Albany 2015:Book of Abstracts

Albany 2015
Conversation 19
June 9-13 2015
©Adenine Press (2012)

2'-Deoxyguanine analogs which enhance hybridization oligonucleotides with complementary DNA

It has been demonstrated previously that some adducts formed between endogenously activated polyaromatic hydrocarbons and DNA lead to significant stabilization of the DNA secondary structure (Lukin et al., 2011; Zaliznyak et al., 2006). Systematic study of the effect of exocyclic bulky aromatic groups on the DNA stability allowed us to identify novel dG analogs that considerably improve oligonucleotide hybridization properties.

Our study demonstrated that incorporation of the nucleoside analog PDZ-dG (3-(deoxyguanosin-N2-yl)-2-acetylamino-5-[(5-phenyloxadiazole)-2-yl]-benzene, or its analogs) into synthetic oligonucleotides significantly stabilizes the duplexes formed by these oligonucleotides and a complementary DNA strand.


When incorporated instead of dG, PDZ-dG analog increases dsDNA stability by 2.5-3.6 kcal/mol per modification in all sequence contexts studied. Enthalpy - entropy compensation was observed in all cases, which suggests the role of hydrophobic effects in the duplex stabilization. The stabilizing effect of PDZ-dG is comparable to the effect of G-clamp, a cytosine analog with increased affinity towards guanine (Ortega et al., 2007).

Solution state NMR study provides insights into the role of the bulky PDZ residue in the duplex stabilization. According to our results (see the figure below), the PDZ moiety occupies the DNA minor groove, thereby minimizing the area of hydrophobic surface exposed to the solvent. The PDZ moiety fits the minor groove without inducing any appreciable distortion in the canonical B-form structure.


All Watson-Crick hydrogen bonds, including the hydrogen bonds between the PDZ-dG and complementary cytosine, are fully preserved in the duplex, and all corresponding imino protons are clearly visible on the NOESY spectra in H2O.

In addition to substantial enhancement of DNA thermal stability, the PDZ-dG containing oligonucleotides demonstrate increased mismatch discrimination, especially when the mismatched base in the opposite strand is adenine or guanine. That makes the PDZ-dG monomer a potentially useful tool for creation of various DNA hybridization methods, especially for detection of point mutations. The PDZ-dG nucleotide can be incorporated into the oligonucleoides using standard phosphoramidite chemistry, and no modification of the synthetic protocol is necessary.

    Lukin M., Zaliznyak T., Johnson F., de los Santos CR. (2011) Incorporation of 3-Aminobenzanthrone into 2'-Deoxyoligonucleotides and Its Impact on Duplex Stability. J. Nucl. Acids., 2011:521035

    Zaliznyak T., Bonala R., Johnson F., de los Santos C. (2006) Structure and Stability of Duplex DNA Containing the 3-(Deoxyguanosin-N2)--yl)-2-acetylaminofluorene (dG(N2)-AAF) Lesion: A Bulky Adduct that Persists in Cellular DNA. Chem. Res. Toxicol., 19, 745-752.

    Ortega J-A., Blas JR, Orozco M, Grandas A., Pedroso E., Robles J. (2007) Binding Affinities of Oligonucleotides and PNAs Containing Phenoxazine and G-Clamp Cytosine Analogues Are Unusually Sequence-Dependent. Org. Lett. 9, 4503-4506.

Mark Lukin
Tatiana Zaliznyak
Leyla Shakirzyanova
Carlos de los Santos

Department of Pharmacological Sciences
School of Medicine
Stony Brook University Medical School
BST 8-140
Stony Brook, NY, 11794-8651