (2000). A DNA enzyme with N-glycosylase activity. Proc Natl Acad Sci U S A 97, 7802-7. PMC 16625

Ordoukhanian P, Taylor JS. (2000). Caged single and double strand breaks. Bioconjug Chem. 11(1):94-103. PMID: 10639091 

Ordoukhanian P, Joyce GF (1999). A molecular description of the evolution of resistance. Chem Biol 6, 881-9.

Ordoukhanian P, Taylor JS (1997). Solid phase-supported thymine dimers for the construction of dimer-containing DNA by combined chemical and enzymatic synthesis: a potentially general method for the efficient incorporation of modified nucleotides into DNA. Nucleic Acids Res 25. 3783-6

Ordoukhanian P, Taylor JS (1995) Design and Synthesis of a Versatile Photocleavable DNA Building Block. Application to Phototriggered Hybridization. J Am Chem Soc. 117 (37), pp 9570–9571, DOI: 10.1021/ja00142a028