nuclease protection assays


Summary: Techniques for measuring specific nucleic acid interaction with another nucleic acid or with a protein by digestion of the non-interacting nucleic acid by various nucleases. After all non-interacting regions are eliminated by nuclease digestion, the protected nucleic acid that remains is analyzed. DNA FOOTPRINTING utilizes this technique to analyze the DNA contact sites of DNA-BINDING PROTEINS.

Top Publications

  1. Freund F, Boulme F, Litvak S, Tarrago Litvak L. Initiation of HIV-2 reverse transcription: a secondary structure model of the RNA-tRNA(Lys3) duplex. Nucleic Acids Res. 2001;29:2757-65 pubmed
    ..In view of these experimental data and sequence comparison between different HIV-2 isolates, we propose a model for the secondary structure of the HIV-2 template-primer initiation complex. ..
  2. Raychaudhuri B, Han Y, Lu T, Vogelbaum M. Aberrant constitutive activation of nuclear factor kappaB in glioblastoma multiforme drives invasive phenotype. J Neurooncol. 2007;85:39-47 pubmed
    ..Interruption of this aberrant NF-kappaB activity may help reduce the spread of this infiltrative tumor. ..
  3. James M, Skaar T, Lee R, MacPherson A, Zwiebel J, Ahluwalia B, et al. Constitutive expression of the steroid sulfatase gene supports the growth of MCF-7 human breast cancer cells in vitro and in vivo. Endocrinology. 2001;142:1497-505 pubmed
    ..These studies directly demonstrate that intratumor STS activity can support estrogen-dependent tumorigenicity in an experimental model and may contribute to the promotion of human breast tumors. ..
  4. Yuan Z, Shioji K, Kihara Y, Takenaka H, Onozawa Y, Kishimoto C. Cardioprotective effects of carvedilol on acute autoimmune myocarditis: anti-inflammatory effects associated with antioxidant property. Am J Physiol Heart Circ Physiol. 2004;286:H83-90 pubmed
  5. Mitchell J, Ting T, Wong S, Mitchell B, Lye S. Parathyroid hormone-related protein treatment of pregnant rats delays the increase in connexin 43 and oxytocin receptor expression in the myometrium. Biol Reprod. 2003;69:556-62 pubmed
    ..PTHrP treatment did not prevent the increase in Cx43 and OTR gene expression on Day 23 or the timing of labor, suggesting that the effects of PTHrP signaling are overridden with the onset of labor. ..
  6. Luo Y, Berman M, Abromson Leeman S, Dorf M. Tumor necrosis factor is required for RANTES-induced astrocyte monocyte chemoattractant protein-1 production. Glia. 2003;43:119-27 pubmed
    ..The results define an astrocyte proinflammatory cascade that amplifies synthesis of proinflammatory mediators. The implications of these findings to inflammatory diseases of the central nervous system are discussed. ..
  7. Cosenza L, Gorgun G, Urbano A, Foss F. Interleukin-7 receptor expression and activation in nonhaematopoietic neoplastic cell lines. Cell Signal. 2002;14:317-25 pubmed
    ..The expression of functional IL-7R on epithelial tumour cells may represent a potential target for receptor-directed therapy. ..
  8. Banerjee P, Weissleder R, Bogdanov A. Linear polyethyleneimine grafted to a hyperbranched poly(ethylene glycol)-like core: a copolymer for gene delivery. Bioconjug Chem. 2006;17:125-31 pubmed
    ..Because of the biocompatibility and higher transfection efficiency, the 'inverted' block copolymer merits further investigation as a gene carrier. ..
  9. Itani O, Stokes J, Thomas C. Nedd4-2 isoforms differentially associate with ENaC and regulate its activity. Am J Physiol Renal Physiol. 2005;289:F334-46 pubmed
    ..Our data illustrate that naturally occurring hNedd4-2 isoforms differentially associate with ENaC to regulate its activity. ..

More Information


  1. Spender L, Cornish G, Rowland B, Kempkes B, Farrell P. Direct and indirect regulation of cytokine and cell cycle proteins by EBNA-2 during Epstein-Barr virus infection. J Virol. 2001;75:3537-46 pubmed
    ..The results indicate that cytokines are an early target of EBNA-2 and that EBNA-2 can regulate cyclin D2 transcription in EBV-infected cells by mechanisms additional to the c-myc pathway. ..
  2. Xu H, Tian W, Fu Y, Oyama T, Anderson S, Cohen D. Functional effects of nonsynonymous polymorphisms in the human TRPV1 gene. Am J Physiol Renal Physiol. 2007;293:F1865-76 pubmed
    ..In aggregate, these data underscore expression-level and functional differences among naturally occurring TRPV1 variants; the implications with respect to human physiology are considered. ..
  3. Faber J, Yang N, Xin X. Expression of alpha-adrenoceptor subtypes by smooth muscle cells and adventitial fibroblasts in rat aorta and in cell culture. J Pharmacol Exp Ther. 2001;298:441-52 pubmed
    ..In addition, we report the intriguing finding that AFBs express alpha1-ARs in similar abundance as medial SMCs and that norepinephrine induced them to proliferate. ..
  4. Carlisle S, Marciano Cabral F, Staab A, Ludwick C, Cabral G. Differential expression of the CB2 cannabinoid receptor by rodent macrophages and macrophage-like cells in relation to cell activation. Int Immunopharmacol. 2002;2:69-82 pubmed
    ..Furthermore, since inflammatory and primed macrophages express the highest levels of CB2, the functional activities of macrophages when in these respective states of activation may be the most sensitive to the action of cannabinoids. ..
  5. Kumar A, Gates P, Brockes J. Positional identity of adult stem cells in salamander limb regeneration. C R Biol. 2007;330:485-90 pubmed
    ..Prod1 protein is up-regulated after treatment of distal blastemas with RA and this is particularly marked in cells of the dermis. These cells have previously been implicated in pattern formation during limb regeneration. ..
  6. Weinberg E, Shimpo M, De Keulenaer G, MacGillivray C, Tominaga S, Solomon S, et al. Expression and regulation of ST2, an interleukin-1 receptor family member, in cardiomyocytes and myocardial infarction. Circulation. 2002;106:2961-6 pubmed
    ..41, P<0.001) and negatively with ejection fraction (P=0.02). These data identify ST2 release in response to myocardial infarction and suggest a role for this innate immune receptor in myocardial injury. ..
  7. Pruznak A, Hong Brown L, Lantry R, She P, Frost R, Vary T, et al. Skeletal and cardiac myopathy in HIV-1 transgenic rats. Am J Physiol Endocrinol Metab. 2008;295:E964-73 pubmed publisher
    ..Hence, HIV-1 Tg rats develop atrophy of cardiac and skeletal muscle, the latter of which results primarily from an increased protein degradation and may be related to the marked reduction in muscle insulin-like growth factor I. ..
  8. Maran A, Hefferan T, Zhang M, Turner R. Unanticipated changes in steady-state mRNA levels for glyceraldehyde-3-phosphate dehydrogenase in rat tibiae. Calcif Tissue Int. 2004;74:204-7 pubmed
    ..Taken together, these findings indicate that it is essential to demonstrate that GAPDH expression is not altered prior to using the gene as an internal control. ..
  9. Nakamura M, Houghtling R, MacArthur L, Bayer B, Bregman B. Differences in cytokine gene expression profile between acute and secondary injury in adult rat spinal cord. Exp Neurol. 2003;184:313-25 pubmed
  10. Long M, Sairam M, Komar C. Initiation of the expression of peroxisome proliferator-activated receptor gamma (PPAR gamma) in the rat ovary and the role of FSH. Reprod Biol Endocrinol. 2009;7:145 pubmed publisher
    ..These data indicate that FSH is not a primary factor initiating the expression of PPARgamma and that other agents play a role in activating its expression in the ovary. ..
  11. Gaupp S, Pitt D, Kuziel W, Cannella B, Raine C. Experimental autoimmune encephalomyelitis (EAE) in CCR2(-/-) mice: susceptibility in multiple strains. Am J Pathol. 2003;162:139-50 pubmed
  12. Bahk J, Li S, Park M, Kim M. Dopamine D1 and D2 receptor mRNA up-regulation in the caudate-putamen and nucleus accumbens of rat brains by smoking. Prog Neuropsychopharmacol Biol Psychiatry. 2002;26:1095-104 pubmed
    ..In conclusion, we believe that smoking up-regulate the DA receptor mRNA expression significantly higher in rat CPu and NAc than nicotine but only a little bit higher in OTu. ..
  13. Hansen L, Kirpekar F, Douthwaite S. Recognition of nucleotide G745 in 23 S ribosomal RNA by the rrmA methyltransferase. J Mol Biol. 2001;310:1001-10 pubmed
    ..After assembly of the 50 S subunit, nucleotides G745, G748 and A2058 come to lie in close proximity lining the peptide exit channel at the site where macrolide, lincosamide and streptogramin B antibiotics bind. ..
  14. Juknevicius I, Segal Y, Kren S, Lee R, Hostetter T. Effect of aldosterone on renal transforming growth factor-beta. Am J Physiol Renal Physiol. 2004;286:F1059-62 pubmed
    ..In summary, aldosterone provokes renal TGF-beta, and this action may contribute to aldosterone's fibrotic propensity. ..
  15. Nosareva O, Nesterov A, Boldyrev A, Smirnova O, Tumanov Y, Kouzmitcheva G, et al. Construction of an encapsulated ESAT-6-based anti-TB DNA vaccine and evaluation of its immunogenic properties. Biol Chem. 2008;389:579-83 pubmed
    ..KpONE6 induces a proliferative T-cell immune response in mice upon intramuscular immunization. ..
  16. Braverman A, Ruggieri M. Muscarinic receptor transcript and protein density in hypertrophied and atrophied rat urinary bladder. Neurourol Urodyn. 2006;25:55-61 pubmed
    ..Extrapolation of functional effects from transcript density data is invalid for M(3) mediated bladder contractions. ..
  17. Fu Z, Noguchi T, Kato H. Differential regulation of IGFBP-2 and IGFBP-5 gene expression by vitamin A status in Japanese quail. Am J Physiol Endocrinol Metab. 2001;281:E138-46 pubmed
  18. He Q, Kim J, Sharma R. Silymarin protects against liver damage in BALB/c mice exposed to fumonisin B1 despite increasing accumulation of free sphingoid bases. Toxicol Sci. 2004;80:335-42 pubmed
    ..These findings suggest that silymarin protected against FB(1) liver damage by inhibiting biological functions of free sphingoid bases and increasing cellular regeneration. ..
  19. Kolb F, Westhof E, Ehresmann C, Ehresmann B, Wagner E, Romby P. Bulged residues promote the progression of a loop-loop interaction to a stable and inhibitory antisense-target RNA complex. Nucleic Acids Res. 2001;29:3145-53 pubmed
    ..In contrast to the four-way junction topology, the loop-loop interaction alone failed to prevent ribosome binding at its loading site and, thus, inhibition of RepA translation was alleviated. ..
  20. Li Y, Seidel K, Marschall P, Klein M, Hope A, Schacherl J, et al. A polymorphic microsatellite repeat within the ECE-1c promoter is involved in transcriptional start site determination, human evolution, and Alzheimer's disease. J Neurosci. 2012;32:16807-20 pubmed publisher
    ..Our data indicate that a short genomic repeat structure constitutes a novel core promoter element, coincides with human evolution, and contributes to the pathogenesis of AD. ..
  21. Okuzawa K, Gen K, Bruysters M, Bogerd J, Gothilf Y, Zohar Y, et al. Seasonal variation of the three native gonadotropin-releasing hormone messenger ribonucleic acids levels in the brain of female red seabream. Gen Comp Endocrinol. 2003;130:324-32 pubmed
    ..The increase in sbGnRH mRNA levels correlates with the increase in day length, water temperature and serum steroids levels, suggesting that these factors are candidates for regulators of sbGnRH synthesis. ..
  22. Bellarosa D, Ciucci A, Bullo A, Nardelli F, Manzini S, Maggi C, et al. Apoptotic events in a human ovarian cancer cell line exposed to anthracyclines. J Pharmacol Exp Ther. 2001;296:276-83 pubmed
    ..The pathway was Fas-independent but likely involved bax and caspase-3 as effectors of the cascade culminating in apoptosis. ..
  23. Zhang Y, Leibowitz M. Folding of the group I intron ribozyme from the 26S rRNA gene of Candida albicans. Nucleic Acids Res. 2001;29:2644-53 pubmed
    ..LSU. However, it appears that the role cations play in the multiple folding pathways leading to the catalytically active form may differ between folding of these two group I introns. ..
  24. Ostrow K, Loeb D. Underrepresentation of the 3' region of the capsid pregenomic RNA of duck hepatitis B virus. J Virol. 2004;78:2179-86 pubmed
    ..Possibly, the 3' region of the pgRNA is not packaged into the interior of the capsid but rather is associated with a part of the capsid where it is susceptible to microccocal nuclease digestion. ..
  25. Husse B, Briest W, Homagk L, Isenberg G, Gekle M. Cyclical mechanical stretch modulates expression of collagen I and collagen III by PKC and tyrosine kinase in cardiac fibroblasts. Am J Physiol Regul Integr Comp Physiol. 2007;293:R1898-907 pubmed
    ..Myocardial fibrosis due to ECM remodeling contributes to the dysfunction of the failing heart, which might be attributed to changes in hemodynamic loading. ..
  26. Huang B, El Sherif T, Gidh Jain M, Qin D, el Sherif N. Alterations of sodium channel kinetics and gene expression in the postinfarction remodeled myocardium. J Cardiovasc Electrophysiol. 2001;12:218-25 pubmed
    ..Additional studies are required to address these questions and to characterize the functional role of the NaCh I subtypes in cardiac myocytes. ..
  27. Jean Harry G, Bruccoleri A, Lefebvre d Hellencourt C. Differential modulation of hippocampal chemical-induced injury response by ebselen, pentoxifylline, and TNFalpha-, IL-1alpha-, and IL-6-neutralizing antibodies. J Neurosci Res. 2003;73:526-36 pubmed
    ..Data suggests a role for TNFalpha in the pathogenesis of hippocampal injury induced by TMT. ..
  28. Kleemann E, Neu M, Jekel N, Fink L, Schmehl T, Gessler T, et al. Nano-carriers for DNA delivery to the lung based upon a TAT-derived peptide covalently coupled to PEG-PEI. J Control Release. 2005;109:299-316 pubmed
    ..Thus, TAT-PEG-PEI represents a new approach to non-viral gene carriers for lung therapy, comprising protection for plasmid DNA, low toxicity and significantly enhanced transfection efficiency under in vivo conditions. ..
  29. Ohlson J, Ensterö M, Sjoberg B, Ohman M. A method to find tissue-specific novel sites of selective adenosine deamination. Nucleic Acids Res. 2005;33:e167 pubmed
    ..The RNA substrates were verified by RT-PCR, RNase protection and microarray. Using this method it is possible to uniquely identify novel single sites of selective A to I editing. ..
  30. Sohail M, Hochegger H, Klotzbucher A, Guellec R, Hunt T, Southern E. Antisense oligonucleotides selected by hybridisation to scanning arrays are effective reagents in vivo. Nucleic Acids Res. 2001;29:2041-51 pubmed
    ..Excellent correlation was found between antisense potency and affinity of oligonucleotides for the cyclin transcripts as measured by the array, despite the complexity of the cellular environment. ..
  31. Koch M, Spillmann F, Dendorfer A, Westermann D, Altmann C, Sahabi M, et al. Cardiac function and remodeling is attenuated in transgenic rats expressing the human kallikrein-1 gene after myocardial infarction. Eur J Pharmacol. 2006;550:143-8 pubmed
    ..Further studies have to show whether these results can be caused by other therapeutically options. Long acting bradykinin receptor agonists might be an alternative option to improve ischemic heart disease. ..
  32. Fumagalli F, Frasca A, Racagni G, Riva M. Antipsychotic drugs modulate Arc expression in the rat brain. Eur Neuropsychopharmacol. 2009;19:109-15 pubmed publisher
  33. Shan K, Qi X, Long Y, Nordberg A, Guan Z. Decreased nicotinic receptors in PC12 cells and rat brains influenced by fluoride toxicity--a mechanism relating to a damage at the level in post-transcription of the receptor genes. Toxicology. 2004;200:169-77 pubmed
    ..The results suggest that the deficit of nAChRs induced by fluoride toxicity occurs at the level of post-transcription of the receptor gene, in which a mechanism might be involved in the damage by oxidative stress. ..
  34. Bhandari N, Sharma R. Fumonisin B(1)-induced alterations in cytokine expression and apoptosis signaling genes in mouse liver and kidney after an acute exposure. Toxicology. 2002;172:81-92 pubmed
    ..Increased expression of caspase 8 involved in the TNFalpha signaling pathway may contribute to the apoptosis, whereas IL-1Ra induction could contribute to the proliferating effects observed in FB(1) toxicity. ..
  35. Piwonska M, Wilczek E, Szewczyk A, Wilczynski G. Differential distribution of Ca2+-activated potassium channel beta4 subunit in rat brain: immunolocalization in neuronal mitochondria. Neuroscience. 2008;153:446-60 pubmed publisher
    ..These findings may support the perspectives for the neuroprotective role of mitochondrial BK(Ca) channel in specific brain structures. ..
  36. Huber W, Rossmanith W, Grusch M, Haslinger E, Prustomersky S, Peter Vörösmarty B, et al. Effects of coffee and its chemopreventive components kahweol and cafestol on cytochrome P450 and sulfotransferase in rat liver. Food Chem Toxicol. 2008;46:1230-8 pubmed
    ..The data confirm that the effects of complex mixtures may deviate from those of their putatively active components. ..
  37. Zhang D, Vuocolo S, Masciullo V, Sava T, Giordano A, Soprano D, et al. Cell cycle genes as targets of retinoid induced ovarian tumor cell growth suppression. Oncogene. 2001;20:7935-44 pubmed
    ..These results suggest that the pocket protein pathways are critical targets for retinoid suppression of ovarian carcinoma cell growth. ..
  38. Zhen Y, Mi T, Yu Z. Detection of Phaeocystis globosa using sandwich hybridization integrated with nuclease protection assay (NPA-SH). J Environ Sci (China). 2008;20:1481-6 pubmed
    ..Sandwich hybridization integrated with nuclease protection assay will provide an efficient alternative to microscopic method for monitoring and investigating the bloom of P. globosa. ..
  39. Lee C, Poovey H, Rando R, Hoyle G. Neuronal modulation of lung injury induced by polymeric hexamethylene diisocyanate in mice. Toxicol Appl Pharmacol. 2007;224:19-28 pubmed
    ..The results indicate that sensory nerves acting through Tacr1 can exert protective or anti-inflammatory effects in the lung following isocyanate exposure. ..
  40. Takano H, Asano K, Beppu T, Ueda K. Role of sigmaH paralogs in intracellular melanin formation and spore development in Streptomyces griseus. Gene. 2007;393:43-52 pubmed
    ..The transcription of the rpp operon is regulated both by the stress-response sigma factors and the A-factor regulatory cascade...
  41. Kumar J, Gupta R. Strand exchange activity of human recombination protein Rad52. Proc Natl Acad Sci U S A. 2004;101:9562-7 pubmed
  42. Yamaguchi Y, Yatsushiro S, Yamamura S, Abe H, Abe K, Watanabe M, et al. Ribonuclease protection assay on microchip electrophoresis. Analyst. 2011;136:2247-51 pubmed publisher
    ..These results clearly indicate the potential of microchip electrophoresis for the analysis of mRNA expression in cells. ..
  43. Hardy P, Lamireau D, Hou X, Dumont I, Abran D, Nuyt A, et al. Major role for neuronal NO synthase in curtailing choroidal blood flow autoregulation in newborn pig. J Appl Physiol (1985). 2001;91:1655-62 pubmed
  44. Brink M, Price S, Chrast J, Bailey J, Anwar A, Mitch W, et al. Angiotensin II induces skeletal muscle wasting through enhanced protein degradation and down-regulates autocrine insulin-like growth factor I. Endocrinology. 2001;142:1489-96 pubmed
    ..Our data suggest that ang II causes a loss in skeletal muscle mass by enhancing protein degradation probably via its inhibitory effect on the autocrine IGF-I system. ..
  45. Hansen R, Stöger R, Wijmenga C, Stanek A, Canfield T, Luo P, et al. Escape from gene silencing in ICF syndrome: evidence for advanced replication time as a major determinant. Hum Mol Genet. 2000;9:2575-87 pubmed
    ..The persistence of inactivation in these latter cases appears to depend critically on delayed replication of DNA because escape from silencing was only seen when replication was advanced to an active X-like pattern. ..
  46. Pradhan S, Mallick S, Chowdhury R. Vibrio cholerae classical biotype is converted to the viable non-culturable state when cultured with the El Tor biotype. PLoS ONE. 2013;8:e53504 pubmed publisher
  47. Mascarenhas R, Dougherty J, Schoenberg D. SMG6 cleavage generates metastable decay intermediates from nonsense-containing ?-globin mRNA. PLoS ONE. 2013;8:e74791 pubmed publisher
    ..Importantly, none of these altered the phosphorylation state of Upf1. These data provide the first proof for accumulation of stable NMD products by SMG6 endonuclease cleavage. ..
  48. Oh J, Olman M, Benveniste E. CXCL12-mediated induction of plasminogen activator inhibitor-1 expression in human CXCR4 positive astroglioma cells. Biol Pharm Bull. 2009;32:573-7 pubmed
    ..These results indicate that CXCL12/CXCR4 signaling in glioma cells may be another mechanism for these cells to express PAI-1, which may be involved in angiogenesis and tumor invasion in brain tumors. ..
  49. Wu C, Travers A. A 'one-pot' assay for the accessibility of DNA in a nucleosome core particle. Nucleic Acids Res. 2004;32:e122 pubmed
    ..We compare this assay to previously described methods. ..
  50. Frohnert P, Stonecypher M, Carroll S. Constitutive activation of the neuregulin-1/ErbB receptor signaling pathway is essential for the proliferation of a neoplastic Schwann cell line. Glia. 2003;43:104-18 pubmed
    ..The absence of EGFR expression in JS1 cells suggests that constitutive activation of the NRG-1/erbB signaling pathway is an alternative means of inducing Schwann cell neoplasia. ..
  51. Fogel B, McNally L, McNally M. Efficient polyadenylation of Rous sarcoma virus RNA requires the negative regulator of splicing element. Nucleic Acids Res. 2002;30:810-7 pubmed
    ..We propose a model in which the NRS serves to enhance polyadenylation of RSV unspliced RNA in a process analogous to the stimulation of cellular pre-mRNA polyadenylation by splicing complexes. ..
  52. Abudula A, Rommerskirch W, Weber E, Gunther D, Wiederanders B. Splice variants of human cathepsin L mRNA show different expression rates. Biol Chem. 2001;382:1583-91 pubmed
    ..Based on these results, we suggest a cis-acting element on human cathepsin L mRNA which can be bound by a negative trans-acting regulator, thus leading to reduced expression rates. ..
  53. Troyer R, LaPatra S, Kurath G. Genetic analyses reveal unusually high diversity of infectious haematopoietic necrosis virus in rainbow trout aquaculture. J Gen Virol. 2000;81:2823-32 pubmed
    ..Three of the four lineages exhibited temporal trends consistent with rapid evolution. ..