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Völker J, Breslauer KJ. How sequence alterations enhance the stability and delay expansion of DNA triplet repeat domains. QRB DISCOVERY 2023; 4:e8. [PMID: 37965436 PMCID: PMC10641665 DOI: 10.1017/qrd.2023.6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/14/2023] [Accepted: 08/17/2023] [Indexed: 11/16/2023] Open
Abstract
DNA sequence alterations within DNA repeat domains inexplicably enhance the stability and delay the expansion of interrupted repeat domains. Here we propose mechanisms that rationalise such unanticipated outcomes. Specifically, we describe how interruption of a DNA repeat domain restricts the ensemble space available to dynamic, slip out, repeat bulge loops by introducing energetic barriers to loop migration. We explain how such barriers arise because some possible loop isomers result in energetically costly mismatches in the duplex portion of the repeat domain. We propose that the reduced ensemble space is the causative feature for the observed delay in repeat DNA expansion. We further posit that the observed loss of the interrupting repeat in some expanded DNAs reflects the transient occupation of loop isomer positions that result in a mismatch in the duplex stem due to 'leakiness' in the energy barrier. We propose that if the lifetime of such a low probability event allows for recognition by the mismatch repair system, then 'repair' of the repeat interruption can occur; thereby rationalising the absence of the interruption in the final expanded DNA 'product.' Our proposed mechanistic pathways provide reasoned explanations for what have been described as 'puzzling' observations, while also yielding insights into a biomedically important set of coupled genotypic phenomena that map the linkage between DNA origami thermodynamics and phenotypic disease states.
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Affiliation(s)
- Jens Völker
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
| | - Kenneth J. Breslauer
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
- The Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
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Breslauer KJ. The shaping of a molecular linguist: How a career studying DNA energetics revealed the language of molecular communication. J Biol Chem 2021; 296:100522. [PMID: 34237886 PMCID: PMC8058554 DOI: 10.1016/j.jbc.2021.100522] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 03/04/2021] [Indexed: 01/31/2023] Open
Abstract
My personal and professional journeys have been far from predictable based on my early childhood. Owing to a range of serendipitous influences, I miraculously transitioned from a rebellious, apathetic teenage street urchin who did poorly in school to a highly motivated, disciplined, and ambitious academic honors student. I was the proverbial “late bloomer.” Ultimately, I earned my PhD in biophysical chemistry at Yale, followed by a postdoc fellowship at Berkeley. These two meccas of thermodynamics, coupled with my deep fascination with biology, instilled in me a passion to pursue an academic career focused on mapping the energy landscapes of biological systems. I viewed differential energetics as the language of molecular communication that would dictate and control biological structures, as well as modulate the modes of action associated with biological functions. I wanted to be a “molecular linguist.” For the next 50 years, my group and I used a combination of spectroscopic and calorimetric techniques to characterize the energy profiles of the polymorphic conformational space of DNA molecules, their differential ligand-binding properties, and the energy landscapes associated with mutagenic DNA damage recognition, repair, and replication. As elaborated below, the resultant energy databases have enabled the development of quantitative molecular biology through the rational design of primers, probes, and arrays for diagnostic, therapeutic, and molecular-profiling protocols, which collectively have contributed to a myriad of biomedical assays. Such profiling is further justified by yielding unique energy-based insights that complement and expand elegant, structure-based understandings of biological processes.
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Affiliation(s)
- Kenneth J Breslauer
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA; The Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA.
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Tomar R, Minko IG, Kellum AH, Voehler MW, Stone MP, McCullough AK, Lloyd RS. DNA Sequence Modulates the Efficiency of NEIL1-Catalyzed Excision of the Aflatoxin B 1-Induced Formamidopyrimidine Guanine Adduct. Chem Res Toxicol 2021; 34:901-911. [PMID: 33595290 DOI: 10.1021/acs.chemrestox.0c00517] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dietary exposure to aflatoxins is a significant risk factor in the development of hepatocellular carcinomas. Following bioactivation by microsomal P450s, the reaction of aflatoxin B1 (AFB1) with guanine (Gua) in DNA leads to the formation of stable, imidazole ring-opened 8,9-dihydro-8-(2,6-diamino-4-oxo-3,4-dihydropyrimid-5-yl-formamido)-9-hydroxyaflatoxin B1 (AFB1-FapyGua) adducts. In contrast to most base modifications that result in destabilization of the DNA duplex, the AFB1-FapyGua adduct increases the thermal stability of DNA via 5'-interface intercalation and base-stacking interactions. Although it was anticipated that this stabilization might make these lesions difficult to repair relative to helix distorting modifications, prior studies have shown that both the nucleotide and base excision repair pathways participate in the removal of the AFB1-FapyGua adduct. Specifically for base excision repair, we previously showed that the DNA glycosylase NEIL1 excises AFB1-FapyGua and catalyzes strand scission in both synthetic oligodeoxynucleotides and liver DNA of exposed mice. Since it is anticipated that error-prone replication bypass of unrepaired AFB1-FapyGua adducts contributes to cellular transformation and carcinogenesis, the structural and thermodynamic parameters that modulate the efficiencies of these repair pathways are of considerable interest. We hypothesized that the DNA sequence context in which the AFB1-FapyGua adduct is formed might modulate duplex stability and consequently alter the efficiencies of NEIL1-initiated repair. To address this hypothesis, site-specific AFB1-FapyGua adducts were synthesized in three sequence contexts, with the 5' neighbor nucleotide being varied. DNA structural stability analyses were conducted using UV absorbance- and NMR-based melting experiments. These data revealed differentials in thermal stabilities associated with the 5'-neighbor base pair. Single turnover kinetic analyses using the NEIL1 glycosylase demonstrated corresponding sequence-dependent differences in the repair of this adduct, such that there was an inverse correlation between the stabilization of the duplex and the efficiency of NEIL1-mediated catalysis.
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Affiliation(s)
- Rachana Tomar
- Department of Chemistry and the Vanderbilt-Ingram Cancer Center, Vanderbilt University, VU Station B, Box 351822, Nashville, Tennessee 37235, United States
| | - Irina G Minko
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, United States
| | - Andrew H Kellum
- Department of Chemistry and the Vanderbilt-Ingram Cancer Center, Vanderbilt University, VU Station B, Box 351822, Nashville, Tennessee 37235, United States
| | - Markus W Voehler
- Department of Chemistry and the Vanderbilt-Ingram Cancer Center, Vanderbilt University, VU Station B, Box 351822, Nashville, Tennessee 37235, United States
| | - Michael P Stone
- Department of Chemistry and the Vanderbilt-Ingram Cancer Center, Vanderbilt University, VU Station B, Box 351822, Nashville, Tennessee 37235, United States
| | - Amanda K McCullough
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, United States.,Department of Molecular and Medical Genetics, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, United States
| | - R Stephen Lloyd
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, United States.,Department of Molecular and Medical Genetics, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, United States
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Conformational and migrational dynamics of slipped-strand DNA three-way junctions containing trinucleotide repeats. Nat Commun 2021; 12:204. [PMID: 33420051 PMCID: PMC7794359 DOI: 10.1038/s41467-020-20426-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 11/30/2020] [Indexed: 12/18/2022] Open
Abstract
Expansions of CAG/CTG trinucleotide repeats in DNA are the cause of at least 17 degenerative human disorders, including Huntington’s Disease. Repeat instability is thought to occur via the formation of intrastrand hairpins during replication, repair, recombination, and transcription though relatively little is known about their structure and dynamics. We use single-molecule Förster resonance energy transfer to study DNA three-way junctions (3WJs) containing slip-outs composed of CAG or CTG repeats. 3WJs that only have repeats in the slip-out show two-state behavior, which we attribute to conformational flexibility at the 3WJ branchpoint. When the triplet repeats extend into the adjacent duplex, additional dynamics are observed, which we assign to interconversion of positional isomers. We propose a branchpoint migration model that involves conformational rearrangement, strand exchange, and bulge-loop movement. This migration has implications for how repeat slip-outs are processed by the cellular machinery, disease progression, and their development as drug targets. DNA three-way junctions are branched structures formed during replication, repair, and recombination, and are involved in models of repeat expansion. Here the authors use single-molecule Förster resonance energy transfer to reveal the dynamics of DNA three-way junctions containing slip-outs composed of CAG or CTG repeats.
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Völker J, Plum GE, Breslauer KJ. Heat Capacity Changes (Δ Cp) for Interconversions between Differentially-Ordered DNA States within Physiological Temperature Domains: Implications for Biological Regulatory Switches. J Phys Chem B 2020; 124:5614-5625. [PMID: 32531155 DOI: 10.1021/acs.jpcb.0c04065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Knowledge of differences in heat capacity changes (ΔCp) between biopolymer states provides essential information about the temperature dependence of the thermodynamic properties of these states, while also revealing insights into the nature of the forces that drive the formation of functional and dysfunctional biopolymer "order." In contrast to proteins, for nucleic acids there is a dearth of direct experimental determination of this information-rich parameter, a deficiency that compromises interpretations of the ever-increasing thermodynamic analyses of nucleic acid properties; particularly as they relate to differential nucleic acid (meta)stability states and their potential biological functions. Here we demonstrate that such heat capacity differences, in fact, exist not only between traditionally measured native to fully unfolded (assumed "random coil") DNA states, but also between competing order-to-order transformations. We illustrate the experimental approach by measuring the heat capacity change between "native"/ordered, sequence homologous, "isomeric" DNA states that differ in conformation but not sequence. Importantly, these heat capacity differences occur within biologically relevant temperature ranges. In short, we describe a new and general method to measure the value of such heat capacity differences anywhere in experimentally accessible conformational and temperature space; in this case, between two metastable bulge loop states, implicated in DNA expansion diseases, and their competing, fully paired, thermodynamically more stable duplex states. This measurement reveals a ΔCp of 61 ± 7 cal molbp -1 K -1. Such heat capacity differences between competing DNA "native" ensemble states must be considered when evaluating equilibria between different DNA "ordered" conformations, including the assessment of the differential stabilizing forces and potential biological functions of competing DNA "structured" motifs.
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Affiliation(s)
- Jens Völker
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854, United States
| | - G Eric Plum
- UNICON International, Inc. 241 Outerbelt Street, Columbus, Ohio 43213, United States
| | - Kenneth J Breslauer
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854, United States.,The Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey 08901, United States
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