Subsections of Labs

Week 1: Pipetting

cover image cover image

Week 2: DNA Gel Art

cover image cover image

Design

Coming from a design background, I find it really interesting that DNA digestion patterns could be treated as a visual medium. I played around with Ronan’s gel art website trying different combination of digest results and I found some band patterns that generated a robot design. After I landed on the design, I used benchling to perform the virtual digest with the corresponding enzymes.

Design using Ronan’s website Design using Ronan’s website Ronan’s website allowed me to scroll through different enzyme combinations and randomize to see what patterns came up, which was much faster for exploring visual patterns.

Virtual digest in Benchling Virtual digest in Benchling Benchling virtual digest of my final 6-lane design, showing predicted band sizes for each enzyme combination against the 1 Kb Plus Thermo ladder.

Lane Assignments

My final design uses 6 lanes cut with different restriction enzyme combinations, mirrored across the center:

Lane assignments Lane assignments

Restriction Digest Preparation

Each digest reaction was prepared in a PCR tube with the following components:

Restriction digest recipe Restriction digest recipe *Reaction setup for each lane. Each tube contained water, CutSmart buffer, Lambda DNA, and the specific enzyme(s). *

The reactions were incubated at 37°C for 30 minutes to allow the enzymes to fully cut the DNA.

Lab Process

Step 1: Prepare the TAE buffer and agarose gel

We used 1× TAE buffer to mix with agarose powder. The flask was microwaved until the cloudy color became completely clear as the solution just bagan to have some bubbles.

Dissolving agarose in the microwave Dissolving agarose in the microwave Waiting for the solution to cool down

Step 2: Add DNA stain and pour the gel

Once the agarose cooled slightly, we added a small amount of SYBR Safe DNA stain which made the solution tinted pink.

SYBR Safe DNA stain SYBR Safe DNA stain The SYBR Safe stain next to the flask of melted agarose.

We then poured the gel into the casting tray with the comb in place and waited for it to solidify.

Poured gel solidifying in the tray Poured gel solidifying in the tray The gel cast in the electrophoresis tray with the comb creating wells at the top.

Step 3: Prepare the digest reactions

While waiting for the gel, we prepared the restriction digest reactions. Each tube was labeled 1-6 corresponding to our lane design. We pipetted water, CutSmart buffer, Lambda DNA, and the specific enzymes into each tube.

Preparing digest reactions Preparing digest reactions Pipetting enzymes and Lambda DNA stored on ice.

This was the most challenging part because the micropipetting was tricky. It was hard to tell whether we had the right amount, since the volumes are so small they’re essentially invisible in the pipette tip.

Labeled digest tubes Labeled digest tubes Six labeled digest tubes ready for incubation.

Step 4: Add loading dye and load the gel

After incubation, we added loading dye to each reaction which would help us visually track how far the gel has run.

Adding loading dye Adding loading dye Adding loading purple dye to the digest reactions before loading into the gel.

We then filled casting wells with 1x TAE and loaded 20 uL of each samples

Step 5: Run the gel

Once loaded, we connected the electrodes and started running the gel. We noticed bubbles in the TAE buffer when the elctricity is on.

Gel electrophoresis running Gel electrophoresis running The electrophoresis setup running.

Gel electrophoresis running Gel electrophoresis running Small bubbles rising to surface

We ran it for about 45 minutes to allow the DNA to travel more than halfway throught the gel.

Results

Gel result — printed from imager Gel result — printed from imager Printed gel image from the lab imager

Gel result — digital capture Gel result — digital capture Digital gel result

The symmetric design concept came through but the overall image was fainter and the lower section was not visible. Possible reasons might be too little DNA samples and shorter runtimes.

Week 3: Opentrons Art

cover image cover image

Design

I designed a mandala-inspired symmetrical pattern using the Opentrons Art Interface, drawing on the visual language of radial symmetry. The script was exported from the GUI and ran on the Opentrons software

Design in the Opentrons Art GUI Design in the Opentrons Art GUIDesign in the Opentrons Art GUI Design in the Opentrons Art GUI

Python Script

from opentrons import types
import string

metadata = {
    'protocolName': '{ANNIE} - Opentrons Art - HTGAA',
    'author': 'HTGAA',
    'source': 'HTGAA 2026',
    'apiLevel': '2.20'
}

Z_VALUE_AGAR = 2.0
POINT_SIZE = 0.75

mjuniper_points = [(-1,31), (1,31), (-13,27), (-11,27), (-1,27), (1,27), (11,27), (13,27), (-15,25), (-13,25), (-1,25), (1,25), (13,25), (15,25), (-5,21), (5,21), (-19,19), (-7,19), (-3,19), (3,19), (7,19), (19,19), (-27,17), (-19,17), (-1,17), (1,17), (19,17), (27,17), (-7,15), (7,15), (-23,13), (-21,13), (-19,13), (19,13), (21,13), (23,13), (-7,11), (7,11), (21,11), (-15,9), (15,9), (-19,7), (-17,7), (17,7), (19,7), (-5,5), (5,5), (-29,3), (29,3), (-31,1), (-29,1), (29,1), (31,1), (-31,-1), (-29,-1), (29,-1), (31,-1), (-29,-3), (29,-3), (-5,-5), (5,-5), (-19,-7), (-17,-7), (17,-7), (19,-7), (-15,-9), (15,-9), (-21,-11), (-7,-11), (7,-11), (21,-11), (-21,-13), (-19,-13), (19,-13), (21,-13), (-7,-15), (7,-15), (-27,-17), (-19,-17), (-1,-17), (1,-17), (19,-17), (27,-17), (-19,-19), (-7,-19), (-3,-19), (3,-19), (19,-19), (-5,-21), (5,-21), (-15,-25), (-13,-25), (-1,-25), (1,-25), (13,-25), (15,-25), (-13,-27), (-11,-27), (-1,-27), (1,-27), (11,-27), (13,-27), (-1,-31), (1,-31)]
mko2_points = [(-3,27), (3,27), (-11,25), (-5,25), (-3,25), (3,25), (5,25), (11,25), (-11,23), (-9,23), (-3,23), (3,23), (9,23), (11,23), (-15,21), (-11,21), (11,21), (15,21), (-15,19), (-13,19), (-1,19), (1,19), (13,19), (15,19), (-13,17), (13,17), (-23,15), (-21,15), (-19,15), (-11,15), (-5,15), (5,15), (11,15), (19,15), (21,15), (-27,13), (-11,13), (-7,13), (-3,13), (3,13), (7,13), (11,13), (27,13), (-25,11), (-5,11), (-3,11), (3,11), (5,11), (25,11), (-23,9), (-21,9), (-11,9), (-9,9), (-5,9), (-3,9), (3,9), (5,9), (9,9), (11,9), (21,9), (23,9), (-11,7), (-7,7), (-5,7), (-3,7), (3,7), (5,7), (7,7), (11,7), (-13,5), (-3,5), (-1,5), (1,5), (3,5), (13,5), (-25,3), (-3,3), (3,3), (25,3), (-27,1), (-25,1), (-23,1), (-11,1), (-9,1), (-7,1), (-5,1), (5,1), (7,1), (9,1), (11,1), (23,1), (25,1), (27,1), (-27,-1), (-25,-1), (-23,-1), (-11,-1), (-9,-1), (-7,-1), (-5,-1), (5,-1), (7,-1), (9,-1), (11,-1), (23,-1), (25,-1), (27,-1), (-25,-3), (-3,-3), (3,-3), (25,-3), (-13,-5), (-3,-5), (-1,-5), (1,-5), (3,-5), (13,-5), (-11,-7), (-7,-7), (-5,-7), (-3,-7), (3,-7), (5,-7), (7,-7), (-23,-9), (-21,-9), (-11,-9), (-9,-9), (-5,-9), (-3,-9), (3,-9), (5,-9), (9,-9), (11,-9), (21,-9), (23,-9), (-25,-11), (-5,-11), (-3,-11), (3,-11), (5,-11), (25,-11), (-27,-13), (-11,-13), (-7,-13), (-3,-13), (3,-13), (7,-13), (11,-13), (27,-13), (-21,-15), (-19,-15), (-11,-15), (-5,-15), (5,-15), (11,-15), (19,-15), (21,-15), (-13,-17), (13,-17), (-17,-19), (-15,-19), (-13,-19), (-1,-19), (13,-19), (15,-19), (-17,-21), (-15,-21), (-11,-21), (11,-21), (15,-21), (-11,-23), (-9,-23), (-3,-23), (3,-23), (9,-23), (11,-23), (-11,-25), (-5,-25), (-3,-25), (3,-25), (5,-25), (11,-25), (-3,-27), (3,-27)]
mrfp1_points = [(-3,31), (3,31), (-5,29), (-3,29), (-1,29), (1,29), (3,29), (5,29), (-17,27), (-15,27), (-7,27), (-5,27), (5,27), (7,27), (15,27), (17,27), (-17,25), (-7,25), (7,25), (17,25), (-17,23), (-15,23), (-7,23), (7,23), (15,23), (17,23), (-7,21), (7,21), (-11,19), (-9,19), (9,19), (11,19), (-25,17), (-23,17), (-17,17), (-15,17), (-11,17), (-9,17), (-7,17), (7,17), (9,17), (11,17), (15,17), (17,17), (23,17), (25,17), (-27,15), (-13,15), (-3,15), (3,15), (13,15), (23,15), (27,15), (-17,13), (-13,13), (-9,13), (9,13), (13,13), (17,13), (-27,11), (-23,11), (-13,11), (-11,11), (11,11), (13,11), (23,11), (27,11), (-25,9), (25,9), (-27,7), (-25,7), (-23,7), (-15,7), (-13,7), (13,7), (15,7), (23,7), (25,7), (27,7), (-29,5), (-25,5), (-23,5), (-17,5), (-15,5), (15,5), (17,5), (23,5), (25,5), (29,5), (-31,3), (-27,3), (-21,3), (-19,3), (-17,3), (-15,3), (-5,3), (5,3), (15,3), (17,3), (19,3), (21,3), (27,3), (31,3), (-21,1), (-19,1), (-13,1), (13,1), (19,1), (21,1), (-21,-1), (-19,-1), (-13,-1), (13,-1), (19,-1), (21,-1), (-31,-3), (-27,-3), (-21,-3), (-19,-3), (-17,-3), (-15,-3), (-5,-3), (5,-3), (15,-3), (17,-3), (19,-3), (21,-3), (27,-3), (31,-3), (-29,-5), (-25,-5), (-23,-5), (-17,-5), (-15,-5), (15,-5), (17,-5), (23,-5), (25,-5), (29,-5), (-27,-7), (-25,-7), (-23,-7), (-15,-7), (-13,-7), (13,-7), (15,-7), (23,-7), (25,-7), (27,-7), (-25,-9), (25,-9), (-27,-11), (-23,-11), (-13,-11), (-11,-11), (11,-11), (13,-11), (23,-11), (27,-11), (-17,-13), (-13,-13), (-9,-13), (9,-13), (13,-13), (17,-13), (-27,-15), (-23,-15), (-13,-15), (-3,-15), (3,-15), (13,-15), (23,-15), (27,-15), (-25,-17), (-23,-17), (-17,-17), (-15,-17), (-11,-17), (-9,-17), (-7,-17), (7,-17), (9,-17), (11,-17), (15,-17), (17,-17), (23,-17), (25,-17), (-11,-19), (-9,-19), (9,-19), (11,-19), (-7,-21), (7,-21), (-17,-23), (-15,-23), (-7,-23), (7,-23), (15,-23), (17,-23), (-17,-25), (-7,-25), (7,-25), (17,-25), (-17,-27), (-15,-27), (-7,-27), (-5,-27), (5,-27), (7,-27), (15,-27), (17,-27), (-5,-29), (-3,-29), (-1,-29), (1,-29), (3,-29), (5,-29), (-3,-31), (3,-31)]
mclover3_points = [(-5,23), (5,23), (-3,21), (3,21), (-17,19), (-5,19), (5,19), (17,19), (-25,15), (25,15), (-11,5), (11,5), (-9,3), (9,3), (-9,-3), (9,-3), (-11,-5), (11,-5), (11,-7), (-25,-15), (25,-15), (-5,-19), (1,-19), (5,-19), (17,-19), (-3,-21), (3,-21), (-5,-23), (5,-23)]
sfgfp_points = [(-21,11), (-23,-13), (23,-13)]

point_name_pairing = [("mjuniper", mjuniper_points),("mko2", mko2_points),("mrfp1", mrfp1_points),("mclover3", mclover3_points),("sfgfp", sfgfp_points)]

TIP_RACK_DECK_SLOT = 9
COLORS_DECK_SLOT = 6
AGAR_DECK_SLOT = 5
PIPETTE_STARTING_TIP_WELL = 'A1'

well_colors = {
    'A1': 'sfGFP', 'A2': 'mRFP1', 'A3': 'mKO2', 'A4': 'Venus',
    'A5': 'mKate2_TF', 'A6': 'Azurite', 'A7': 'mCerulean3', 'A8': 'mClover3',
    'A9': 'mJuniper', 'A10': 'mTurquoise2', 'A11': 'mBanana', 'A12': 'mPlum',
    'B1': 'Electra2', 'B2': 'mWasabi', 'B3': 'mScarlet_I', 'B4': 'mPapaya',
    'B5': 'eqFP578', 'B6': 'tdTomato', 'B7': 'DsRed', 'B8': 'mKate2',
    'B9': 'EGFP', 'B10': 'mRuby2', 'B11': 'TagBFP', 'B12': 'mChartreuse_TF',
    'C1': 'mLychee_TF', 'C2': 'mTagBFP2', 'C3': 'mEGFP', 'C4': 'mNeonGreen',
    'C5': 'mAzamiGreen', 'C6': 'mWatermelon', 'C7': 'avGFP', 'C8': 'mCitrine',
    'C9': 'mVenus', 'C10': 'mCherry', 'C11': 'mHoneydew', 'C12': 'TagRFP',
    'D1': 'mTFP1', 'D2': 'Ultramarine', 'D3': 'ZsGreen1', 'D4': 'mMiCy',
    'D5': 'mStayGold2', 'D6': 'PA_GFP'
}

volume_used = {
    'mjuniper': 0, 'mko2': 0, 'mrfp1': 0, 'mclover3': 0, 'sfgfp': 0
}

def update_volume_remaining(current_color, quantity_to_aspirate):
    rows = string.ascii_uppercase
    for well, color in list(well_colors.items()):
        if color == current_color:
            if (volume_used[current_color] + quantity_to_aspirate) > 250:
                row = well[0]
                col = well[1:]
                next_row = rows[rows.index(row) + 1]
                next_well = f"{next_row}{col}"
                del well_colors[well]
                well_colors[next_well] = current_color
                volume_used[current_color] = quantity_to_aspirate
            else:
                volume_used[current_color] += quantity_to_aspirate
            break

def run(protocol):
    protocol.home()
    tips_20ul = protocol.load_labware('opentrons_96_tiprack_20ul', TIP_RACK_DECK_SLOT, 'Opentrons 20uL Tips')
    pipette_20ul = protocol.load_instrument("p20_single_gen2", "right", [tips_20ul])
    temperature_plate = protocol.load_labware('opentrons_96_aluminumblock_generic_pcr_strip_200ul', 6)
    agar_plate = protocol.load_labware('htgaa_agar_plate', AGAR_DECK_SLOT, 'Agar Plate')
    agar_plate.set_offset(x=0.00, y=0.00, z=Z_VALUE_AGAR)
    center_location = agar_plate['A1'].top()
    pipette_20ul.starting_tip = tips_20ul.well(PIPETTE_STARTING_TIP_WELL)

    def dispense_and_jog(pipette, volume, location):
        assert(isinstance(volume, (int, float)))
        above_location = location.move(types.Point(z=location.point.z + 2))
        pipette.move_to(above_location)
        pipette.dispense(volume, location)
        pipette.move_to(above_location)

    def location_of_color(color_string):
        for well, color in well_colors.items():
            if color.lower() == color_string.lower():
                return temperature_plate[well]
        raise ValueError(f"No well found with color {color_string}")

    for i, (current_color, point_list) in enumerate(point_name_pairing):
        if not point_list:
            continue
        pipette_20ul.pick_up_tip()
        max_aspirate = int(18 // POINT_SIZE) * POINT_SIZE
        quantity_to_aspirate = min(len(point_list)*POINT_SIZE, max_aspirate)
        update_volume_remaining(current_color, quantity_to_aspirate)
        pipette_20ul.aspirate(quantity_to_aspirate, location_of_color(current_color))

        for i in range(len(point_list)):
            x, y = point_list[i]
            adjusted_location = center_location.move(types.Point(x, y))
            dispense_and_jog(pipette_20ul, POINT_SIZE, adjusted_location)
            if pipette_20ul.current_volume == 0 and len(point_list[i+1:]) > 0:
                quantity_to_aspirate = min(len(point_list[i:])*POINT_SIZE, max_aspirate)
                update_volume_remaining(current_color, quantity_to_aspirate)
                pipette_20ul.aspirate(quantity_to_aspirate, location_of_color(current_color))
        pipette_20ul.drop_tip()

Printing

The OT-2 dispensed 0.75 µL drops of each fluorescent strain onto the charcoal agar plate.

Opentrons OT-2 dispensing onto the agar plate Opentrons OT-2 dispensing onto the agar plate Printing in progress Printing in progress

Result

After overnight incubation, the plate was imaged under UV light.

Final plate under UV illumination Final plate under UV illumination