Teaching with Schrödinger

Updated: 1-23-22

DNA and RNA
Created with:

Release 2022-2

Prerequisites:

working knowledge of Maestro

Files Supplied:

DNA_RNA_worksheet

Categories:

high school biology, AP/college general biology

About this Lesson:
DNA (or Deoxyribonucleic Acid) is the master code of life that is present in nearly all
living organisms. When DNA is passed down from parent to child, it can determine how
the child looks, like their eye and hair color. However, DNA alone cannot account for
the expression of genes. RNA (Ribonucleic Acid) is also needed to help carry out the
instructions in DNA. In this lesson, you will learn about the molecular structures of DNA
and RNA. This is important for learning about genes and the production of amino acids
to form proteins. Using Maestro, students will learn how to use the Build Biopolymer
function to create DNA and RNA, look at noncovalent bond interactions within the two
strands, as well as measure distances between the bases in DNA.

1
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

Learning Objectives:
●

●
●
●
●

●

Break down the molecular structures of DNA and RNA
Review and dive deeper into the central dogma of molecular biology
Build and interpret the structure of DNA and RNA using Build Biopolymer fromthe Protein Preparation and Refinement Panel
Analyze hydrogen bonding within DNA and RNA from the Maestro graphical userinterface
Generate electrostatic potential surfaces to view a DNA’s overall shape
Calculate distances between the nitrogenous bases using the Measurements
panelStandards:●

NY State Core Curriculum:●

Connections to AP:○○

DNA Bonding (Standard 4, Key Idea 5.2)
Gene Expression and Regulation (IST 1)● IB Diploma Programme:○ Structures of DNA & RNA ( Core Topic 2.6)
● ACS Guidelines:○●

ETS Chemistry GRE:○●

Biological Structures and Interactions - (Conceptual Topics)
Organic Chemistry - Nucleic Acids (3F)

AAMC MCAT:○

Biological and Biochemical Foundations of Living Systems (1B)

Assessments:
The following types of formative assessments are embedded in this lesson:●●

Assessment of student understanding through discussion of warm-up questions andfilling in any knowledge gaps about the structures of DNA and RNA
Visual assessment of student-generated DNA double stranded structure, RNA single
stranded structure, and measurements of DNA clefts

2
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

Warm-Up Questions: To be done on their own or at the beginning of class
Read the Khan Academy article on Nucleic Acids and answer the following questions:
1)

What is the basic subunit of DNA and RNA called? What is this subunit made of?

2) What is the difference between a purine and pyrimidine?

3) What is the central dogma of molecular biology?

Lesson Outline:
1.
2.
3.
4.
5.
6.
7.
8.

What you will need for this lesson - p. 4
Introduction to DNA structure - p. 6
Introduction to RNA structure - p. 7
DNA to RNA to Proteins - p. 8
Creating DNA and RNA - p. 10
Individual Exercises - p. 17
Summary, Additional Resources, and References - p. 20
Glossary of Terms - p. 20

3The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

1.

What you will need for this lesson
1. Go to the ‘Data’ folder and open yourClass Folder found on the virtual
cluster’s desktop.
2. Right-click on the folder called“DNA_RNA” and copy folder to
Desktop● Here, you will find the lesson
plan, worksheet, and any
additional resources
3. Open Maestro
a. See Starting Maestro if you
need help

Figure 1-1. Open Maestro.
4. Go to File > Change Working
Directory
5. Find your “DNA_RNA” folder that you
duplicated to your Desktop, and click
ChooseFigure 1-2. Change Working Directory option.

4
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

6. Go to File > Save Project As
7. Type “DNA_RNA_tutorial” and click
Savea. The project will be titled
DNA_RNA_tutorial.prj

Figure 1-3. Save Project panel.

Figure 1-4. Choose the best mouse option foryour set up.

2.

8. Finally, check your Mouse Actions
a. PC : Edit > Customize Mouse
Actionsb. Mac : Workspace >Customize Mouse Actions
9. Make sure you have the best option
chosen for your set up. This lesson
was written with a three-button mousewith a scroll wheel, meaning the scroll
wheel is a button as well as a wheel. If
you do not have a mouse, choose
Trackpad.

Introduction to DNA Structure

DNA is a nucleic acid, which is one of four major groups of biologicalmacromolecules that sustain life. Nucleic acids are composed of nucleotides. In DNA,each nucleotide is made up of three main parts: a 5-carbon sugar called deoxyribose, aphosphate group, and a nitrogenous base. There are four types of nitrogenous bases
found in DNA: adenine (A), cytosine (C), guanine (G), and thymine (T). To understandhow DNA forms into its well-known double helical structure, we have to zoom into DNA’ssugar-phosphate backbone in Figure 2-1 below. The sugar-phosphate backbone
consists of a chain of nucleotides linked by covalent bonds called phosphodiester
linkages, which form between the deoxyribose sugar of one nucleotide and thephosphate group of the next. This arrangement makes up two alternating chains or
strands of deoxyribose sugar and phosphate groups in the DNA polymer that run in
5
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

opposite directions of one another. This results in DNA molecules having anantiparallel structure with complementary strands: one strand runs from its 5’ end to 3’
end and is paired with a matching strand that runs from its 3’ end to 5’ end.

Figure 2-1. Molecular structure of DNA
As you can see in Figure 2-1, the sugar-phosphate backbone of the DNA
molecule lies on the outside of the helix. At the 5’ end of one DNA strand, the 5’
phosphate group of the first nucleotide sticks out. At the other end, called the 3’ end, the3’ hydroxyl group sticks out of the last nucleotide in the chain. The nitrogenous baseson the other hand, extend into the interior of the helix and form base pairs. Base pairing
is highly specific, A can only pair with T and G can only pair with C, and bases arebound together by hydrogen bonds. This means that we can predict the arrangement ofbases in the complementary DNA strand for a given strand of DNA. Try it out for
yourself in the exercise below!

6
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

Example #1. Complete the complementary DNA strand for each given strand of DNA
a. CGTAAGCGCTAATTA

b. TCTTAAATGATCGATC

c. GGCATTCGCGATCATG

3.

Introduction to RNA Structure

RNA is a nucleic acid that carries out the instructions coded by DNA. Like DNA,RNA is also made up of nucleotides consisting of a 5-carbon sugar, phosphate group,and nitrogenous base. However, there are three main differences between the
structures of DNA and RNA as pictured in Figure 3-1. First, RNA uses the sugar ribose
instead of deoxyribose. In ribose, there is a hydroxyl group on the 2’ end of the carbon.
Second, RNA is usually single stranded not double stranded. Third, RNA replaces thenitrogenous base thymine (T) with uracil (U).

7
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

Figure 3-1. Molecular structure of RNA

4. DNA to RNA to Proteins
So we now know what the structures of DNA and RNA look like and how thechain of nucleotides are arranged in each polymer. But what’s next? How does a DNA
molecule actually transmit its genetic information to affect a human or other organism’s
features?
Recall the central dogma of molecular biology. The central dogma states that
information flows from DNA → RNA → proteins. Transcription is the DNA → RNA partof the central dogma. It occurs in the nucleus. During transcription, a copy of mRNA
(messenger RNA) is made that is complementary to a strand of DNA. mRNA is anintermediary molecule that carries information from DNA in the nucleus to ribosomes in
the cytoplasm, where proteins are made. After transcription, an mRNA molecule isready to initiate protein synthesis in the cytoplasm. This process is called translation.
During translation, the nucleotide sequence of an mRNA molecule is translated into theamino acid sequence of a polypeptide with the help of tRNA (transfer RNA). However,
because there are only four different types of nucleotides present in an mRNA molecule8
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

and 20 different types of amino acids in a protein, the sequence of nucleotides in themRNA is read in groups of three. Each group of three consecutive nucleotides in RNA iscalled a codon, and each codon specifies either one amino acid or a stop to thetranslation process based on a set of rules called the genetic code.
Example #2. Complete the complementary mRNA strand for each given strand of DNA
a. ATGTCGCTGATACTGT

b. GGCATTCGCGATCATG

c. ACTAACGGTAGCTAGC

Example #3. Using the genetic code, translate the amino acid sequence of each givenmRNA strand.
a. AUG CAC UGU CCU UUC GCU GAC

b. GAG AUC UGG UUG GAA UCG

c. AGC GUA UUA ACG UAU CAU

9
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

5.

Creating DNA and RNA

Recap: genetic information carried in DNA is used to synthesize proteins throughintermediary RNA molecules. Now it’s time to switch gears and use Maestro to visualize thestructures of DNA and RNA that we have learned so far.

Computational Exercise: Creating DNA and RNA strands in Maestro
This exercise involves four parts:
1) Create DNA and RNA structures using Build Biopolymer and visualize hydrogenbonding within the DNA and RNA
2) Compare and contrast the structures of DNA and RNA using Tile View
3) Visualize the overall shape of DNA using Surfaces
4) Measure the distance between base pairs in DNA

Part 1. Creating DNA and RNA using Build
Biopolymer and visualizing H-bonding

Figure 5-1. Opening Build Biopolymer.

1. Open the Tasks Bar
2. In the search bar, type “Build
Biopolymer from Sequence”
3. Click on > Build Biopolymer from
Sequence
4. Select > DNA as Biopolymer typefrom the dropdown menu
5. Name the molecule “Short_DNA”
6. Enter the Sequence >CGCCTAAATTGAA○ Looking at the picture you can
see that the sequence is
automatically completed below
in gray○ Reminder: Checkmark Build
double-stranded
7. Change the Shape > B-DNA
8. Click > Build

Figure 5-2. Input DNA Sequence into Build
Biopolymer.

10
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

9. Go to the Workplace toggles in thebottom right hand corner and selectthe interactions toggle.
10. Select the “Non-Covalent bonds”(drop down) > All
11. Select the “Pi interactions” (dropdown) > All

Figure 5-3. Opening Non-Covalent bonds.

Figure 5-4. Visualizing hydrogen bonds in
DNA.

Pause here and zoom into the DNA moleculeusing your scroll wheel to get a closer look at
the hydrogen bonds. Remember, theHydrogen Bonds appear as yellow dottedlines in the DNA structure.
12. Open the Tasks Bar
13. In the search bar, type “Build
Biopolymer from Sequence”
14. Click on > Build Biopolymer from
Sequence
15. Select > RNA as Biopolymer typefrom the dropdown menu
16. Name the molecule “Short_RNA”
17. Enter the Sequence >AUGAUCUCGUAA○ Reminder: Toggle off Build
double-stranded
18. Click > Build
19. Select the “Non-Covalent bonds”(drop down) > All
20. Select the “Pi interactions” (dropdown) > All
Pause here and zoom into the RNA moleculeusing your scroll wheel to get a closer look at
the hydrogen bonds. Remember, theHydrogen Bonds appear as yellow dottedlines in the RNA structure.

Figure 5-5. Input RNA Sequence into Build
Biopolymer.
11
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

Figure 5-6. Visualizing hydrogen bonds in
RNA.
Question #1: Roughly how many Hydrogen Bonds can you count in the DNA and RNA
molecules? Remember, the Hydrogen Bonds appear as yellow dotted lines on the Maestro
interface.

Part 2. Compare and contrast the DNA andRNA molecules

Figure 5-7. Including short_DNA andshort_RNA in the workspace.

21. Right click on > short_DNA in the
project table
22. Click > Include
23. Right click on > short_RNA in the
project table
24. Click > Include○ When a structure has been
included in the workspace, youwill notice blue circles next toeach entry list.
25. Click on the “plus sign” at thebottom-right of the Maestro interface
26. Click > Tile by > Entry

Figure 5-8. short_DNA and short_RNA havebeen included in the workspace.
12
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

Pause here and zoom in/out, rotate the DNA
and RNA molecules. What similarities can
you observe between the two structures?
What differences are most noticeable?

Figure 5-9. Toggle on Tile view.
Question #2: Take a screenshot of your short_DNA and short_RNA structures side-by-side in
the tile view. Paste your screenshot in the table below. What are some similarities anddifferences you can observe between the DNA and RNA structures? Note them down in thetable below.
DNA and RNA side-by-side screenshot:

Similarities

Differences

13
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

Part 3. Adding a surface to the DNA

Figure 5-10. Excluding short_RNA from theworkspace.

Figure 5-11. Adding a surface to the DNA
structure.

27. Right click on > short_RNA in the
project table
28. Click > Exclude
29. Click on the “plus sign” at thebottom-right of the Maestro interface
30. Toggle off Tile view
31. Click on the surface icon at thebottom-right of the Maestro interface
to add a surface to the DNA molecule
32. Click on > Workspace > Surface >Manage Surfaces in the toolbar
33. Click on > Display Options
34. Keep Style > as Solid
35. Change the Color Scheme > Other
Property
36. Then select Residue Charge andClick > OK
Learn more: Electrostatic surface potentials
are colored red for negatively charged
residues and blue for positively charged
residues, while white/gray represents neutral
residues. See the chemical bonding lesson
for more information!

Figure 5-12. Opening the Manage Surfaces
panel.

14
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

Figure 5-13. Opening Display Options.

Figure 5-14. Changing the Color Scheme to
Other Property.

Figure 5-15. Selecting Residue Charge.

15
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

Figure 5-16. Click OK.
Question #3: Read the following two articles on DNA and the sugar-phosphate backbone.
Why is the sugar-phosphate backbone of DNA negatively charged? What function does thisserve?

Figure 4-19. Click on Measure in Favorites
Toolbar.

Part 4. Measuring distance between basesin the DNA
37. Toggle off the surface○ To activate and deactivate
surfaces, in the bottom-righthand corner there is a “Patch”
icon. Click that icon to turn thesurface on and off.
38. In your Favorites Toolbar click
Measure○ Keep the dropdown menu toDistances16
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

39. Measure the distance of the hydrogenbonds in each base pair
○ To measure the length, click
the start of one of the bases
and click to its matching basein the pair to see the distance
between them
40. When you are finished click OK

Figure 4-20. Measuring distance of hydrogenbonds in each base pair.
Question #4: List what hydrogen bond distances (in units of Ångstroms) you see between the
DNA base pairs.

Question #5: Other than hydrogen bonds, what are other non covalent interactions that you
see within the DNA?

17
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

6.

Individual Exercises

Part A: Calculate the distance between bases in your short_RNA structure. You canfollow the same steps from Part 4 of the computational exercise.
1) List some of the hydrogen bond distances (in units of Angstroms) between the
RNA bases. What do you notice about the hydrogen bond lengths in RNA?

2) What overall conclusion can you draw about hydrogen bond lengths in the
structures of DNA and RNA?

Part B: Identifying base pairs in DNA.
1) Zoom into your short_DNA structure and identify an instance where A is pairedwith T and where G is paired with C. Take screenshots of each base pair.
A - T screenshot:G - C screenshot:2) How did you identify which base pair was which?

18
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

Part C: Oxygen and nitrogen are electronegative atoms found in nitrogenous bases.
They are represented in models by the color conventions: red for oxygen, and blue fornitrogen. Electronegative O and N atoms with free lone pairs are potential hydrogenbond acceptors. Hydrogen atoms attached to very electronegative atoms like O and N
have strong partial positive charge and are potential hydrogen bond donors.
1) In the structures of adenine and thymine below, where are the hydrogen bondacceptors and donors? Draw an arrow pointing outwards to indicate a hydrogenbond donor, and draw an arrow pointing inwards to indicate a hydrogen bondacceptor.

19
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

2) In the structures of guanine and cytosine below, where are the hydrogen bondacceptors and donors? Draw an arrow pointing outwards to indicate a hydrogenbond donor, and draw an arrow pointing inwards to indicate a hydrogen bondacceptor.

7.

Summary, Additional Resources, and References

In this lesson, students learned how to use the Biopolymer Builder to create a DNA andRNA molecule, visualize hydrogen bonding, measure distances within base pairs, aswell as generate electrostatic potential surfaces of DNA. Using Maestro, students wereable to interact with the DNA and RNA structures by using the graphical user interface
to zoom in/out, measure bond lengths, and move around the molecules.
For further learning:
●
●
●
●
●
●
●

https://proteopedia.org/wiki/index.php/DNA
https://proteopedia.org/wiki/index.php/RNA
From RNA to Protein
Introduction to Computational Chemistry, 3rd Edition
Essentials of Computational Chemistry: Theories and Models, 2nd Edition
Molecular Modelling: Principles and Applications, 2nd Edition
See the Build Biopolymer help documentation

20
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

8.

Glossary of Terms

Entry List - a simplified view of the Project Table that allows you to perform basic
operations such as selection and inclusion
Included - the entry is represented in the Workspace, the circle in the In column is blue
Project Table - displays the contents of a project and is also an interface for performing
operations on selected entries, viewing properties, and organizing structures and data
Recent actions - This is a list of your recent actions, which you can use to reopen apanel, displayed below the Browse row. (Right-click to delete.)
Scratch Project - a temporary project in which work is not saved. Closing a scratch
project removes all current work and begins a new scratch project
Selected - (1) the atoms are chosen in the Workspace. These atoms are referred to as"the selection" or "the atom selection". Workspace operations are performed on theselected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row
for the entry is highlighted. Project operations are performed on all selected entries
Working Directory - the location that files are saved
Workspace - the 3D display area in the center of the main window, where molecular
structures are displayed
Nucleic acid - one of the four major groups of biological macromolecules that make up
life
DNA - a nucleic acid that carries genetic material found nearly in all living cells on earth
RNA - a single stranded nucleic acid that carries out the instructions coded in DNA
Base pairing - the principle by which nitrogenous bases in DNA bond with each other
Sugar-phosphate backbone - a polynucleotide chain linked by covalent bonds found in
the structures of DNA and RNA

21
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.