DNA bending by photolyase in specific and non-specific complexes studied by atomic force microscopy

Noort, S.J.T. van; Orsini, F.; Eker, A.P.M.; Wyman, Claire; Grooth, B.G. de; Greve, Jan

doi:10.1093/nar/27.19.3875

Cited by 43 publications

(23 citation statements)

References 19 publications

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“…This enzyme might initially recognize the 30°bend in the DNA or its bendability. In favor of such a mechanism, it has been found by atomic force microscopy that dimer-containing DNA is bent by 36°when bound by Anacystis nidulans photolyase, although the CPDcontaining DNA did not appear to cause significant bending on its own (52). This enzyme may also initially recognize the altered phosphate backbone, because this and other photolyases have been found to make specific contacts with the phosphate immediately 5Ј and the three phosphates immediately 3Ј to the dimer as well as the phosphate across from the dimer (53).…”

Section: Discussionmentioning

confidence: 99%

Crystal structure of a DNA decamer containing a cis-syn thymine dimer

Park

Zhang²,

Ren³

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

212

209

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It is well known that exposure to UV induces DNA damage, which is the first step in mutagenesis and a major cause of skin cancer. Among a variety of photoproducts, cyclobutane-type pyrimidine photodimers (CPD) are the most abundant primary lesion. Despite its biological importance, the precise relationship between the structure and properties of DNA containing CPD has remained to be elucidated. Here, we report the free (unbound) crystal structure of duplex DNA containing a CPD lesion at a resolution of 2.0 Å. Our crystal structure shows that the overall helical axis bends Ϸ30°t oward the major groove and unwinds Ϸ9°, in remarkable agreement with some previous theoretical and experimental studies. There are also significant differences in local structure compared with standard B-DNA, including pinching of the minor groove at the 3 side of the CPD lesion, a severe change of the base pair parameter in the 5 side, and serious widening of both minor and major groves both 3 and 5 of the CPD. Overall, the structure of the damaged DNA differs from undamaged DNA to an extent that DNA repair proteins may recognize this conformation, and the various components of the replicational and transcriptional machinery may be interfered with due to the perturbed local and global structure. The cis-syn pyrimidine dimer (cyclobutane-type pyrimidine photodimer, CPD) is the major photoproduct induced by UV light present in sunlight (1) and is one of the principal causes of skin cancer (2). Evidence for the formation of the thymine dimer in DNA was first obtained Ͼ40 years ago (3, 4) and a few years later for cytosine-containing CPDs (5). Because of the mutagenic and protein-DNA-disrupting properties of CPDs, many organisms have evolved enzymes to specifically recognize and repair cis-syn dimers, such as Escherichia coli photolyase (6, 7), T4 endoV (8), as well as general repair enzymes such as E. coli uvrABC (9) and human excinuclease (10). Additionally, dimers are efficiently repaired in transcription-coupled repair by virtue of their ability to block synthesis by RNA polymerases (11,12). CPDs also block DNA replication (13) and are efficiently bypassed in a nonmutagenic manner by DNA damage bypass polymerases such as E. coli pol V (14) and the recently discovered yeast (15) and human polymerase (16,17). There is also evidence that the mismatch repair system can recognize mismatches opposite thymine dimers (18). Understanding the mechanism by which these proteins recognize and process CPDs will be greatly aided by a structure for CPD-containing DNA.The efficiency of damage repair is likely to depend on the extent to which those changes alter the structure of the DNA, hence making it recognizable for the repair enzymes involved. It has been suggested that the binding affinities of the repair enzymes for the CPD-containing DNA depend on the degree of DNA unwinding or kinking caused by those lesions (19,20). The first evidence that CPD formation causes large alterations in the structure of DNA is offered by circular dichroism studies and...

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Section: Discussionmentioning

confidence: 99%

Crystal structure of a DNA decamer containing a cis-syn thymine dimer

Park

Zhang²,

Ren³

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

212

209

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“…HS-AFM work builds upon two decades of biological studies with conventional AFM [14] which, to-date, has achieved significant success on model systems such as RNA polymerase [15,16], bacteriophage Lambda Cro protein [17], DNA photolyase [18], nucleosomes [19], and restriction enzymes [20]. HS-AFM may therefore have a central role to play in bionanotechnology and experimental biology, complementing current biochemical techniques and crystallography while elucidating fundamental biological processes.…”

Section: Introductionmentioning

confidence: 99%

Tuning the translational freedom of DNA for high speed AFM

et al. 2015

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Direct observation is arguably the preferred way to investigate the interactions between two molecular complexes. With the development of high speed atomic force microscopy (AFM), it is becoming possible to observe directly DNA-protein interactions with relevant spatial and temporal resolutions. These interactions are of central importance to biology, bionanotechnology, and functional biologically inspired materials. As in all microscopy studies, sample preparation plays a central role in AFM observation and minimal perturbation of the sample is desired. Here, we demonstrate the ability to tune the interactions between DNA molecules and the surface to create an association strong enough to enable high-resolution AFM imaging while also providing sufficient translational freedom to allow the relevant protein-DNA interactions to take place. Furthermore, we describe a quantitative method for measuring DNA mobility, while also determining the individual forces contributing to DNA movement. We found that for a weak surface association, a significant contribution to the movement arises from the interaction of the AFM tip with the DNA. In combination, these methods enable the tuning of the surface translational freedom of DNA molecules to allow the direct study of a wide range of nucleo-protein interactions by high speed atomic force microscopy.

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“…To locally determine flexibility in a polymer, we used and extended a method derived from quantifying bending angles of protein-DNA complexes (13). A slightly different method has been used to identify subtle sequence-dependent differences in flexibility in DNA molecules (14).…”

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confidence: 99%

The coiled-coil of the human Rad50 DNA repair protein contains specific segments of increased flexibility

Noort

Heijden

Jager

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

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Protein structural features are usually determined by defining regularities in a large population of homogeneous molecules. However, irregular features such as structural variation and flexibility are likely to be missed, despite their vital role for their biological function. In this paper, we report the observation of striking irregularities in the flexibility of the coiled-coil region of the human Rad50 DNA repair protein. Existing methods to quantitatively analyze flexibility are applicable to homogeneous polymers only. Because protein coiled-coils cannot be assumed to be homogeneous, we develop a method to quantify the local flexibility from high-resolution atomic force microscopy images. Indeed, in Rad50 coiled-coils, two positions of increased flexibility are observed. We discuss how this dynamic structural feature is integral to Rad50 function.

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DNA bending by photolyase in specific and non-specific complexes studied by atomic force microscopy

Cited by 43 publications

References 19 publications

Crystal structure of a DNA decamer containing a cis-syn thymine dimer

Crystal structure of a DNA decamer containing a cis-syn thymine dimer

Tuning the translational freedom of DNA for high speed AFM

The coiled-coil of the human Rad50 DNA repair protein contains specific segments of increased flexibility

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