Anti-DNA-RNA Hybrid [S9.6] Antibody

This mouse monoclonal antibody was generated against a ΦX174 bacteriophage-derived synthetic DNA–RNA antigen and recognizes RNA-DNA hybrids of various lengths.


  • High specificity and affinity for DNA-RNA hybrids
  • Useful in the detection of R-loops
  • Does NOT cross-react with single-stranded DNA or double-stranded DNA
  • Minor cross-reaction (~5-fold less) has been observed for AU-rich double-stranded RNA.
  • High affinity binding shown for hybrids of 8, 10, 15, and 23 base pairs in length

DNA-RNA hybrids are a natural occurrence within eukaryotic cells, with levels of these hybrids increasing at sites with high transcriptional activity, such as during transcription initiation, repression, and elongation. Because RNA-DNA hybrids influence genomic instability, the S9.6 antibody is a useful reagent to help study the consequences of R-loops and lesions formed by these hybrids during DNA replication or other cellular processes. In addition, the S9.6 antibody is effective in recognizing RNA-DNA hybridization for microarray studies.

From the laboratory of Stephen H. Leppla, PhD, National Institute of Allergy and Infectious Diseases/NIH.

Catalog Number Product Size AVAILABILITY Price Qty
Anti-DNA-RNA Hybrid [S9.6] Antibody, 100ug
100ug In stock
Price: $405.00
Anti-DNA-RNA Hybrid [S9.6] Antibody, 1mg (10x100ug)
1mg (10x100ug) In stock
Price: $3,500.00
Antigen: S9.6 ΦX174 bacteriophage-derived synthetic DNA/RNA antigen
Isotype: IgG2a
Clonality: Monoclonal
Clone Name: S9.6
Reactivity: High specificity and affinity for DNA/RNA hybrids and other A-form nucleic acid hybrids
Immunogen: ΦX174 bacteriophage-derived synthetic DNA/RNA
Species Immunized: BALB/c mouse
Paratope: DYYGSRWFDY (proposed)
Purification Method: Protein G
Buffer: 0.1M Sodium Phosphate, pH 7.4, 0.15M NaCl, 0.05% (w/v) Sodium Azide
Tested Applications: Various (see publications below)
Storage: -20C
Shipped: Cold packs
From the laboratory of Stephen H. Leppla, PhD, National Institute of Allergy and Infectious Diseases/NIH.

PDF Anti-DNA-RNA Hybrid [S9.6] Antibody – Publications »

  1. Phillips DD, Garboczi DN, Singh K, Hu Z, Leppla SH, Leysath CE. The sub-nanomolar binding of DNA-RNA hybrids by the single-chain Fv fragment of antibody S9.6. J Mol Recognit. 2013 Aug;26(8):376-81.
  2. Sridhara SC, Carvalho S, Grosso AR, Gallego-Paez LM, Carmo-Fonseca M, de Almeida SF. Transcription Dynamics Prevent RNA-Mediated Genomic Instability through SRPK2-Dependent DDX23 Phosphorylation. View Article
  3. Starokadomskyy P, Gemelli T, Rios JJ, Xing C, Wang RC, Li H, Pokatayev V, Dozmorov I, Khan S, Miyata N, Fraile G, Raj P, Xu Z, Xu Z, Ma L, Lin Z, Wang H, Yang Y, Ben-Amitai D, Orenstein N, Mussaffi H, Baselga E, Tadini G, Grunebaum E, Sarajlija A, Krzewski K, Wakeland EK, Yan N, de la Morena MT, Zinn AR, Burstein E. DNA polymerase-α regulates the activation of type I interferons through cytosolic RNA:DNA synthesis. Nat Immunol. 2016 May;17(5):495-504. doi: 10.1038/ni.3409. PubMed PMID: 27019227; PubMed Central PMCID: PMC4836962. View Article
  4. Krishnan S, Petchiappan A, Singh A, Bhatt A, Chatterji D. R-loop induced stress response by second (p)ppGpp synthetase in Mycobacterium smegmatis: functional and domain interdependence. Mol Microbiol. 2016 Oct;102(1):168-82. doi: 10.1111/mmi.13453. PubMed PMID: 27349932. View Article
  5. Wiedemann EM, Peycheva M, Pavri R. DNA Replication Origins in Immunoglobulin Switch Regions Regulate Class Switch Recombination in an R-Loop-Dependent Manner. Cell Rep. 2016 Dec 13;17(11):2927-2942 View Article
  6. Torrente-Rodríguez RM, Ruiz-Valdepeñas Montiel V, Campuzano S, Farchado-Dinia M, Barderas R, San Segundo-Acosta P, Montoya JJ, Pingarron JM. Fast Electrochemical miRNAs Determination in Cancer Cells and Tumor Tissues with Antibody-Functionalized Magnetic Microcarriers. ACS Sensors. 2016 Jun 10;1(7):896-903. View Article
  7. Abraham KJ, Chan JN, Salvi JS, Ho B, Hall A, Vidya E, Guo R, Killackey SA, LiuN, Lee JE, Brown GW, Mekhail K. Intersection of calorie restriction and magnesiumin the suppression of genome-destabilizing RNA-DNA hybrids. Nucleic Acids Res.2016 Aug 29. pii: gkw752. View Article
  8. Lima WF, Murray HM, Damle SS, Hart CE, Hung G, De Hoyos CL, Liang XH, Crooke ST. Viable RNaseH1 knockout mice show RNaseH1 is essential for R loop processing, mitochondrial and liver function. Nucleic Acids Res. 2016 Apr 29. View Article
  9. Starokadomskyy P, Gemelli T, Rios JJ, Xing C, Wang RC, Li H, Pokatayev V, Dozmorov I, Khan S, Miyata N, Fraile G, Raj P, Xu Z, Xu Z, Ma L, Lin Z, Wang H, Yang Y, Ben-Amitai D, Orenstein N, Mussaffi H, Baselga E, Tadini G, Grunebaum E, Sarajlija A, Krzewski K, Wakeland EK, Yan N, de la Morena MT, Zinn AR, Burstein E. DNA polymerase-? regulates the activation of type I interferons throughcytosolic RNA:DNA synthesis. Nat Immunol. 2016 Mar 28. View Article
  10. Li L, Matsui M, Corey DR. Activating frataxin expression by repeat-targeted nucleic acids. Nat Commun. 2016 Feb 4;7:10606. doi: 10.1038/ncomms 10606. View Article
  11. Aronica L, Kasparek T, Ruchman D, Marquez Y, Cipak L, Cipakova I, Anrather D, Mikolaskova B, Radtke M, Sarkar S, Pai CC, Blaikley E, Walker C, Shen KF, Schroeder R, Barta A, Forsburg SL, Humphrey TC. The spliceosome-associated protein Nrl1 suppresses homologous recombination-dependent R-loop formation in fission yeast. Nucleic Acids Res. 2015 Dec 17. pii: gkv1473. View Article
  12. Boguslawski SJ, Smith DE, Michalak MA, Mickelson KE, Yehle CO, Patterson WL, Carrico RJ. Characterization of monoclonal antibody to DNA.RNA and its application to immunodetection of hybrids. J Immunol Methods. 1986 May 1;89(1):123-30.
  13. El Hage A, Webb S, Kerr A, Tollervey D. Genome-Wide Distribution of RNA-DNA Hybrids Identifies RNase H Targets in tRNA Genes, Retrotransposons and Mitochondria. PLoS Genet. 2014 Oct 30;10(10):e1004716.
  14. Bhatia V, Barroso SI, García-Rubio ML, Tumini E, Herrera-Moyano E, Aguilera A. BRCA2 prevents R-loop accumulation and associates with TREX-2 mRNA export factor PCID2. Nature. 2014 Jul 17;511(7509):362-5.
  15. Rigby RE, Webb LM, Mackenzie KJ, Li Y, Leitch A, Reijns MA, Lundie RJ, Revuelta A, Davidson DJ, Diebold S, Modis Y, Macdonald AS, Jackson AP. RNA:DNA hybrids are a novel molecular pattern sensed by TLR9. EMBO J. 2014 Mar 18;33(6):542-58.
  16. Tran HV, Piro B, Reisberg S, Duc HT, Pham MC. Antibodies directed to RNA/DNA hybrids: an electrochemical immunosensor for microRNAs detection using graphene-composite electrodes. Anal Chem. 2013 Sep 3;85(17):8469-74.
  17. Ginno PA, Lott PL, Christensen HC, Korf I, Chédin F. R-loop formation is a distinctive characteristic of unmethylated human CpG island promoters. Mol Cell. 2012 Mar 30;45(6):814-25.
  18. Skourti-Stathaki K, Proudfoot NJ, Gromak N. Human senataxin resolves RNA/DNA hybrids formed at transcriptional pause sites to promote Xrn2-dependent termination. Mol Cell. 2011 Jun 24;42(6):794-805.
  19. Sípová H, Zhang S, Dudley AM, Galas D, Wang K, Homola J. Surface plasmon resonance biosensor for rapid label-free detection of microribonucleic acid at subfemtomole level. Anal Chem. 2010 Dec 15;82(24):10110-5.
  20. El Hage A, French SL, Beyer AL, Tollervey D. Loss of Topoisomerase I leads to R-loop-mediated transcriptional blocks during ribosomal RNA synthesis. Genes Dev. 2010 Jul 15;24(14):1546-58.
  21. Pohjoismäki JL, Holmes JB, Wood SR, Yang MY, Yasukawa T, Reyes A, Bailey LJ, Cluett TJ, Goffart S, Willcox S, Rigby RE, Jackson AP, Spelbrink JN, Griffith JD, Crouch RJ, Jacobs HT, Holt IJ. Mammalian mitochondrial DNA replication intermediates are essentially duplex but contain extensive tracts of RNA/DNA hybrid. J Mol Biol. 2010 Apr 16;397(5):1144-55.
  22. Dutrow N, Nix DA, Holt D, Milash B, Dalley B, Westbroek E, Parnell TJ, Cairns BR. Dynamic transcriptome of Schizosaccharomyces pombe shown by RNA-DNA hybrid mapping. Nat Genet. 2008 Aug;40(8):977-86.
  23. Székvölgyi L, Rákosy Z, Bálint BL, Kókai E, Imre L, Vereb G, Bacsó Z, Goda K, Varga S, Balázs M, Dombrádi V, Nagy L, Szabó G. Ribonucleoprotein-masked nicks at 50-kbp intervals in the eukaryotic genomic DNA. Proc Natl Acad Sci U S A. 2007 Sep 18;104(38):14964-9.
  24. Hu Z, Zhang A, Storz G, Gottesman S, Leppla SH. An antibody-based microarray assay for small RNA detection. Nucleic Acids Res. 2006 Apr 13;34(7):e52.
  25. Casebolt DB, Stephensen CB. Monoclonal antibody solution hybridization assay for detection of mouse hepatitis virus infection. J Clin Microbiol. 1992 Mar;30(3):608-12.
  26. Miller CA, Patterson WL, Johnson PK, Swartzell CT, Wogoman F, Albarella JP, Carrico RJ. Detection of bacteria by hybridization of rRNA with DNA-latex and immunodetection of hybrids. J Clin Microbiol. 1988 Jul;26(7):1271-6.
  27. Yehle CO, Patterson WL, Boguslawski SJ, Albarella JP, Yip KF, Carrico RJ. A solution hybridization assay for ribosomal RNA from bacteria using biotinylated DNA probes and enzyme-labeled antibody to DNA:RNA. Mol Cell Probes. 1987 Jun;1(2):177-93.
  28. Molès JP, Griez A, Guilhou JJ, Girard C, Nagot N, Van de Perre P, Dujols P. Cytosolic RNA:DNA Duplexes Generated by Endogenous Reverse Transcriptase Activity as Autonomous Inducers of Skin Inflammation in Psoriasis. PLoS One. 2017 Jan 17;12(1):e0169879. doi: 10.1371/journal.pone.0169879. PubMed PMID: 28095445; PubMed Central PMCID: PMC5240966. View Article
  29. Jangi M, Fleet C, Cullen P, Gupta SV, Mekhoubad S, Chiao E, Allaire N, Bennett CF, Rigo F, Krainer AR, Hurt JA, Carulli JP, Staropoli JF. SMN deficiency in severe models of spinal muscular atrophy causes widespread intron retention and DNA damage. Proc Natl Acad Sci U S A. 2017 Mar 21;114(12):E2347-E2356. doi: 10.1073/pnas.1613181114. PubMed PMID: 28270613. View Article
  30. Sagie S, Toubiana S, Hartono SR, Katzir H, Tzur-Gilat A, Havazelet S, Francastel C, Velasco G, Chédin F, Selig S. Telomeres in ICF syndrome cells are vulnerable to DNA damage due to elevated DNA:RNA hybrids. Nat Commun. 2017 Jan 24;8:14015. doi: 10.1038/ncomms14015. PubMed PMID: 28117327; PubMed Central PMCID: PMC5286223. View Article

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