Skip to main content
PMC home page
Biochemical Journal logoLink to Biochemical Journal
. 1968 Jul;108(4):599–610. doi: 10.1042/bj1080599

A spectrophotometric study of the denaturation of deoxyribonucleic acid in the presence of urea or formaldehyde and its relevance to the secondary structure of single-stranded polynucleotides

R A Cox 1, K Kanagalingam 1
PMCID: PMC1198857  PMID: 5667272

Abstract

1. The thermal denaturation of DNA from rat liver was studied spectrophotometrically. In sodium phosphate buffers denaturation led to a single-stranded form having, at 25°, about 25% of the hypochromism of the intact double helix. 2. The hypochromism of the denatured form was the same in 1mm- as in 10mm-sodium phosphate buffer and was scarcely affected by reaction with formaldehyde. The hypochromism was decreased by about 40% in the presence of 8m-urea. 3. The hypochromism of denatured DNA at low ionic strengths was about the same as that of fragments of reticulocyte ribosomal RNA that were too short to form double-helical secondary structure and about the same as that of RNA after reaction with formaldehyde. 4. The spectrum of DNA was slightly affected by the presence of 8m-urea or 4m-guanidinium chloride. The differences in the spectrum of the native and denatured forms of DNA in 0·1m-sodium phosphate buffer, in 8m-urea–10mm-sodium phosphate buffer and in 4m-guanidinium chloride–10mm-sodium phosphate buffer, pH7·6, were similar but not identical. 5. Denatured rat liver DNA appears to have no double-helical character at 25° in 10mm-sodium phosphate buffer, pH7·6; increasing the buffer concentration to 0·1m leads to a more compact form in which about 40% of the residues form base pairs.

Full text

PDF
599

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Arnstein H. R., Cox R. A., Hunt J. A. The function of high-molecular-weight ribonucleic acid from rabbit reticulocytes in haemoglobin biosynthesis. Biochem J. 1964 Sep;92(3):648–661. doi: 10.1042/bj0920648. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. BAUTZ E. K., BAUTZ F. A. THE INFLUENCE OF NONCOMPLEMENTARY BASES ON THE STABILITY OF ORDERED POLYNUCLEOTIDES. Proc Natl Acad Sci U S A. 1964 Dec;52:1476–1481. doi: 10.1073/pnas.52.6.1476. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Boedtker H. The reaction of ribonucleic acid with formaldehyde. I. Optical absorbance studies. Biochemistry. 1967 Sep;6(9):2718–2727. doi: 10.1021/bi00861a011. [DOI] [PubMed] [Google Scholar]
  4. Brahms J., Michelson A. M., Van Holde K. E. Adenylate oligomers in single- and double-strand conformation. J Mol Biol. 1966 Feb;15(2):467–488. doi: 10.1016/s0022-2836(66)80122-5. [DOI] [PubMed] [Google Scholar]
  5. COX R. A., LITTAUER U. Z. Ribonucleic acid from Escherichia coli. III. The influence of ionic strength and temperature on hydrodynamic and optical properties. Biochim Biophys Acta. 1962 Aug 20;61:197–208. [PubMed] [Google Scholar]
  6. Cox R. A. A possible method for characterizing the secondary structure of ribonucleic acids. Biochem J. 1966 Jul;100(1):146–168. doi: 10.1042/bj1000146. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Cox R. A., Gould H. J., Kanagalingam K. A study of the alkaline hydrolysis of fractionated reticulocyte ribosomal ribonucleic acid and its relevance to secondary structure. Biochem J. 1968 Feb;106(3):733–741. doi: 10.1042/bj1060733. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Cox R. A. Hydrolysis of polynucleotides and the characterization of their secondary structure. A theoretical study. Biochem J. 1968 Feb;106(3):725–731. doi: 10.1042/bj1060725. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Cox R. A., Kanagalingam K. A spectrophotometric study of the secondary structure of ribonucleic acid based on a method for diminishing single-stranded base-'stacking' without affecting multi-helical structures. Biochem J. 1967 Jun;103(3):749–758. doi: 10.1042/bj1030749. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Cox R. A., Kanagalingam K. A study of the hydrolysis of unfractionated reticulocyte ribosomal ribonucleic acid by pancreatic ribonuclease and its relevance to secondary structure. Biochem J. 1967 May;103(2):431–452. doi: 10.1042/bj1030431. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Cox R. A. The secondary structure of ribosomal ribonucleic acid in solution. Biochem J. 1966 Mar;98(3):841–857. doi: 10.1042/bj0980841. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Eigner J., Doty P. The native, denatured and renatured states of deoxyribonucleic acid. J Mol Biol. 1965 Jul;12(3):549–580. doi: 10.1016/s0022-2836(65)80312-6. [DOI] [PubMed] [Google Scholar]
  13. FASMAN G. D., LINDBLOW C., GROSSMAN L. THE HELICAL CONFORMATIONS OF POLYCYTIDYLIC ACID: STUDIES ON THE FORCES INVOLVED. Biochemistry. 1964 Aug;3:1015–1021. doi: 10.1021/bi00896a002. [DOI] [PubMed] [Google Scholar]
  14. FELSENFELD G., CANTONI G. L. USE OF THERMAL DENATURATION STUDIES TO INVESTIGATE THE BASE SEQUENCE OF YEAST SERINE SRNA. Proc Natl Acad Sci U S A. 1964 May;51:818–826. doi: 10.1073/pnas.51.5.818. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Gould H. J., Arnstein H. R., Cox R. A. The dissociation of reticulocyte polysomes into subunits and the location of messenger RNA. J Mol Biol. 1966 Feb;15(2):600–618. doi: 10.1016/s0022-2836(66)80130-4. [DOI] [PubMed] [Google Scholar]
  16. Guschlbauer W. Helical regions in transfer ribonucleic acid. Biophysik. 1966;3(2):156–164. doi: 10.1007/BF01191609. [DOI] [PubMed] [Google Scholar]
  17. Hanlon S. The importance of London dispersion forces in the maintenance of the deoxyribonucleic acid helix. Biochem Biophys Res Commun. 1966 Jun 21;23(6):861–867. doi: 10.1016/0006-291x(66)90567-5. [DOI] [PubMed] [Google Scholar]
  18. Klucis E. S., Gould H. J. Zonal ultracentrifuge for the separation of ribosomal subunits. Science. 1966 Apr 15;152(3720):378–378. doi: 10.1126/science.152.3720.378. [DOI] [PubMed] [Google Scholar]
  19. LIPSETT M. N. COMPLEX FORMATION BETWEEN POLYCYTIDYLIC ACID AND GUANINE OLIGONUCLEOTIDES. J Biol Chem. 1964 Apr;239:1256–1260. [PubMed] [Google Scholar]
  20. LIPSETT M. N., HEPPEP L. A., BRADLEY D. F. Complex formation between oligonucleotides and polymers. J Biol Chem. 1961 Mar;236:857–863. [PubMed] [Google Scholar]
  21. LITTAUER U. Z., EISENBERG H. Ribonucleic acid from Escherichia coli; preparation, characterization and physical properties. Biochim Biophys Acta. 1959 Apr;32:320–337. doi: 10.1016/0006-3002(59)90604-3. [DOI] [PubMed] [Google Scholar]
  22. Leng M., Felsenfeld G. A study of polyadenylic acid at neutral pH. J Mol Biol. 1966 Feb;15(2):455–466. doi: 10.1016/s0022-2836(66)80121-3. [DOI] [PubMed] [Google Scholar]
  23. MAHLER H. R., KLINE B., MEHROTRA B. D. SOME OBSERVATIONS ON THE HYPOCHROMISM OF DNA. J Mol Biol. 1964 Sep;9:801–811. doi: 10.1016/s0022-2836(64)80186-8. [DOI] [PubMed] [Google Scholar]
  24. MARMUR J., DOTY P. Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J Mol Biol. 1962 Jul;5:109–118. doi: 10.1016/s0022-2836(62)80066-7. [DOI] [PubMed] [Google Scholar]
  25. SPENCER M., POOLE J. ON THE ORIGIN OF CRYSTALLIZABLE RNA FROM YEAST. J Mol Biol. 1965 Feb;11:314–326. doi: 10.1016/s0022-2836(65)80060-2. [DOI] [PubMed] [Google Scholar]
  26. STOCKX J. The influence of strong solutions of uerea and poly alcohols on the spectroscopic behavior of ribonucleic acid and nucleotides. Biochim Biophys Acta. 1963 Apr 30;68:535–546. doi: 10.1016/0006-3002(63)90182-3. [DOI] [PubMed] [Google Scholar]
  27. Schildkraut C. Dependence of the melting temperature of DNA on salt concentration. Biopolymers. 1965;3(2):195–208. doi: 10.1002/bip.360030207. [DOI] [PubMed] [Google Scholar]
  28. Stevens C. L., Rosenfeld A. The secondary structure of polyadenylic acid Inferences from its reaction with formaldehyde. Biochemistry. 1966 Aug;5(8):2714–2721. doi: 10.1021/bi00872a031. [DOI] [PubMed] [Google Scholar]
  29. Widnell C. C., Tata J. R. A procedure for the isolation of enzymically active rat-liver nuclei. Biochem J. 1964 Aug;92(2):313–317. doi: 10.1042/bj0920313. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Biochemical Journal are provided here courtesy of The Biochemical Society

RESOURCES