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)_<i>n</i> and (CTG)_<i>n</i>, as well as the canonical (CAG)_<i>n</i>/(CTG)_<i>n</i> 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>^⧧ describing this process. We report that the thermodynamic parameters of unfolding the stem-loop (CTG)_<i>n</i> and (CAG)_<i>n</i> 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 spiroimino­dihydantoin-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^–) 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^– 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>_pol/<i>K</i>_d 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^– 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^– 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 22 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 55 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 70 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 3: of Distinct tissue-specific transcriptional regulation revealed by gene regulatory networks in maize

Evaluation of tissue GRNs generated by MRNET and CLR. (XLSX 9 kb