# EDGAR Filing Document

**Accession Number:** 0001894562
**File Stem:** 0001072613-25-000536
**Filing Date:** 2025-8
**Character Count:** 41447
**Document Hash:** e7c3474bfe47a6a1c4e013aae232710b
**Contains OCR:** False
**Source Format:** 

## Filing Content

## Filing Summary
**0001072613-25-000536.hdr.sgml**: 20250811

**ACCESSION NUMBER**: 0001072613-25-000536

**CONFORMED SUBMISSION TYPE**: SCHEDULE 13D/A

**PUBLIC DOCUMENT COUNT**: 3

**FILED AS OF DATE**: 20250811

**DATE AS OF CHANGE**: 20250811

**SUBJECT COMPANY**: 

**COMPANY DATA:**
- **COMPANY CONFORMED NAME:** Prime Medicine, Inc.
- **CENTRAL INDEX KEY:** 0001894562
- **STANDARD INDUSTRIAL CLASSIFICATION:** BIOLOGICAL PRODUCTS (NO DIAGNOSTIC SUBSTANCES) [2836]
- **ORGANIZATION NAME:** 03 Life Sciences
- **EIN:** 000000000
- **STATE OF INCORPORATION:** DE
- **FISCAL YEAR END:** 1231

**FILING VALUES:**
- **FORM TYPE:** SCHEDULE 13D/A
- **SEC ACT:** 1934 Act
- **SEC FILE NUMBER:** 005-93800
- **FILM NUMBER:** 251203823

**BUSINESS ADDRESS:**
- **STREET 1:** 60 FIRST ST.
- **CITY:** CAMBRIDGE
- **STATE:** MA
- **ZIP:** 02141
- **BUSINESS PHONE:** 617-465-0013

**MAIL ADDRESS:**
- **STREET 1:** 60 FIRST ST.
- **CITY:** CAMBRIDGE
- **STATE:** MA
- **ZIP:** 02141
**FILED BY**: 

**COMPANY DATA:**
- **COMPANY CONFORMED NAME:** ARCH Venture Fund XII, L.P.
- **CENTRAL INDEX KEY:** 0001906837

**ORGANIZATION NAME:**
- **EIN:** 873448430
- **STATE OF INCORPORATION:** DE
- **FISCAL YEAR END:** 1231

**FILING VALUES:**
- **FORM TYPE:** SCHEDULE 13D/A

**BUSINESS ADDRESS:**
- **STREET 1:** 8755 W. HIGGINS ROAD, SUITE 1025
- **CITY:** CHICAGO
- **STATE:** IL
- **ZIP:** 60631
- **BUSINESS PHONE:** 773-380-6600

**MAIL ADDRESS:**
- **STREET 1:** 8755 W. HIGGINS ROAD, SUITE 1025
- **CITY:** CHICAGO
- **STATE:** IL
- **ZIP:** 60631

## Ex-1

**<u>Exhibit</u>** **<u>1</u>**

**<u>AGREEMENT OF JOINT FILING</u>**

Pursuant to Rule 13d-1(k)(1) under the Securities Exchange Act of 1934, the undersigned hereby agree that only one statement containing the information required by Schedule 13D need be filed with respect to the ownership by each of the undersigned of shares of Common Stock of Prime Medicine, Inc.

This Agreement may be executed in any number of counterparts, each of which shall be deemed an original.

Date: August 11, 2025

ARCH VENTURE FUND X, L.P.

By: ARCH Venture Partners IX, L.P.

its General Partner

By: ARCH Venture Partners X, LLC

its General Partner

By: <u>\*</u> 

Robert Nelsen

Managing Director

ARCH VENTURE PARTNERS X, L.P.

By: ARCH Venture Partners X, LLC

its General Partner

By: <u>\*</u> 

Robert Nelsen

Managing Director

ARCH VENTURE PARTNERS X, LLC

By: <u>\*</u> 

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Robert Nelsen

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Managing Director

ARCH VENTURE FUND X OVERAGE, L.P.

By: ARCH Venture Partners X Overage, L.P.

its General Partner

By: ARCH Venture Partners X, LLC

its General Partner

By: <u>\*</u> 

Robert Nelsen

Managing Director

ARCH VENTURE PARTNERS X OVERAGE, L.P.

By: ARCH Venture Partners X, LLC

its General Partner

By: <u>\*</u> 

Robert Nelsen

Managing Director

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <u>\*</u> 

Keith Crandell

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <u>\*</u> 

Robert Nelsen

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <u>\*</u> 

Kristina Burow

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <u>\*</u> 

Steven Gillis

\* By: <u>/s/ Mark McDonnell</u> 

Mark McDonnell as

Attorney-in-Fact

\* This Agreement of Joint Filing was executed by Mark McDonnell pursuant to a Powers of Attorney filed as Exhibit 24 and 24.1 to the Form 3 relating to the beneficial ownership of shares of Prime Medicine, Inc. by the Reporting Persons filed with the Securities Exchange Commission on October 19, 2022 and incorporated herein in its entirety by reference.

## Ex-2

**<u>EXHIBIT 2</u>**

**<u>AGREEMENT OF JOINT FILING</u>**

Pursuant to Rule 13d-1(k)(1) under the Securities Exchange Act of 1934, the undersigned hereby agree that only one statement containing the information required by Schedule 13D need be filed with respect to the ownership by each of the undersigned of shares of Common Stock of Prime Medicine, Inc.

This Agreement may be executed in any number of counterparts, each of which shall be deemed an original.

Date: August 11, 2025

ARCH VENTURE FUND XII, L.P.

By: ARCH Venture Partners XII, L.P.

its General Partner

By: ARCH Venture Partners XII, LLC

its General Partner

By: <u>\*</u> 

Keith Crandell

Managing Director

ARCH VENTURE PARTNERS XII, L.P.

By: ARCH Venture Partners XII, LLC

its General Partner

By: <u>\*</u> 

Keith Crandell

Managing Director

ARCH VENTURE PARTNERS XII, LLC

By: <u>\*</u> 

Keith Crandell

Managing Director

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <u>\*</u> 

Keith Crandell

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <u>\*</u> 

Robert Nelsen

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <u>\*</u> 

Kristina Burow

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <u>\*</u> 

Steven Gillis

\* By: <u>/s/ Mark McDonnell</u> 

Mark McDonnell as

Attorney-in-Fact

\* This Agreement of Joint Filing was executed by Mark McDonnell pursuant to a Power of Attorney filed as Exhibit 24.4 to the Form 3 relating to the beneficial ownership of shares of Neumora Therapeutics, Inc. by the Reporting Persons filed with the Securities Exchange Commission on September 14, 2023 and incorporated herein in its entirety by reference.

### UNITED STATES SECURITIES AND EXCHANGE COMMISSION
**Washington, D.C. 20549**

## SCHEDULE 13D

### Under the Securities Exchange Act of 1934

**(Amendment No. 2)**

**Prime Medicine, Inc.**

*(Name of Issuer)*

**Common Stock, $0.00001 par value**

*(Title of Class of Securities)*

**74168J101**

*(CUSIP Number)*

**Mark McDonnell**<br>ARCH Venture Management, LLC<br>8755 W. Higgins Road Suite 1025<br>Chicago IL 60631<br>(773)380-6600

*(Name, Address and Telephone Number of Person Authorized to Receive Notices and Communications)*

**08/07/2025**

*(Date of Event Which Requires Filing of this Statement)*

| **CUSIP No.** | **74168J101** |

---

| | | | |
|:--|:--|:--|:--|
| 1 | Name of reporting person<br>**ARCH Venture Fund X, L.P.** | Name of reporting person<br>**ARCH Venture Fund X, L.P.** | |
| 2 | Check the appropriate box if a member of a Group (See Instructions)<br>[x] (a)<br>[ ] (b) | Check the appropriate box if a member of a Group (See Instructions)<br>[x] (a)<br>[ ] (b) | |
| 3 | SEC use only | SEC use only | |
| 4 | Source of funds (See Instructions)<br>**WC** | Source of funds (See Instructions)<br>**WC** | |
| 5 | Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)<br>[ ] | Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)<br>[ ] | |
| 6 | Citizenship or place of organization<br>**DELAWARE** | Citizenship or place of organization<br>**DELAWARE** | |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 7 | Sole Voting Power<br>**0.00** |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 8 | Shared Voting Power<br>**18486894.00** |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 9 | Sole Dispositive Power<br>**0.00** |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 10 | Shared Dispositive Power<br>**18486894.00** |
| 11 | Aggregate amount beneficially owned by each reporting person<br>**18486894.00** | Aggregate amount beneficially owned by each reporting person<br>**18486894.00** | |
| 12 | Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)<br>[ ] | Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)<br>[ ] | |
| 13 | Percent of class represented by amount in Row (11)<br>**10.4%** | Percent of class represented by amount in Row (11)<br>**10.4%** | |
| 14 | Type of Reporting Person (See Instructions)<br>**PN** | Type of Reporting Person (See Instructions)<br>**PN** | |

---

| **CUSIP No.** | **74168J101** |

---

| | | | |
|:--|:--|:--|:--|
| 1 | Name of reporting person<br>**ARCH Venture Fund X Overage, L.P.** | Name of reporting person<br>**ARCH Venture Fund X Overage, L.P.** | |
| 2 | Check the appropriate box if a member of a Group (See Instructions)<br>[x] (a)<br>[ ] (b) | Check the appropriate box if a member of a Group (See Instructions)<br>[x] (a)<br>[ ] (b) | |
| 3 | SEC use only | SEC use only | |
| 4 | Source of funds (See Instructions)<br>**WC** | Source of funds (See Instructions)<br>**WC** | |
| 5 | Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)<br>[ ] | Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)<br>[ ] | |
| 6 | Citizenship or place of organization<br>**DELAWARE** | Citizenship or place of organization<br>**DELAWARE** | |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 7 | Sole Voting Power<br>**0.00** |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 8 | Shared Voting Power<br>**18486894.00** |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 9 | Sole Dispositive Power<br>**0.00** |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 10 | Shared Dispositive Power<br>**18486894.00** |
| 11 | Aggregate amount beneficially owned by each reporting person<br>**18486894.00** | Aggregate amount beneficially owned by each reporting person<br>**18486894.00** | |
| 12 | Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)<br>[ ] | Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)<br>[ ] | |
| 13 | Percent of class represented by amount in Row (11)<br>**10.4%** | Percent of class represented by amount in Row (11)<br>**10.4%** | |
| 14 | Type of Reporting Person (See Instructions)<br>**PN** | Type of Reporting Person (See Instructions)<br>**PN** | |

---

| **CUSIP No.** | **74168J101** |

---

| | | | |
|:--|:--|:--|:--|
| 1 | Name of reporting person<br>**ARCH Venture Fund XII, L.P.** | Name of reporting person<br>**ARCH Venture Fund XII, L.P.** | |
| 2 | Check the appropriate box if a member of a Group (See Instructions)<br>[x] (a)<br>[ ] (b) | Check the appropriate box if a member of a Group (See Instructions)<br>[x] (a)<br>[ ] (b) | |
| 3 | SEC use only | SEC use only | |
| 4 | Source of funds (See Instructions)<br>**WC** | Source of funds (See Instructions)<br>**WC** | |
| 5 | Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)<br>[ ] | Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)<br>[ ] | |
| 6 | Citizenship or place of organization<br>**DELAWARE** | Citizenship or place of organization<br>**DELAWARE** | |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 7 | Sole Voting Power<br>**0.00** |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 8 | Shared Voting Power<br>**18486894.00** |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 9 | Sole Dispositive Power<br>**0.00** |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 10 | Shared Dispositive Power<br>**18486894.00** |
| 11 | Aggregate amount beneficially owned by each reporting person<br>**18486894.00** | Aggregate amount beneficially owned by each reporting person<br>**18486894.00** | |
| 12 | Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)<br>[ ] | Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)<br>[ ] | |
| 13 | Percent of class represented by amount in Row (11)<br>**10.4%** | Percent of class represented by amount in Row (11)<br>**10.4%** | |
| 14 | Type of Reporting Person (See Instructions)<br>**PN** | Type of Reporting Person (See Instructions)<br>**PN** | |

---

| **CUSIP No.** | **74168J101** |

---

| | | | |
|:--|:--|:--|:--|
| 1 | Name of reporting person<br>**ARCH Venture Partners X, L.P.** | Name of reporting person<br>**ARCH Venture Partners X, L.P.** | |
| 2 | Check the appropriate box if a member of a Group (See Instructions)<br>[x] (a)<br>[ ] (b) | Check the appropriate box if a member of a Group (See Instructions)<br>[x] (a)<br>[ ] (b) | |
| 3 | SEC use only | SEC use only | |
| 4 | Source of funds (See Instructions)<br>**AF** | Source of funds (See Instructions)<br>**AF** | |
| 5 | Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)<br>[ ] | Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)<br>[ ] | |
| 6 | Citizenship or place of organization<br>**DELAWARE** | Citizenship or place of organization<br>**DELAWARE** | |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 7 | Sole Voting Power<br>**0.00** |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 8 | Shared Voting Power<br>**18486894.00** |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 9 | Sole Dispositive Power<br>**0.00** |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 10 | Shared Dispositive Power<br>**18486894.00** |
| 11 | Aggregate amount beneficially owned by each reporting person<br>**18486894.00** | Aggregate amount beneficially owned by each reporting person<br>**18486894.00** | |
| 12 | Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)<br>[ ] | Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)<br>[ ] | |
| 13 | Percent of class represented by amount in Row (11)<br>**10.4%** | Percent of class represented by amount in Row (11)<br>**10.4%** | |
| 14 | Type of Reporting Person (See Instructions)<br>**PN** | Type of Reporting Person (See Instructions)<br>**PN** | |

---

| **CUSIP No.** | **74168J101** |

---

| | | | |
|:--|:--|:--|:--|
| 1 | Name of reporting person<br>**ARCH Venture Partners X Overage, L.P.** | Name of reporting person<br>**ARCH Venture Partners X Overage, L.P.** | |
| 2 | Check the appropriate box if a member of a Group (See Instructions)<br>[x] (a)<br>[ ] (b) | Check the appropriate box if a member of a Group (See Instructions)<br>[x] (a)<br>[ ] (b) | |
| 3 | SEC use only | SEC use only | |
| 4 | Source of funds (See Instructions)<br>**AF** | Source of funds (See Instructions)<br>**AF** | |
| 5 | Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)<br>[ ] | Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)<br>[ ] | |
| 6 | Citizenship or place of organization<br>**DELAWARE** | Citizenship or place of organization<br>**DELAWARE** | |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 7 | Sole Voting Power<br>**0.00** |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 8 | Shared Voting Power<br>**18486894.00** |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 9 | Sole Dispositive Power<br>**0.00** |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 10 | Shared Dispositive Power<br>**18486894.00** |
| 11 | Aggregate amount beneficially owned by each reporting person<br>**18486894.00** | Aggregate amount beneficially owned by each reporting person<br>**18486894.00** | |
| 12 | Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)<br>[ ] | Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)<br>[ ] | |
| 13 | Percent of class represented by amount in Row (11)<br>**10.4%** | Percent of class represented by amount in Row (11)<br>**10.4%** | |
| 14 | Type of Reporting Person (See Instructions)<br>**PN** | Type of Reporting Person (See Instructions)<br>**PN** | |

---

| **CUSIP No.** | **74168J101** |

---

| | | | |
|:--|:--|:--|:--|
| 1 | Name of reporting person<br>**ARCH Venture Partners XII, L.P.** | Name of reporting person<br>**ARCH Venture Partners XII, L.P.** | |
| 2 | Check the appropriate box if a member of a Group (See Instructions)<br>[x] (a)<br>[ ] (b) | Check the appropriate box if a member of a Group (See Instructions)<br>[x] (a)<br>[ ] (b) | |
| 3 | SEC use only | SEC use only | |
| 4 | Source of funds (See Instructions)<br>**WC** | Source of funds (See Instructions)<br>**WC** | |
| 5 | Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)<br>[ ] | Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)<br>[ ] | |
| 6 | Citizenship or place of organization<br>**DELAWARE** | Citizenship or place of organization<br>**DELAWARE** | |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 7 | Sole Voting Power<br>**0.00** |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 8 | Shared Voting Power<br>**18486894.00** |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 9 | Sole Dispositive Power<br>**0.00** |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 10 | Shared Dispositive Power<br>**18486894.00** |
| 11 | Aggregate amount beneficially owned by each reporting person<br>**18486894.00** | Aggregate amount beneficially owned by each reporting person<br>**18486894.00** | |
| 12 | Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)<br>[ ] | Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)<br>[ ] | |
| 13 | Percent of class represented by amount in Row (11)<br>**10.4%** | Percent of class represented by amount in Row (11)<br>**10.4%** | |
| 14 | Type of Reporting Person (See Instructions)<br>**PN** | Type of Reporting Person (See Instructions)<br>**PN** | |

---

| **CUSIP No.** | **74168J101** |

---

| | | | |
|:--|:--|:--|:--|
| 1 | Name of reporting person<br>**ARCH Venture Partners X, LLC** | Name of reporting person<br>**ARCH Venture Partners X, LLC** | |
| 2 | Check the appropriate box if a member of a Group (See Instructions)<br>[x] (a)<br>[ ] (b) | Check the appropriate box if a member of a Group (See Instructions)<br>[x] (a)<br>[ ] (b) | |
| 3 | SEC use only | SEC use only | |
| 4 | Source of funds (See Instructions)<br>**AF** | Source of funds (See Instructions)<br>**AF** | |
| 5 | Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)<br>[ ] | Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)<br>[ ] | |
| 6 | Citizenship or place of organization<br>**DELAWARE** | Citizenship or place of organization<br>**DELAWARE** | |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 7 | Sole Voting Power<br>**0.00** |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 8 | Shared Voting Power<br>**18486894.00** |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 9 | Sole Dispositive Power<br>**0.00** |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 10 | Shared Dispositive Power<br>**18486894.00** |
| 11 | Aggregate amount beneficially owned by each reporting person<br>**18486894.00** | Aggregate amount beneficially owned by each reporting person<br>**18486894.00** | |
| 12 | Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)<br>[ ] | Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)<br>[ ] | |
| 13 | Percent of class represented by amount in Row (11)<br>**10.4%** | Percent of class represented by amount in Row (11)<br>**10.4%** | |
| 14 | Type of Reporting Person (See Instructions)<br>**OO** | Type of Reporting Person (See Instructions)<br>**OO** | |

---

| **CUSIP No.** | **74168J101** |

---

| | | | |
|:--|:--|:--|:--|
| 1 | Name of reporting person<br>**ARCH Venture Partners XII, LLC** | Name of reporting person<br>**ARCH Venture Partners XII, LLC** | |
| 2 | Check the appropriate box if a member of a Group (See Instructions)<br>[x] (a)<br>[ ] (b) | Check the appropriate box if a member of a Group (See Instructions)<br>[x] (a)<br>[ ] (b) | |
| 3 | SEC use only | SEC use only | |
| 4 | Source of funds (See Instructions)<br>**AF** | Source of funds (See Instructions)<br>**AF** | |
| 5 | Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)<br>[ ] | Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)<br>[ ] | |
| 6 | Citizenship or place of organization<br>**DELAWARE** | Citizenship or place of organization<br>**DELAWARE** | |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 7 | Sole Voting Power<br>**0.00** |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 8 | Shared Voting Power<br>**18486894.00** |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 9 | Sole Dispositive Power<br>**0.00** |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 10 | Shared Dispositive Power<br>**18486894.00** |
| 11 | Aggregate amount beneficially owned by each reporting person<br>**18486894.00** | Aggregate amount beneficially owned by each reporting person<br>**18486894.00** | |
| 12 | Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)<br>[ ] | Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)<br>[ ] | |
| 13 | Percent of class represented by amount in Row (11)<br>**10.4%** | Percent of class represented by amount in Row (11)<br>**10.4%** | |
| 14 | Type of Reporting Person (See Instructions)<br>**OO** | Type of Reporting Person (See Instructions)<br>**OO** | |

---

| **CUSIP No.** | **74168J101** |

---

| | | | |
|:--|:--|:--|:--|
| 1 | Name of reporting person<br>**Robert Nelsen** | Name of reporting person<br>**Robert Nelsen** | |
| 2 | Check the appropriate box if a member of a Group (See Instructions)<br>[x] (a)<br>[ ] (b) | Check the appropriate box if a member of a Group (See Instructions)<br>[x] (a)<br>[ ] (b) | |
| 3 | SEC use only | SEC use only | |
| 4 | Source of funds (See Instructions)<br>**AF** | Source of funds (See Instructions)<br>**AF** | |
| 5 | Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)<br>[ ] | Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)<br>[ ] | |
| 6 | Citizenship or place of organization<br>**X1** | Citizenship or place of organization<br>**X1** | |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 7 | Sole Voting Power<br>**100142.00** |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 8 | Shared Voting Power<br>**18486894.00** |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 9 | Sole Dispositive Power<br>**100142.00** |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 10 | Shared Dispositive Power<br>**18486894.00** |
| 11 | Aggregate amount beneficially owned by each reporting person<br>**18587036.00** | Aggregate amount beneficially owned by each reporting person<br>**18587036.00** | |
| 12 | Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)<br>[ ] | Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)<br>[ ] | |
| 13 | Percent of class represented by amount in Row (11)<br>**10.4%** | Percent of class represented by amount in Row (11)<br>**10.4%** | |
| 14 | Type of Reporting Person (See Instructions)<br>**IN** | Type of Reporting Person (See Instructions)<br>**IN** | |

---

| **CUSIP No.** | **74168J101** |

---

| | | | |
|:--|:--|:--|:--|
| 1 | Name of reporting person<br>**Keith Crandell** | Name of reporting person<br>**Keith Crandell** | |
| 2 | Check the appropriate box if a member of a Group (See Instructions)<br>[x] (a)<br>[ ] (b) | Check the appropriate box if a member of a Group (See Instructions)<br>[x] (a)<br>[ ] (b) | |
| 3 | SEC use only | SEC use only | |
| 4 | Source of funds (See Instructions)<br>**AF** | Source of funds (See Instructions)<br>**AF** | |
| 5 | Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)<br>[ ] | Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)<br>[ ] | |
| 6 | Citizenship or place of organization<br>**X1** | Citizenship or place of organization<br>**X1** | |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 7 | Sole Voting Power<br>**0.00** |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 8 | Shared Voting Power<br>**18486894.00** |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 9 | Sole Dispositive Power<br>**0.00** |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 10 | Shared Dispositive Power<br>**18486894.00** |
| 11 | Aggregate amount beneficially owned by each reporting person<br>**18486894.00** | Aggregate amount beneficially owned by each reporting person<br>**18486894.00** | |
| 12 | Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)<br>[ ] | Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)<br>[ ] | |
| 13 | Percent of class represented by amount in Row (11)<br>**10.4%** | Percent of class represented by amount in Row (11)<br>**10.4%** | |
| 14 | Type of Reporting Person (See Instructions)<br>**IN** | Type of Reporting Person (See Instructions)<br>**IN** | |

---

| **CUSIP No.** | **74168J101** |

---

| | | | |
|:--|:--|:--|:--|
| 1 | Name of reporting person<br>**Kristina Burow** | Name of reporting person<br>**Kristina Burow** | |
| 2 | Check the appropriate box if a member of a Group (See Instructions)<br>[x] (a)<br>[ ] (b) | Check the appropriate box if a member of a Group (See Instructions)<br>[x] (a)<br>[ ] (b) | |
| 3 | SEC use only | SEC use only | |
| 4 | Source of funds (See Instructions)<br>**AF** | Source of funds (See Instructions)<br>**AF** | |
| 5 | Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)<br>[ ] | Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)<br>[ ] | |
| 6 | Citizenship or place of organization<br>**X1** | Citizenship or place of organization<br>**X1** | |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 7 | Sole Voting Power<br>**0.00** |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 8 | Shared Voting Power<br>**18486894.00** |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 9 | Sole Dispositive Power<br>**0.00** |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 10 | Shared Dispositive Power<br>**18486894.00** |
| 11 | Aggregate amount beneficially owned by each reporting person<br>**18486894.00** | Aggregate amount beneficially owned by each reporting person<br>**18486894.00** | |
| 12 | Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)<br>[ ] | Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)<br>[ ] | |
| 13 | Percent of class represented by amount in Row (11)<br>**10.4%** | Percent of class represented by amount in Row (11)<br>**10.4%** | |
| 14 | Type of Reporting Person (See Instructions)<br>**IN** | Type of Reporting Person (See Instructions)<br>**IN** | |

---

| **CUSIP No.** | **74168J101** |

---

| | | | |
|:--|:--|:--|:--|
| 1 | Name of reporting person<br>**Steven Gillis** | Name of reporting person<br>**Steven Gillis** | |
| 2 | Check the appropriate box if a member of a Group (See Instructions)<br>[x] (a)<br>[ ] (b) | Check the appropriate box if a member of a Group (See Instructions)<br>[x] (a)<br>[ ] (b) | |
| 3 | SEC use only | SEC use only | |
| 4 | Source of funds (See Instructions)<br>**AF** | Source of funds (See Instructions)<br>**AF** | |
| 5 | Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)<br>[ ] | Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)<br>[ ] | |
| 6 | Citizenship or place of organization<br>**X1** | Citizenship or place of organization<br>**X1** | |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 7 | Sole Voting Power<br>**0.00** |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 8 | Shared Voting Power<br>**18486894.00** |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 9 | Sole Dispositive Power<br>**0.00** |
| Number of Shares<br>Beneficially Owned by<br>Each Reporting Person With: | 10 | Shared Dispositive Power<br>**18486894.00** |
| 11 | Aggregate amount beneficially owned by each reporting person<br>**18486894.00** | Aggregate amount beneficially owned by each reporting person<br>**18486894.00** | |
| 12 | Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)<br>[ ] | Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)<br>[ ] | |
| 13 | Percent of class represented by amount in Row (11)<br>**10.4%** | Percent of class represented by amount in Row (11)<br>**10.4%** | |
| 14 | Type of Reporting Person (See Instructions)<br>**IN** | Type of Reporting Person (See Instructions)<br>**IN** | |

---

**Item 1. Security and Issuer**

**(a) Title of Class of Securities:**
Common Stock, $0.00001 par value

**(b) Name of Issuer:**
Prime Medicine, Inc.

**(c) Address of Issuer's Principal Executive Offices:**
21 Erie Street, 175 Greenwich Street, Cambridge, MA, 02139

This statement relates to the Common Stock, $0.00001 par value per share (the "Common Stock"), of Prime Medicine, Inc. (the "Issuer") having its principal executive office at 21 Erie St., Cambridge, MA 02139 USA.

**Item 5. Interest in Securities of the Issuer**

**(a)**
AVF X is the record owner of 6,128,297 shares of Common Stock ("AVF X Record Shares"). AVP X LP, as the sole general partner of AVF X LP, may be deemed to beneficially own the AVF X Record Shares.  AVP X LLC, as the sole general partner of AVP X LP, may be deemed to beneficially own the AVF X Record Shares.

AVF X Overage is the record holder of 6,128,297 shares of Common Stock ("AVF X Overage Record Shares").  AVP X Overage LP, as the sole general partner of AVF X Overage, may be deemed to beneficially own the AVF X Overage Record Shares.  AVP X LLC, as the sole general partner of AVP X Overage LP, may be deemed to beneficially own the AVF X Overage Record Shares.

AVF XII is the record holder of 6,230,300 shares of Common Stock ("AVF XII Record Shares").  AVP XII LP, as the sole general partner of AVF XII LP, may be deemed to beneficially own the AVF XII Record Shares.  AVP XII LLC, as the sole general partner of AVP XII LP, may be deemed to beneficially own the AVF XII Overage Record Shares.

By virtue of their relationship as affiliated entities who have overlapping general partners and investment committee members, each of the Committee Members and direct and indirect general partners of AVF X, AVF X Overage and AVF XII may be deemed to share the power to direct AVF X Record Shares, AVF Overage X Record Shares and AVF XII Record Shares (collectively the "Record Shares").

Nelsen and his related trusts are also the owner of 16,080 shares of Common Stock of the Issuer and is the holder of vested options to purchase 84,062 shares of Common Stock ("Nelsen Options").

Each Reporting Person disclaims beneficial ownership of the Record Shares except for the shares, if any, held of record by such Reporting Person.

The percentage of outstanding Common Stock of the Issuer which may be deemed to be beneficially owned by each Reporting Person (other than Nelsen) is set forth on Line 13 of such Reporting Person's cover sheet.  Such percentage was calculated based on the 134,573,998 shares of Common Stock reported by the Issuer to be outstanding on July 31, 2025 in the Issuer's Form 10-Q filed with the Securities and Exchange Commission on August 7, 2025, plus 43,700,000 shares sold in an offering in August 2025. For Nelsen, the Nelsen Options were included in the number of shares of Common Stock outstanding.

**(b)**
Regarding the number of shares as to which such person has:

(i) sole power to vote or to direct the vote:  See line 7 of cover sheets.

(ii) shared power to vote or to direct the vote:  See line 8 of cover sheets.

(iii) sole power to dispose or to direct the disposition:  See line 9 of cover sheets.

(iv) shared power to dispose or to direct the disposition:  See line 10 of cover sheets.

**(c)**
On August 1, 2025, AVF XII purchased 3,030,300 shares of Common Stock at purchase price of $3.30 in a public offering.

The working capital of AVF XII was the source of the funds for the purchase.

No part of the purchase price paid by AVF XII was represented by funds or other consideration borrowed or otherwise obtained for the purpose of acquiring, holding, trading or voting the shares of Common Stock described above.  The total amount paid by for securities purchased in the above-listed transactions is as follows:

                                                   AVF XII:                                 $9,999,990.00

This Amendment No. 2 is being filed voluntarily due to an issuance of securities by the Issuer as reported on the Issuer's 10-Q filed with the Securities and Exchange Commission on August 7, 2025, which caused the percentage of outstanding Common Stock of the Issuer deemed to be beneficial owned by the Reporting Persons to reduce by one percent or more.

**Item 6. Contracts, Arrangements, Understandings or Relationships With Respect to Securities of the Issuer.**

AVF X and AVF X Overage are parties to that certain Amended and Restated Investors' Rights Agreement, dated April 20, 2021, the "Investor Rights Agreement"), which is attached as Exhibit 4.1+ to the Issuer's Form S-1 filed on September 23, 2022.  Effective as of the closing of the Issuer's initial public offering, the covenants relating to delivery of financial statements and inspection rights set forth in Section 3 were terminated and rights of first offer were terminated.  Pursuant to the Investor Rights Agreement, AVF X and AVF X Overage have certain registration rights with respect to its Common Stock.  Specifically, the Issuer has granted demand, piggyback and Form S-3 registration rights, which will terminate upon the earlier of (i) with respect to each stockholder, such date on which all registrable shares held by such stockholder may immediately be sold during any three-month period pursuant to Rule 144 of the Securities Act of 1933, as amended, (ii) the occurrence of a deemed liquidation event, as defined in the Issuer's amended and restated certificate of incorporation, as currently in effect, and (iii) the fifth anniversary of the IPO.

The foregoing description of the Investor Rights Agreement does not purport to be complete and is qualified in its entirety by reference to the full text of such agreement filed as an exhibit to this Schedule 13D and is incorporated herein by reference.

### SIGNATURE

After reasonable inquiry and to the best of my knowledge and belief, I certify that the information set forth in this statement is true, complete and correct.

**Reporting Person:** ARCH Venture Fund X, L.P.

**Signature:** ARCH Venture Partners X, L.P.

**Name/Title:** its General Partner

**Date:** 08/11/2025

After reasonable inquiry and to the best of my knowledge and belief, I certify that the information set forth in this statement is true, complete and correct.

**Reporting Person:** ARCH Venture Fund X Overage, L.P.

**Signature:** ARCH Venture Partners X Overage, L.P.

**Name/Title:** its General Partner

**Date:** 08/11/2025

After reasonable inquiry and to the best of my knowledge and belief, I certify that the information set forth in this statement is true, complete and correct.

**Reporting Person:** ARCH Venture Fund XII, L.P.

**Signature:** ARCH Venture Partners XII, L.P.

**Name/Title:** its General Partner

**Date:** 08/11/2025

After reasonable inquiry and to the best of my knowledge and belief, I certify that the information set forth in this statement is true, complete and correct.

**Reporting Person:** ARCH Venture Partners X, L.P.

**Signature:** ARCH Venture Partners X, LLC

**Name/Title:** its General Partner

**Date:** 08/11/2025

After reasonable inquiry and to the best of my knowledge and belief, I certify that the information set forth in this statement is true, complete and correct.

**Reporting Person:** ARCH Venture Partners X Overage, L.P.

**Signature:** ARCH Venture Partners X, LLC

**Name/Title:** its General Partner

**Date:** 08/11/2025

After reasonable inquiry and to the best of my knowledge and belief, I certify that the information set forth in this statement is true, complete and correct.

**Reporting Person:** ARCH Venture Partners XII, L.P.

**Signature:** ARCH Venture Partners XII, LLC

**Name/Title:** its General Partner

**Date:** 08/11/2025

After reasonable inquiry and to the best of my knowledge and belief, I certify that the information set forth in this statement is true, complete and correct.

**Reporting Person:** ARCH Venture Partners X, LLC

**Signature:** /s/ Mark McDonnell

**Name/Title:** Mark McDonnell, as Attorney-in-Fact for Robert Nelsen, Managing Director

**Date:** 08/11/2025

After reasonable inquiry and to the best of my knowledge and belief, I certify that the information set forth in this statement is true, complete and correct.

**Reporting Person:** ARCH Venture Partners XII, LLC

**Signature:** /s/ Mark McDonnell

**Name/Title:** Mark McDonnell, as Attorney-in-Fact for Keith Crandell, Managing Director

**Date:** 08/11/2025

After reasonable inquiry and to the best of my knowledge and belief, I certify that the information set forth in this statement is true, complete and correct.

**Reporting Person:** Robert Nelsen

**Signature:** /s/ Mark McDonnell

**Name/Title:** Mark McDonnell, as Attorney-in-Fact for Robert Nelsen

**Date:** 08/11/2025

After reasonable inquiry and to the best of my knowledge and belief, I certify that the information set forth in this statement is true, complete and correct.

**Reporting Person:** Keith Crandell

**Signature:** /s/ Mark McDonnell

**Name/Title:** Mark McDonnell, as Attorney-in-Fact for Keith Crandell

**Date:** 08/11/2025

After reasonable inquiry and to the best of my knowledge and belief, I certify that the information set forth in this statement is true, complete and correct.

**Reporting Person:** Kristina Burow

**Signature:** /s/ Mark McDonnell

**Name/Title:** Mark McDonnell, as Attorney-in-Fact for Kristina Burow

**Date:** 08/11/2025

After reasonable inquiry and to the best of my knowledge and belief, I certify that the information set forth in this statement is true, complete and correct.

**Reporting Person:** Steven Gillis

**Signature:** /s/ Mark McDonnell

**Name/Title:** Mark McDonnell, as Attorney-in-Fact for Steven Gillis

**Date:** 08/11/2025