Printable Biology Molecules

The Printable Biology Molecules project provides teaching tools for all students and provides access to students who are blind or visually impaired. The project has been supported by a number of different partners including a grant from the UMass Open Education Initiative, a UMass Campus Climate Grant, and UMass IT. We are always looking to improve our offerings and welcome new models, feedback, and comments. Contact us here.

DNA Helix

Image of DNA helix model

Description: This space-filling DNA model is ideal for showing the concept of the major and minor groove. Feeling the two grooves in the model, you can tell that one groove is larger than the other. This is the result of the angle of the bases and is important as more chemical information is available to proteins in the major groove. Conversely, many proteins that do not bind to a specific DNA sequence interact with the minor groove, which has less specific chemical information available from the outside of the helix.

  • Download STL file for printing
  • Reference:
    • Watson, James D., editor. Molecular Biology of the Gene. Seventh edition, Pearson, 2014.
      • Chapter 4
  • Source: PDB:1BNA

DNA Polymerase

Image of DNA Polymerase

Description: This model represents DNA Polymerase I bound to DNA. DNA polymerases are shaped like a right hand and have three distinct domains: fingers, thumb, and palm. Orient the model, so the double stranded DNA is facing towards you and the single stranded DNA, is facing upwards. The 3’ end of DNA is bound to the palm. The fingers found on the left side of the model are the site of dNTP binding and the thumb domain, found on the right side of the model, curves around the duplex DNA.

  • Download STL file for printing
  • References:
    • Watson, James D., editor. Molecular Biology of the Gene. Seventh edition, Pearson, 2014.
      • Chapter 11
  • Source: DNA Polymerase I from Thermus aquaticus bound to a Primer/Template DNA
    PDB ID: 4KTQ
  • Edited using: Chimera, MeshLab, MeshMixer, and Fusion360

Helicase

Image of Helicase

Description: Orient the model so the DNA double helix is facing upwards. Note how the double helix is separated into two single strands, one of which enters the core of the protein. The DNA double helix feeds into the helicase model and is converted from its duplex form to two single strands. The helicase forms a ring-like complex composed of six subunits which surround a single strand of DNA and separate the duplex DNA using ATP hydrolysis to power its motion.

  • Download STL file for printing
  • References:
  • Watson, James D., editor. Molecular Biology of the Gene. Seventh edition, Pearson, 2014.
    • Chapter 5
    • Chapter 11
  • Source: Structure of bacteriophage T7 E343Q mutant gp4 helicase-primase in complex with ssDNA, dTTP, AC dinucleotide and CTP (form II)
    PBD ID: 6N7S
  • Edited using: Chimera, MeshLab, MeshMixer, and Fusion360

DNA Replication Fork

Image of replication fork model

Description: This model is a cartoon representation of the DNA Replication fork during the elongation phase of DNA replication. Using the double-stranded DNA helix to orient the model, there is a round disk that represents topoisomerase II which relaxes supercoiled DNA at the origin of replication. There is a cone pointing towards the topoisomerase, in between both strands of DNA. This cone represents the helicase protein, which separates double-stranded DNA into single-stranded DNA. Following the single strands of DNA, there are three spherical bumps on each strand, representing single-stranded binding proteins which function to keep DNA strands separated. One of the strands is the leading stand, and the other, the lagging strand. The leading strand contains one rectangular prism, or DNA polymerase III, and a short stretch of newly synthesized DNA that contains an arrow at the end of the phosphate backbone, indicating the direction of synthesis. The lagging strand also contains a DNA polymerase III and a short stretch of newly synthesized DNA. Additionally, there is a circular ring shortly after the single-stranded binding proteins which represents RNA primase. An Okazaki fragment is represented by a short stretch of fragmented double-stranded DNA placed between the ring-shaped RNA primase and the long stretch of double-stranded DNA. Between the Okazaki fragment and the DNA polymerase is DNA ligase, bound to the phosphate backbone of the newly synthesized DNA.

  • Download STL file for printing
  • Reference:
    • Watson, James D., editor. Molecular Biology of the Gene. Seventh edition, Pearson, 2014.
      • Chapter 11
  • Source: This model was inspired off of this public domain diagram.
    The DNA Double Helix was sourced from
    PBD ID: 5NT5
  • Edited using: Chimera, MeshLab, MeshMixer, and Fusion360

RNA Polymerase

Image of RNA-Polymerase Model

Description: This model of a small RNA polymerase shows a transcription bubble with two strands of DNA and an RNA strand that is found in the active site. Note how the DNA strands form a double helix at the top of the model, the polymerase separates them, builds a strand of RNA and the DNA strands join back together forming a double helix once again.

  • Download STL file for printing
  • References:
    • Watson, James D., editor. Molecular Biology of the Gene. Seventh edition, Pearson, 2014.
      • Chapter 15
  • Source: Structural basis for the transition from initiation to elongation transcription in T7 RNA polymerase
    PBD ID: 1MSW
  • Edited using: Chimera, MeshLab, MeshMixer and Fusion360

tRNA-Phe from Escherichia coli

Image of tRNA model

Description and educational walkthrough: This tRNA model is in its three-dimensional structure which takes the shape of the uppercase letter “L.” If held within the L position, there are three prongs at the upper tip of the L. Those three prongs are the anticodon loop, which is responsible for recognizing the codon on the mRNA via base pairing. The short end of the L is the acceptor stem, where the specific amino acid (Phenylalanine in this case) binds to the tRNA. Next to the acceptor arm is the ?U loop and between the ?U loop and the anticodon loop is the D loop.

Isoleucyl-transfer RNA (tRNA) synthetase

Image of tRNA-synthetase model

Description and educational walkthrough: Print a dual print with the top and the tRNA. Print a single color with the bottom. Then glue the top to the bottom. Isoleucyl-transfer RNA (tRNA) synthetase (IleRS) joins Ile to tRNA(Ile) at its synthetic active site and hydrolyzes incorrectly acylated amino acids at its editing active site.

Small Ribosomal Subunit with tRNAs bound

Image of small ribosomal subunit

Description and educational walkthrough: It is highly recommended to find the tRNA molecule before proceeding with this model. Using the tRNA model, there are three miniature versions in this model. Those three tRNAs are nestled in the E, P, and A sites of the ribosome.

Large Ribosomal Subunit

Image of large ribosomal subunit

Description and educational walkthrough: The large ribosomal subunit and the small ribosomal subunit are designed in a way that they fit together. If you have found the tRNAs on the small ribosomal subunit model, try to find a groove or pit that could house the tRNAs on the small ribosomal subunit. This “groove” should be located near the center of the large subunit. The groove is angled in such a way that the “L” shape of the tRNA can only be fitted in a single direction. If the large and small subunits feel to align with each other and they make an “egg” shape, then most likely the two subunits are fitted properly. The large subunit has the three chambers (aminoacyl-tRNA site, peptidyl-tRNA binding site, and exit site) that the tRNAs go through to generate a polypeptide chain.