Abstract
Specific DNA breaks underlie many morphological changes in normal and damaged cells. They can serve as important markers in cell and tissue research. Yet historically, the labeling of DNA breaks in situ was most often limited to the identification of apoptotic cells. Consequently, the major techniques for analysis of DNA cleavage in tissue sections were initially developed for the visualization of apoptotic death. These assays rely on enzymatic labeling of DNA breaks to detect the characteristic DNA fragmentation seen in apoptosis. One of two methods is typically employed: a) terminal transferase (TdT) digoxigenin dUTP nick end labeling (TUNEL), or b) the Klenow fragment of DNA polymerase I based in situ end labeling. In order to identify various pathological states in situ based on structural DNA changes, a technique to selectively detect the various types of DNA damage is required. However, due to the properties of the enzymes involved in these assays, multiple types of DNA breaks are labeled. The terminal transferase-based assay labels free 3′ hydroxyl groups, which can be present in different types of breaks. As a result, it can detect stretches of single-stranded DNA (gaps) and also both single- and double-stranded breaks of various configurations (blunt-ended, 3′ and 5′ overhangs) (1). The Klenow polymerase-based assay in turn labels gaps and various 5′ overhangs (2). This prevents the selective visualization of specific types of DNA breaks in situ using these approaches.
References
Walker P. R., Carson C., Leblanc J., and Sikorska M. (2002) Labeling DNA damage with terminal transferase: applicability, specificity and limitations, in In Situ Detection of DNA Damage: Methods and Protocols (Didenko V. V. ed.) pp. 3–20.
Dierendonck J. H. (2002) DNA damage detection using DNA polymerase I or its Klenow fragment: applicability, specificity, limitations, in In Situ Detection of DNA Damage: Methods and Protocols (Didenko V. V. ed.) pp. 81–108.
Didenko V. V., and Hornsby P. J. (1996) Presence of double-strand breaks with single-base 3′ overhangs in cells undergoing apoptosis but not necrosis. J. Cell Biol. 135, 1369–1376.
Didenko V. V., Tunstead J. R., and Hornsby P. J. (1998) Biotin-labeled hairpin oligonucleotides. Probes to detect double-strand breaks in DNA in apoptotic cells. Am. J. Pathol. 152, 897–902.
Didenko V. V., Boudreaux D. J., and Baskin D. S. (1999) Substantial background reduction in ligase-based apoptosis detection using newly designed hairpin oligonucleotide probes. Biotechniques 27, 1130–1132.
Sikorska M., and Walker P. R. (1998) Endonuclease activities and apoptosis, in When Cells Die (eiLockshin R. A., Zakeri Z., and Tilly J. L., eds.), Wiley-Liss New York, pp. 211–242.
Liu Q. Y., Ribecco M., Pandey S., Walker P. R., and Sikorska M. (1999) Apoptosis-related functional features of the DNaseI-like family of nucleases. Ann. NYAcad. Sci. 887, 60–76.
Enari M., Sakahira H., Yokoyama H., Okawa K., Iwamatsu A., and Nagata S. (1998) A caspase-activated DNase that degrades DNA during apoptosis, and its inhibitor ICAD. Nature 391, 43–50.
Barry M. A. and Eastman A. (1993) Identification of deoxyribonuclease II as an endonuclease involved in apoptosis. Arch. Biochem. Biophys. 300, 440–450.
Sollner-Webb B., Melchior W.,Jr., and Felsenfeld G., (1978) DNAase I, DNAase II and staphylococcal nuclease cut at different, yet symmetrically located, sites in the nucleosome core. Cell 14, 611–627.
Weir F. A. (1993) Deoxyribonuclease I (EC 3.1.21.1) and II (EC 3.1.22.1), in Enzymes of Molecular Biology (Burrell M. M. ed.), Humana Totowa, NJ, pp. 7–16.
Lutter L. C., (1979) Precise location of DNase I cutting sites in the nucleosome core determined by high resolution gel electrophoresis. Nucleic Acids Res. 6, 41–56.
Liu X., Zou H., Slaughter C., and Wang X. (1997) DFF, a heterodimeric protein that functions downstream of caspase-3 to trigger DNA fragmentation during apoptosis. Cell 89, 175–184.
Widlak P., Li P., Wang X., and Garrard W. T. (2000) Cleavage preferences of the apoptotic endonuclease DFF40 (caspase-activated DNase or nuclease) on naked DNA and chromatin substrates. J Biol Chem. 275, 8226–8232.
Staley K., Blaschke A. J., and Chun J. (1997) Apoptotic DNA fragmentation is detected by a semiquantitative ligation-mediated PCR of blunt DNA ends. Cell Death Diff. 4, 66–75.
Alnemri E. S., and Litwack G. (1990) Activation of internucleosomal DNA cleavage in human CEM lymphocytes by glucocorticoid and novobiocin. Evidence for a non-Ca2(+)-requiring mechanism(s). J. Biol. Chem. 265, 17,323–17,333.
Collins M. K., Furlong I. J., Malde P., Ascaso R., Oliver J., and Lopez Rivas A. (1996) An apoptotic endonuclease activated either by decreasing pH or by increasing calcium. J. Cell Sci. 109, 2393–2399.
Dong Z., Saikumar P., Weinberg J. M., and Venkatachalam M. A. (1997) Internucleosomal DNA cleavage triggered by plasma membrane damage during necrotic cell death. Involvement of serine but not cysteine proteases. Am. J. Pathol. 151, 1205–1213.
Lieber M. R. (1998) Warner-Lambert/Parke-Davis Award Lecture. Pathological and physiological double-strand breaks: roles in cancer, aging, and the immune system. Am J Pathol. 153, 1323–1332.
Maunders M..J. (1993) DNA and RNA ligases (EC 6.5.1.1, EC 6.5.1.2, EC 6.5.1.3), in Enzymes of Molecular Biology (Burrell M. M., ed.), Humana Totowa, NJ, pp. 213–230.
Sweeney P. J. and Walker J. M. (1993) Proteinase K (EC 3.4.21.14), in Enzymes of Molecular Biology (Burrell M. M., ed.), Humana Totowa, NJ, pp. 305–311.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2002 Humana Press Inc.
About this protocol
Cite this protocol
Didenko, V.V. (2002). Detection of Specific Double-Strand DNA Breaks and Apoptosis In Situ Using T4 DNA Ligase. In: Didenko, V.V. (eds) In Situ Detection of DNA Damage. Methods in Molecular Biology, vol 203. Humana Press. https://doi.org/10.1385/1-59259-179-5:143
Download citation
DOI: https://doi.org/10.1385/1-59259-179-5:143
Publisher Name: Humana Press
Print ISBN: 978-0-89603-952-0
Online ISBN: 978-1-59259-179-4
eBook Packages: Springer Protocols