Tag Archives: crystallography

SCIENTISTS TELL US ABOUT THEIR LIFE AND WORK, PART 8

 

Quotations by Prof. Nadrian (Ned) C. Seeman (from pages 20 and 23 of his Living History essay in ACA RefleXions, American Crystallographic Association, Summer 2014, Number 2, pages 19-23)
Quotations by Prof. Nadrian (Ned) C. Seeman (from pages 20 and 23 of his Living History essay in ACA RefleXions, American Crystallographic Association, Summer 2014, Number 2, pages 19-23)

 

In this series, I am recommending to you a few life stories about real scientists.  I prefer to let these scientists tell their own stories where possible.  Autobiographical accounts are interesting and entertaining for both non-scientists and other scientists.  My selections here mostly involve scientists I either know personally or at least know about.  If further materials like this are needed, they can be obtained readily on the internet or with input from librarians at public or university libraries, science teachers, and other scientists.

In the preceding segment of this series, the story of a very celebrated basic research scientist working on Protein Dynamics in Cell Biology was recommended (see “Scientists Tell Us About Their Life and Work, Part 7”).  Part 8 presents the life story of a research scientist who dreamed up and established an amazingly novel new branch of chemical engineering based upon the well-known double-helix of DNA.

Part 8 Recommendations:  NEW NANOSTRUCTURES BASED ON DNA

Prof. Nadrian (Ned) C. Seeman (1945 – present) originated several new fields of science and engineering: DNA Nanotechnology, DNA-Based Crystallography, and DNA-Based Computation.  His very creative investigations and innovative new concepts for “Structural DNA Technology” often were developed for practical applications (e.g., better production of highly ordered macromolecular crystals, nanocomputation, nano-electronics, nanomedicine, and nanorobotics); thus, he is both a basic and an applied researcher.  All of his dramatic innovations and unusual research topics are based on the structure and properties of DNA.  Numerous other research labs around the world now also are working with DNA-based nanostructures.

DNA is known to most as the double-stranded genetic material making up chromosomes.  The binding between each of the 2 associated strands takes place by specific pairing between their individual nucleotide bases; this binding is very specific and fairly strong.  In the laboratory, segments of synthetic single-stranded DNA can be  hybridized (reassociated) to form new double-stranded DNA; branch points and unpaired base sequences at the termini can be produced as desired, and are key points of technology for using DNA to produce new nanostructures.  Seeman developed and used these characteristic features from the early 1980’s to form self-assembled DNA polygons, and, 2-D and 3-D lattices; subsequently, he went on to invent nanomechanical devices (e.g., synthetic computers, robots, translators, and walkers), and other nanostructures (e.g., superstructures of DNA associated with other species, and nano-assembly lines).  In 2004-5, he was the founding president of a new professional science association, the International Society for Nanoscale Science, Computation and Engineering (see:  http://isnsce.org/ ).

Seeman’s unconventional research involves unique combinations of biochemistry, biophysics, chemical engineering, computer science, crystallography, nanoscience and nanotechnology, structural biology, and, thermodynamics.  His creative ideas and amazing lab studies for making new nanostructures involve both theory and practice, and are also being used to advance scientific knowledge and understanding about the biophysics of intermediates in the recombination of chromosomal DNA during its replication.

Prof. Seeman chairs the Department of Chemistry at New York University.  He has received many honors for his pioneering research, including the Sidhu Award from the Pittsburg Diffraction Society (1974), a Research Career Development Award from the National Institutes of Health (1982), the Science and Technology Award from Popular Science Magazine (1993), the Feynman Prize in Nanotechnology (1995), and the Nichols Medal from the NY Section of the American Chemical Society (2008).  He is an elected member of the Norwegian Academy of Science and Letters, a Fellow of the Royal Society of Chemistry (U.K.), and holds an Einstein Professorship from the Chinese Academy of Sciences.  In 2010, Prof Seeman and Prof. Donald Eigler (IBM Almaden Research Center, San Jose, California) were jointly honored as awardees of the Kavli Prize in Nanoscience [1]; also see the photo of these 2 awardees receiving their Kavli Prize from H. M. King Harald of Norway [2].  Seeman is without question an embodiment of what Dr.M wrote about in an earlier essay on the significance of curiosity, creativity, inventiveness, and individualism in science (see:  http://dr-monsrs.net/2014/02/25/curiosity-creativity-inventiveness-and-individualism-in-science/ ).

[1]  Kavli Foundation, 2010.  2010 Kavli Prize in Nanoscience.  Available on the internet at:
http://www.kavlifoundation.org/2010-nanoscience-citation .

[2]   Kavli Foundation, 2010.  The Kavli Prize in Nanoscience (2010).  Available on the internet at:  http://registration.kavliprize.org/seksjon/vis.html?tid=27454 .

Lots of interesting information about Prof. Seeman is displayed on his laboratory home page (see: http://seemanlab4.chem.nyu.edu/ ).  My recommendations (below) start with Seeman’s own explanation of his research in DNA Nanotechnology, as written for non-scientists (1A).  For working scientists, his review article provides a stimulating overview (1B).  The second recommendation (2) is an official summary of why Seeman and Eigler were selected for the Kavli Prize in Nanoscience in 2010.  The third item is Prof. Seeman’s personal description about his own career in science (3), and is filled with stories and anecdotes about both his difficulties and his triumphs; all readers will find this to be a very fascinating account.  Dr.M considers that essay to be extraordinary, since it is probably the most unusually forthright and outspoken piece ever authored by a modern scientist.

(1A)  Seeman, N. C., 2004.  Nanotechnology and the double helix (preview).  Scientific American  290:64-75.  Available on the internet at:
 http://www.scientificamerican.com/article/nanotechnology-and-the-double-helix .

(1B)  Seeman, N. C., 2010.  Nanomaterials based on DNA.  Annual Review of Biochemistry  79:65-87.  Available on the internet at:
http://www.annualreviews.org/doi/pdf/10.1146/annurev-biochem-060308-102244 .

(2)  Kavli Foundation, 2010.  2010 Nanoscience Prize explanatory notes.  Available on the internet at:
http://www.kavlifoundation.org/2010-nanoscience-prize-explanatory-notes .

(3)  Seeman, N. C., 2014.  The crystallographic roots of DNA nanotechnology.  ACA RefleXions, American Crystallographic Association, Number 2, Summer 2014, pages 19-23.  Available on the internet at: http://www.amercrystalassn.org/documents/2014%20newsletters/Summer%202014%20WEB.pdf .

 

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LET’S JOIN IN CELEBRATING THE INTERNATIONAL YEAR OF CRYSTALLOGRAPHY!!

 

Schematic of ordering in 1, 2, and 3 dimensions.  Top view looks downward onto the flat object; side view is at 90 degrees and looks onto the edge.  1-D ordering is a row of 5 associated subunits.  2-D ordering has 4 associated rows of 5 subunits. 3-D ordering has a layer of 12 subunits on top of the 20 subunits in the 2-D array.   (http:dr-monsrs.net)
Schematic of ordering in 1, 2, and 3 dimensions. Top view looks downward onto the flat object; side view is at 90 degrees and looks onto the edge. 1-D ordering is a row of 5 associated subunits. 2-D ordering has 4 associated rows of 5 subunits. 3-D ordering has a layer of 12 subunits above the 20 subunits in 2-D array.  (http://dr-monsrs.net)

2014 is the 100th year since the discovery that a beam of x-rays directed onto a single crystal comes out as multiple beams forming discrete spots.  That monumental finding has been called one the most important scientific research discoveries of all time.  Everyone in the entire public now is invited to celebrate this special 2014, designated by the United Nations as the International Year of Crystallography (IYCr2014)!  Below, I give the briefest possible non-mathematical introduction to the basic essentials of crystals and crystallography, along with some recommended internet websites where much further information is available.

What are crystals? 

We all encounter crystals every day, but most know little about them.  Crystals consist of matter whose smallest subunits (i.e., molecules or macromolecules) are very highly ordered in all 3 dimensions (3-D), as depicted in the opening figure above.  Some typical examples of the numerous crystals we commonly see are table salt (sodium chloride), diamonds in rings and jewelry (carbon), ice (water), and small granules of sugar (glucose).  If you have a magnifier, take a look now at what is in your salt shaker and you will observe many tiny crystals!

The 3-D ordering of the components making up crystals is so perfect that each and every subunit has exactly the same orientation and positioning as do all its neighbors.  This means that the atoms making up each subunit also have identical positioning to those in other subunits.  When a beam of x-rays is directed onto a single crystal in a suitable manner, each atom in the highly ordered complex scatters the incoming radiation identically into discrete spots.  The array of different spots produced from one crystal is the sum of the rays scattered by all its component atoms; because the innumerable atoms are so highly ordered, the many scattered rays join to form discrete spots.

What is diffraction? 

Diffraction is a fundamental property of atoms whereby incoming x-rays, electrons, or neutrons are scattered at characteristic angles and intensities.  The numerous scattered rays form an ordered array of diffraction spots and rings known as a diffraction pattern.  A single crystal produces one set of periodic diffraction spots, 2 crystals produce 2 sets of spots (at different rotations), and multiple crystals in polycrystalline materials will produce diffraction rings (i.e., many sets of the same spots at numerous different rotations).  The periodic order in diffraction patterns directly corresponds to the ordered position of the different atoms inside crystals; this means that diffraction patterns show atomic structure of the material making up each crystal.  The diffraction pattern is totally distinctive for each crystalline material, since the locations (atomic spacings) and brightness (kinds and numbers of atoms) of spots or rings are unique for each kind of crystalline matter.

What is crystallography? 

Crystallography is a research methodology for studying crystals.  Diffraction patterns are used in crystallography to tell us about the arrangement of the component atoms inside many different materials.  Since the beginning of x-ray crystallography one century ago, many thousands of materials have been crystallized and examined by crystallography; these include catalysts, enzymes, metals, minerals and biominerals, newly synthesized chemical compounds, proteins, salts, viruses, etc.   Because the atoms inside crystals are so highly ordered in an identical manner, diffraction patterns can be recorded, measured, and then processed by computation to determine structure down to the level of individual atoms.  This atomic structure determination of crystalline matter is the magic of crystallography!

Crystallography is a global activity for both science and industry, and almost all countries have scientists working as crystallographers.  X-ray diffraction is the most frequently used approach for crystallography, and now is quite automated through the use of computers to carry out the extensive numerical calculations needed to define an unknown structure to a high level of resolution.  Crystallography can be performed with laboratory x-ray sources or with very powerful and very fast x-rays produced by synchrotrons.   The hugely expensive synchrotron facilities are rather few in number, but have well-organized programs permitting their use by many visiting scientists.  Diffraction of electrons or neutrons also provides valuable special knowledge about structure at the atomic level.  When all is said and done, crystallography simply is a special way of looking at structure.

Not all materials are crystalline

Not all substances are naturally crystalline or can be induced to form crystals.  If the atoms in some substance are not ordered at all (i.e., they are randomly distributed), then this material is said to be in the amorphous state.  Examples of amorphous materials we see frequently include liquid water, many plastics, and air.  Inducing the formation of very highly ordered crystals is an essential requirement for structure determination by x-ray crystallography, since amorphous materials do not produce any diffraction spots or rings.

How does crystallography matter to you and me? 

Why do research scientists spend so much time and effort to use the magic of crystallography for determining the atomic structure of many kinds of physical, chemical, and biological materials?  The answer is that this knowledge about structure always provides information about functional capabilities and mechanisms for activities.  As one example, consider what can be derived from new knowledge about the high resolution structure of a virus; this will often increase  understanding about its biogenesis, mechanism for infecting host cells, immunoreactivity, and differences from other viruses.  Knowledge about functional capabilities  always is immensely valuable for both science and industry; for example: functioning of some inorganic catalyst or enzyme (e.g., mechanisms for activity and activation), interactions with other ions and molecules (e.g., changed functioning upon binding), formation of functional complexes (e.g., complex multi-protein assemblies), arrangement to form some more complex object (e.g., associations of 2-D polymers), changes producing specific toxic effects, prerequisites for binding to various ligands. sequential steps in genesis, characteristics of new materials (e.g., nano-materials made in university or industrial labs), etc.

Where can more information be found about crystals, crystallography, and IYCr2014? 

In the year-long world-wide celebration of crystallography and crystallographers during IYCr2014, many very fascinating programs for non-scientists now are being featured on the internet.  A large directory of instructive videos about crystals and crystallography for IYCr2014 is available at:  http://iycr2014.org/learn/watch .  Dr.M gives a rating of ‘outstanding’ to “Diving into the Heart of the Molecules of Life”, which shows how modern protein crystallography is done (http://www.youtube.com/watch?v=GfOyZch6llo ); regardless of which branch of science you prefer, Dr.M encourages everyone to see this video.

The International Union of Crystallography, which coordinates the international congresses on crystallography, has a special area on its website explaining the current celebration of IYCr2014 (see  http://www.iycr2014.org/about/video , and,  http://www.iycr2014.org/about  ).  Other large areas provide a listing of many internet resources and web tutorials dealing with crystals and crystallography; these include educational materials for students and teachers, and, recipes and instructions for growing your own crystals ( http://www.iycr2014.org/learn/educational-materials ).  The American Crystallographic Association has annual meetings that always include a special presentation aimed to instruct ordinary people about crystals and crystallography ( http://www.amercrystalassn.org/ ); this and many other national or regional crystallography societies also feature special IYCr2014 programs on their websites.

Visitors to Dr.M’s website are urged to take a look at any of these internet resources.  You don’t have to be a scientist to love crystals!  The IYCr2014 is for everyone, and that includes you!

 

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