Proton NMR relaxation studies of the hydrogen-bonded imino protons of poly(dA-dT)

Assa‐Munt, Nuria; Granot, Joseph; Behling, Ronald W.; Kearns, David R.

doi:10.1021/bi00300a023

Cited by 63 publications

(42 citation statements)

References 53 publications

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“…'~ Zn ( I1 ) is required for the function of many regulatory proteins. As the protein binds to dA-dT rich regions, the water activity around the DNA will be lowered and the presence of the Zn (11) near these regions may induce the C structure. Even though the C structure is only slightly overwound with respect to the B structure, this small change could maximize the protein-DNA interactions required to produce the specific binding.…”

Section: Discussionmentioning

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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Section: Discussionmentioning

confidence: 99%

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

Loprete

Hartman

1990

Biopolymers

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“…Poly[d(G-C)] (P-L Biochemicals, lot 676-7) was sonicated to =60 base pairs (14,15), precipitated with ethanol, dissolved in 0.125 ml of buffer containing 4.5 M NaCl (or 3.25 M Na-C104) and 0.01 M sodium cacodylate at pH 7, and placed in a Wilmad 508-CP NMR microcell. Real-time solvent-exchange experiments were performed by first equilibrating the Z-DNA in buffer containing 'H20.…”

Section: Methodsmentioning

confidence: 99%

“…We have been studying the exchange of the imino protons in short (-60-base-pair) DNA polymers by NMR relaxation techniques (13)(14)(15)), but we found that exchange from Z-form poly[d(G-C)] was too slow (<1 s-1 at 850C) to use this approach. Nevertheless, using our data to estimate the exchange rate at high temperature and the Ramstein and Leng (10) rate obtained at low temperature, we calculated an apparent exchange activation energy of only 12 kcal/mol (1 kcal = 4.18 kJ).…”

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confidence: 99%

Unusual proton exchange properties of Z-form poly[d(G-C)]

Mirau

Kearns

1985

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

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Real-time solvent-exchange NMR has been used to study the proton exchange in Z-form poly [d(G-C)]. In 4.5 M NaCl the most slowly exchanging protons (about two orders of magnitude slower than in B-DNA) are identified as the guanine imino proton and the cytosine amino proton hydrogen bonded to the guanine carbonyl. Both protons exchange at the same rate and the exchange follows single-exponential kinetics and cannot be catalyzed, implying that the exchanges of the two protons both occur from the same transient solvent-exposed state. The exchange depends strongly on temperature and the activation energy for exchange (=22 kcal/ mol) is the same as the activation energy for the B -* Z transition. The rate of proton exchange is identical with the B -* Z transition rate, both measured in 4.5 M NaCl. The correlation between the B -+ Z kinetics and the proton exchange also extends to 3.25 M NaCIO4 solutions, in which both rates are 5 times faster. This unexpected parallelism between the B -* Z transition kinetics and the Z exchange kinetics indicates that the rate-limiting steps in the two processes are similar. (16) and the values for double-stranded DNA and RNA polymers are typically 16-22 kcal/mol (13-17). Since exchange in Z-DNA is so slow, an activation energy of at least 22 kcal/mol is expected (14). To examine the slowly exchanging protons in Z-DNA, we have used the real-time solvent-exchange technique previously used to study proton exchange in proteins (18) and tRNA (19). Contrary to the proposed assignments, we find that the most slowly exchanging pair of protons in Z-DNA are not the C., but rather the guanine imino (Gim) and the cytosine amino proton hydrogen bonded to the G carbonyl, and this indicates that the rate of opening of base pairs in Z-DNA is 1/20th as fast (half-life of 7 hr at 00C) as the very slow rate previously inferred (10). There is a remarkable similarity in the rate constant for the B -b Z transition and the exchange rate for the most slowly exchanging proton in Z-DNA in that: (i) the activation energies are nearly identical (""22 kcal/mol), (ii) the absolute rate constants are identical, and (iii) both rates are 5 times faster in 3.25 M NaCl04 than in 4.5 M NaCl. These results suggest that the rate-limiting steps in the B --Z transition are similar to those leading to exchange from Z-DNA. Studies on Z-form polymers containing both AFT and G-C base pairs show that the same considerations apply to other Z-forming sequences (unpublished results). MATERIALS AND METHODSPoly[d(G-C)] (P-L Biochemicals, lot 676-7) was sonicated to =60 base pairs (14,15), precipitated with ethanol, dissolved in 0.125 ml of buffer containing 4.5 M NaCl (or 3.25 M Na-C104) and 0.01 M sodium cacodylate at pH 7, and placed in a Wilmad 508-CP NMR microcell. Real-time solvent-exchange experiments were performed by first equilibrating the Z-DNA in buffer containing 'H20. The sample was placed in the NMR spectrometer and the instrumental parameters were adjusted at the desired temperature. The solvent was removed...

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“…A good tit is obtained with a model featuring torsional motions (0.1 -1.5 ns, f 30" amplitude) in addition to out of plane motions (1 -100 ns, f30" amplitude). The combination of these two motions can also be simulated by a 'jumping on a cone' model (1 ns, $30" amplitude) [110]. In-plane and out-of-plane motions of the bases, with amplitudes of about lo", are also implied by 2H relaxation data of G(2H8) [8-'H]G-deuterated calf thymus DNA in the, oriented, hydrated, solid state [118].…”

Section: Intru-molecular Mobilitymentioning

confidence: 99%