Solution structure of poly(dA-dT).poly(dA-dT) in low and high salt: a 500 MHz 1H NMR study using one-dimensional NOE

CD spectra of poly(dA-dT).poly(dA-dT) in low salt (10-100 mM NaCl) and high salt (4-6 M CsF) are different i.e. 275 nm band gets inverted in going from low to high salt (Vorhickova et. al., J. Mol. Biol. 166, 85, 1983). However, from CD spectra alone it is not possible to decipher any structural differences that might exist between the low and high salt forms of poly(dA-dT).poly(dA-dT). Hence, we took recourse to high resolution NMR spectroscopy to understand the structural properties of poly(dA-dT).poly(dA-dT) in low and high salt. A detailed analysis of shielding constants and extensive use of NOE studies under minimum spin diffusion conditions using C(8)-deuterated poly(dA-dT).poly(dA-dT) enabled us to come up with the following conclusions (i) base-pairing is Watson-Crick under low and high salt conditions. (ii) under both the conditions of salt the experimental data can be explained in terms of an equilibrium blend of right and left-handed B-DNA duplexes with the left-handed form 70% and the right-handed 30%. In a 400 base pairs long poly(dA-dT).poly(dA-dT) (as used in this study), equilibrium between right and left-handed helices can also mean the existence of both helical domains in the same molecule with fast interchange between these domains or/and unhindered motion/propagation of these domains along the helix axis. (iii) However, there are other structural differences between the low and high salt forms of poly(dA-dT).poly(dA-dT); under the low salt condition, right- and left-handed B-DNA duplexes have mononucleotide as a structural repeat while under the high salt conditions, right- and left-handed B-DNA duplexes have dinucleotide as a structural repeat. In the text we provide the listing of torsion angles for the low and high salt structural forms. (iv) Salt (CsF) induced structural transition in poly(dA-dT).poly(dA-dT) occurs without any breakage of Watson-Crick pairing. (v) The high salt form of poly(dA-dT).poly(dA-dT) is not the left-handed Z-helix. Although the results above from NMR data are quite unambiguous, a question still remains i.e. what does the salt (CsF) induced change in the CD spectra of poly(dA-dT).poly(dA-dT) really indicate? Interestingly, we could show that the salt (CsF) induced change in poly(dA-dT).poly(dA-dT) is quite similar to that caused by a basic polypeptide viz. poly-L(Lys2-Ala)n i.e. both the agents induced a psi-structure in DNA.

Poly(dA-dT).poly(dA-dT) in low salt appears to be a left-handed B-helix combined use of chemical theory, fiber diffraction and NMR spectroscopy

Poly(dA-dT).poly(dA-dT) can adopt the B- and D- forms in the fibrous state. Theoretical energy calculations and fiber diffraction analyses suggest that there can be three structural models of poly(dA-dT).poly(dA-dT) in each of these two forms viz right and left-handed Watson Crick models and left-handed Hoogsteen--a total of six possible models. Fiber data for the polymer in the B- or the D-form or energy calculations cannot distinguish any one model from the other. However, a comparison of observed proton chemical shifts with the theoretically computed ones and the NOE studies on exchangeable and nonexchangeable protons suggest that poly(dA-dT).poly(dA-dT) in low salt solution exists predominantly in the left-handed B-conformation.

Determination of handedness of DNA double helices from NOE difference spectra: the structure of poly(dG-dC).poly(dG-dC) in low salt

Combined use of shielding constant computations, measurements of chemical shifts and NOE studies reveal that poly(dG-dC).(poly)dG-dC) in low salt solutions exist as a right-handed B-DNA double helix described by Gupta, Dhingra, Sarma, Sarma, Rajagopalan and Sasisekharan, J. Biomole. Str. Dyn. 1. 395, 1983. We present a simple and direct method to determine the handedness of DNA double helices from NOE difference spectra. This method takes advantage of the NOE between base protons and the H2'H2" sugar protons; and in the difference NOE spectra in the H2'H2" region the signatures of the right and left-handed helices become imprinted.

Left-handed intercalated DNA double helix: rendezvous of ethidium and actinomycin D in the Z-helical conformation space

It is now very well recognized that the DNA double helix is conformationally pluralistic and that this flexibility is derived from internal motions due to backbone torsions. But what is less apparent is that such internal motions can occur in a correlated fashion and express themselves in a wide variety of structural motifs and phenomena. For example, flexibility inherent in the DNA molecule can lead to a family of Z-DNA, LZ1 and LZ2 being the two extremes and correlated internal motion can cause LZ1 in equilibrium LZ2 transition. More interestingly, such motions manifest themselves as breathing modes on the DNA lattice resulting in the sequence specific intercalation sites. Following a detailed stereochemical analyses we observed that the intercalation site for ethidium is located at the dCpdG sequence of the intercalated LZ1 helix (LZ1*) while that for actinomycin D is located at the dGpdC sequence of the intercalated LZ2 helix (LZ2*). From the stereochemistry of the drug binding we make experimentally testable predictions which are in fact supported by a few recent experimental studies. These studies also show that a left-handed intercalated B-DNA model is a viable intermediate in the Z to B transition which can hold the drug with binding energy comparable to that of the intercalated right-handed B-DNA.

During B-Z transition there is no large scale breakage of Watson-Crick base pairs. A direct demonstration using 500 MHz 1H NMR spectroscopy

Monitoring of the Watson-Crick GNH1 proton in poly(dG-dC).poly(dG-dC) at 500 MHz in 90% H2O:10% D2O at 30 degrees C as a function of NaCl concentration (1.5 to 3.6 M), demonstrates that the bases retain Watson-Crick pairing throughout the transition. This observation unequivocally demonstrates that during the B-Z transition there is no large scale and detectable base pair opening and that macroscopically the phenomenon can be described as a direct helix to helix transition. We present frame by frame, an energetically sound stereodynamical trajectory for this transfiguration from right-handed B-DNA to left-handed Z-DNA.

Structure of D-DNA: 8-fold or 7-fold helix?

We have shown that both right- and left-handed uniform helical models (RU and LU models) could be built to give satisfactory agreement with the fibre diffraction data of poly[d(I-C)] in the D-form. Atomic coordinates of these two models are reported in the present work. Molecular transforms of these two models, as well as of the recently published Hoogsteen base-paired 7-fold helical structure of Drew and Dickerson, are given. In view of the work of Drew and Dickerson, attention is drawn to the presence of clear 004 and 008 reflections in the diffraction patterns of poly[d(I-C)] and poly[d(A-T)]. The available data strongly suggest an 8-fold helical structure for the D-form of DNA.

Base-base interactions in nucleic acids containing A-T base pairs. Structure of poly[d(A-T)]

The Watson-Crick type of base pairing is considered to be mandatory for the formation of duplex DNA. However, conformational calculations carried out in our laboratory, have shown that some combinations of backbone torsion angles and sugar pucker lead to duplexes with Hoogsteen type of base pairing also. Here we present the results of energy calculations performed on A-T containing doublet sequences in the D-form with both Hoogsteen and Watson-Crick type of base pairing and the 3 viable models for the A-T containing polynucleotide duplex poly[d(A-T)].

Left-handed helices for DNA: studies on poly[d(I-C)]

Earlier, we showed that, for the D form (n = 8 and h = 3.03 A, where n is number of nucleotide units per turn and h is height per nucleotide unit) of poly[d(A-T)], both right- and left-handed double helical models are stereochemically satisfactory and give good agreement with the observed fiber diffraction data. It was also noted that the conformations of the right- and left-handed D-DNA models are very similar to those of the right- and left-handed B-DNA models. This observation was consistent with the D leads to B transition in the solid phase. As a continuation of our earlier studies, we have carried out similar experiments with poly[d(I-C)]. We could obtain a crystalline D-form pattern (n = 8, h = 3.13 A) of the fiber at 75% relative humidity (r.h.); the hydrated (r.h. approximately equal to 95%) form of the same fiber gave the classical B-form pattern (n = 10, h = 3.40 A). In the present report, we show that both right- and left-handed double-helical models are consistent with the fiber diffraction data of poly[d(I-C)] in the D-form. Theoretical energy calculations also suggest that the right- and left-handed B- and D-DNA models are almost equally stable. Hence, we conclude that the right- and left-handed double-helical models of poly[d(I-C)] in a given form (B or D) are equally likely and that the fiber diffraction data do not permit discrimination.

Hemoperfusion for chronic schizophrenia: preliminary psychiatric results

Six patients with chronic schizophrenia unresponsive to accepted therapy were assigned randomly to receive as adjunctive therapy either (A) weekly coated-charcoal hemoperfusion (CCHP) or (B) sham hemoperfusion (Sham HP) in a double-blind study using two independent psychiatric raters. Four weeks of treatment suggested that (1) CCHP was associated with significant improvement in some psychiatric measures, (2) improvement was early in the treatment course, and (3) neither CCHP nor Sham-HP was associated with deterioration in any of the psychiatric measures. When one patient from each group was "crossed-over" to receive the opposite treatment these conclusions were supported. Further studies appear to be warranted.

Conformational flexibility of DNA: polymorphism and handedness

It is shown that left-handed duplexes are possible for A, B, and D forms of DNA. These duplexes are stereochemically satisfactory and are consistent with the observed x-ray intensity data. On scrutiny the refined right-handed models of B and D DNA by Arnott and coworkers are found to be stereochemically unacceptable. It was possible to formulate a stereochemical guideline for molecular model building based on theory and analysis of single-crystal structure data of dinucleoside monophosphate and higher oligomers. This led to both right- and left-handed DNA duplexes. The right-handed B and D DNA duplexes so obtained are stereochemically superior to earlier models and agree well with the observed x-ray intensity data. The observation that DNA can exist in either handedness for all the polymorphous forms of DNA at once explained A in equilibrium B and B in equilibrium D transitions. Hence it is confirmed that polymorphism of DNA is a reflection on the conformational flexibility inherent in DNA, the same cause that ultimately allows DNA in either handedness. The possibility of various types of right- and left-handed duplexes generated by using dinucleoside monophosphate and trinucleoside diphosphate as repeating units resulted in a variety of models, called RL models. All these models have alternating right and left helical segments and inverted stacking at the bend region as suggested by us earlier. It turns out that the B-Z DNA model of Wang et al. is only an example of RL models.

The selection and evaluation of new chelating agents for the treatment of iron overload

A large-scale systematic evaluation of potential iron chelators for the treatment of hemosiderosis was conducted. The compounds were identified and evaluated using a hypertransfused mouse screen in which deferrioxamine B was a standard. This screen was designed to measure iron depletion in the tissues as well as iron excretion. Groups of 10 previously hypertransfused BDF1 male mice received a single daily i.p. injection of either vehicle, standard, or test compound for 7 days. Iron in daily urine pools and individual spleen and liver homogenates was determined by atomic absorption. More than 70 chelators were evaluated, including natural and synthetic hydroxamic acids, phenols, catechols and tropolones known to have a high affinity for iron (III) in vitro. Ethylenediamine-N,N'-bis(2-hydroxyphenylacetic acid) was shown to be considerably more effective than deferrioxamine B (i.p.) and, in addition, was orally active. Factors determining the efficacy of this and other chelating agents are discussed.

Some implications of an alternative structure for DNA

We have constructed a space-filling (Corey-Pauling-Koltun) model of an alternative structure for DNA. This structure is not a double helix, but consists of a pair of polynucleotide strands lying side by side and held together by Watson-Crick base pairing. Each of the two strands has alternating right- and left-handed helical segments approximately five base pairs in length. Sugar residues in alternating segments along a strand point in opposite directions. A structure slightly different from the present one proposed earlier by ourselves and another group and in which sugars in a strand all point in the same direction is ruled out. The present structure yields natural solutions to the problems of supercoiling of DNA and of strand separation during DNA replication. This model is energetically more favorable than the double helix.

Theoretical calculations of base-base interactions in nucleic acids: I. Stacking interactions in free bases

Stacking interactions in free bases were computed on the basis of molecular association. The results of the calculations were compared with the stacking patterns observed in a few single crystals of nucleic acid components as examples. The following are the conclusions: (i) there can be two types of stacking pattern classified as normal and inverted types for any two interacting bases and both can be energetically favourable (ii) in both the types the stacking interaction is a combined effect of the overlap of the interacting bases and relative positions and orientations of the atomic centres of the two bases (iii) crystal symmetry and H-bonding interaction may influence stacking patterns.

Theoretical calculations of base-base interactions in nucleic acids: II. Stacking interactions in polynucleotides

Base-base interactions were computed for single- and double stranded poly,ucleotides, for all possible base sequences. In each case, both right and left stacking arrangements are energetically possible. The preference of one over the other depends upon the base-sequence and the orientation of the bases with respect to helix-axis. Inverted stacking arrangement is also energetically possible for both single- and double-stranded polynucleotides. Finally, interacting energies of a regular duplex and the alternative structures were compared. It was found that the type II model is energetically more favourable than the rest.

Physiology of the epididymis and induction of functional sterility in the male

The factors regulating the physiology of the epididymis and the induction of functional sterility by alteration of epididymal function are discussed. The threshold requirement of androgens to maintain the structural and functional integrity of the epididymis in the rat, hamster and monkey is much higher than that needed by the accessory glands. Further, the cauda epididymidis has a higher threshold requirement of androgens than the caput epididymidis and may reflect the differences in the availability and metabolism of androgens to these two segments. An inverse relationship exists between the levels of sialic acid (sialoproteins) in the epididymal luminal plasma and that bound to the spermatozoa in the cauda epididymidis. Androgen deprivation and consequent alteration of the secretory activity of the epididymis either by castration or by treatment with antiserum to LH or by the antiandrogen, cyproterone acetate, caused concurrent decrease in the levels of sialic acid in the luminal plasma and in the spermatozoa of the different regions of the epididymis. These changing patterns of sialic acid in the spermatozoa and luminal plasma may be associated with changes in the surface charge of the spermatozoa and the stabilization of the acrosome and its membranes during sperm maturation.