Time-Resolved X-Ray Diffraction Studies of the B⇆D Structural Transition in the DNA Double Helix

Mahendrasingam, A.; Forsyth, V. T.; Hussain, Rohanah; Greenall, R. J.; Pigram, W. J.; Fuller, W.

doi:10.1126/science.3726529

Cited by 50 publications

(13 citation statements)

References 21 publications

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“…At one extreme the A ↔ B transition appeared to be similar to a first-order phase transition, with little evidence of intermediate structures; the time-resolved datasets recorded at the Daresbury SRS for this transition were of the A or B type or simple mixtures of the A and B patterns. By contrast, the D ↔ B transition exhibited a gradual distortion of the doublestranded helix as its pitch increased over a period of minutes from 24 Å to 34 Å Mahendrasingam et al 1986). However, the A ↔ B and D ↔ B transitions have a number of important features in common.…”

Section: Time-resolved X-ray Fibre-diffraction Studies Of Structural mentioning

confidence: 97%

Water–DNA interactions as studied by X–ray and neutron fibre diffraction

Fuller

Forsyth

Mahendrasingam

2004

Phil. Trans. R. Soc. Lond. B

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X-ray fibre-diffraction studies indicate a high degree of stereochemical specificity in interactions between water and the DNA double helix. Evidence for this comes from data that show that the molecular conformations assumed by DNA in fibres are highly reproducible and that the hydration-driven transitions between these conformations are fully reversible. These conformational transitions are induced by varying the relative humidity of the fibre environment and hence its water content. Further evidence for stereochemical specificity comes from the observed dependence of the conformation assumed on the ionic content of the fibre and the nucleotide sequence of the DNA. For some transitions, information on stereochemical pathways has come from real-time X-ray fibre diffraction using synchrotron radiation; information on the location of water with respect to the double helix for a number of DNA conformations has come from neutron fibre diffraction. This structural information from fibre-diffraction studies of DNA is complemented by information from X-ray single-crystal studies of oligonucleotides. If the biochemical processes involving DNA have evolved to exploit the structural features observed in DNA fibres and oligonucleotide single crystals, the challenges in developing alternatives to a water environment can be expected to be very severe.

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Section: Time-resolved X-ray Fibre-diffraction Studies Of Structural mentioning

confidence: 97%

Water–DNA interactions as studied by X–ray and neutron fibre diffraction

Fuller

Forsyth

Mahendrasingam

2004

Phil. Trans. R. Soc. Lond. B

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“…The plots show data measured in these experiments and previously reported data for poly[d(A-T)]. 18 From these data we calculate that ∆V T ) 0 cm 3 We calculated the number of base pairs in the cooperative unit of a heat-induced transition (or the cooperative length) N T by taking the ratio of ∆H vH /∆H cal . 19,31,40 The data in Figure 7 show that N T is independent of pressure to a good approximation and that it decreases with salt concentration.…”

Section: A Representative Heat-induced Helix-coil Transition Of Poly[mentioning

confidence: 98%

Comparison of the Heat- and Pressure-Induced Helix−Coil Transition of Two DNA Copolymers

Rayan

Macgregor

2005

J. Phys. Chem. B

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The helix-coil transition of poly[d(I-C)] and poly[d(A-T)] was studied as a function of hydrostatic pressure, temperature, and sodium ion concentration. These studies were undertaken in light of a recently published phase diagram for double stranded nucleic acids [Dubins et al. J. Am. Chem. Soc. 2001, 123, 9254-9259]. The sign and magnitude of the volume change for the heat-induced helix-coil transition, DeltaV(T), of poly[d(I-C)] and poly[d(A-T)] were dependent on the helix-coil transition temperature, T(M), at atmospheric pressure. The sign of DeltaV(T) changed from negative to positive as T(M) was increased by increasing the sodium ion concentration. For poly[d(I-C)], DeltaV(T) = 0 cm(3) mol(-1), when the sodium ion concentration is such that the spectroscopically monitored T(M) = 55 degrees C at atmospheric pressure. For poly[d(A-T)], the value of DeltaV(T) = 0 under conditions such that T(M) = 47 degrees C at atmospheric pressure. Negative values of DeltaV(T) imply that the helical form is destabilized at high pressure. Under experimental conditions where the DeltaV(T) for the transition is negative, the transition could be caused by increasing the pressure under isothermal conditions. At temperatures below T(M) measured at atmospheric pressure the midpoint of the pressure-induced helix-coil transition, P(M), decreases with increasing temperature. The volume change of the pressure-induced transitions helix-coil transition, DeltaV(P), was calculated assuming a two-state model. The magnitude of DeltaV(P) (per cooperative length) was much larger than the volume change (per base pair) measured for the heat-induced transition, DeltaV(T), calculated using the Clapeyron equation. The ratio of these two volume changes was used to calculate the cooperative length for the pressure-induced transition. This parameter depends strongly on temperature, becoming greater closer to T(M) measured at atmospheric pressure. At temperatures approaching T(M) the magnitude of the cooperative length of the pressure-induced transition is approximately twice that observed for the heat-induced transition (N(T)). On the basis of the temperature dependence of the DeltaV(T) for the two polymers the coefficient of thermal expansion of the two polymers was found to be 0.17 and 0.16 cm(3) K(-1) mol(-1) for poly[d(I-C)] and poly[d(A-T)], respectively.

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“…At least one sample of poly (dAd T ) -Na ( r value not stated) could be rapidly cycled from B to D to B as rh was changed from 98 to 80 and back to 98% rh. The transition time was about 1 h. 6 Infrared dichroic spectra of oriented gels of poly (dA-dT) -Na containing added NaCl ( r = 0.20)…”

Section: B C and D Structures Of Poly (Da-dt)mentioning

confidence: 99%

Conditions for the stability of the alternative structures of duplex poly(dA‐dT)

Loprete

Hartman

1990

Biopolymers

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SYNOPSISThe alternative structures of the lithium, sodium, potassium, and rubidium salts of poly(dAd T ) were studied using ir spectra of hydrated, nonoriented gels. Poly (dA-dT) Na existed as the B structure a t high hydration and as the A structure a t moderate hydration. A disordered state occurred a t low hydration. No hint of the C, D, or other structures was observed a t any hydration for nonoriented gels containing NaCl up to 0.56 moles NaC1/ mole of nucleotide residue. Poly (dA-dT) -Li existed as the B structure a t high hydration, made a gradual transition to the C structure a t moderate hydration, and became disordered at low hydration. Poly (dA-dT) K and poly( dA-dT) -Rb existed as the B structure a t high hydration and as the presumptive D structure at lower hydration. The addition of Zn ( 11) to poly(dA-dT)-Na produced a gradual transition from the B to the C structure upon dehydration. The addition of NaN03 to poly (dA-dT) * Na gave only the A and B structures, and not the C or Z structures that are promoted by NO, in other base sequences. The D N A secondary structure stabilized by a given ion is determined by a specific base sequence and not simply by the properties of the ion INTRODUCTIONThe nature of the alternative structures of poly (dAdr) and the conditions for the stability of these structures have received much study (reviewed in Ref'. 1 ) . Crystallographic studies of oriented gels of poly ( dA-dT) have demonstrated the existence of the A, B, C, and D structures depending on the counterion to the polymer, the salt content of the gel, and the hydration (or water activity) of the Raman studies have confirmed the existence of the B structure in ~o l u t i o n s~~~~ and the A structure in partially oriented and unoriented gels.' Nuclear magnetic resonance spectra of solutions of poly (dA- Biopolymers, Vol. 30, 753-761 (1990) ('CC OOOS-:~525/90/7-80753-09 $04.00* To whom correspondence should be addressed.nonoriented 16*17 gels, have been assigned to the A, B, C, and D structures of poly (dA-dT) . Although the existence of the A, B, C, and D structures of poly (dA-dT ) has been broadly supported, the stabilizing conditions for these structures are less certain. We have therefore made a systematic survey of the structures that exist and the conditions for stability for the Li, Na, K, and Rb salts of poly(dA-dT) using nonoriented gels in which shifts in equilibrium due to crystal-lattice forces should be minimized.A brief review of the salient results for the conditions of stability of alternative structures of poly (dA-dT) follows.Davies and Baldwin first observed the diffraction patterns of the sodium, lithium, and ammonium salts of poly (dA-dT) using hydrated oriented gels.' They found the A and B structures for the Na and Li salts of poly(dA-dT), respectively. A C-like structure and a new structure, which they called D, were observed for poly (dA-dT) * NH4. Samples of poly (dA-dT) -Na containing ca. 0.2 moles of NaCl per mole of nucleotide (hereafter designated r = 0.2) also gave the D s...

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Time-Resolved X-Ray Diffraction Studies of the B⇆D Structural Transition in the DNA Double Helix

Cited by 50 publications

References 21 publications

Water–DNA interactions as studied by X–ray and neutron fibre diffraction

Water–DNA interactions as studied by X–ray and neutron fibre diffraction

Comparison of the Heat- and Pressure-Induced Helix−Coil Transition of Two DNA Copolymers

Conditions for the stability of the alternative structures of duplex poly(dA‐dT)

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