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ABSTRACT: Human ADAR1, which has two left-handed Z-DNA binding domains, preferentially binds Z-DNA rather than B-DNA with a high binding affinity. Z-DNA can be induced in long genomic DNA by Z-DNA binding proteins through the formation of two B-Z junctions with the extrusion of one base pair from each junction. We performed NMR experiments on complexes of Zα(ADAR1) with three DNA duplexes at a variety of protein-to-DNA molar ratios. This study confirmed that the Zα(ADAR1) first binds to an 8-bp CG-rich DNA segment via a unique conformation during B-Z transition and the neighboring AT-rich region becomes destabilized. We also found that, when DNA duplexes have only 6-bp CG-rich segment, the interaction with Zα(ADAR1) did not affect the thermal stabilities of the 6-bp CG-rich segment as well as the neighboring two A·T base pairs. These results indicate that four Zα(ADAR1) proteins interact with the 8-bp DNA sequence containing a 6-bp CG-repeat segment as well as a dinucleotide step, even though the dinucleotid step contains A∙T base pairs. Thus this study suggests that the length of the CG-rich region is more important than the specific DNA sequence for determining which base-pair is extruded from the B-Z junction structure. This study also found that the Zα(ADAR1) in complex with a 11-bp DNA duplex exhibits a Z-DNA-bound conformation distinct from that of free Zα(ADAR1) and the initial contact conformations of Zα(ADAR1) complexed with 13-bp DNA duplexes.
Biophysical chemistry 12/2012; 172C:18-25. · 2.28 Impact Factor
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ABSTRACT: The Z-DNA binding domain of human ADAR1 (Zα(ADAR1)) preferentially binds Z-DNA rather than B-DNA with high binding affinity. Here, we have carried out chemical shift perturbation and backbone dynamics studies of Zα(ADAR1) in the free form and in complex with three DNA duplexes, d(CGCGCG)(2), d(CACGTG)(2), and d(CGTACG)(2). This study reveals that Zα(ADAR1) initially binds to d(CGCGCG)(2) through the distinct conformation, especially in the unusually flexible β1-loop-α2 region, from the d(CGCGCG)(2)-(Zα(ADAR1))(2) complex. This study also suggests that Zα(ADAR1) exhibits a distinct conformational change during the B-Z transition of non-CG-repeat DNA duplexes with low binding affinities compared to the CG-repeat DNA duplex.
Biochemical and Biophysical Research Communications 10/2012; · 2.48 Impact Factor
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ABSTRACT: Z-DNA is produced in a long genomic DNA by Z-DNA binding proteins, through formation of two B-Z junctions with the extrusion of one base pair from each junction. To answer the question of how Z-DNA binding proteins induce B-Z transitions in CG-rich segments while maintaining the B-conformation of surrounding segments, we investigated the kinetics and thermodynamics of base-pair openings of a 13-bp DNA in complex with the Z-DNA binding protein, Zα(ADAR1). We also studied perturbations in the backbone of Zα(ADAR1) upon binding to DNA. Our study demonstrates the initial contact conformation as an intermediate structure during B-Z junction formation induced by Zα(ADAR1), in which the Zα(ADAR1) protein displays unique backbone conformational changes, but the 13-bp DNA duplex maintains the B-form helix. We also found the unique structural features of the 13-bp DNA duplex in the initial contact conformation: (i) instability of the AT-rich region II and (ii) longer lifetime for the opening state of the CG-rich region I. Our findings suggest a three-step mechanism of B-Z junction formation: (i) Zα(ADAR1) specifically interacts with a CG-rich DNA segment maintaining B-form helix via a unique conformation; (ii) the neighboring AT-rich region becomes very unstable, and the CG-rich DNA segment is easily converted to Z-DNA; and (iii) the AT-rich regions are base-paired again, and the B-Z junction structure is formed.
Journal of the American Chemical Society 03/2012; 134(11):5276-83. · 9.91 Impact Factor
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ABSTRACT: G-quadruplexes, formed of four stranded guanine bases stabilized by monovalent cations, serve important role in cancer cell growth and control gene expression in telomere. Since there are various types of quadruplex structures, rapid and simple screening methods with high selectivity, sensitivity and nontoxicity are required for understanding about the biological roles of quadruplex DNA as well as in designing therapeutics. Herein, we report a pyrene-imidazolium derivative, JY-1, which can with high selectivity recognize G-quadruplex using fluorescence and NMR spectroscopy. This is the first example based on the imidazolium derivative, which can detect the G-quadruplex directly to utilize the excimer/monomer emission change in pyrene fluorophore. The selectivity of strong binding to a specific sequence can allow for quadruplex sensing and the detection method presented here is very simple, using fluorescence and NMR study. Also, the groove binding characteristic of JY-1 to the G-quadruplex has a relatively low nonspecific toxicity and the structure-specific differences in fluorescent character between DNA duplex and G-quadruplex may offer more discovery and application in biological study.
Biomaterials 12/2011; 33(7):2282-8. · 7.40 Impact Factor
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ABSTRACT: Peptide nucleic acids (PNA) are one of the most widely used synthetic DNA mimics where the four bases are attached to a N-(2-aminoethyl)glycine (aeg) backbone instead of the negative-charged phosphate backbone in DNA. We have developed a chimeric PNA (chiPNA), in which a chiral GNA-like γ(3)T monomer is incorporated into aegPNA backbone. The base pair opening kinetics of the aegPNA:DNA and chiPNA:DNA hybrid duplexes were studied by NMR hydrogen exchange experiments. This study revealed that the aegPNA:DNA hybrid is much more stable duplex and is less dynamic compared to DNA duplex, meaning that base pairs are opened and reclosed much more slowly. The site-specific incorporation of γ(3)T monomer in the aegPNA:DNA hybrid can destabilize a specific base pair and its neighbors, maintaining the thermal stabilities and dynamic properties of other base pairs. Our hydrogen exchange study firstly revealed the unique kinetic features of base pairs in the aegPNA:DNA and chiPNA:DNA hybrids, which will provide an insight into the development of methodology for specific DNA recognition using PNA fragments.
Nucleic Acids Research 05/2011; 39(16):7329-35. · 8.03 Impact Factor
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Chemistry - An Asian Journal 04/2011; 6(8):1996-9. · 4.50 Impact Factor
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ABSTRACT: The human DNA-dependent activator of IFN-regulatory factor (DAI) protein, which activates the innate immune response in response to DNA, contains two tandem Z-DNA binding domains (Zα and Zβ) at the NH(2) terminus. The hZβ(DAI) structure is similar to other Z-DNA binding proteins, although it demonstrates an unusual Z-DNA recognition. We performed NMR experiments on complexes of hZβ(DAI) with DNA duplex, d(CGCGCG)(2), at a variety of protein-to-DNA molar ratios. The results suggest that hZβ(DAI) binds to Z-DNA via an active-di B-Z transition mechanism, where two hZβ(DAI) proteins bind to B-DNA to form the hZβ(DAI)-B-DNA complex; the B-DNA is subsequently converted to left-handed Z-DNA. This novel mechanism of DNA binding and B-Z conversion is distinct from Z-DNA binding of the human ADAR1 protein.
FEBS letters 02/2011; 585(5):772-8. · 3.54 Impact Factor
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ABSTRACT: The Yaba-like disease viruses (YLDV) are members of the Yatapoxvirus family and have double-stranded DNA genomes. The E3L protein, which is essential for pathogenesis in the vaccinia virus, consists of two domains: an N-terminal Z-DNA binding domain and a C-terminal RNA binding domain. The crystal structure of the E3L orthologue of YLDV (yabZα(E3L)) bound to Z-DNA revealed that the overall structure of yabZα(E3L) and its interaction with Z-DNA are very similar to those of hZα(ADAR1). Here we have performed NMR hydrogen exchange experiments on the complexes between yabZα(E3L) and d(CGCGCG)(2) with a variety of protein-to-DNA molar ratios. This study revealed that yabZα(E3L) could efficiently change the B-form helix of the d(CGCGCG)(2) to left-handed Z-DNA via the active-mono B-Z transition pathway like hZα(ADAR1).
FEBS letters 10/2010; 584(21):4453-7. · 3.54 Impact Factor
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ABSTRACT: In Escherichia coli, the very short patch (VSP) repair system is a major pathway for removal of T.G mismatches in Dcm target sequences. In the VSP repair pathway, the very short patch repair (Vsr) endonuclease selectively recognizes a T.G mismatch in Dcm target sequences and hydrolyzes the 5'-phosphate group of the mismatched thymine. The hydrogen exchange NMR studies here revealed that the T5.G18 mismatch in the Dcm target sequence significantly stabilizes own base pair but destabilizes the two neighboring G4.C19 and A6.T17 base pairs compare to other T.G mismatches. These unusual patterns of base pair stability in the Dcm target sequence can explain how the Vsr endonuclease specifically recognizes the mismatched Dcm target sequence and intercalates into the DNA.
Archives of Biochemistry and Biophysics 09/2010; 501(2):201-6. · 2.93 Impact Factor
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ABSTRACT: The Zα domain of human ADAR1 (Zα(ADAR1)) preferentially binds Z-DNA rather than B-DNA with high binding affinity. Zα(ADAR1) binds to the Z-conformation of both non-CG-repeat DNA duplexes and a d(CGCGCG)(2) duplex similarly. We performed NMR experiments on complexes between the Zα(ADAR1) and non-CG-repeat DNA duplexes, d(CACGTG)(2) or d(CGTACG)(2), with a variety of protein-DNA molar ratios. Comparison of these results with those from the analysis of d(CGCGCG)(2) in the previous study suggests that Zα(ADAR1) exhibits the sequence preference of d(CGCGCG)(2)≫d(CACGTG)(2)>d(CGTACG)(2) through multiple sequence discrimination steps during the B-Z transition.
FEBS letters 09/2010; 584(20):4344-50. · 3.54 Impact Factor
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Automatica. 01/2010; 46:1806-1811.
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ABSTRACT: The human RNA editing enzyme ADAR1 (double-stranded RNA deaminase I) deaminates adenine in pre-mRNA to yield inosine, which codes as guanine. ADAR1 has two left-handed Z-DNA binding domains, Z alpha and Z beta, at its NH(2)-terminus and preferentially binds Z-DNA, rather than B-DNA, with high binding affinity. The cocrystal structure of Z alpha(ADAR1) complexed to Z-DNA showed that one monomeric Z alpha(ADAR1) domain binds to one strand of double-stranded DNA and a second Z alpha(ADAR1) monomer binds to the opposite strand with 2-fold symmetry with respect to DNA helical axis. It remains unclear how Z alpha(ADAR1) protein specifically recognizes Z-DNA sequence in a sea of B-DNA to produce the stable Z alpha(ADAR1)-Z-DNA complex during the B-Z transition induced by Z alpha(ADAR1). In order to characterize the molecular recognition of Z-DNA by Z alpha(ADAR1), we performed circular dichroism (CD) and NMR experiments with complexes of Zalpha(ADAR1) bound to d(CGCGCG)(2) (referred to as CG6) produced at a variety of protein-to-DNA molar ratios. From this study, we identified the intermediate states of the CG6-Z alpha(ADAR1) complex and calculated their relative populations as a function of the Z alpha(ADAR1) concentration. These findings support an active B-Z transition mechanism in which the Z alpha(ADAR1) protein first binds to B-DNA and then converts it to left-handed Z-DNA, a conformation that is then stabilized by the additional binding of a second Z alpha(ADAR1) molecule.
Journal of the American Chemical Society 08/2009; 131(32):11485-91. · 9.91 Impact Factor
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ABSTRACT: The cyclobutane pyrimidine dimer (CPD) is one of the major classes of cytotoxic and carcinogenic DNA photoproducts induced by UV light. Hydrogen exchange rates of the imino protons were measured for various CPD-containing DNA duplexes to better understand the mechanism for CPD recognition by XPC-hHR23B. The results here revealed that double T.G mismatches in a CPD lesion significantly destabilized six consecutive base pairs compared to other DNA duplexes. This flexibility in a DNA duplex caused at the CPD lesions with double T.G mismatches might be the key factor for damage recognition by XPC-hHR23B.
FEBS letters 06/2009; 583(12):2037-41. · 3.54 Impact Factor
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ABSTRACT: Methylation of DNA plays a regulatory role in DNA metabolism. The Escherichia coli DNA adenine methyltransferase methylates the N6 positions of adenines in the sequence 5'-GATC-3', which exists in the fully methylated state during most of the cell cycle. Just after DNA replication, however, the GATC sites transiently become hemimethylated, a condition that is indispensable for various cellular processes, such as negative modulation of replication initiation at oriC by SeqA. The lack of structural and dynamic information on DNA duplexes that contain fully methylated GATC sites makes it difficult to explain how hemimethylated GATC sites are recognized in vivo by proteins in a sea of fully methylated ones. Here, we used NMR spectroscopy to characterize the solution structure of a dodecamer DNA duplex that contained a fully methylated GATC site and the dynamics of the unmethylated, hemimethylated, and fully methylated GATC duplexes. Only the hemimethylated GATC duplex displays a unique major groove conformation, which is optimized for entrance into the cleft structure of SeqA. The apparent equilibrium constants for base-pair opening of the three differentially methylated GATC duplexes revealed that N6-methylation of the adenine residue affects the thermodynamics and kinetics of its own and neighboring base pairs. The equilibrium constants for base-pair opening of three GATC duplexes were determined using proton exchange catalyzed by TRIS. The two G.C base pairs of the hemimethylated GATC duplex displayed a faster base-pair opening rate and required less energy for the base-pair opening reaction than did those of the fully methylated one.
Journal of the American Chemical Society 01/2009; 130(52):17688-96. · 9.91 Impact Factor
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ABSTRACT: In this paper, the bounds of allowable parameter variations in the LQG regulator for fixed weighting matrices are obtained and the asymptotic properties of these bounds with respect to weighting matrices are analysed. It is shown that the guaranteed bounds of allowable parameter variations, which are independent of weighting matrices, are often small but not necessarily small under some conditions. It is also shown that under some conditions, the allowable bounds of the LQG regulator can become as large as those of the LQ regulator. In addition, a loop transfer recovery method for perturbed systems is derived under which the LQG regulator may possess the same robustness as the LQ regulator. Examples are given to validate these results.
International Journal of Robust and Nonlinear Control 03/2007; 1(1):33 - 42. · 1.55 Impact Factor
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ABSTRACT: In this note, sufficient conditions for H<sub>∞</sub> output feedback stabilization of linear discrete-time systems are proposed via linear matrix inequalities (LMIs). In order to reduce conservatism existing in earlier LMI methods, auxiliary slack variables with structure are employed. It is shown that degree of freedoms by the introduction of auxiliary slack variables lead to more flexibility in obtaining an approximate solution of H<sub>∞</sub> output feedback stabilization problems. Consequently, the proposed method can yield a less conservative result than earlier LMI methods. In particular, typical output feedback control problems, such as decentralized H<sub>∞</sub> output feedback control and simultaneous H<sub>∞</sub> output feedback control, can be more efficiently solved. Numerical examples are included to illustrate the advantages of the proposed LMI method.
IEEE Transactions on Automatic Control 05/2006; · 2.11 Impact Factor
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Journal of Biomolecular NMR 10/2005; 33(1):75. · 3.61 Impact Factor
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ABSTRACT: Replication protein A (RPA) is a three-subunit complex with multiple roles in DNA metabolism. DNA-binding domain A in the large subunit of human RPA (hRPA70A) binds to single-stranded DNA (ssDNA) and is responsible for the species-specific RPA-T antigen (T-ag) interaction required for Simian virus 40 replication. Although Saccharomyces cerevisiae RPA70A (scRPA70A) shares high sequence homology with hRPA70A, the two are not functionally equivalent. To elucidate the similarities and differences between these two homologous proteins, we determined the solution structure of scRPA70A, which closely resembled the structure of hRPA70A. The structure of ssDNA-bound scRPA70A, as simulated by residual dipolar coupling-based homology modeling, suggested that the positioning of the ssDNA is the same for scRPA70A and hRPA70A, although the conformational changes that occur in the two proteins upon ssDNA binding are not identical. NMR titrations of hRPA70A with T-ag showed that the T-ag binding surface is separate from the ssDNA-binding region and is more neutral than the corresponding part of scRPA70A. These differences might account for the species-specific nature of the hRPA70A-T-ag interaction. Our results provide insight into how these two homologous RPA proteins can exhibit functional differences, but still both retain their ability to bind ssDNA.
Nucleic Acids Research 02/2005; 33(13):4172-81. · 8.03 Impact Factor
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ABSTRACT: In this note, sufficient LMI conditions for the H<sub>∞</sub> output feedback control design of linear discrete-time systems are proposed. In order to reduce conservatism existing in earlier sufficient LMI methods, auxiliary slack variables with structure are employed. It is shown that the slack variables employed in this note provide additional flexibility in solving the H<sub>∞</sub> output feedback control problem. Consequently, the proposed method can yield a less conservative result than that of earlier LMI methods. In particular, typical output feedback control problems, such as decentralized H<sub>∞</sub> output feedback control and simultaneous H<sub>∞</sub> output feedback control, can be more efficiently solved. Numerical examples are included to illustrate the advantages of the proposed LMI method.
Decision and Control, 2004. CDC. 43rd IEEE Conference on; 01/2005
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ABSTRACT: In this paper, a nonlinear minimization approach is proposed for multiobjective and structured controls for discrete-time systems. The problem of finding multiobjective and structured controls for discrete-time systems is represented as a quadratic matrix inequality problem. It is shown that the problem is reduced to a nonlinear minimization problem that has a concave objective function and linear matrix inequality constraints. An algorithm for the nonlinear minimization problem is proposed, which is easily implemented with existing semidefinite programming algorithms. The validity of the proposed algorithm is illustrated by comparisons with existing methods. In addition, applications of this work are demonstrated via numerical examples. Copyright © 2004 John Wiley & Sons, Ltd.
International Journal of Robust and Nonlinear Control 08/2004; 14(16):1327 - 1343. · 1.55 Impact Factor
