1
|
Belotserkovskii BP, Mirkin SM, Hanawalt PC. DNA sequences that interfere with transcription: implications for genome function and stability. Chem Rev 2013; 113:8620-37. [PMID: 23972098 DOI: 10.1021/cr400078y] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
2
|
Svingen R, Takahashi M, Åkerman B. Gel-Shift Assays: Migrative Dissociation of a RecA−Oligonucleotide Complex during Electrophoresis in Hydroxyethylated Agarose Gels. J Phys Chem B 2001. [DOI: 10.1021/jp011674e] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Roine Svingen
- Department of Physical Chemistry, Chalmers University of Technology, Göteborg, Sweden, and Department of Biocatalysis, University of Nantes and Centre National de la Recherche Scientifique, Nantes, France
| | - Masayuki Takahashi
- Department of Physical Chemistry, Chalmers University of Technology, Göteborg, Sweden, and Department of Biocatalysis, University of Nantes and Centre National de la Recherche Scientifique, Nantes, France
| | - Björn Åkerman
- Department of Physical Chemistry, Chalmers University of Technology, Göteborg, Sweden, and Department of Biocatalysis, University of Nantes and Centre National de la Recherche Scientifique, Nantes, France
| |
Collapse
|
3
|
Shchyolkina AK, Timofeev EN, Lysov YP, Florentiev VL, Jovin TM, Arndt-Jovin DJ. Protein-free parallel triple-stranded DNA complex formation. Nucleic Acids Res 2001; 29:986-95. [PMID: 11160932 PMCID: PMC29604 DOI: 10.1093/nar/29.4.986] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A 14 nt DNA sequence 5'-AGAATGTGGCAAAG-3' from the zinc finger repeat of the human KRAB zinc finger protein gene ZNF91 bearing the intercalator 2-methoxy,6-chloro,9-amino acridine (Acr) attached to the sugar-phosphate backbone in various positions has been shown to form a specific triple helix (triplex) with a 16 bp hairpin (intramolecular) or a two-stranded (intermolecular) duplex having the identical sequence in the same (parallel) orientation. Intramolecular targets with the identical sequence in the antiparallel orientation and a non-specific target sequence were tested as controls. Apparent binding constants for formation of the triplex were determined by quantitating electrophoretic band shifts. Binding of the single-stranded oligonucleotide probe sequence to the target led to an increase in the fluorescence anisotropy of acridine. The parallel orientation of the two identical sequence segments was confirmed by measurement of fluorescence resonance energy transfer between the acridine on the 5'-end of the probe strand as donor and BODIPY-Texas Red on the 3'-amino group of either strand of the target duplex as acceptor. There was full protection from OsO(4)-bipyridine modification of thymines in the probe strand of the triplex, in accordance with the presumed triplex formation, which excluded displacement of the homologous duplex strand by the probe-intercalator conjugate. The implications of these results for the existence of protein-independent parallel triplexes are discussed.
Collapse
Affiliation(s)
- A K Shchyolkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Science, 117984 Moscow, Russia.
| | | | | | | | | | | |
Collapse
|
4
|
Bertucat G, Lavery R, Prévost C. A molecular model for RecA-promoted strand exchange via parallel triple-stranded helices. Biophys J 1999; 77:1562-76. [PMID: 10465767 PMCID: PMC1300444 DOI: 10.1016/s0006-3495(99)77004-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
A number of studies have concluded that strand exchange between a RecA-complexed DNA single strand and a homologous DNA duplex occurs via a single-strand invasion of the minor groove of the duplex. Using molecular modeling, we have previously demonstrated the possibility of forming a parallel triple helix in which the single strand interacts with the intact duplex in the minor groove, via novel base interactions (Bertucat et al., J. Biomol. Struct. Dynam. 16:535-546). This triplex is stabilized by the stretching and unwinding imposed by RecA. In the present study, we show that the bases within this triplex are appropriately placed to undergo strand exchange. Strand exchange is found to be exothermic and to result in a triple helix in which the new single strand occupies the major groove. This structure, which can be equated to so-called R-form DNA, can be further stabilized by compression and rewinding. We are consequently able to propose a detailed, atomic-scale model of RecA-promoted strand exchange. This model, which is supported by a variety of experimental data, suggests that the role of RecA is principally to prepare the single strand for its future interactions, to guide a minor groove attack on duplex DNA, and to stabilize the resulting, stretched triplex, which intrinsically favors strand exchange. We also discuss how this mechanism can incorporate homologous recognition.
Collapse
Affiliation(s)
- G Bertucat
- Laboratoire de Biochimie Théorique, CNRS UPR 9080, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | | | | |
Collapse
|
5
|
Kosikov KM, Gorin AA, Zhurkin VB, Olson WK. DNA stretching and compression: large-scale simulations of double helical structures. J Mol Biol 1999; 289:1301-26. [PMID: 10373369 DOI: 10.1006/jmbi.1999.2798] [Citation(s) in RCA: 119] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Computer-simulated elongation and compression of A - and B -DNA structures beyond the range of thermal fluctuations provide new insights into high energy "activated" forms of DNA implicated in biochemical processes, such as recombination and transcription. All-atom potential energy studies of regular poly(dG).poly(dC) and poly(dA).poly(dT) double helices, stretched from compressed states of 2.0 A per base-pair step to highly extended forms of 7.0 A per residue, uncover four different hyperfamilies of right-handed structures that differ in mutual base-pair orientation and sugar-phosphate backbone conformation. The optimized structures embrace all currently known right-handed forms of double-helical DNA identified in single crystals as well as non-canonical forms, such as the original "Watson-Crick" duplex with trans conformations about the P-O5' and C5'-C4' backbone bonds. The lowest energy minima correspond to canonical A and B -form duplexes. The calculations further reveal a number of unusual helical conformations that are energetically disfavored under equilibrium conditions but become favored when DNA is highly stretched or compressed. The variation of potential energy versus stretching provides a detailed picture of dramatic conformational changes that accompany the transitions between various families of double-helical forms. In particular, the interchanges between extended canonical and non-canonical states are reminiscent of the cooperative transitions identified by direct stretching experiments. The large-scale, concerted changes in base-pair inclination, brought about by changes in backbone and glycosyl torsion angles, could easily give rise to the observed sharp increase in force required to stretch single DNA molecules more than 1.6-1.65 times their canonical extension. Our extended duplexes also help to tie together a number of previously known structural features of the RecA-DNA complex and offer a self-consistent stereochemical model for the single-stranded/duplex DNA recognition brought in register by recombination proteins. The compression of model duplexes, by contrast, yields non-canonical structures resembling the deformed steps in crystal complexes of DNA with the TATA-box binding protein (TBP). The crystalline TBP-bound DNA steps follow the calculated compression-elongation pattern of an unusual "vertical" duplex with base planes highly inclined with respect to the helical axis, exposed into the minor groove, and accordingly accessible for recognition.Significantly, the double helix can be stretched by a factor of two and compressed roughly in half before its computed internal energy rises sharply. The energy profiles show that DNA extension-compression is related not only to the variation of base-pair Rise but also to concerted changes of Twist, Roll, and Slide. We suggest that the high energy "activated" forms calculated here are critical for DNA processing, e.g. nucleo-protein recognition, DNA/RNA synthesis, and strand exchange.
Collapse
Affiliation(s)
- K M Kosikov
- Department of Chemistry, Rutgers, the State University of New Jersey, Wright-Rieman Laboratories, 610 Taylor Road, Piscataway, NJ, 08854-8087, USA
| | | | | | | |
Collapse
|
6
|
Bertucat G, Lavery R, Prévost C. A model for parallel triple helix formation by RecA: single-single association with a homologous duplex via the minor groove. J Biomol Struct Dyn 1998; 16:535-46. [PMID: 10052612 DOI: 10.1080/07391102.1998.10508268] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The nucleoproteic filaments of RecA polymerized on single stranded DNA are able to integrate double stranded DNA in a coaxial arrangement (with DNA stretched by a factor 1.5), to recognize homologous sequences in the duplex and to perform strand exchange between the single stranded and double stranded molecules. While experimental results favor the hypothesis of an invasion of the minor groove of the duplex by the single strand, parallel minor groove triple helices have never been isolated or even modeled, the minor groove offering little space for a third strand to interact. Based on an internal coordinate modeling study, we show here that such a structure is perfectly conceivable when the two interacting oligomers are stretched by a factor 1.5, in order to open the minor groove of the duplex. The model helix presents characteristics that coincide with known experimental data on unwinding, base pair inclination and inter-proton distances. Moreover, we show that extension and unwinding stabilize the triple helix. New patterns of triplet interaction via the minor groove are presented.
Collapse
Affiliation(s)
- G Bertucat
- Laboratoire de Biochimie Théorique, UPR 9080, Institut de Biologie Physico-Chimique, Paris, France
| | | | | |
Collapse
|
7
|
Nishinaka T, Shinohara A, Ito Y, Yokoyama S, Shibata T. Base pair switching by interconversion of sugar puckers in DNA extended by proteins of RecA-family: a model for homology search in homologous genetic recombination. Proc Natl Acad Sci U S A 1998; 95:11071-6. [PMID: 9736691 PMCID: PMC21597 DOI: 10.1073/pnas.95.19.11071] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Escherichia coli RecA is a representative of proteins from the RecA family, which promote homologous pairing and strand exchange between double-stranded DNA and single-stranded DNA. These reactions are essential for homologous genetic recombination in various organisms. From NMR studies, we previously reported a novel deoxyribose-base stacking interaction between adjacent residues on the extended single-stranded DNA bound to RecA protein. In this study, we found that the same DNA structure was induced by the binding to Saccharomyces cerevisiae Rad51 protein, indicating that the unique DNA structure induced by the binding to RecA-homologs was conserved from prokaryotes to eukaryotes. On the basis of this structure, we have formulated the structure of duplex DNA within filaments formed by RecA protein and its homologs. Two types of molecular structures are presented. One is the duplex structure that has the N-type sugar pucker. Its helical pitch is approximately 95 A (18.6 bp/turn), corresponding to that of an active, or ATP-form of the RecA filament. The other is one that has the S-type sugar pucker. Its helical pitch is approximately 64 A (12.5 bp/turn), corresponding to that of an inactive, or ADP-form of the RecA filament. During this modeling, we found that the interconversion of sugar puckers between the N-type and the S-type rotates bases horizontally, while maintaining the deoxyribose-base stacking interaction. We propose that this base rotation enables base pair switching between double-stranded DNA and single-stranded DNA to take place, facilitating homologous pairing and strand exchange. A possible mechanism for strand exchange involving DNA rotation also is discussed.
Collapse
Affiliation(s)
- T Nishinaka
- Cellular and Molecular Biology Laboratory, The Institute of Physical and Chemical Research (RIKEN), Saitama 351-0198, Japan
| | | | | | | | | |
Collapse
|
8
|
Kiran MR, Bansal M. Sequence-independent recombination triple helices: a molecular dynamics study. J Biomol Struct Dyn 1997; 15:333-45. [PMID: 9399159 DOI: 10.1080/07391102.1997.10508196] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Recent experimental studies have shown that the Rec-A mediated homologous recombination reaction involves a triple helical intermediate, in which the third strand base forms hydrogen bonds with both the bases in the major groove of the Watson-Crick duplex. Such 'mixed' hydrogen bonds allow formation of sequence independent triplexes. DNA triple helices involving 'mixed' hydrogen bonds have been studied, using model building, molecular mechanics (MM) and molecular dynamics (MD). Models were built for a triplex comprising all four possible triplets viz., G.C*C, C.G*G, A.T*T and T.A*A. To check the stability of all the 'mixed' hydrogen bonds in such triplexes and the conformational preferences of such triplex structures, MD studies were carried out starting from two structures with 30 degrees and 36 degrees twist between the basepairs. It was observed that though the two triplexes converged towards a similar structure, the various hydrogen bonds between the WC duplex and the third strand showed differential stabilities. An MD simulation with restrained hydrogen bonds showed that the resulting structure was stable and remained close to the starting structure. These studies help us in defining stable hydrogen bond geometries involving the third strand and the WC duplex. It was observed that in the C.G*G triplets the N7 atom of the second strand is always involved in hydrogen bonding. In the G.C*C triplets, either N3 or O2 in the third strand cytosine can interchangeably act as a hydrogen bond acceptor.
Collapse
Affiliation(s)
- M R Kiran
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | | |
Collapse
|
9
|
Dagneaux C, Gousset H, Shchyolkina AK, Ouali M, Letellier R, Liquier J, Florentiev VL, Taillandier E. Parallel and antiparallel A*A-T intramolecular triple helices. Nucleic Acids Res 1996; 24:4506-12. [PMID: 8948642 PMCID: PMC146268 DOI: 10.1093/nar/24.22.4506] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Intramolecular triple helices have been obtained by folding back twice oligonucleotides formed by decamers bound by non-nucleotide linkers: dA10-linker-dA10-linker-dT10 and dA10-linker-dT10-linker-dA10. We have thus prepared two triple helices with forced third strand orientation, respectively antiparallel (apA*A-T) and parallel (pA*A-T) with respect to the adenosine strand of the Watson-Crick duplex. The existence of the triple helices has been shown by FTIR, UV and fluorescence spectroscopies. Similar melting temperatures have been obtained in very different oligomer concentration conditions (micromolar solutions for thermal denaturation classically followed by UV spectroscopy, milimolar solutions in the case of melting monitored by FTIR spectroscopy) showing that the triple helices are intramolecular. The stability of the parallel triplex is found to be slightly lower than that of the antiparallel (deltaT(m) = 6 degrees C). The sugar conformations determined by FTIR are different for both triplexes. Only South-type sugars are found in the antiparallel triplex whereas both South- and North-type sugars are detected in the parallel triplex. In this case, thymidine sugars have a South-type geometry, and the adenosine strand of the Watson-Crick duplex has North-type sugars. For the antiparallel triplex the experimental results and molecular modeling data are consistent with a reverse-Hoogsteen like third-strand base pairing and South-type sugar conformation. An energetically optimized model of the parallel A*A-T triple helix with a non-uniform distribution of sugar conformations is discussed.
Collapse
Affiliation(s)
- C Dagneaux
- Laboratoire CSSB - URA CNRS 1430, UFR de Santé-Médecine-Biologie-Humaine, Université Paris XIII, Bobigny, France
| | | | | | | | | | | | | | | |
Collapse
|
10
|
Balatskaya SV, Belotserkovskii BP, Johnston BH. Alternate-strand triplex formation: modulation of binding to matched and mismatched duplexes by sequence choice in the Pu-Pu-Py block. Biochemistry 1996; 35:13328-37. [PMID: 8873599 DOI: 10.1021/bi961405s] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
In double-stranded DNA, tandem blocks of purines (Pu) and pyrimidines (Py) can form triplexes by pairing with oligonucleotides which also consist of blocks of purines and pyrimidines, using both Py.Pu.Py (Y-type) and Pu.Pu.Py (R-type) pairing motifs in a scheme called "alternate-strand recognition," or ASR [Jayasena, S. D., & Johnston, B. H. (1992) Biochemistry 31, 320-327; Beal P. A., & Dervan, P. B. (1992) J. Am. Chem. Soc. 114, 1470-1478]. We investigated the relative contributions of the Py.Pu.Py and Pu.Pu.Py blocks in the 16-bp duplex sequence 5'-AAGGAGAATTCCCTCT-3' paired with the third-strand oligonucleotides 5'-TTCCTCTTXXGGGZGZ-3' (XZ-16), where X and Z are either T or A and C is 5-methylcytosine, using chemical footprinting and get electrophoretic mobility shift measurements. We found that the left-hand, pyrimidine half (Y-block) of the third strand (TTCCTCTT, Y-8) forms a Py.Pu.Py triplex as detected by both dimethyl sulfate (DMS) probing and a gel-shift assay; in contrast, the triplex formed by the right-hand half alone (R-block) with X = T (TTGGGTGT, R-8) is not detectable under the conditions tested. However, when tethered to the Y-block (i.e., as XZ-16), the R-block contributes greatly increased specificity of target recognition and confers protection from DMS onto the duplex even under conditions unfavorable for Pu-Pu-Py triplexes (lack of divalent cations). In general, the 16-mer (XZ-16) can bind with apparent strength either greater or lesser than Y-8, depending on whether X and Z are A or T. The order of apparent binding strength, as measured by the target duplex concentration necessary to cause retardation of the third strand during gel electrophoresis, is TT-16 approximately AT-16 > Y-8 > AA-16 > TA-16. Chemical probing experiments showed that both halves of the triplex form even for AA-16, which binds with less apparent binding strength than the pyrimidine block alone (Y-8). The presence of the right half of the 16-mers, although detracting from affinity in cases of AA-16 and TA-16, provides strong specificity for the correct target compared to a target incapable of forming the Pu.Pu.Py part of the triplex. We discuss possible explanations for these observations in terms of alternate oligonucleotide conformations and suggest practical applications of affinity modulation by A-to-T replacements.
Collapse
Affiliation(s)
- S V Balatskaya
- Cell and Molecular Biology Laboratory, SRI International, Mento Park, California 94025, USA
| | | | | |
Collapse
|