Conformation of denatured and renatured DNA

Bagchi, B.; Misra, D.N.; Basu, S.; Gupta, Nandini

doi:10.1016/0005-2787(69)90207-x

Cited by 6 publications

(3 citation statements)

References 13 publications

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“…These structures were isolated first as cores of single-stranded DNA that resist digestion by S 1 nuclease or other enzymes specific for unpaired nucleic acids. S 1 nuclease-resistant cores with fold-back helical structure also occur in more complex samples such as bacterial and mammalian DNA (18,33,34). In a situation that may parallel the ability of antibodies to recognize secondary structure in denatured DNA, duplex structure within single-stranded OX 174 DNA appears to be responsible for recognition and cleavage by restriction endonucleases (35).…”

Section: Discussionmentioning

confidence: 99%

“…One of the lines of evidence for the existence it DNA, it of secondary structure in denatured DNA is the relative the closer resistance of a portion of the DNA to digestion by SI ompetitive nuclease (18). When digestion of denatured DNA by may have Si nuclease was monitored at room temperature, a secondary rapid early rate of digestion was followed by a second, slower phase (Fig.…”

Section: Methodsmentioning

confidence: 99%

“…Three possibilities raised by these observations are, first, that the reaction is due to exposure ofthe bases in local single-stranded regions ofthe DNA; second, that the reaction is with the sugar-phosphate backbone of one polydeoxyribonucleotide strand and that such a structure is accessible in both the native and denatured DNA (it should be noted that antibodies to such a determinant, even in combining with denatured DNA, would differ from those that recognize bases or base sequences; and third, that the antibodies react with a determinant that does involve the backbone of both strands, and that denatured DNA competes for binding because there is in fact a significant amount of helical secondary structure (either stable or transient) in denatured DNA (18). Such antibodies would resemble the experimentally induced antibodies to double-stranded RNA or RNA-DNA hybrids, which recognize specific helical shape (19).…”

Section: Introductionmentioning

confidence: 99%

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Secondary Structure in Denatured DNA is Responsible for Its Reaction with Antinative DNA Antibodies of Systemic Lupus Erythematosus Sera

Stollar¹,

Papalian²

1980

J. Clin. Invest.

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A B S T R A C T Experiments were designed to determine the basis for the strong competitive reaction of denatured DNA with systemic lupus erythematosus (SLE) antinative DNA antibodies. Secondary structure in denatured DNA was reflected in hyperchromicity upon heating and in multiphase kinetics ofits digestion by Si nuclease. Partial digestion by Si nuclease completely eliminated the ability of denatured DNA to react with antidenatured DNA antibodies, but not its ability to react with SLE sera. Sl nuclease-resistant cores were isolated from extensively digested denatured DNA. These cores had secondary structure, including some stable fold-back helical regions. The cores, from 20 to several hundred base pairs in size, competed with native DNA for binding by SLE sera. Other experiments measured reactions of denatured DNA under conditions that affected its secondary structure content. Its competitive activity decreased as temperature was increased from 00 to 37°C, whereas the activity of native DNA was not altered in this temperature range. With DNA pieces of 90-110 base pairs, native fragments were much more effective than the denatured fragments, in which stable helical structure is less likely to occur than in high molecular weight denatured DNA. Competitive assays with mononucleotides, oligonucleotides, homopolymers, and RNA-DNA hybrids also indicated that two strands of polydeoxyribonucleotide were required for optimal reactions with these SLE serum antibodies. The antibodies can measure stable helical regions in denatured DNA; they may also stabilize short helical regions that occur in an equilibrium of conformational forms.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Secondary Structure in Denatured DNA is Responsible for Its Reaction with Antinative DNA Antibodies of Systemic Lupus Erythematosus Sera

Stollar¹,

Papalian²

1980

J. Clin. Invest.

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The interaction of antibody/dna immune complexes with complement

Taylor

Edberg

Kujala

et al. 1987

Arthritis & Rheumatism

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In 28 serum and plasma samples from patients with systemic lupus erythematosus, we examined the importance of antibody class with respect to complement-mediated binding to human red blood cells (RBC) of antibody/DNA immune complexes (IC) prepared with anti-DNA antibodies. We used both 3H-double-stranded DNA and 3H-single-stranded DNA (ssDNA). Generally, double-stranded DNA IC showed considerably higher binding than did ssDNA IC in the RBC binding assay. Further analysis indicated that although ssDNA IC fix complement, it is necessary that these IC contain IgM anti-DNA antibodies in order for them to bind to RBC. The results suggest that the mechanisms of clearance and pathogenic potential of these IC may depend upon both the DNA conformation and antibody class. In particular, complement-fixing IC which contain IgG anti-DNA antibodies and ssDNA may not be cleared via the erythrocyte clearance mechanism, and therefore, Address reprint requests to Ronald P. Taylor, PhD, Department of Biochemistry, University of Virginia School of Medicine, Charlottesville, VA 22908.Submitted for publication March 19, 1986; accepted in revised form September 10, 1986. could be more likely to deposit in certain tissues and initiate inflammatory reactions.The results of extensive studies from a number of different laboratories indicate that complementfixing (CF) IgG antibody/double-stranded DNA (dsDNA) immune complexes (IC) play a significant role in the pathogenesis of systemic lupus erythematosus (SLE) (1-5). Although it is also believed that IC containing single-stranded DNA (ssDNA) may contribute to the pathogenesis of SLE (6,7), studies of these IC have been less frequent. This is because antibodies to dsDNA are more specific for SLE (3,8,9). In fact, care has often been taken to ensure that the DNA antigen used in SLE studies is not contaminated with ss regions (9-11). However, it has been demonstrated that IC prepared with ssDNA, and SLE sera containing anti-DNA antibodies, do fix complement, as defined by immune hemolysis techniques (12).Recently, Cornacoff and colleagues' findings in baboons (13) have raised considerable interest in the role of red blood cells (RBC) in the clearance of CF IC from the circulation. Their studies indicate that injected CF bovine serum albumin (BSA)/anti-BSA IC rapidly bind to the complement receptors of the baboon RBCs and are then taken to the liver, where the IC (but not the RBC) are removed from the circulation. In vitro studies (14) have shown that C F antibody/dsDNA IC also bind to the C3b receptors of human RBC, so it is likely that a similar clearance mechanism is operative in humans. The recent finding of a reduction in either the number of RBC C3b receptors or in their IC binding capacity, in ICmediated diseases such as SLE and rheumatoid arthri-

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Synergistic Regulation of DNA Morphology by Metal Cations and Low pH

Wang,

Gao

et al. 2024

Microscopy Res & Technique

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As a flexible biomolecule, the spatial structure of DNA is variable. The effects of concentration, metal cations, and low pH on DNA morphology were studied. For the high concentration of DNA, the cross‐linked branch‐like or network structures were formed. For the low concentration of DNA, isolated, random and freely loose linear DNA chains were presented. These phenomena were related to the intermolecular interactions. Branch‐like DNA structures were reformed with the addition of metal cations to the low concentration of DNA at pH 7–4, suggesting the negative charges of DNA were neutralized, thus transforming the spatial structure of DNA into a low charge density morphology and presenting the hypochromic effect. Compared to the monovalent alkaline metal cations, more negative charges of DNA were screened by the alkaline‐earth metal cations. Distinct DNA morphologies were observed for pH 3. The linear and condensed DNA structures were simultaneously observed, which was met regardless of the solution with or without the addition of metal cations. This was further confirmed by the absorbance of DNA. Compared to the pure DNA, bulky and aggregated DNA collapsed structures were formed when the sodium and magnesium cations were added to the reaction solution. In addition, it was verified that the condensed DNA structures failed to revert back to the chain structure by neutralizing acidic solutions with alkali, but the compacted DNA spheres became loose. The conductivities of various DNA morphologies were measured. They were morphology‐dependent. This study provides guidance for the behavior of DNA in the acidic solutions and further promotes the application of DNA in DNA‐based nano‐optoelectronic devices.

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Conformation of denatured and renatured DNA

Cited by 6 publications

References 13 publications

Secondary Structure in Denatured DNA is Responsible for Its Reaction with Antinative DNA Antibodies of Systemic Lupus Erythematosus Sera

Secondary Structure in Denatured DNA is Responsible for Its Reaction with Antinative DNA Antibodies of Systemic Lupus Erythematosus Sera

The interaction of antibody/dna immune complexes with complement

Synergistic Regulation of DNA Morphology by Metal Cations and Low pH

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