The Experts below are selected from a list of 9978 Experts worldwide ranked by ideXlab platform
Shrikant Kukreti - One of the best experts on this subject based on the ideXlab platform.
-
differential structural status of the rna counterpart of an undecamer quasi Palindromic DNA sequence present in lcr of human β globin gene cluster
Journal of Biomolecular Structure & Dynamics, 2015Co-Authors: Mahima Kaushik, Shrikant KukretiAbstract:Our previous work on structural polymorphism shown at a single nucleotide polymorphism (SNP) (A→G) site located on HS4 region of locus control region (LCR) of β-globin gene has established a hairpin→duplex equilibrium corresponding to A→B like DNA transition (Kaushik M, Kukreti, R., Grover, D., Brahmachari, S.K. and Kukreti S. Nucleic Acids Res. 2003; Kaushik M, Kukreti S. Nucleic Acids Res. 2006). The G-allele of A→G SNP has been shown to be significantly associated with the occurrence of β-thalassemia. Considering the significance of this 11-nt long quasi-Palindromic sequence [5′-TGGGG(G/A)CCCCA; HP(G/A)11] of β-globin gene LCR, we further explored the differential behavior of the same DNA sequence with its RNA counterpart, using various biophysical and biochemical techniques. In contrast to its DNA counterpart exhibiting a A→B structural transition and an equilibrium between duplex and hairpin forms, the studied RNA oligonucleotide sequence [5′-UGGGG(G/A)CCCCA; RHP(G/A)11] existed only in duplex form (...
-
differential structural status of the rna counterpart of an undecamer quasi Palindromic DNA sequence present in lcr of human β globin gene cluster
Journal of Biomolecular Structure & Dynamics, 2015Co-Authors: Mahima Kaushik, Shrikant KukretiAbstract:Our previous work on structural polymorphism shown at a single nucleotide polymorphism (SNP) (A→G) site located on HS4 region of locus control region (LCR) of β-globin gene has established a hairpi...
Francois Heslot - One of the best experts on this subject based on the ideXlab platform.
-
mechanically controlled DNA extrusion from a Palindromic sequence by single molecule micromanipulation
Physical Review Letters, 2006Co-Authors: Alexandre Dawid, Camille Breme, Fabien Guillemot, Vincent Croquette, Francois HeslotAbstract:A magnetic tweezers setup is used to control both the stretching force and the relative linking number $\ensuremath{\Delta}\mathrm{Lk}$ of a Palindromic DNA molecule. We show here, in absence of divalent ions, that twisting negatively the molecule while stretching it at $\ensuremath{\sim}1\text{ }\text{ }\mathrm{pN}$ induces the formation of a cruciform DNA structure. Furthermore, once the cruciform DNA structure is formed, the extrusion of several kilo-base pairs of Palindromic DNA sequence is directly and reversibly controlled by varying $\ensuremath{\Delta}\mathrm{Lk}$. Indeed the branch point behaves as a nanomechanical gear that links rotation with translation, a feature related to the helicity of DNA. We obtain experimentally a very good linear relationship between the extension of the molecule and $\ensuremath{\Delta}\mathrm{Lk}$. We use then this experiment to obtain a precise measurement of the pitch of B-DNA in solution : $3.61\ifmmode\pm\else\textpm\fi{}0.03$ nm/turn.
-
mechanically controlled DNA extrusion from a Palindromic sequence by single molecule micromanipulation
Physical Review Letters, 2006Co-Authors: Alexandre Dawid, Camille Breme, Fabien Guillemot, Vincent Croquette, Francois HeslotAbstract:A magnetic tweezers setup is used to control both the stretching force and the relative linking number DeltaLk of a Palindromic DNA molecule. We show here, in absence of divalent ions, that twisting negatively the molecule while stretching it at approximately 1 pN induces the formation of a cruciform DNA structure. Furthermore, once the cruciform DNA structure is formed, the extrusion of several kilo-base pairs of Palindromic DNA sequence is directly and reversibly controlled by varying DeltaLk. Indeed the branch point behaves as a nanomechanical gear that links rotation with translation, a feature related to the helicity of DNA. We obtain experimentally a very good linear relationship between the extension of the molecule and DeltaLk. We use then this experiment to obtain a precise measurement of the pitch of B-DNA in solution: 3.61 +/- 0.03 nm/turn.
Mahima Kaushik - One of the best experts on this subject based on the ideXlab platform.
-
differential structural status of the rna counterpart of an undecamer quasi Palindromic DNA sequence present in lcr of human β globin gene cluster
Journal of Biomolecular Structure & Dynamics, 2015Co-Authors: Mahima Kaushik, Shrikant KukretiAbstract:Our previous work on structural polymorphism shown at a single nucleotide polymorphism (SNP) (A→G) site located on HS4 region of locus control region (LCR) of β-globin gene has established a hairpin→duplex equilibrium corresponding to A→B like DNA transition (Kaushik M, Kukreti, R., Grover, D., Brahmachari, S.K. and Kukreti S. Nucleic Acids Res. 2003; Kaushik M, Kukreti S. Nucleic Acids Res. 2006). The G-allele of A→G SNP has been shown to be significantly associated with the occurrence of β-thalassemia. Considering the significance of this 11-nt long quasi-Palindromic sequence [5′-TGGGG(G/A)CCCCA; HP(G/A)11] of β-globin gene LCR, we further explored the differential behavior of the same DNA sequence with its RNA counterpart, using various biophysical and biochemical techniques. In contrast to its DNA counterpart exhibiting a A→B structural transition and an equilibrium between duplex and hairpin forms, the studied RNA oligonucleotide sequence [5′-UGGGG(G/A)CCCCA; RHP(G/A)11] existed only in duplex form (...
-
differential structural status of the rna counterpart of an undecamer quasi Palindromic DNA sequence present in lcr of human β globin gene cluster
Journal of Biomolecular Structure & Dynamics, 2015Co-Authors: Mahima Kaushik, Shrikant KukretiAbstract:Our previous work on structural polymorphism shown at a single nucleotide polymorphism (SNP) (A→G) site located on HS4 region of locus control region (LCR) of β-globin gene has established a hairpi...
Lin Chen - One of the best experts on this subject based on the ideXlab platform.
-
mechanism of forkhead transcription factors binding to a novel Palindromic DNA site
Nucleic Acids Research, 2021Co-Authors: Shuyan Dai, Xiaojuan Chen, Xujun Liang, Longying Jiang, Ming Guo, Zhan Zhou, Hudie Wei, Huajun Zhang, Zhuchu Chen, Lin ChenAbstract:Forkhead transcription factors bind a canonical consensus DNA motif, RYAAAYA (R = A/G, Y = C/T), as a monomer. However, the molecular mechanisms by which forkhead transcription factors bind DNA as a dimer are not well understood. In this study, we show that FOXO1 recognizes a Palindromic DNA element DIV2, and mediates transcriptional regulation. The crystal structure of FOXO1/DIV2 reveals that the FOXO1 DNA binding domain (DBD) binds the DIV2 site as a homodimer. The wing1 region of FOXO1 mediates the dimerization, which enhances FOXO1 DNA binding affinity and complex stability. Further biochemical assays show that FOXO3, FOXM1 and FOXI1 also bind the DIV2 site as homodimer, while FOXC2 can only bind this site as a monomer. Our structural, biochemical and bioinformatics analyses not only provide a novel mechanism by which FOXO1 binds DNA as a homodimer, but also shed light on the target selection of forkhead transcription factors.
-
an asymmetric nfat1 dimer on a pseudo Palindromic κb like DNA site
Nature Structural & Molecular Biology, 2003Co-Authors: Lei Jin, Lin Chen, Piotr Sliz, Fernando Macian, Anjana Rao, Patrick G Hogan, Stephen C HarrisonAbstract:The crystal structure of the NFAT1 Rel homology region (RHR) bound to a pseudo-Palindromic DNA site reveals an asymmetric dimer interaction between the RHR-C domains, unrelated to the contact seen in Rel dimers such as NF kappa B. Binding studies with a form of the NFAT1 RHR defective in the dimer contact show loss of cooperativity and demonstrate that the same interaction is present in solution. The structure we have determined may correspond to a functional NFAT binding mode at Palindromic sites of genes induced during the anergic response to weak TCR signaling.
Jean Swings - One of the best experts on this subject based on the ideXlab platform.
-
flavobacterium fryxellicola sp nov and flavobacterium psychrolimnae sp nov novel psychrophilic bacteria isolated from microbial mats in antarctic lakes
International Journal of Systematic and Evolutionary Microbiology, 2005Co-Authors: Stefanie Van Trappen, Joris Mergaert, Ilse Vandecandelaere, Jean SwingsAbstract:Taxonomic studies were performed on seven strains isolated from microbial mats in Antarctic lakes of the McMurdo Dry Valleys. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these strains are related to the genus Flavobacterium; sequence similarity values with their nearest phylogenetic neighbours ranged from 97.0 to 98.7 %. Results of DNA-DNA hybridization and comparison of repetitive extragenic Palindromic DNA-PCR fingerprinting patterns revealed that these strains are members of two distinct species. Genotypic results, together with phenotypic characteristics, allowed these species to be differentiated from related recognized Flavobacterium species. The isolates are psychrophilic, Gram-negative, chemoheterotrophic, rod-shaped cells. Their whole-cell fatty acid profiles are similar and include C(15 : 0), C(15 : 0) anteiso, C(15 : 0) iso, C(15 : 1)omega6c, C(16 : 0) iso, C(16 : 0) iso 3-OH, C(16 : 1) iso and summed feature 3 (which comprises C(15 : 0) iso 2-OH and/or C(16 : 1)omega7c) as the major fatty acid components. On the basis of these results, two novel species are proposed: Flavobacterium fryxellicola sp. nov., consisting of three strains with LMG 22022(T) (=CIP 108325(T)) as the type strain; and Flavobacterium psychrolimnae sp. nov., consisting of four strains with LMG 22018(T) (=CIP 108326(T)) as the type strain. DNA G+C contents of F. fryxellicola and F. psychrolimnae are 35.2-35.9 and 33.8-34.5 mol%, respectively.
-
loktanella salsilacus gen nov sp nov loktanella fryxellensis sp nov and loktanella vestfoldensis sp nov new members of the rhodobacter group isolated from microbial mats in antarctic lakes
International Journal of Systematic and Evolutionary Microbiology, 2004Co-Authors: Stefanie Van Trappen, Joris Mergaert, Jean SwingsAbstract:A taxonomic study was performed on 26 strains isolated from microbial mats in Antarctic lakes of the Vestfold Hills and the McMurdo Dry Valleys. Phylogenetic analysis based on 16S rRNA gene sequences placed these strains within the Rhodobacter group of the alpha-subclass of the Proteobacteria. Sequence similarity values for the strains with their nearest phylogenetic neighbours (Jannaschia, Octadecabacter and Ketogulonicigenium) ranged between 94.0 and 95.8%. DNA-DNA hybridizations and comparison of repetitive extragenic Palindromic DNA-PCR (rep-PCR) fingerprinting patterns revealed that these strains are members of three distinct species. The isolates are Gram-negative, chemoheterotrophic, non-motile rods and their DNA G+C contents range from 59.4 to 66.4 mol%. Whole-cell fatty acid profiles are similar and the primary fatty acid in all the strains is 18 : 1 omega7c (74.1-87.7% of total). Genotypic results together with phenotypic characteristics allowed the differentiation of these species from related recognized species of the alpha-Proteobacteria and the strains are assigned to a new genus, Loktanella gen. nov., with three novel species: Loktanella salsilacus sp. nov. (type species), consisting of ten strains with LMG 21507T (=CIP 108322T) as type strain; Loktanella fryxellensis sp. nov., consisting of 12 strains with LMG 22007T (=CIP 108323T) as type strain; and Loktanella vestfoldensis sp. nov., consisting of four strains with LMG 22003T (=CIP 108321TT) as type strain.
-
flavobacterium degerlachei sp nov flavobacterium frigoris sp nov and flavobacterium micromati sp nov novel psychrophilic bacteria isolated from microbial mats in antarctic lakes
International Journal of Systematic and Evolutionary Microbiology, 2004Co-Authors: Stefanie Van Trappen, Joris Mergaert, Ilse Vandecandelaere, Jean SwingsAbstract:Taxonomic studies were performed on 36 strains that were isolated from microbial mats in Antarctic lakes of the Vestfold Hills, the Larsemann Hills and the McMurdo Dry Valleys. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these strains are related to members of the genus Flavobacterium; sequence similarity values with their nearest phylogenetic neighbours ranged from 96.8 to 98.5%. Results of DNA-DNA hybridization and comparison of repetitive extragenic Palindromic DNA-PCR fingerprinting patterns revealed that these strains are members of three distinct species. Genotypic results, together with phenotypic characteristics, allowed the differentiation of these species from related Flavobacterium species with validly published names. The isolates are Gram-negative, chemoheterotrophic, rod-shaped cells that are psychrophilic and moderately halotolerant; their DNA G+C contents range from 33.1 to 34.5 mol%. Their whole-cell fatty acid profiles are similar and include C(15:0), anteiso-C(15:0), iso-C(15:0), C(15:1)omega6c, iso-C(16:0), iso-C(16:0) 3-OH and summed feature 3 (which comprises iso-C(15:0) 2-OH, C(16:1)omega7c or both) as major fatty acid components. On the basis of these results, three novel species are proposed, namely Flavobacterium degerlachei sp. nov. (consisting of 14 strains, with LMG 21915T=DSM 15718T as the type strain), Flavobacterium micromati sp. nov. (consisting of three strains, with LMG 21919T=CIP 108161T as the type strain) and Flavobacterium frigoris sp. nov. (consisting of 19 strains, with LMG 21922T=DSM 15719T as the type strain).