How to Make a DNA Model

Figure 1

One of the students I tutor had to build a DNA model for an assignment for 9^th grade biology. We built our model, photographed it and posted it on Facebook. Some friends saw the picture and asked me to post instructions, so they could build similar models with their kids.

Let’s start with the basics.

DNA consists of several units:

• Phosphates and ribose molecules comprise the backbone. The phosphates and riboses alternate.
• The two strands of the phosphate-ribose backbone are antiparallel. That means the two strands go in opposite directions.
• The cross-links are the nucleotide base pairs.
• The nucleotides are: Adenine (A), Guanine (G), Cytosine (C) and Thymidine (T).
• Adenine and Guanine are purines. Cytosine and Thymidine are pyrimidines.
• Correct base pairing is A with T and G with C. (Figure 1)
• A-T base pairs are connected by two hydrogen bonds.  G-C base pairs are connected with three hydrogen bonds. (Figure 1)
• DNA forms a right-handed helix. In other words, when you look down from the end, the twist is counterclockwise.
• One twist occurs about every ten base pairs.

The assignment stated that the model must be made with household items, not a molecular model kit. We chose wire and beads. The assignment also had several criteria to make the finished model as realistic as possible. The criteria were:

• The phosphate-ribose backbones must be antiparallel. This means that if you start with a ribose on one strand, start with a phosphate on the opposite strand. In our model, the ribose molecules were five-pointed stars, so we were able to emphasize the directionality with the star beads. (Figure 1)
• The ribose molecules must be larger than the phosphate molecules.
• The ribose and phosphate molecules must be different shapes or different colors.
• Base pairing must be correct. (A with T and G with C)
• Purines (A and G) must be larger than pyrimidines (C and T).
• Base pairs must be attached to the ribose molecules only.
• The hydrogen bonds must be smaller than the nucleotides.
• The model must include at least 15 base pairs.
• The model must include at least two twists.

Materials:

• 18-gauge plastic-coated steel wire for the phosphate-ribose backbone. (This wire is sturdy enough to support the structure, yet malleable enough to bend and twist.)
• 22-gauge dark annealed steel wire for the cross-links. (This wire was bendable and worked for the project. However, the dark coating rubbed off on our hands. Another type of thin malleable wire might work better.)
• Pony beads for the phosphate molecules – at least 60.
• Star-shaped crafting beads for the ribose molecules – at least 60. (The ones I bought were plastic with a metallic-sheen coating.) Make sure the hole in the bead is big enough to allow both the 18 gauge and 22 gauge wires to go through at the same time.
• Wooden beads of assorted shapes and colors for the nucleotides. You’ll need four types of beads and approximately 15 beads of each. The A and G beads must be larger than the C and T beads. The A beads should be a different color than the T beads. The G beads should be a different color than the C beads. Make sure the 22 gauge wire will go through the hole in the beads.
• Drinking straws in two colors
• A sharpie marker
• Scissors
• Wire cutters
• Needle-nosed pliers
• A platform (We used a piece of Styrofoam. Clay would also work. Alternately, the model can hang from a string.)

Methods:

Create the phosphate-ribose backbone.

• Cut two 2.5-foot lengths of the 18-gauge wire.
• Bend a small loop in one end of each wire so the beads don’t slide off.
• Start one strand with a phosphate (pony bead). Alternate riboses (stars) and phosphates (pony beads) until you have 30 beads on the wire.
• The second strand must be antiparallel. That means you need to start with a ribose (star) and follow with a phosphate (pony bead). Make sure the stars point in opposite directions on the two strands. String 30 beads on the wire.
• Bend a small loop in the far end of the wire so no beads slide off.

Create the nucleotide cross-links.

• Remember the nucleotides must be connected to the ribose molecules. (The nucleotides are supposed to be connected only to the ribose molecules, but we twisted the 22-gauge wire around the 18-gauge wire for stability. This slight structural convenience is hidden by the beads.)
• Use the sharpie to label the wooden beads with A, G, C or T. Make sure the As and Gs are larger than the Cs and Ts.
• Flatten two drinking straws. Make two vertical lines on both sides on one straw with the marker. Make three vertical lines on both sides of the other straw.
• Cut straws into short pieces (smaller than the nucleotide beads). The pieces of straw are hydrogen bonds.
• Cut 30 seven-inch pieces of 22-gauge wire.
• Loop the 22-gauge wire once or twice around the 18-gauge wire between the phosphate and the ribose beads.
• Twist the 22-gauge wire around the arms of the ribose star. Do not use all of the seven inches.
• String a nucleotide bead on the 22-gauge wire.
• String the appropriate hydrogen bond (straw pieces) next. Remember A-T base pairs have 2 hydrogen bonds and C-G base pairs have 3 hydrogen bonds.
• String the appropriate nucleotide bead to pair with the first on the cross-bridge. (If the first was a C, string a G. If the first was a T, string an A, etc.)
• Twist the end of the 22-gauge wire around the star on the opposite strand to secure.
• Repeat until all of the ribose molecules (stars) on the two strands have cross-bridges. 

Create the double helix.

• You may have extra 18-gauge wire at the top of the phosphate ribose backbones that needs to be trimmed.
• We made one-inch loops at the top to insert into the Styrofoam platform. Other types of platforms may require different wire accommodations.
• When you figure out how much wire you’ll need to attach the DNA to the platform, trim the 18-gauge wire and make loops in the ends.
• Look at the DNA molecule end-on so the loops in the wire are facing you.
• Twist the structure counterclockwise to create a right-handed helix.
• Try to get about ten base pairs per turn.
• Attach the structure to the platform or hang it with string.

Asymptote Anecdote

During a discussion of science jokes with a group of friends, I mentioned that the asymptote is the mathematical model for my writing career. It’s a joke many people don’t get. 

Merriam Webster’s definition of asymptote is "a straight line associated with a curve such that as a point moves along an infinite branch of the curve the distance from the point to the line approaches zero and the slope of the curve at the point approaches the slope of the line," 

In other words, the curve approaches the line, gets infinitely close to it, yet never crosses it.  

One person asked about the origin of the word. Asymptote likely comes from Greek asymptōtos not meeting, from a- + sympiptein to meet.” (also Merriam Webster) 

To my surprise, I discovered Merriam Webster lists rhyming words. I don’t write in rhyme, but consider the possibilities of billy goat, sticky note, or even quarter note. Here’s Merriam Webster’s list: 

anecdote, antidote, assault boat, billy goat, Capriote, cashmere goat, casting vote, Corfiote, creosote, dead man's float, entrecôte, ferryboat, flying boat, get one's goat, Huhehot, locomote, matelote, miss the boat, morning coat, motorboat, mountain goat, nanny goat, overcoat, paddleboat, papillote, passing note, pedal-note, petticoat, picketboat, polo coat, powerboat, quarter note, redingote, riverboat, rock the boat, rubythroat, Shabuoth, Sialkot, sixteenth note, sticky note, sugarcoat, symbiote, table d'hôte, undercoat, yellowthroat

Pass the Mustard

Here’s an addition to my ancient pottery series. (link, link, link) 

Archaeologists analyzing food remains on the inside of ancient pottery discovered that 6000 years ago humans seasoned their food with mustard seeds (article). From other food remains in the pottery shards, they can tell that the mustard was added to meat from land animals and marine life as well as starchy plants. Mustard is not a significant source of calories or nutrients, so the seeds were probably a flavor enhancer. Previously, the earliest known use of seasoning was 4500 years ago in Northern India where turmeric and ginger were used. 

No actual mustard can be found in the pottery after 6000 years. Scientists studied phytoliths, silica crystals that remain when plants decay, and determined the phytoliths are characteristic of mustard plants.

Links

This is what I found most interesting this week. 

Preliminary research suggests that different parts of the brain are involved when people are immersed in what they’re reading as opposed to skimming.

At Literary Rambles, Lorin Oberweger offers excellent advice on putting an emotional hook in a query letter summary. 

The Swagger Writers are doing an fascinating series called The October Memoir and Backstory Blog Challenge. Members recount a childhood memory for each year starting at age one. Today is year 11, so scroll back for what has already been posted.

Tendril Links

For a reprise to last week's Overheard statement and some old nature pictures, check out this video from Science Friday on plant movement and cucumber tendrils.

How Old is That Hunk of Clay?

While researching my WIP, I wondered how archaeologists determine the age of pottery fragments. ¹⁴C dating is useful for organic substances (bones, teeth, parchment, fabric, pollen, or other remnants of carbon-based life forms). The clays used in ceramics are made from inorganic silica compounds that don’t contain much carbon. Pottery fragments can be dated by: 

¹⁴C dating of burned food residues (link) 
In the days before dishwashers, steel wool and foaming detergents, food stuck to the crockery. 

¹⁴C dating of lipids that were absorbed by unglazed pottery (link)
It’s always been hard to scrub grease off dirty dishes. This method was used to demonstrate that dairy farming has existed in Britain for 6000 years. 

Determining the water of re-hydroxylation (link, link)
After bricks or pottery are removed from a kiln and exposed to the atmosphere, the clay begins to chemically combine with water at a time-dependent rate. This water can be removed with heat. The change in mass (before and after heating) is used to determine when the ceramic was first fired. This method appears to be accurate except for bricks from buildings bombed during WWWII where high temperatures reset the hydroxylation clock. 

The age of ¹⁴C-dated objects is expressed in years BP (Before Present) (link) with January 1, 1950 as the origin because radiocarbon dating expanded in use in the 1950s. BP is sometimes interpreted as Before Physics since nuclear testing during the 1950s spiked the atmosphere with radioisotopes of carbon and increased the amount of ¹⁴C in samples.

Passage of Venus

A friend took this picture with an iPhone held up to a telescope. 

photo by Greg Glenn

Civil War Code

The Washington Post ran a fascinating article on a newly deciphered Civil War message. Believe it or not, the Museum of the Confederacy had this message in a bottle since 1896, and it remained unopened, un-deciphered and unread until collections manager Catherine M. Wright decided to investigate. The other thing that amazed me was retired CIA code breaker, David Gaddy and Navy cryptologist Cmdr. John B. Hunter, solved the code by brain, not by computer. It goes to show that spies like to play as much as anybody.

The description of the Vigenere Cipher isn’t completely clear in the article. A Vigenere Cipher is not a simple substitution or Caesar cipher (a frame shift). A Vigenere Cipher is a series of shifts based on a code word or key. This makes decoding the message by frequency analysis much more complicated because the most common letter is not necessarily E. Frequency analysis is how Sherlock Holmes decoded messages in “The Adventure of the Dancing Men.”

I loved finding out about this newly deciphered code. I wish the picture of the message was more legible and that they’d told us what the key was.

Thanks to Debbie Diesen for the link.

A Bit More on Speaking Your Truth

The attack on my friend Fang Shimin was covered in Time Magazine.

Shimin (web name Fang Zhouzi) is the author of seventeen books, many of which expose scientific corruption in China. His writing has put his life in danger.

Speaking Your Truth

When children ask Patricia Polacco if her stories are true, she says, “Yes, but it might not have happened.”

As a writer, I appreciate the importance of truth in expressing emotion, rendering dialog and detailing description – whether the story is fiction or nonfiction.

As a former scientist, I think of truth in a different way. Textbooks relate facts, but working scientists rarely speak of truth. We talk about replicating controlled experiments and data that are consistent with a larger hypothesis because often it takes a long time to figure out how nature actually works.

Lately, I’ve been thinking about truth in a political sense. In America, we expect truth, and find fraud, cover-ups and misappropriation of funds scandalous. But this isn’t true of every country. My friend, Fang Shimin (net name Fang Zhouzi), has devoted his career to exposing scientific corruption in China. Last weekend Shimin was attacked by two thugs, apparently in retribution for his role as a whistleblower. Fortunately, he escaped with only minor injuries.

Today, I’m thinking of freedom of speech, the privilege of living in a place where truth is expected, and the great gift of a legal system equipped to fight dishonesty.

Zombie Spiders

Imagine you’re a wolf spider that lives in salt marshes. When the tide comes in, your number one priority should be to get to higher ground. Spiders are terrestrial organisms that require oxygen, so rising water seems detrimental to survival.

Recent work by Julien Pétillon and his graduate student (unnamed in the article) at France’s Université de Rennes, demonstrated that one species of marsh-dwelling spider, Arctosa fulvolineata, can survive up to forty hours of submersion in salt water by lapsing into a “coma”. If the spiders are allowed to dry out for a few hours, they recover.

While this adaptive mechanism is interesting, I do not think that drowning spiders is an appropriate activity for scientists.

References:
Science: 324: 571 (2009).
MSNBC

Seasonal Links

Pumpkins
Some creative elementary school kids decorated pumpkins to honor their favorite characters in children's books. My personal fave is the one modeled to look like The Pout Pout Fish, a picture book by Debbie Diesen and illustrated by Dan Hanna.

This year, I'm carving only one pumpkin, the Viking, to honor the local high school.

Costumes
I have to miss the Halloween band performance. The Sousaphones are going as Pacmen this year.

Vampires
An east African spider called Evarcha culicivora prefers mates that have recently fed on blood-filled mosquitoes. This could explain a lot about current literary trends.

NaNoWriMo
I'm in revising mode, plus I'll be attending the Highlights Founders Workshop on Writing YA novels in November, so no NaNo for me.

Raptorex

60-70 million years before Tyrannosaurus rex dominated the dinosaur world, a smaller version of the famous and fearsome predator lived and hunted in what is now China. The newly discovered fossil resembles T. rex but is 1/100th the size (8 feet long and 175 pounds). Scientists named the dinosaur, Raptorex, the king of thieves. Raptorex shares many characteristics with its gigantic evolutionary cousin, such as huge jaws, well developed brain and olfactory center, powerful hind legs and tiny arms. These traits therefore developed before massive size.

The skeleton is nearly complete. Isn’t it beautiful?

Dr. Paul Serano discusses Raptorex and shares his ideas about the purpose of those tiny arms in this video.

References:
Science Express
New York Times
The Guardian
Not Exactly Rocket Science blog

Stone Age Rock and Roll

No one knows when prehistoric people started making and using complex musical instruments. The August 6, 2009 issue of Nature reports the discovery of bone and ivory flutes dating from 35,000 years ago. The flutes were found in caves in southwestern Germany.

The bone flute (picture) was made from the radius of a griffon vulture. Bird bones are hollow, which makes them ideal for flute construction. The flute had five finger holes, and was marked with fine evenly-placed scratches near the finger holes. The scratches may have been used to measure the location of the holes for tone calibration. Anthropologists believe the two V-shaped notches in one end of the flute served as a mouthpiece.

Fragments of two ivory flutes were also unearthed. An ivory flute was more difficult to make than a bone flute. First the mammoth tusk was shaped to the rough form of a flute. Next, the tusk was split longitudinally so the inside could be hollowed out. Finger holes were drilled, and the two halves were cemented together with air-tight seals.

It's hard to guess what the earliest music sounded like, but it probably wasn't like this.

Conard, N.J., Malina, M. and Munzel, S.C., New Flutes Document the Earliest Musical Tradition in Southwestern Germany, Nature, 460:737-740 (2009).

Frog Identified

Thanks to Tim Bogar*, the frog in last Sunday's photo has been identified as a Gray Treefrog (Hyla versicolor or Hyla chrysoscelis). Here is some great information from the Department of Natural Resources on Gray Treefrogs. These frogs can change color to match their surroundings, but fortunately for my photograph, fuchsia is not in their repertoire.


*You can read some of Tim's ideas on our critique group's blog, Write Brainers.