DNA conformation is determined by economics in the hydration of phosphate groups

Mixed sequence DNA can exist in two right-handed and one left-handed double helical conformations--A, B and Z. Under conditions of high water activity the B conformation prevails. If the water activity is reduced on addition of salt or organic solvents, transformation occurs to A-DNA or, in DNAs with alternating purine-pyrimidine sequences, to the left-handed Z-DNA. In crystal structure analyses of oligonucleotides, the free oxygen atoms of adjacent phosphate groups along the polynucleotide chain in B-DNA are found at least 6.6 A apart and individually hydrated whereas they are as close as 5.3 A in A-DNA and 4.4 A in Z-DNA, and bridged by water molecules. We suggest that this more economical hydration in A- and Z-DNA compared with B-DNA is the underlying cause of B----A and B----Z transitions.     

The three-dimensional structure of a DNA duplex containing looped-out bases

Unpaired bases in DNA have been assigned a possible role in the mechanism of frameshift mutagenesis in sequences with repeated base pairs. They also occur in quasipalindromic DNA sequences, which have been implicated in mutagenesis where there are no repeated base pairs, through the formation of single-stranded hairpin loops. The conformation of unpaired bases in DNA has been the subject of numerous thermodynamic as well as high resolution NMR (nuclear magnetic resonance) studies (reviewed in ref. 4). The NMR studies in solution have shown that the duplex of the tridecamer DNA fragment d(CGCAGAATTCGCG) remains intact, and that the unpaired adenosines are stacked into the duplex. Having crystallized this oligonucleotide and determined its structure, we find its conformation in the crystal is close to that of a B-DNA duplex, with the two additional adenosines looped out from the double helix and causing little disruption of the rest of the structure.     

Poly(dA).poly(dT) is a B-type double helix with a distinctively narrow minor groove

The structure of poly(dA).poly(dT) currently arouses great interest, mainly because dAn.dTn stretches are associated with considerable DNA bending. Until recently the heteronomous DNA described by Arnott et al., with the poly(dA) and poly(dT) chains in A and B conformations respectively, was the only detailed model of this structure. Following our earlier studies of the interaction of DNA and monovalent ions, we examined the X-ray diffraction of the bivalent Ca2+ salt of poly(dA).poly(dT) (Ca-poly(dA).poly(dT)) and found no sign of a heteronomous structure: Ca-poly(dA).poly(dT) in fibres shows fully equivalent B-type conformations of the opposite sugar-phosphate chains. A revision of the structure of the sodium salt, Na-poly(dA).poly(dT), based on this result, yields only a slightly heteronomous structure with each chain in a B-type conformation, which is in much better agreement with the experimental data underlying the original heteronomous model. Both structures, Ca- and Na-poly(dA).poly(dT), have a minor groove narrower than that of the B form: this peculiarity seems to be very important for the interaction of poly(dA).poly(dT) and biologically significant molecules (including proteins and antibiotics). The specific base-pair positions in poly(dA).poly(dT) may account for the DNA bending adjacent to dAn.dTn tracts.     

Use of an 125I-labelled DNA ligand to probe DNA structure

It no longer seems likely that DNA molecules in situ have a uniform conformation, represented by the classical B-form helix. For example, recent structural studies have shown that in certain conditions DNA can have a left-handed (so-called Z-form) helix, and have revealed extensive sequence-dependent variations of B-DNA helical parameters. Such sequence-dependent variations in DNA structure can be investigated in solution with reagents that bind to DNA in a conformation-dependent manner, and cut one or both strands of the double-helix at the site of binding, as, for example, has been shown for the endonuclease DNase I3. We describe here a simple way to endow a DNA-binding ligand with the ability to cleave DNA--labelling with 125I. The radiochemical damage associated with 125I decay induces a double-stranded DNA break. Using this technique we have shown that a sequence of four consecutive A X T base pairs is a necessary, but not sufficient, condition for strong binding to DNA of the bis-benzamide Hoechst 33258--presumably the other important factor is the conformation of the double-helix at the site of the (A/T)4 sequence. We suggest 125I-Hoechst 33258 may be a useful new probe of DNA structure.     

Tetramerization of an RNA oligonucleotide containing a GGGG sequence.

Poly rG can form four-stranded helices. The Hoogsteen-paired quartets of G residues on which such structures depend are so stable that they will form in 5'-GMP solutions, provided that Na+ or K+ are present (see for example, refs 2-4). Telomeric DNA sequences, which are G-rich, adopt four-stranded antiparallel G-quartet conformations in vitro, and parallel tetramerization of G-rich sequences may be involved in meiosis. Here we show that RNAs containing short runs of Gs can also tetramerize. A 19-base oligonucleotide derived from the 5S RNA of Escherichia coli (strand III), 5'GCCGAUGGUAGUGUGGGGU3', forms a K(+)-stabilized tetrameric aggregate that depends on the G residues at its 3' end. This complex is so stable that it would be surprising if similar structures do not occur in nature.     

Interconversion of single and double helices formed from synthetic molecular strands

Synthetic single-helical conformations are quite common, but the formation of double helices based on recognition between the two constituent strands is relatively rare. Known examples include duplex formation through base-pair-specific hydrogen bonding and stacking, as found in nucleic acids and their analogues, and polypeptides composed of amino acids with alternating L and D configurations. Some synthetic polymers and self-assembled fibres have double-helical winding induced by van der Waals interactions. A third mode of non-covalent interaction, coordination of organic ligands to metal ions, can give rise to double, triple and quadruple helices, although in this case the assembly is driven by the coordination geometry of the metal and the structure of the ligands, rather than by direct inter-strand complementarity. Here we describe a family of oligomeric molecules with bent conformations, which exhibit dynamic exchange between single and double molecular helices in solution, through spiral sliding of the synthetic oligomer strands. The bent conformations leading to the helical shape of the molecules result from intramolecular hydrogen bonding within 2'-pyridyl-2-pyridinecarboxamide units, with extensive intermolecular aromatic stacking stabilizing the double-stranded helices that form through dimerization.     

Circular dichroism spectra of different structures formed by the oligonucleotides

Under different conditions, oligonucleotides can form several different DNA structures such as duplex, triplex and quadruplex. All these structures exhibit an obvious difference in their CD spectra. The common characteristic is that they show a negative band at 240 nm, while in the range of 260–300 nm, the spectra are different from each other. Many factors such as chain direction, sugar puckering mode, orientation of the glycosyl bond, base stacking and sequence can affect their conformation and then show diversity and complexity in their spectra. By studying and comparing these spectra, more information about their conformations can be obtained to help predict some new structures. Furthermore, the spectra can also provide a base to study their potential biological functions.     

异优呫吨酮及其衍生物与DNA相互作用的研究

采用紫外光谱、荧光光谱、圆二色谱以及红外差谱法研究了异优呫吨酮(1,6-二羟基吨酮)(A)及其哌啶衍生物(1-羟基-6-(2-(1-哌啶基)乙氧基)呫吨酮)(B)与小牛胸腺DNA(CT-DNA)的作用方式和作用强度。结果表明,这两种化合物的紫外吸收光谱随DNA浓度的增加表现出减色效应;化合物A和B与DNA作用的结合常数分别为1.5×104,2.8×104 L/mol;DNA-EB体系的荧光强度随着两种化合物浓度的增加发生淬灭现象,化合物A和B的淬灭常数Kq分别是1.9×104,3.7×104 L/mol;两种化合物主要以嵌入方式与CT-DNA发生作用,B与DNA的结合能力比A强;并且呫吨酮芳环的嵌入使DNA螺旋变得松散、碱基堆积增强;化合物B插入后使CT-DNA的构象变化更为明显。研究结果对抗肿瘤药物的研发有一定的指导意义。     

Structure of the membrane-pore-forming fragment of colicin A

Colicins are antibiotic proteins produced by and active against sensitive Escherichia coli and closely related bacteria. They can adsorb to specific receptors located at the external surface of the outer membrane of sensitive cells, and are then translocated to their specific targets within these cells. The largest group of colicins comprises those which can form voltage-dependent channels in membranes, thereby destroying the cell's energy potential. Colicin molecules are organized in structural domains, each domain carrying one function associated with the toxin's lethal activity. The pore-forming activity seems to be located at the carboxyl terminus. A thermolytic fragment comprising amino acids 389-592 from colicin A has pore-forming properties very similar to those of the entire molecule. This fragment is soluble in aqueous medium and spontaneously inserts into lipid bilayers. We have determined the structure of the pore-forming fragment of colicin A by X-ray crystallography and refinement at 2.5 A resolution. The protein consists of ten alpha-helices organized in a three-layer structure. Two of the helices are completely buried within the structure and form a hydrophobic hairpin loop similar to that proposed for signal sequences which function in translocation. We present a model for insertion of the protein into lipid bilayers the features of which may be applicable in other biological systems involving protein insertion or translocation across membranes.     

Structure of an adenine-cytosine base pair in DNA and its implications for mismatch repair

Mutational pathways rely on introducing changes in the DNA double helix. This may be achieved by the incorporation of a noncomplementary base on replication or during genetic recombination, leading to substitution mutation. In vivo studies have shown that most combinations of base-pair mismatches can be accommodated in the DNA double helix, albeit with varying efficiencies. Fidelity of replication requires the recognition and excision of mismatched bases by proofreading enzymes and post-replicative mismatch repair systems. Rates of excision vary with the type of mismatch and there is some evidence that these are influenced by the nature of the neighbouring sequences. However, there is little experimental information about the molecular structure of mismatches and their effect on the DNA double helix. We have recently determined the crystal structures of several DNA fragments with guanine X thymine and adenine X guanine mismatches in a full turn of a B-DNA helix and now report the nature of the base pairing between adenine and cytosine in an isomorphous fragment. The base pair found in the present study is novel and we believe has not previously been demonstrated. Our results suggest that the enzymatic recognition of mismatches is likely to occur at the level of the base pairs and that the efficiency of repair can be correlated with structural features.     

Ring-opened alkylated guanine is not repaired in Z-DNA

Since the discovery of Z-DNA by X-ray analysis of the alternated hexanucleotide d(C-G)3 crystals, numerous studies have shown that fragments of natural DNAs can adopt the Z conformation, topological constraints being a major factor stabilizing this conformation. Immunochemical assays using antibodies to Z-DNA provide strong evidence for the presence of Z fragments in chromosomes. The biological role of Z-DNA is not yet known, but it might be involved in gene regulation. Proteins which bind specifically to Z-DNA have been isolated and interactions between Z-DNA and several cellular proteins have been studied. The ability of DNA repair enzymes to maintain the genome's integrity is of major importance to the cell. On alkylation of DNA by chemical carcinogens such as dimethyl sulphate, methyl methanesulphonate, methylnitrosourea or methylnitrosoguanidine, the main target is the N7 of the guanosine residue, yielding 7-methylguanine (mG). In alkaline conditions, the imidazole ring of mG opens up, yielding the ring-opened form 2,6-diamino-4-oxo-5-methylformamidopyrimidine (rom7G); this lesion is a block to DNA replication. It occurs in vivo and is enzymatically removed by the DNA glycosylase. Here we report that the lesion is not excised when present in DNA in the left-handed Z conformation.     

Conformational variations in an infectious protein determine prion strain differences

A remarkable feature of prion biology is the strain phenomenon wherein prion particles apparently composed of the same protein lead to phenotypically distinct transmissible states. To reconcile the existence of strains with the 'protein-only' hypothesis of prion transmission, it has been proposed that a single protein can misfold into multiple distinct infectious forms, one for each different strain. Several studies have found correlations between strain phenotypes and conformations of prion particles; however, whether such differences cause or are simply a secondary manifestation of prion strains remains unclear, largely due to the difficulty of creating infectious material from pure protein. Here we report a high-efficiency protocol for infecting yeast with the [PSI+] prion using amyloids composed of a recombinant Sup35 fragment (Sup-NM). Using thermal stability and electron paramagnetic resonance spectroscopy, we demonstrate that Sup-NM amyloids formed at different temperatures adopt distinct, stably propagating conformations. Infection of yeast with these different amyloid conformations leads to different [PSI+] strains. These results establish that Sup-NM adopts an infectious conformation before entering the cell--fulfilling a key prediction of the prion hypothesis--and directly demonstrate that differences in the conformation of the infectious protein determine prion strain variation.     

DNA主链构象与脱氧鸟苷组分构象相关性的喇曼分析

对小牛胸腺ＤＮＡ纤维样品溶解３ｈ内的空间构象变化过程进行了喇曼光谱分析，结果显示了表征脱氧鸟苷糖环折迭不同类型的６７２ｃｍ＾－１与６８３ｃｍ＾－１峰的同时存在，与ＤＮＡ分子主链不同特征峰的同时出现之间有着明显的联系。     

丙氨酸甘氨酸混合三、四肽构象稳定性的快速预测

使用特殊氢方法预测丙氨酸甘氨酸混合三肽和四肽分子共111个构象的相对稳定性,并与B3LYP/6-31G^＊方法的相对能量比较,得到了满意的结果.在所有111个构象中,特殊氢方法相对能量与B3LYP/6-31G^＊方法相对能量偏差绝对值大于2.0 kcal/mol的只有3个,偏差在1.0～2.0 kcal/mol之间的有18个,其余均小于1.0 kcal/mol.本文结果表明特殊氢原子在决定多肽构象稳定性方面的内秉重要性.     

Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP

The 3.3-A resolution crystal structure of the large proteolytic fragment of Escherichia coli DNA polymerase I complexed with deoxythymidine monophosphate consists of two domains, the smaller of which binds zinc-deoxythymidine monophosphate. The most striking feature of the larger domain is a deep crevice of the appropriate size and shape for binding double-stranded B-DNA. A flexible subdomain may allow the enzyme to surround completely the DNA substrate, thereby allowing processive nucleotide polymerization without enzyme dissociation.     

黄原胶水溶液结构流变性质的研究

黄原胶水溶液是石油３次开采中的新型聚合物驱油剂，研究了３种黄原胶水溶液在不同溶液浓度，不同离子强度下的流变性质，并用透射电镜观察黄原胶水溶液链的结构形态，结果表明，黄原胶水溶液的粘度和浓度间具有奇特的性质，它对应于黄原胶水溶液内在结构形态的变化，在不同离子强度下，黄原胶水溶液的螺旋结构可被诱发转变，而其结构转变的过程与所测黄原胶水溶液的流变性质吻合。     

The conformation of the DNA double helix in the crystal is dependent on its environment

Studies of the crystal structures of more than 30 synthetic DNA fragments have provided structural information about three basic forms of the double helix: A-, B- and Z-form DNA. These studies have demonstrated that the DNA double helix adopts a highly variable structure which is related to its base sequence. The extent to which such observed structures are influenced by the crystalline environment can be found by studying the same molecule in different crystalline forms. We have recently crystallized one particular oligomer in various crystal forms. Here we report the results of structural analyses of the different crystal structures and demonstrate that the DNA double helix can adopt a range of conformations in the crystalline state depending on hydration, molecular packing and temperature. These results have implications on our understanding of the influence of the environment on DNA structure, and on the modes of DNA recognition by proteins.     

The open pore conformation of potassium channels

Living cells regulate the activity of their ion channels through a process known as gating. To open the pore, protein conformational changes must occur within a channel's membrane-spanning ion pathway. KcsA and MthK, closed and opened K(+) channels, respectively, reveal how such gating transitions occur. Pore-lining 'inner' helices contain a 'gating hinge' that bends by approximately 30 degrees. In a straight conformation four inner helices form a bundle, closing the pore near its intracellular surface. In a bent configuration the inner helices splay open creating a wide (12 A) entryway. Amino-acid sequence conservation suggests a common structural basis for gating in a wide range of K(+) channels, both ligand- and voltage-gated. The open conformation favours high conduction by compressing the membrane field to the selectivity filter, and also permits large organic cations and inactivation peptides to enter the pore from the intracellular solution.