53 research outputs found
Unique Length-Dependent Biophysical Properties of Repetitive DNA
Expansion
of a trinucleotide repeat (TNR) sequence is the molecular
signature of several neurological disorders. The formation of noncanonical
structures by the TNR sequence is proposed to contribute to the expansion
mechanism. Furthermore, it is known that the propensity for expansion
increases with repeat length. In this work, we use calorimetry to
describe the thermodynamic parameters (Δ<i>H</i>, <i>T</i>Δ<i>S</i>, and Δ<i>G</i>) of the noncanonical stem-loop hairpins formed by the TNR sequences
(CAG)<sub><i>n</i></sub> and (CTG)<sub><i>n</i></sub>, as well as the canonical (CAG)<sub><i>n</i></sub>/(CTG)<sub><i>n</i></sub> duplexes, for <i>n</i> = 6–14. Using a thermodynamic cycle, we calculated the same
thermodynamic parameters describing the process of converting from
noncanonical stem-loop hairpins to a canonical duplex. In addition
to these thermodynamic analyses, we used spectroscopic techniques
to determine the rate at which the noncanonical structures convert
to duplex and the activation enthalpy Δ<i>H</i><sup>⧧</sup> describing this process. We report that the thermodynamic
parameters of unfolding the stem-loop (CTG)<sub><i>n</i></sub> and (CAG)<sub><i>n</i></sub> hairpins, along with
the thermodynamic and kinetic properties of hairpin to duplex conversion,
do not proportionally correspond to the increase in length, but rather
show a unique pattern that depends on whether the sequence has an
even or odd number of repeats
Klenow Fragment Discriminates against the Incorporation of the Hyperoxidized dGTP Lesion Spiroiminodihydantoin into DNA
Defining
the biological consequences of oxidative DNA damage remains
an important and ongoing area of investigation. At the foundation
of understanding the repercussions of such damage is a molecular-level
description of the action of DNA-processing enzymes, such as polymerases.
In this work, we focus on a secondary, or hyperoxidized, oxidative
lesion of dG that is formed by oxidation of the primary oxidative
lesion, 2′-deoxy-8-oxo-7,8-dihydroguanosine (8-oxodG). In particular,
we examine incorporation into DNA of the diastereomers of the hyperoxidized
guanosine triphosphate lesion spiroiminoÂdihydantoin-2′-deoxynucleoside-5′-triphosphate
(dSpTP). Using kinetic parameters, we describe the ability of the
Klenow fragment of Escherichia coli DNA polymerase I lacking 3′ → 5′ exonuclease
activity (KF<sup>–</sup>) to utilize (<i>S</i>)-dSpTP
and (<i>R</i>)-dSpTP as building blocks during replication.
We find that both diastereomers act as covert lesions, similar to
a Trojan horse: KF<sup>–</sup> incorporates the lesion dNTP
opposite dC, which is a nonmutagenic event; however, during the subsequent
replication, it is known that dSp is nearly 100% mutagenic. Nevertheless,
using <i>k</i><sub>pol</sub>/<i>K</i><sub>d</sub> to define the nucleotide incorporation specificity, we find that
the extent of oxidation of the dGTP-derived lesion correlates with
its ability to be incorporated into DNA. KF<sup>–</sup> has
the highest specificity for incorporation of dGTP opposite dC. The
selection factors for incorporating 8-oxodGTP, (<i>S</i>)-dSpTP, and (<i>R</i>)-dSpTP are 1700-, 64000-, and 850000-fold
lower, respectively. Thus, KF<sup>–</sup> is rigorous in its
discrimination against incorporation of the hyperoxidized lesion,
and these results suggest that the specificity of cellular polymerases
provides an effective mechanism to avoid incorporating dSpTP lesions
into DNA from the nucleotide pool
Legislative Documents
Also, variously referred to as: House bills; House documents; House legislative documents; legislative documents; General Court documents
Additional file 6: of Distinct tissue-specific transcriptional regulation revealed by gene regulatory networks in maize
GO enrichment analysis for 1657 conserved targets in four tissue GRNs. (XLSX 22Ă‚Â kb
Additional file 4: of Distinct tissue-specific transcriptional regulation revealed by gene regulatory networks in maize
A Venn diagram showing the overlap among top 1 million edges of each tissue-specific GRN. (PDF 55Ă‚Â kb
Legislative Documents
Also, variously referred to as: House bills; House documents; House legislative documents; legislative documents; General Court documents
Additional file 5: of Distinct tissue-specific transcriptional regulation revealed by gene regulatory networks in maize
The 353 TFs and 1657 targets included in the 2679 edges shared by four tissue GRNs. (XLSX 70Ă‚Â kb
Additional file 11: of Distinct tissue-specific transcriptional regulation revealed by gene regulatory networks in maize
Predicted TF targets from top 1 million edges in each tissue. “max _tissue” means which tissue has the highest number of interactions. “CV” is the coefficient of variance. (XLSX 76 kb
Additional file 14: of Distinct tissue-specific transcriptional regulation revealed by gene regulatory networks in maize
Homologs of shared TF by more than two tissues in Arabidopsis. Genes without homologs identified by BioMart were left blank. (XLSX 11 kb
Additional file 7: of Distinct tissue-specific transcriptional regulation revealed by gene regulatory networks in maize
GO enrichment analysis for KN1, FEA4 and O2 targets in four tissue GRNs. (XLSX 19Ă‚Â kb
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