A Non-Canonical Linker between Zinc Fingers 10 and 11 of Miz-1 Promotes Conformational Exchange: Implications for the Mechanism of Recognition of the Consensus DNA Sequence

2021 ◽  
Author(s):  
Olivier Boisvert ◽  
Danny Létourneau ◽  
Patrick Delattre ◽  
Cynthia Tremblay ◽  
Émilie Jolibois ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Zinc Fingers ◽  
Conformational Exchange ◽  
Mechanism Of Recognition

scholarly journals Rational design of DNA sequence-specific zinc fingers

FEBS Letters ◽  
2012 ◽  
Vol 586 (6) ◽  
pp. 918-923 ◽  
Author(s):  
Hidetoshi Kono ◽  
Miki Imanishi ◽  
Shigeru Negi ◽  
Kazuya Tatsutani ◽  
Yui Sakaeda ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Rational Design ◽  
Zinc Fingers

Solution structure of the first three zinc fingers of TFIIIA bound to the cognate DNA sequence: determinants of affinity and sequence specificity

1997 ◽  
Vol 273 (1) ◽  
pp. 183-206 ◽  
Author(s):  
Deborah S. Wuttke ◽  
Mark P. Foster ◽  
David A. Case ◽  
Joel M. Gottesfeld ◽  
Peter E. Wright
Keyword(s):  
Dna Sequence ◽  
Solution Structure ◽  
Zinc Fingers ◽  
Sequence Specificity

scholarly journals Slow motions in A·T rich DNA sequence

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
A. Ben Imeddourene ◽  
L. Zargarian ◽  
M. Buckle ◽  
B. Hartmann ◽  
O. Mauffret
Keyword(s):  
Dna Sequence ◽  
Relaxation Dispersion ◽  
Conformational Exchange ◽  
Spatial Proximity ◽  
Protein Assemblies ◽  
Base Pairs ◽  
Nmr Data ◽  
Nucleosome Formation ◽  
Nmr Methods

Abstract In free B-DNA, slow (microsecond-to-millisecond) motions that involve equilibrium between Watson–Crick (WC) and Hoogsteen (HG) base-pairing expand the DNA dynamic repertoire that could mediate DNA–protein assemblies. R1ρ relaxation dispersion NMR methods are powerful tools to capture such slow conformational exchanges in solution using 13C/15 N labelled DNA. Here, these approaches were applied to a dodecamer containing a TTAAA element that was assumed to facilitate nucleosome formation. NMR data and inferred exchange parameters assign HG base pairs as the minor, transient conformers specifically observed in three successive A·T base pairs forming the TAA·TTA segment. The abundance of these HG A·T base pairs can be up to 1.2% which is high compared to what has previously been observed. Data analyses support a scenario in which the three adenines undergo non-simultaneous motions despite their spatial proximity, thus optimising the probability of having one HG base pair in the TAA·TTA segment. Finally, revisiting previous NMR data on H2 resonance linewidths on the basis of our results promotes the idea of there being a special propensity of A·T base pairs in TAA·TTA tracts to adopt HG pairing. In summary, this study provides an example of a DNA functional element submitted to slow conformational exchange. More generally, it strengthens the importance of the role of the DNA sequence in modulating its dynamics, over a nano- to milli-second time scale.

scholarly journals Zinc Fingers 10 and 11 of Miz-1 undergo conformational exchange to achieve specific DNA binding

Structure ◽  
2021 ◽  
Author(s):  
Olivier Boisvert ◽  
Danny Létourneau ◽  
Patrick Delattre ◽  
Cynthia Tremblay ◽  
Émilie Jolibois ◽  
...  
Keyword(s):  
Dna Binding ◽  
Zinc Fingers ◽  
Conformational Exchange

scholarly journals CTCF As an Example of DNA-Binding Transcription Factors Containing Clusters of C2H2-Type Zinc Fingers

Acta Naturae ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 31-46
Author(s):  
Oksana G. Maksimenko ◽  
Dariya V. Fursenko ◽  
Elena V. Belova ◽  
Pavel G. Georgiev
Keyword(s):  
Experimental Data ◽  
Transcription Factors ◽  
Dna Binding ◽  
Characteristic Feature ◽  
Dna Sequence ◽  
Binding Sites ◽  
Zinc Fingers ◽  
Topologically Associating Domains ◽  
Key Factor

In mammals, most of the boundaries of topologically associating domains and all well-studied insulators are rich in binding sites for the CTCF protein. According to existing experimental data, CTCF is a key factor in the organization of the architecture of mammalian chromosomes. A characteristic feature of the CTCF is that the central part of the protein contains a cluster consisting of eleven domains of C2H2-type zinc fingers, five of which specifically bind to a long DNA sequence conserved in most animals. The class of transcription factors that carry a cluster of C2H2-type zinc fingers consisting of five or more domains (C2H2 proteins) is widely represented in all groups of animals. The functions of most C2H2 proteins still remain unknown. This review presents data on the structure and possible functions of these proteins, using the example of the vertebrate CTCF protein and several well- characterized C2H2 proteins in Drosophila and mammals.

DNA sequence mapping in interphase and metaphase chromosomes by fluorescence in situ hybridization

1992 ◽  
Vol 50 (1) ◽  
pp. 496-497
Author(s):  
Barbara Trask ◽  
Susan Allen ◽  
Anne Bergmann ◽  
Mari Christensen ◽  
Anne Fertitta ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Dual Band ◽  
Nick Translation ◽  
Metaphase Chromosomes ◽  
Band Pass ◽  
Texas Red ◽  
Fluorescent Spot

Using fluorescence in situ hybridization (FISH), the positions of DNA sequences can be discretely marked with a fluorescent spot. The efficiency of marking DNA sequences of the size cloned in cosmids is 90-95%, and the fluorescent spots produced after FISH are ≈0.3 μm in diameter. Sites of two sequences can be distinguished using two-color FISH. Different reporter molecules, such as biotin or digoxigenin, are incorporated into DNA sequence probes by nick translation. These reporter molecules are labeled after hybridization with different fluorochromes, e.g., FITC and Texas Red. The development of dual band pass filters (Chromatechnology) allows these fluorochromes to be photographed simultaneously without registration shift.

Phylogenetic relationships ofSalvia(Lamiaceae) in China: Evidence from DNA sequence datasets

2012 ◽  
pp. n/a-n/a
Author(s):  
Qian-Quan Li ◽  
Min-Hui Li ◽  
Qing-Jun Yuan ◽  
Zhan-Hu Cui ◽  
Lu-Qi Huang ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Phylogenetic Relationships

Corrected DNA Sequence of the Platelet Glycoprotein IX Gene

1997 ◽  
Vol 77 (05) ◽  
pp. 1034-1035 ◽  
Author(s):  
Tomohiro Hayashi ◽  
Keijiroh Suzuki ◽  
Akito Yahagi ◽  
Jiroh Akiba ◽  
Katsushi Tajima ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Platelet Glycoprotein

The Conceptualist Ends of Writing and the End of Conceptualism

CounterText ◽  
2020 ◽  
Vol 6 (1) ◽  
pp. 63-77
Author(s):  
Louis Armand
Keyword(s):  
Dna Sequence ◽  
Life Form ◽  
The Sun

This essay examines the convergence of conceptualist poetics with evolutionary code as a form of ‘becoming alien’. The focus is Christian Bök's The Xenotext project: an attempt at translating a ‘short verse about language and genetics’, using a chemical alphabet, into a DNA sequence implanted into the genome of a polyextremophile bacterium capable of enduring conditions in outerspace. Bök describes the project as, ‘in effect, engineering a life-form so that it becomes not only a durable archive for storing a poem, but also as an operant machine for writing a poem – one that can persist on the planet until the sun itself explodes …’. The concrete, constraint-based character of Bök's project evokes a mode of writing between posthumanist aesthetics and a positivist grammatology by turns deconstructive and itself requiring of deconstruction.

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