{"id":4089,"date":"2011-05-18T14:34:27","date_gmt":"2011-05-18T14:34:27","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=4089"},"modified":"2023-07-02T08:30:05","modified_gmt":"2023-07-02T07:30:05","slug":"the-inner-secrets-of-the-dna-structure","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=4089","title":{"rendered":"The inner secrets of the DNA structure."},"content":{"rendered":"
\n

In earlier posts<\/a>, I alluded to what might make DNA wind into a left or a right-handed helix. Here I switch the magnification of our structural microscope up a notch to take a look at some more inner secrets.<\/p>\n

\"\"

A fragment of a single chain of DNA, taken from a Z-helix. Click for 3D.<\/p><\/div>The 3D coordinates of this fragment were obtained by taking a crystal structure of a Z-d(CGCG)2 containing oligomer, editing (to remove water, and superfluous bases) and subjecting it to \u03c9B97XD\/6-311G(d,p)\/SCRF=water geometry refinement. This should be accurate enough to recover dispersion attractions, and various electronic and electrostatic interactions. Z-d(CGCG)2 was then reduced to the fragment you see above, which\u00a0is large enough to capture the essence of the Z-helical wind, but small enough to be able to spot things which a larger fragment might overwhelm.<\/p>\n

    \n
  1. The 3D model (click on above to obtain it) reveals that the oxygen of one of the five-membered (tetrahydrofuran) rings has a close contact to the guanine base of 2.85\u00c5. This is some 0.3\u00c5 shorter than the combined van der Waals radii, and very typical of oxygen…electrophilic carbon interactions (see discussion here<\/a> for more details). We can reasonably assume its real<\/em>. It is supported by a small NBO perturbation term (~1.1<\/strong> kcal\/mol) corresponding to donation of the oxygen lone pair into a C-N \u03c0*<\/sup> orbital.<\/li>\n
  2. The next interaction detected comes from a furanose C-H bond, in which the hydrogen approaches to within\u00a02.48\u00c5 of the oxygen on the furanose the other side of the phosphate. This is\u00a0~0.14\u00c5 shorter than the combined van der Waals distances (remember, even at the actual vdW sum, the attraction is still attractive). Why would an apparently inert C-H bond do that? Such bonds are not normally considered in such analyses. Well, this one is special.<\/li>\n
  3. It may well be (slightly) more acidic than normal due to a\u00a0C-H\u03c3<\/sub>\/C-O\u03c3<\/sub>* anti-periplanar interaction (E2 5.8<\/strong>, magenta bonds in 3D model) into the CH2<\/sub>-OH bond of the furanose. Hence the acidified H can form a weak(ish) hydrogen bond to the oxygen. The NBO E2 energy is 1.4<\/strong> from the Olp<\/sub> to the C-H*<\/sup> bond (larger E2 interactions normally occur through bonds, but this one is through space, <\/em>which is why it is smaller).<\/li>\n
  4. These two interactions in turn set up a good orientation for the guanine to create a strong anomeric effect\u00a0between it and the ribose; NLp<\/sub>\/C-O\u03c3<\/sub>*<\/sup>;\u00a0E2 11.6<\/strong> (violet bond in 3D model, blue bond b<\/em><\/strong> in above diagram). To calibrate this interaction, anomeric effects in sugars are of the order of 14-16 kcal\/mol. These stereoelectronic effect helps to slightly rigidify the relationship between the guanine base and the furanose it is connected to.<\/li>\n
  5. In contrast, the cytosine-furanose link avoids the classical anomeric effect, and instead sets up a weaker one with a C-C bond instead (E2 6.8<\/strong>, indigo bond, blue bond a<\/strong><\/em> in above diagram). The Nlp <\/sub>is not as good a donor, because it is sequestered into the adjacent carbonyl group on the cytosine. The guanine has no such adjacent group, and so its Nlp <\/sub> is a better donor. The outcome of all of this is that the two bases, C<\/strong> and G<\/strong> end up having a different geometrical relationship to the furanose they are each connected to.<\/li>\n
  6. Notice the\u00a0gauche<\/em>-like conformation of the ethane-1,2-diol fragment (gold bond in 3D model), which is again due to stereoelectronic alignments<\/a>.<\/li>\n
  7. Notice the Nlp<\/sub> …H-C distance of 2.51\u00c5, which like 2<\/strong> above, is around the sum of the vdW radii. It might be slightly more than just a dispersion attraction, since the NBO E2 Nlp<\/sub>\/C-H* <\/sub>through space<\/em> interaction is ~2<\/strong> kcal\/mol.<\/li>\n
  8. There are some other relatively close atom-atom approaches, but I do not list them here.\u00a0Do explore them yourself (they are labelled 8 in the diagram below).<\/li>\n<\/ol>\n

    To complete the present analysis, I include an ELF diagram. This can locate lone-pairs (as monosynaptic basins) as well as bond pairs (disynaptic basins) and so is useful for visualising the anti-periplanar anomeric effects between a lone pair and a bond (connecting a mono and a disynaptic basin if you like). Some of the interactions described in the list above are shown below with dotted lines (note that some of the lone pairs appear as two basins, distributed either face of the aromatic base).<\/p>\n

    \"\"

    ELF analysis. Click for 3D.<\/p><\/div>Well, cranking up the magnification on a microscope will always reveal new details. You might ask if these new details matter? Well, since DNA is such a very long polymer, repeating even a very weak (but predictable) interaction millions of times is bound to have some sort of cumulative effect. Who knows which of the ones above might play an important role in the super-winding of DNA, or its packing into a cell, or interaction with proteins, and so on. I do wonder how many of the terms I have identified above have been previously considered for such roles. Anyone know?<\/p>\n

    Postscript<\/strong>: Shown below is a \u00a0non-covalent-analysis (NCI, \u00a0see earlier post<\/a>). A reminder that the interaction surface is colour coded with orange or red tinge if repulsive, blue if attractive, and green for weaker interactions. These surfaces pretty much recapitulate what it itemised above, adding also other interactions not listed above (labelled 8 in diagram).<\/p>\n

    \"\"

    NCI analysis for Z-CG fragment. Click for 3D.<\/p><\/div>\n

    \n

    This post has DOI: 10.14469\/hpc\/12767<\/p>\n

    \n\n<\/div> ","protected":false},"excerpt":{"rendered":"

    In earlier posts, I alluded to what might make DNA wind into a left or a right-handed helix. Here I switch the magnification of our structural microscope up a notch to take a look at some more inner secrets. The 3D coordinates of this fragment were obtained by taking a crystal structure of a Z-d(CGCG)2 […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"activitypub_content_warning":"","activitypub_content_visibility":"","activitypub_max_image_attachments":5,"activitypub_interaction_policy_quote":"anyone","activitypub_status":"","footnotes":"","jetpack_publicize_message":"","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":false,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2},"jetpack_post_was_ever_published":false},"categories":[1,4],"tags":[534,533,17,24,249,535,317,373,572],"ppma_author":[2661],"class_list":["post-4089","post","type-post","status-publish","format-standard","hentry","category-general","category-interesting-chemistry","tag-adjacent","tag-adjacent-carbonyl","tag-conformational-analysis","tag-energy","tag-julia-contreras-garcia","tag-n-lp","tag-postscript","tag-tutorial-material","tag-watoc11"],"yoast_head":"\nThe inner secrets of the DNA structure. - Henry Rzepa's Blog<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=4089\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"The inner secrets of the DNA structure. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"In earlier posts, I alluded to what might make DNA wind into a left or a right-handed helix. 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These calculations involved optimising the positions of around 250-254 atoms, for d(CGCG)2 and d(ATAT)2, an undertaking which has taken about two months of computer time! The geometries are finally optimised to the\u2026","rel":"","context":"In "Interesting chemistry"","block_context":{"text":"Interesting chemistry","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=4"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":3326,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=3326","url_meta":{"origin":4089,"position":1},"title":"A comparison of left and right handed DNA double-helix models.","author":"Henry Rzepa","date":"January 1, 2011","format":false,"excerpt":"When Watson and Crick (WC) constructed their famous 3D model for DNA, they had to decide whether to make the double helix left or right handed. They chose a right-handed turn, on the grounds that their attempts at left-handed models all \"violated permissible van der Waals contacts\". No details of\u2026","rel":"","context":"In "Interesting chemistry"","block_context":{"text":"Interesting chemistry","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=4"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/01\/CGCG.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":19159,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=19159","url_meta":{"origin":4089,"position":2},"title":"A form of life that can stably store genetic information using a six-letter, three-base-pair alphabet?","author":"Henry Rzepa","date":"December 2, 2017","format":false,"excerpt":"For around 16 years, Floyd Romesberg's group has been exploring un-natural alternatives (UBPs) to the Watson-Crick base pairs (C-G and A-T) that form part of the genetic code in DNA. Recently they have had remarkable success with one such base\u00a0pair, called X and Y (for the press) and dNaMTP and\u2026","rel":"","context":"In "Interesting chemistry"","block_context":{"text":"Interesting chemistry","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=4"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":3235,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=3235","url_meta":{"origin":4089,"position":3},"title":"The handedness of DNA: an unheralded connection.","author":"Henry Rzepa","date":"December 29, 2010","format":false,"excerpt":"Science is about making connections. Plenty are on show in Watson and Crick's famous 1953 article on the structure of DNA but often with the tersest of explanations. Take for example their statement \"Both chains follow right-handed helices\". Where did that come from? This post will explore the subtle implications\u2026","rel":"","context":"In "Interesting chemistry"","block_context":{"text":"Interesting chemistry","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=4"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/12\/tartrate.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":3802,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=3802","url_meta":{"origin":4089,"position":4},"title":"Why are \u03b1-helices in proteins mostly right handed?","author":"Henry Rzepa","date":"April 9, 2011","format":false,"excerpt":"Understanding why and how proteins fold continues to be a grand challenge in science. I have described how Wrinch in 1936 made a bold proposal for the mechanism, which however flew in the face of much of then known chemistry. Linus Pauling took most of the credit (and a Nobel\u2026","rel":"","context":"In "Interesting chemistry"","block_context":{"text":"Interesting chemistry","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=4"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/04\/left-n.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":16997,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16997","url_meta":{"origin":4089,"position":5},"title":"An inorganic double helix: SnIP.","author":"Henry Rzepa","date":"October 16, 2016","format":false,"excerpt":"After sixty years of searching, the first non-templated double helical carbon-free inorganic molecular structure has been reported. That is so neat that I thought to load the 3D coordinates here for you to interact with\u00a0and then to explore the prospect of using these coordinates to add some\u00a0value with\u00a0e.g. some chiroptical\u2026","rel":"","context":"In "Chemical IT"","block_context":{"text":"Chemical IT","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2"},"img":{"alt_text":"snip","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/10\/SnIP.jpg?resize=350%2C200","width":350,"height":200},"classes":[]}],"jetpack_likes_enabled":false,"authors":[{"term_id":2661,"user_id":1,"is_guest":0,"slug":"admin","display_name":"Henry Rzepa","avatar_url":"https:\/\/secure.gravatar.com\/avatar\/897b6740f7f599bca7942cdf7d7914af5988937ae0e3869ab09aebb87f26a731?s=96&d=blank&r=g","0":null,"1":"","2":"","3":"","4":"","5":"","6":"","7":"","8":""}],"_links":{"self":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/4089","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=4089"}],"version-history":[{"count":2,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/4089\/revisions"}],"predecessor-version":[{"id":26197,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/4089\/revisions\/26197"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=4089"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=4089"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=4089"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=4089"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}