Stereochemical details of the side-by-side model for DNA

The probable structure of the protamine–DNA complex

A detailed molecular structure is proposed for the human protamine-DNA complex, which has hitherto been largely a mystery. The structure was created with virtual modeling software (AmiraMol), employing logical deduction as the primary investigative tool. A beta-sheet structure for the protein component is essentially mandated, as the alternatives can be decisively excluded. A dimeric structure too is essentially mandated, since the cysteine residues of protamines P1 and P2 are invariably aligned in all species having both chains. The cross-sectional and axial spacings of arginine guanidinium groups in this protein structure can be perfectly aligned with those of phosphate groups in DNA according to the DNA structure proposed by Wu. This is a non-helical structure, whose possible occurrence in certain plasmids has been suggested by experimental observations. The unit cell of this protamine-DNA complex is essentially devoid of steric hindrances, and heavily favored by a multitude of ionic and hydrogen bonds. The packing of adjacent "unit cells" of the protamine-DNA structure is based on a complex array of salt bridges, the mere existence of which is so fortuitous that it is virtually inconceivable that it comes about through a mere modeling "coincidence". The possible significance of the structure beyond the sperm cell is discussed.

Crystal structure of a partly self-complementary peptide nucleic acid (PNA) oligomer showing a duplex-triplex network

The X-ray structure of a partly self-complementary peptide nucleic acid (PNA) decamer (H-GTAGATCACT-l-Lys-NH(2)) to 2.60 A resolution is reported. The structure is mainly controlled by the canonical Watson-Crick base pairs formed by the self-complementary stretch of four bases in the middle of the decamer (G(4)A(5)T(6)C(7)). One right- and one left-handed Watson-Crick duplex are formed. The two PNA units C(9)T(10) change helical handedness, so that each PNA strand contains both a right- and a left-handed section. The changed handedness in C(9)T(10) allows formation of Hoogsteen hydrogen bonding between C(9)T(10) and G(4)A(5) of a PNA strand in an adjacent Watson-Crick double helix of the same handedness. Thereby, a PNA-PNA-PNA triplex is formed. The PNA unit A(3) forms a noncanonical base pair with A(8) in a symmetry-related strand of opposite handedness; the base pair is of the A-A reverse Hoogsteen type. The structural diversity of this PNA demonstrates how the PNA backbone is able to adapt to structures governed by the stacking and hydrogen-bonding interactions between the nucleobases. The crystal structure further shows how PNA oligomers containing limited sequence complementarity may form complex hydrogen-bonding networks.

The DNA double helix fifty years on

This year marks the 50th anniversary of the proposal of a double helical structure for DNA by James Watson and Francis Crick. The place of this proposal in the history and development of molecular biology is discussed. Several other discoveries that occurred in the middle of the twentieth century were perhaps equally important to our understanding of cellular processes; however, none of these captured the attention and imagination of the public to the same extent as the double helix. The existence of multiple forms of DNA and the uses of DNA in biological technologies is presented. DNA is also finding increasing use as a material due to its rather unusual structural and physical characteristics as well as its ready availability.

Mental tools for thinking about DNA technologies in new ways

OBJECTIVE

To investigate the nature of creative thinking in biomedical science with specific applications to molecular pathologies and DNA technologies.

DATA SOURCES

Accounts of breakthroughs and inventions contained in autobiographies, biographies, interviews, and archival sources.

STUDY SELECTION

Discoveries that have altered, or may yet alter, basic textbook accounts of biomedical sciences for which appropriate data sources exist.

DATA EXTRACTION

Approximately 1000 data sources were analyzed, both within appropriate sciences and in other creative fields, such as the arts.

DATA SYNTHESIS

The current analysis is based on a framework described in our previous book, Sparks of Genius, which outlines a general approach to understanding creative thinking.

CONCLUSIONS

Creative thinking in all disciplines depends on a common mental "toolkit" that consists of 13 fundamental tools: observing, imaging, abstracting, pattern recognition, pattern forming, analogizing, body thinking, empathizing, dimensional thinking, modeling, playing, transforming, and synthesizing. Scientists recognize and solve problems by observing data that break the patterns established by theories; exploring a system by creating an abstract model with which they can play; and transforming data into feelings, sounds, and other forms that create surprising analogies to already-understood principles. The result of such personal thinking is knowledge combined with sensation and emotion--feeling and understanding synthesized into complete awareness. We illustrate some of these modes of thinking with reference to recent breakthroughs in DNA-related areas and suggest ways in which the use of "tools for thinking" can increase the probability of making further discoveries in the biomedical sciences.

Crystal studies of B-DNA: the answers and the questions

The history of DNA crystallography is reviewed and is followed by discussion of the methods used for structure determination. The features of B-DNA molecular and crystal structures are described.

Structure factor calculations for a side-by-side model of B-DNA

In this paper, the side-by-side model of DNA proposed by Premilat and Albiser is investigated. The axial repeat of the model is equal to the c-axis repeat in the observed B-DNA unit cell in fibres. However, the model does not pack into the unit cell as efficiently as the B-DNA double helix does, nor is it as successful as the double helix in predicting the observed Bragg amplitudes. When the azimuthal orientations and the relative axial displacements of the two molecules in the unit cell are allowed to take general values, the best crystallographic R factor for the side-by-side model is 43.43% compared with 34.33% for the double helix. If constraints consistent with the accepted B-DNA space group, P2(1)2(1)2(1), are applied, the best R factors are 45.53% for the side-by-side model and 34.51% for the double helix. Therefore, the side-by-side model can be rejected as a possible conformation for B-DNA in crystalline fibres.

Paranemic structures of DNA and their role in DNA unwinding

A DNA structure is defined as paranemic if the participating strands can be separated without mutual rotation of the opposite strands. The experimental methods employed to detect paranemic, unwound, DNA regions is described, including probing by single-strand specific nucleases (SNN), conformation-specific chemical probes, topoisomer analysis, NMR, and other physical methods. The available evidence for the following paranemic structures is surveyed: single-stranded DNA, slippage structures, cruciforms, alternating B-Z regions, triplexes (H-DNA), paranemic duplexes and RNA, protein-stabilized paranemic DNA. The problem of DNA unwinding during gene copying processes is analyzed; the possibility that extended paranemic DNA regions are transiently formed during replication, transcription, and recombination is considered, and the evidence supporting the participation of paranemic DNA forms in genes committed to or undergoing copying processes is summarized.

Reason in the Zeitgeist

The pages of the history of science record thousands of instances of similar discoveries having been made by scientists working independently of one another. Sometimes the discoveries are simultaneous or almost so; sometimes a scientist will make anew a discovery which, unknown to him, somebody else had made years before.

NMR studies of conformational states and dynamics of DNA

The application of high resolution NMR techniques to the investigation of DNA double helices in solution is currently in a rapid state of change as a result of advances in three different fields. First, new methods (cloning, enzymatic degradation, sonication, and chemical synthesis) have been developed for producing large quantities of short DNA suitable for NMR studies. Second, there have been major advances in the field of NMR in terms of the introduction of new pulse techniques and improvements in instrumentation. Finally, as a result of recent X-ray diffraction studies on short DNA helices and the discovery of left-handed Z-DNA there is heightened interest in the study of DNA structures in solution and the effect of sequence on structure. In the present review, we discuss the way in which NMR techniques have been used to probe various aspects of the DNA properties, including base pairing structure, dynamics of breathing, effect of sequence on DNA structure, internal molecular motions, the effect of environment on the DNA, and the interaction of DNA with small ligands.