• Molecules and Cells
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• 제45권1호
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• pp.33-40
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• 2022

The various DNA-protein interactions associated with the expression of genetic information involve double-stranded DNA (dsDNA) bending. Due to the importance of the formation of the dsDNA bending structure, dsDNA bending properties have long been investigated in the biophysics field. Conventionally, DNA bendability is characterized by innate averaging data from bulk experiments. The advent of single-molecule methods, such as atomic force microscopy, optical and magnetic tweezers, tethered particle motion, and single-molecule fluorescence resonance energy transfer measurement, has provided valuable tools to investigate not only the static structures but also the dynamic properties of bent dsDNA. Here, we reviewed the single-molecule methods that have been used for investigating dsDNA bendability and new findings related to dsDNA bending. Single-molecule approaches are promising tools for revealing the unknown properties of dsDNA related to its bending, particularly in cells.

• 생명과학회지
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• 제16권7호
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• pp.1225-1228
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• 2006

cAMP와 복합체를 형성한 cAMP 수용성 단백질은 DNA와 결합하여 ${\sim}90$도 정도의 예리한 DNA bending을 유도한다. 그러나 이전의 논문[5]에 의하면 돌연변이 CRP:cGMP 복합체는 돌연변이 CRP:cAMP 복합체보다 아크릴아미드 겔에서 상대적으로 빠른 이동속도를 보였다. CRP와 cyclic nucleotide 존재하에서 DNA의 구조 변화를 알아보기 위하여 6가지 준비된 DNA조각들을 사용하여 몰 고리화 인자(molar cyclization factor)[13]를 측정하였다. 이들 자료를 사용하여 nonlinear regression analysis를 통하여 cGMP 존재하에서 돌연변이 CRP는 DNA bending을 형성하지 않으나 CAMP 존재하에서 나선 꼬임과 같은 DNA 구조 변화없이 DNA bending을 형성한다.

• 생명과학회지
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• 제4권3호
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• pp.119-123
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• 1994

CRP에 의한 DNA bending의 첫 실험은 cAMP, CRP, DNA complex의 gelelectrophoresis에 의해 확인되었다. Bent DNA fragment의 이동은 같은 크기의 linear fragment보다 느리며, EH cAMP, CRP, DNA 결합위치에 따라서 상이한 이동 pattern을 나타낸다. 즉, DNA 단편의 중앙에 CRP binding site가 있을 때는 말단부분에 있을 때보다 이동도가 느리다. benting각의 크기는 일반적으로 안정한 복합체의 형성에 관계하며, 큰 각을 갖는 것이 보다 더 안정된 구조를 형성하여 전사가 촉진되는 것으로 밝혀져 있다. 본고에서는 CRP에 의한 bending과 CRP에 의한 전사조절 관계와 bending의 관계에 대하여 알아보았다.

• BMB Reports
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• 제30권6호
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• pp.426-430
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• 1997

The helical periodicity of the triple-stranded $(dT)_n{\cdot}(dA)_n{\cdot}(dT)_n$ sequence was determined by measuring gel-mobilities of bent DNA fragments containing the sequence. In the bent DNA fragments, a $GA_{22}G$ $CT_{22}C$ sequence was located between two bent DNA loci composed of six $A_{6}{\cdot}T_{6}$ repeats. and the DNA length between the bent DNA loci was varied by 1 base pair over a full helical turn. The gel mobility of each bent DNA fragment reflected the overall extent of DNA bending and varied with the DNA length between the two bent loci. Mobilities of the bent DNA fragments in 5% polyacrylamide gel were measured after preincubating the DNA fragments both in the presence and absence of $CT_{22}C$ oligonucleotide. By comparing the bent DNA fragments containing an intermolecular triplex structure with those of a genuine duplex structure in the gel mobilities, the helical periodicity of the $T_n{\cdot}A_n{\cdot}T_n$ triplex DNA was determined to be $11.5({\pm}0.3)bp/turn$.

• Interaction and multiscale mechanics
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• 제6권4호
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• pp.395-409
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• 2013

Molecular dynamics (MD) systems are highly nonlinear and nonlocal, and the conventional model order reduction methods are ineffective for MD systems. The RBF-POD method (Lee and Chen, 2013) employed a radial basis function (RBF) approximated potential energies and inter-atomic forces of MD systems under the framework of the proper orthogonal decomposition (POD) method for the reduced-order modeling of MD systems. In this work, we focus on the numerical procedures of the RBF-POD method and demonstrate how to apply this approach to the modeling of ds-DNA molecules under stretching and bending conditions.

• 미생물학회지
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• 제47권2호
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• pp.158-162
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• 2011

Proteus mirabilis 전사 조절($\underline{P}$roteus $\underline{m}$irabilis $\underline{t}$ranscription $\underline{r}$egulator ) 단백질의 중금속 결합 부위에 대한 아미노산 서열분석에서 PMTR 단백질은 ZntR (아연 저항성) 단백질이 아닌 CueR (구리 저항성) 단백질과 동일한 환경이다. 그리고 겔시프트 법(gel shift assay) 실험에 의하면 PMTR 단백질은 Escherichia coli의 zntA (zinc-translocating P-type ATPase gene) 프로모터에 결합하지 않고 copA (copper-translocating P-type ATPase gene) 프로모터와 Proteus mirabilis에서 atpase (copper-translocating P-type ATPase gene) 프로모터에 결합하였다. DNase I protection 실험에서 PMTR 단백질 결합부위와 DNase I 민감성 염기들이 관찰되었다. P. mirabilis atpase 프로모터에서 민감성 염기로 주형가닥(template strand)에서 C와 A 그리고 비주형가닥(non-template strand)에서 G와 C 염기들이다. 이런 민감성 염기들은 다른 MerR 패밀리 단백질에서 또한 관찰되었으며, 이것은 단백질에 의한 DNA bending을 의미한다.

• Bulletin of the Korean Chemical Society
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• 제17권4호
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• pp.358-362
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• 1996

The ionic strength dependent binding mode of 9-aminoacridine (9AA), a well-known DNA intercalator, to DNA is studied by flow linear dichroism, circular dichroism, fluorescence techniques and equilibrium dialysis. The DNA-bound 9AA exhibits spectral properties corresponding to the intercalative binding mode disregarding the salt concentrations; the angle between the long-axis transition moment of the 9AA molecule and DNA helix axis is calculated to be about 65°, indicating a significant deviation from the classical intercalation. At low salt concentrations, however, upwards bending curve in Stern-Volmer plot is observed (where 9AA is a fluorophore and DNA a quencher), indicating the coexistence of both static and dynamic quenching mechanisms or the existence of an additional binding site.

• 센서학회지
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• 제19권3호
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• pp.214-220
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• 2010

Three-dimensional(3D) structure of specific DNA can be changed between two conformations under an external environmental transition such as pH and salt concentration variations. We have experimentally observed the conformational transitions of i-motif DNA using AFM cantilever bioassay. It is shown that pH change of a solvent induces the bending defleciton change of a cantilever functionalized by i-motif DNA. This indicates that cantilever bioassay enables the label-free detection of DNA structural changes upon pH change. It is implied that cantilever bioassay can be a de novo route to quantitatively understand the conformational transitions of biological molecules under environmental changes.

• 한국자기공명학회논문지
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• 제1권1호
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• pp.31-44
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• 1997

The effect of the binding of CRP to the symmetrically synthetic 22, 28, and 30 bp lac promoter was investigated by 1H NMR. The binding of cAMP*CRP to the 22 bp DNA did not bring about any changes in the chemical shift values, but did cause selective line broadening of imino proton resonances of specific base pairs. However, The binding of cAMP*CRP to the 28 and 30 bp DNA brought about large changes on the imino proton resonances that seems to be induced by DNA bending. We studied also the role of cAMP as an activator of DNA/CRP complex formation by gel mobility shift assay. Gel mobility shift assay revealed that the cAMP*CRP complex was not able to bind to the 22 bp DNA fragment, but was able to bind to the 28 bp DNA fragment of lac promoter region.

• Korea-Australia Rheology Journal
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• 제19권3호
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• pp.141-146
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• 2007

We examine the wall contact of a $3\;{\mu}m$ tethered DNA chain's free end under shear with a focus on developing schemes for double-tethering in the application of making scaffolds for molecular wires. At this scale our results are found to be highly dependent on small length scale rigidity. Chain-end-wall contact frequency, mean fractional extension deficit upon contact, and standard deviation in extension upon contact are examined for scaling with dimensionless flow strength, Wi. Predictions made using a one dimensional approximation to the Smoluchowski equation for a dumbbell and three dimensional dumbbell simulations produce extension deficit, standard deviation, and frequency scaling exponents of -1/3, -1/3, and 2/3, respectively whereas more fine-grained Kratky-Porod (KP) simulations produce scaling exponents of -0.48, -0.42, and 0.76. The contact frequency scaling of 2/3 is derived from the known results regarding cyclic dynamics Analytical scaling predictions are in agreement with those previously proposed for ${\lambda}-DNA$. [Ladoux and Doyle, 2000, Doyle et al., 2000]. Our results suggest that the differences between the dumbbell and the KP model are associated with the addition of chain discretization and the correct bending potential in the latter. These scaling results will aide future exploration in double tethering of DNA to a surface.