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Kinking the double helix by bending deformation.

Du Q, Kotlyar A, Vologodskii A - Nucleic Acids Res. (2007)

Bottom Line: By probing the structure of very small DNA circles, we determined that bending stress disrupts the regular helical structure when the radius of DNA curvature is smaller than 3.5 nm.To detect structural disruptions in the minicircles we treated them by single-strand-specific endonucleases.Our results suggest that strong DNA bending initiates kink formation while preserving base pairing.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, New York University, New York, NY 10003, USA.

ABSTRACT
DNA bending and torsional deformations that often occur during its functioning inside the cell can cause local disruptions of the regular helical structure. The disruptions created by negative torsional stress have been studied in detail, but those caused by bending stress have only been analyzed theoretically. By probing the structure of very small DNA circles, we determined that bending stress disrupts the regular helical structure when the radius of DNA curvature is smaller than 3.5 nm. First, we developed an efficient method to obtain covalently closed DNA minicircles. To detect structural disruptions in the minicircles we treated them by single-strand-specific endonucleases. The data showed that the regular DNA structure is disrupted by bending deformation in the 64-65-bp minicircles, but not in the 85-86-bp minicircles. Our results suggest that strong DNA bending initiates kink formation while preserving base pairing.

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Related in: MedlinePlus

Probing the structure of 200 bp and 205 bp DNA circles by single-strand-specific endonucleases. The 6% denaturing polyacrylamide gels show results of 60 min treatment by BAL 31 (a) and 30 min treatment by S1 (b). The only topoisomer of the 200 bp minicircles (CM, Lk = 19) is relaxed; the two topoisomers of the 205 bp minicircles (Lk of 19 and 20) have ΔLk of –0.5 and 0.5. The minicircles of 400 and 410 bp (CD) are relaxed. The size of linear fragments which served as a substrate in the minicircles preparation is shown at the bottom of the figure.
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Figure 4: Probing the structure of 200 bp and 205 bp DNA circles by single-strand-specific endonucleases. The 6% denaturing polyacrylamide gels show results of 60 min treatment by BAL 31 (a) and 30 min treatment by S1 (b). The only topoisomer of the 200 bp minicircles (CM, Lk = 19) is relaxed; the two topoisomers of the 205 bp minicircles (Lk of 19 and 20) have ΔLk of –0.5 and 0.5. The minicircles of 400 and 410 bp (CD) are relaxed. The size of linear fragments which served as a substrate in the minicircles preparation is shown at the bottom of the figure.

Mentions: First, we investigated 200 bp and 205 bp minicircles. For the 200 bp minicircles ΔLk is close to zero (25), so they are represented by a single topoisomer. The minicircles are very stable to the digestion by both nucleases (under chosen standard conditions), as was expected (Figure 4). The fragments of 205 bp in length have ∼19.5 helix turns and therefore form two topoisomers after cyclization, with and (Figure 4). The topoisomers are not digested by either BAL 31 or S1 nuclease. This result shows that even the (–) topoisomer keeps essentially intact regular structure in the minicircles of this size.Figure 4.


Kinking the double helix by bending deformation.

Du Q, Kotlyar A, Vologodskii A - Nucleic Acids Res. (2007)

Probing the structure of 200 bp and 205 bp DNA circles by single-strand-specific endonucleases. The 6% denaturing polyacrylamide gels show results of 60 min treatment by BAL 31 (a) and 30 min treatment by S1 (b). The only topoisomer of the 200 bp minicircles (CM, Lk = 19) is relaxed; the two topoisomers of the 205 bp minicircles (Lk of 19 and 20) have ΔLk of –0.5 and 0.5. The minicircles of 400 and 410 bp (CD) are relaxed. The size of linear fragments which served as a substrate in the minicircles preparation is shown at the bottom of the figure.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2275110&req=5

Figure 4: Probing the structure of 200 bp and 205 bp DNA circles by single-strand-specific endonucleases. The 6% denaturing polyacrylamide gels show results of 60 min treatment by BAL 31 (a) and 30 min treatment by S1 (b). The only topoisomer of the 200 bp minicircles (CM, Lk = 19) is relaxed; the two topoisomers of the 205 bp minicircles (Lk of 19 and 20) have ΔLk of –0.5 and 0.5. The minicircles of 400 and 410 bp (CD) are relaxed. The size of linear fragments which served as a substrate in the minicircles preparation is shown at the bottom of the figure.
Mentions: First, we investigated 200 bp and 205 bp minicircles. For the 200 bp minicircles ΔLk is close to zero (25), so they are represented by a single topoisomer. The minicircles are very stable to the digestion by both nucleases (under chosen standard conditions), as was expected (Figure 4). The fragments of 205 bp in length have ∼19.5 helix turns and therefore form two topoisomers after cyclization, with and (Figure 4). The topoisomers are not digested by either BAL 31 or S1 nuclease. This result shows that even the (–) topoisomer keeps essentially intact regular structure in the minicircles of this size.Figure 4.

Bottom Line: By probing the structure of very small DNA circles, we determined that bending stress disrupts the regular helical structure when the radius of DNA curvature is smaller than 3.5 nm.To detect structural disruptions in the minicircles we treated them by single-strand-specific endonucleases.Our results suggest that strong DNA bending initiates kink formation while preserving base pairing.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, New York University, New York, NY 10003, USA.

ABSTRACT
DNA bending and torsional deformations that often occur during its functioning inside the cell can cause local disruptions of the regular helical structure. The disruptions created by negative torsional stress have been studied in detail, but those caused by bending stress have only been analyzed theoretically. By probing the structure of very small DNA circles, we determined that bending stress disrupts the regular helical structure when the radius of DNA curvature is smaller than 3.5 nm. First, we developed an efficient method to obtain covalently closed DNA minicircles. To detect structural disruptions in the minicircles we treated them by single-strand-specific endonucleases. The data showed that the regular DNA structure is disrupted by bending deformation in the 64-65-bp minicircles, but not in the 85-86-bp minicircles. Our results suggest that strong DNA bending initiates kink formation while preserving base pairing.

Show MeSH
Related in: MedlinePlus