Magnetic torque tweezers: measuring torsional stiffness in DNA and RecA-DNA filaments

Lipfert, Jan; Kerssemakers, Jacob; Jager, Tessa; Dekker, Nynke H.

doi:10.1038/nmeth.1520

Cited by 282 publications

(377 citation statements)

References 27 publications

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“…Since their invention (28)(29)(30), MT techniques have often been used to analyze the interactions between DNA and DNA ligands, including small drug molecules (25,31,32) and proteins (33)(34)(35)(36)(37)(38). MT can be used to apply controlled force and torsion to single DNA molecules and enables measurement of the influence of such nanomechanical stresses on the DNA structure, primarily through the assessment of end-to-end distance at nanometric resolution.…”

Section: Introductionmentioning

confidence: 99%

Platinum-Based Drugs and DNA Interactions Studied by Single-Molecule and Bulk Measurements

Salerno

Beretta

Zanchetta

et al. 2016

Biophysical Journal

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Platinum-containing molecules are widely used as anticancer drugs. These molecules exert cytotoxic effects by binding to DNA through various mechanisms. The binding between DNA and platinum-based drugs hinders the opening of DNA, and therefore, DNA duplication and transcription are severely hampered. Overall, impeding the above-mentioned important DNA mechanisms results in irreversible DNA damage and the induction of apoptosis. Several molecules, including multinuclear platinum compounds, belong to the family of platinum drugs, and there is a body of research devoted to developing more efficient and less toxic versions of these compounds. In this study, we combined different biophysical methods, including single-molecule assays (magnetic tweezers) and bulk experiments (ultraviolet absorption for thermal denaturation) to analyze the differential stability of double-stranded DNA in complex with either cisplatin or multinuclear platinum agents. Specifically, we analyzed how the binding of BBR3005 and BBR3464, two representative multinuclear platinum-based compounds, to DNA affects its stability as compared with cisplatin binding. Our results suggest that single-molecule approaches can provide insights into the drug-DNA interactions that underlie drug potency and provide information that is complementary to that generated from bulk analysis; thus, single-molecule approaches have the potential to facilitate the selection and design of optimized drug compounds. In particular, relevant differences in DNA stability at the single-molecule level are demonstrated by analyzing nanomechanically induced DNA denaturation. On the basis of the comparison between the single-molecule and bulk analyses, we suggest that transplatinated drugs are able to locally destabilize small portions of the DNA chain, whereas other regions are stabilized.

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Section: Introductionmentioning

confidence: 99%

Platinum-Based Drugs and DNA Interactions Studied by Single-Molecule and Bulk Measurements

Salerno

Beretta

Zanchetta

et al. 2016

Biophysical Journal

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“…In single stretched DNA molecules, B-DNA ceases to display linear torsional elasticity at a critical torque of approximately −10 pNnm, entering an apparent cooperative structural transition to an underwound form (11,12). This transition has been proposed to represent strand separation (13), but it has been noted that other noncanonical structures such as Z-DNA may also be simultaneously populated in random sequences under negative torques (14, 15).…”

mentioning

confidence: 99%

“…The rotor bead tracking assay (11) was the first of a number of methods introduced over the past decade (11,12,(21)(22)(23)(24) for measuring torque on single stretched DNA molecules. Torque is measured by observing the angular velocity of a submicron bead attached to the side of the DNA.…”

mentioning

confidence: 99%

Torque measurements reveal sequence-specific cooperative transitions in supercoiled DNA

Oberstrass

Fernandes

Bryant

2012

Proc. Natl. Acad. Sci. U.S.A.

117

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B-DNA becomes unstable under superhelical stress and is able to adopt a wide range of alternative conformations including strand-separated DNA and Z-DNA. Localized sequence-dependent structural transitions are important for the regulation of biological processes such as DNA replication and transcription. To directly probe the effect of sequence on structural transitions driven by torque, we have measured the torsional response of a panel of DNA sequences using single molecule assays that employ nanosphere rotational probes to achieve high torque resolution. The responses of Z-forming d(pGpC) n sequences match our predictions based on a theoretical treatment of cooperative transitions in helical polymers. “Bubble” templates containing 50–100 bp mismatch regions show cooperative structural transitions similar to B-DNA, although less torque is required to disrupt strand–strand interactions. Our mechanical measurements, including direct characterization of the torsional rigidity of strand-separated DNA, establish a framework for quantitative predictions of the complex torsional response of arbitrary sequences in their biological context.

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“…Предложены различные методики, позволяющие непосредственно измерять величину крутильного момента [1]. Среди них особый интерес представляют метод оптического динамометрического ключа или угловой оптической ловушки (angular optical trap -АОТ) [2, 3] и метод магнитного пинцета [4,5,6]. Каждый из этих методов имеет свои преимущества и недостатки.…”

Section: Introductionunclassified

On the DNA Kink Motion Under the Action of Constant Torque

Якушевич¹,

Yakushevich²

2016

Math.Biol.Bioinf.

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Аннотация. Влияние торсионного момента на движение кинка ДНК исследуется методами математического моделирования. Найдены временные зависимости координаты, скорости, размера и энергии кинка при разных значениях параметров внешнего торсионного момента. Показано, что изменяя эти параметры, включая и выключая внешнее воздействие, можно регулировать скорость и направление движения кинка. Приводится оценка значения торсионного момента, необходимого для движения кинка (открытого состояния) со скоростью, сравнимой со скоростью транскрипции. ВВЕДЕНИЕКонформационная подвижность является одним из важнейших свойств, присущих молекуле ДНК. Среди разнообразных внутренних движений молекулы особую роль играют вращательные движения и вызываемый ими крутильный (или торсионный) момент, который значительное число исследователей рассматривают в качестве механического регулятора во многих биологических процессах, включая процессы транскрипции и репликации [1].К настоящему времени достигнут значительный прогресс в экспериментальных исследованиях вращательных движений одиночных молекул ДНК. Предложены различные методики, позволяющие непосредственно измерять величину крутильного момента [1]. Среди них особый интерес представляют метод оптического динамометрического ключа или угловой оптической ловушки (angular optical trap -АОТ) [2, 3] и метод магнитного пинцета [4,5,6]. Каждый из этих методов имеет свои преимущества и недостатки. Так, например, в методе магнитного пинцета скорость сбора данных меньше, чем в методе АОТ, но зато он не наносит повреждений молекуле, вызванных нагреванием от лазера [7]. С другой стороны, АОТ предлагает гибкое управление, как силой, так и вращательным моментом, позволяя быстро переключаться между разными режимами работы [8]. Однако эти и другие существующие на сегодняшний день экспериментальные методики не дают возможности проводить измерения торсионного момента непосредственно в биологических процессах, в которых участвует молекула ДНК. Это приводит к необходимости привлечь другие методы и с их помощью попытаться оценить значения торсионного момента.В настоящей работе мы исследуем вращательные движения и торсионный момент в молекуле ДНК методами математического моделирования. Для математического

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Magnetic torque tweezers: measuring torsional stiffness in DNA and RecA-DNA filaments

Cited by 282 publications

References 27 publications

Platinum-Based Drugs and DNA Interactions Studied by Single-Molecule and Bulk Measurements

Platinum-Based Drugs and DNA Interactions Studied by Single-Molecule and Bulk Measurements

Torque measurements reveal sequence-specific cooperative transitions in supercoiled DNA

On the DNA Kink Motion Under the Action of Constant Torque

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